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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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2
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Monjaraz-Ruedas R, Starrett J, Leavitt D, Hedin M. Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga). Am Nat 2024; 204:55-72. [PMID: 38857341 DOI: 10.1086/730262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
AbstractIdealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies.
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Lehmann Albornoz P, Bartzen CS, Malabarba LR. The barcode trap-Description of a new species of Microglanis, with a review of the status of Microglanis cibelae (Siluriformes: Pseudopimelodidae). JOURNAL OF FISH BIOLOGY 2024; 105:110-123. [PMID: 38646664 DOI: 10.1111/jfb.15764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
In a recent study based on the generalized mixed Yule coalescent method for delimiting species, a threshold of 2% genetic distance using cytochrome c oxidase subunit I sequences was used to delimit the species of Microglanis. That action resulted in assembling several populations of Microglanis from Atlantic coastal rivers between Rio Grande do Sul and São Paulo states as a single species, Microglanis cottoides, including Microglanis cibelae as a junior synonym. We reexamined these populations and found three species diagnosed by their morphology and that constitute separate mtDNA lineages, including a new species. The synonym of M. cibelae and M. cottoides is reviewed and refuted based on morphological and molecular evidence. M. cibelae and the new species are sympatric and occasionally syntopic in the Tramandaí, Mampituba, and Araranguá river basins. The new species is distinguished from M. cibelae and M. cottoides by the anterior margin of the posttemporosupracleitrum narrow articulated with the epioccipital, the short mental and maxillary barbels, and depressed head and body.
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Affiliation(s)
| | - César Sá Bartzen
- Universidade do Vale do Rio dos Sinos (Unisinos), São Leopoldo, Brazil
| | - Luiz R Malabarba
- Departamento de Zoologia, IB, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends Ecol Evol 2024:S0169-5347(23)00296-3. [PMID: 38849221 DOI: 10.1016/j.tree.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 06/09/2024]
Abstract
Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.
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Affiliation(s)
- Kevin Karbstein
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany.
| | - Lara Kösters
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Ladislav Hodač
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Martin Hofmann
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany
| | - Elvira Hörandl
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Salvatore Tomasello
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Natascha D Wagner
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Brent C Emerson
- Institute of Natural Products and Agrobiology (IPNA-CSIC), Island Ecology and Evolution Research Group, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - Dirk C Albach
- Carl von Ossietzky-Universität Oldenburg, Institute of Biology and Environmental Science, 26129 Oldenburg, Germany
| | - Stefan Scheu
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany; University of Göttingen, Centre of Biodiversity and Sustainable Land Use (CBL), 37073 Göttingen, Germany
| | - Sven Bradler
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, 37077 Göttingen, Germany; University of Göttingen, Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, 37077 Göttingen, Germany
| | - Iker Irisarri
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Centre for Molecular Biodiversity Research, Phylogenomics Section, Museum of Nature, 20146 Hamburg, Germany
| | - He Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Chenshan Botanical Garden, 201602 Shanghai, China
| | - Pamela Soltis
- University of Florida, Florida Museum of Natural History, 32611 Gainesville, USA
| | - Patrick Mäder
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Ecology and Evolution, Philosophenweg 16, 07743 Jena, Germany
| | - Jana Wäldchen
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
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Heine HLA, Derkarabetian S, Morisawa R, Fu PA, Moyes NHW, Boyer SL. Machine learning approaches delimit cryptic taxa in a previously intractable species complex. Mol Phylogenet Evol 2024; 195:108061. [PMID: 38485107 DOI: 10.1016/j.ympev.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.
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Affiliation(s)
- Haley L A Heine
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Rina Morisawa
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Phoebe A Fu
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Nathaniel H W Moyes
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Sarah L Boyer
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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7
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Lo YY, Cheng RC, Lin CP. Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan. PLoS One 2024; 19:e0301776. [PMID: 38722906 PMCID: PMC11081396 DOI: 10.1371/journal.pone.0301776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 05/13/2024] Open
Abstract
An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.
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Affiliation(s)
- Ying-Yuan Lo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Wild Animals Division, Biodiversity Research Institute, Nantou, Taiwan
| | - Ren-Chung Cheng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Research Center for Global Change Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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8
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Burroughs RW, Parham JF, Stuart BL, Smits PD, Angielczyk KD. Morphological Species Delimitation in The Western Pond Turtle ( Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification? Integr Org Biol 2024; 6:obae010. [PMID: 38689939 PMCID: PMC11058871 DOI: 10.1093/iob/obae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.
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Affiliation(s)
- R W Burroughs
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Center for Inclusive Education, Stony Brook University, Stony Brook, NY 11794, USA
| | - J F Parham
- Department of Geological Sciences, California State University, Fullerton, CA 92834, USA
| | - B L Stuart
- Section of Research and Collections, NC Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - P D Smits
- 952 NW 60th St., Seattle, Washington, WA 98107, USA
| | - K D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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Wang HL, Lei T, Wang XW, Cameron S, Navas-Castillo J, Liu YQ, Maruthi MN, Omongo CA, Delatte H, Lee KY, Krause-Sakate R, Ng J, Seal S, Fiallo-Olivé E, Bushley K, Colvin J, Liu SS. A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group. INSECT SCIENCE 2024. [PMID: 38562016 DOI: 10.1111/1744-7917.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou, Zhejiang Province, China
| | - Xiao-Wei Wang
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Stephen Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Yin-Quan Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Kent, UK
| | | | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD, Pôle de Protection des Plantes, Saint-Pierre, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | | | - James Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Kathryn Bushley
- USDA Agricultural Research Service, 17123, Emerging Pests and Pathogens Research Unit, Ithaca, NY, USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Shu-Sheng Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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10
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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11
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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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12
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Sánchez KI, Recknagel H, Elmer KR, Avila LJ, Morando M. Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group). Evolution 2024; 78:716-733. [PMID: 38262697 DOI: 10.1093/evolut/qpae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/17/2024] [Indexed: 01/25/2024]
Abstract
Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (Liolaemus kingii group). Specifically, we (a) inferred the population structure of the group and contrasted it with the phenotypic variability; (b) assessed the role of postdivergence gene flow in shaping phylogeographic and phenotypic patterns; and (c) explored ecogeographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic transitions. We also found evidence of postdivergence gene flow resulting in transgressive phenotypic evolution in one species. Predicted ancestral niches unveiled suitable areas in southern and eastern Patagonia during glacial and interglacial periods. Our study underscores integrating different data and model-based approaches to determine the underlying causes of diversification, a challenge faced in the study of recently diverged groups. We also highlight Liolaemus as a model system for phylogeographic and broader evolutionary studies.
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Hans Recknagel
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kathryn R Elmer
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
- Departamento de Biología y Ambiente, Universidad Nacional de la Patagonia San Juan Bosco, Sede Puerto Madryn, Puerto Madryn, Chubut, Argentina
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13
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Rodrigues BL, da Silva Costa G, Godoy RE, Pereira Júnior AM, Cella W, Ferreira GEM, de Medeiros JF, Shimabukuro PHF. Molecular and morphometric study of Brazilian populations of Psychodopygus davisi. MEDICAL AND VETERINARY ENTOMOLOGY 2024; 38:83-98. [PMID: 37867259 DOI: 10.1111/mve.12701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
In this study, we analysed the molecular and morphometric differences of several populations of the putative sand fly vector Psychodopygus davisi (Root, 1934) (Diptera, Psychodidae, Phlebotominae) in Brazil. We amplified the 658 base pair fragments of the DNA barcoding region-cytochrome c oxidase subunit 1 (COI) gene-for 57 specimens of P. davisi and three specimens of Psychodopygus claustrei (Abonnenc, Léger & Fauran, 1979). We merged our data with public sequences of the same species available from GenBank. Then, the combined dataset-87 sequences and 20 localities-was analysed using population structure analysis and different species delimitation approaches. Geometric morphometry of wings was performed for 155 specimens of P. davisi populations from the North, Midwest and Southeast Brazilian regions, analysing the differences in centroid sizes and canonical variates. Molecular analysis indicated high intraspecific genetic distance values for P. davisi (maximum p distance = 5.52%). All algorithms identified P. davisi and P. claustrei as distinct molecular taxonomic units, despite the low interspecific distance (p distance to the nearest neighbour = 4.79%). P. davisi sequences were split into four genetic clusters by population structure analysis and at least five genetic lineages using intermediate scenarios of the species delimitation algorithms. The species validation analysis of BPP strongly supported the five-species model in our dataset. We found high genetic diversity in this taxon, which is in agreement with its wide geographic distribution in Brazil. Furthermore, the wing analysis showed that specimens from the Southeast Region of Brazil are different from those in the North and the Midwest. The evolutionary patterns of P. davisi populations in Brazil suggest the presence of candidate species, which need to be validated in future studies using a more comprehensive approach with both genomic data and morphological characters.
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Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP), São Paulo, Brazil
| | - Glaucilene da Silva Costa
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório Central de Saúde Pública do Estado de Rondônia, LACEN-RO, Porto Velho, Brazil
| | | | | | - Wilsandrei Cella
- Programa de Pós Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense, Paraná, Brazil
- Universidade do Estado do Amazonas (UEA), Tefé, Brazil
| | - Gabriel Eduardo Melim Ferreira
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Epidemiologia Genética, Fiocruz Rondônia, Porto Velho, Brazil
| | - Jansen Fernandes de Medeiros
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Entomologia, Fiocruz Rondônia, Porto Velho, Brazil
| | - Paloma Helena Fernandes Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- Coleção de Flebotomíneos (Fiocruz/COLFLEB), Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
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14
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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Spirin V, Runnel K, Vlasák J, Viner I, Barrett M, Ryvarden L, Bernicchia A, Rivoire B, Ainsworth A, Grebenc T, Cartabia M, Niemelä T, Larsson KH, Miettinen O. The genus Fomitopsis ( Polyporales, Basidiomycota) reconsidered. Stud Mycol 2024; 107:149-249. [PMID: 38600960 PMCID: PMC11003443 DOI: 10.3114/sim.2024.107.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/10/2023] [Indexed: 04/12/2024] Open
Abstract
Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia and Fomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + TEF1, ITS + TEF1 + RPB1 and ITS + TEF1 + RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided. Taxonomic novelties: New species: Fomitopsis algumicola Grebenc & Spirin, F. caseosa Vlasák & Spirin, F. cupressicola Vlasák, J. Vlasák Jr. & Spirin, F. derelicta Vlasák & Spirin, F. dollingeri Vlasák & Spirin, F. fissa Vlasák & Spirin, F. lapidosa Miettinen & Spirin, F. lignicolor Vlasák & Spirin, F. maculosa Miettinen & Spirin, F. pannucea Runnel & Spirin, F. perhiemata Viner & Spirin, F. purpurea Spirin & Ryvarden, F. retorrida Spirin & Kotiranta, F. solaris Rivoire, A.M. Ainsworth & Vlasák, F. tristis Miettinen & Spirin, F. tunicata Miettinen & Spirin, F. visenda Miettinen & Spirin. New combinations: Fomitopsis aculeata (Cooke) Spirin & Miettinen, F. aethalodes (Mont.) Spirin, F. alaskana (D.V. Baxter) Spirin & Vlasák, F. albidoides (A. David & Dequatre) Bernicchia & Vlasák, F. amygdalina (Berk. & Ravenel) Spirin & Vlasák, F. angusta (Spirin & Vlasák) Spirin & Vlasák, F. atypa (Lév.) Spirin & Vlasák, F. caespitosa (Murrill) Spirin & Miettinen, F. calcitrosa (Spirin & Miettinen) Spirin & Miettinen, F. circularis (B.K. Cui & Hai J. Li) Spirin, F. concentrica (G. Cunn.) M.D. Barrett, F. cyclopis (Miettinen & Spirin) Miettinen & Spirin, F. dickinsii (Berk. ex Cooke) Spirin, F. elevata (Corner) Spirin & Miettinen, F. eucalypti (Kalchbr.) Spirin, F. ferrea (Cooke) Spirin & Viner, F. flavimontis (Vlasák & Spirin) Vlasák & Spirin, F. foedata (Berk.) Spirin & Miettinen, F. gilvidula (Bres.) Spirin & Miettinen, F. glabricystidia (Ipulet & Ryvarden) Miettinen & Ryvarden, F. globispora (Ryvarden & Aime) Spirin, F. hartmannii (Cooke) M.D. Barrett & Spirin, F. hyalina (Spirin, Miettinen & Kotir.) Spirin & Miettinen, F. hypoxantha (Bres.) Spirin & Miettinen, F. incana (Lév.) Spirin & V. Malysheva, F. infirma (Renvall & Niemelä) Miettinen & Niemelä, F. juniperina (Murrill) Spirin & Vlasák, F. kuzyana (Pilát ex Pilát) Spirin & Vlasák, F. leioderma (Mont.) Spirin & Vlasak, F. leucaena (Y.C. Dai & Niemelä) Spirin & Miettinen, F. luzonensis (Murrill) Spirin & Miettinen, F. maculatissima (Lloyd) Spirin, F. madronae (Vlasák & Ryvarden) Vlasák & Ryvarden, F. malicola (Berk. & M.A. Curtis) Spirin, F. marchionica (Mont.) Spirin & Miettinen, F. marianii (Bres.) Spirin, Vlasák & Cartabia, F. mellita (Niemelä & Penttilä) Niemelä & Miettinen, F. microcarpa (B.K. Cui & Shun Liu) Spirin, F. micropora (B.K. Cui & Shun Liu) Spirin, F. modesta (Kuntze ex Fr.) Vlasák & Spirin, F. monomitica (Yuan Y. Chen) Spirin & Viner, F. morganii (Lloyd) Spirin & Vlasák, F. moritziana (Lév.) Spirin & Miettinen, F. neotropica (D.L. Lindner, Ryvarden & T.J. Baroni) Vlasák, F. nigra (Berk.) Spirin & Miettinen, F. nivosella (Murrill) Spirin & Vlasák, F. oboensis (Decock, Amalfi & Ryvarden) Spirin, F. oleracea (R.W. Davidson & Lombard) Spirin & Vlasák, F. philippinensis (Murrill) Spirin & Vlasák, F. primaeva (Renvall & Niemelä) Miettinen & Niemelä, F. psilodermea (Berk. & Mont.) Spirin & Vlasák, F. pulverulenta (Rivoire) Rivoire, F. pulvina (Pers.) Spirin & Vlasák, F. pulvinascens (Pilát ex Pilát) Niemelä & Miettinen, F. quercina (L.) Spirin & Miettinen, F. ramentacea (Berk. & Broome) Spirin & Vlasák, F. renehenticii (Rivoire, Trichies & Vlasák) Rivoire & Vlasák, F. roseofusca (Romell) Spirin & Vlasák, F. sagraeana (Mont.) Vlasák & Spirin, F. sandaliae (Bernicchia & Ryvarden) Bernicchia & Vlasák, F. sclerotina (Rodway) M.D. Barrett & Spirin, F. serialiformis (Kout & Vlasák) Vlasák, F. serialis (Fr.) Spirin & Runnel, F. serrata (Vlasák & Spirin) Vlasák & Spirin, F. squamosella (Bernicchia & Ryvarden) Bernicchia & Ryvarden, F. stereoides (Fr.) Spirin, F. subectypa (Murrill) Spirin & Vlasák, F. substratosa (Malençon) Spirin & Miettinen, F. tropica (B.K. Cui) Spirin, F. tumulosa (Cooke) M.D. Barrett & Spirin, F. tuvensis (Spirin, Vlasák & Kotir.) Spirin & Vlasák, F. uralensis (Pilát) Spirin & Miettinen, F. ussuriensis (Bondartsev & Ljub.) Spirin & Miettinen, F. variiformis (Peck) Vlasák & Spirin, F. yunnanensis (M.L. Han & Q. An) Spirin, Daedaleopsis candicans (P. Karst.) Spirin, Megasporoporia eutelea (Har. & Pat.) Spirin & Viner, Neofomitella hemitephra (Berk.) M.D. Barrett, Pseudophaeolus soloniensis (Dubois) Spirin & Rivoire, P. trichrous (Berk. & M.A. Curtis) Vlasák & Spirin. New synonyms: Antrodia bondartsevae Spirin, A. huangshanensis Y.C. Dai & B.K. Cui, A. taxa T.T. Chang & W.N. Chou, A. wangii Y.C. Dai & H.S. Yuan, Antrodiella subnigra Oba, Mossebo & Ryvarden, Antrodiopsis Audet, Boletus quercinus Schrad., Brunneoporus Audet, Buglossoporus Kotl. & Pouzar, Buglossoporus eucalypticola M.L. Han, B.K. Cui & Y.C. Dai, Caloporus P. Karst., Cartilosoma Kotlaba & Pouzar, Coriolus clemensiae Murrill, C. cuneatiformis Murrill, C. hollickii Murrill, C. parthenius Hariot & Pat., C. rubritinctus Murrill, Daedalea Pers., Daedalea allantoidea M.L. Han, B.K. Cui & Y.C. Dai, D. americana M.L. Han, Vlasák & B.K. Cui, D. radiata B.K. Cui & Hai J. Li, D. rajchenbergiana Kossmann & Drechsler-Santos, D. sinensis Lloyd, Daedalella B.K. Cui & Shun Liu, Dentiporus Audet, Flavidoporia Audet, Fomes subferreus Murrill, Fomitopsis cana B.K. Cui, Hai J. Li & M.L. Han, F. caribensis B.K. Cui & Shun Liu, F. cystidiata B.K. Cui & M.L. Han, F. ginkgonis B.K. Cui & Shun Liu, F. iberica Melo & Ryvarden, F. incarnata K.M. Kim, J.S. Lee & H.S. Jung, F. subfeei B.K. Cui & M.L. Han, F. subtropica B.K. Cui & Hai J. Li, Fragifomes B.K. Cui, M.L. Han & Y.C. Dai, Leptoporus epileucinus Pilát, Melanoporia Murrill, Neoantrodia Audet, Neolentiporus Rajchenb., Nigroporus macroporus Ryvarden & Iturr., Niveoporofomes B.K. Cui, M.L. Han & Y.C. Dai, Pilatoporus Kotl. & Pouzar, Piptoporus P. Karst., Polyporus aurora Ces., P. durescens Overh. ex J. Lowe, P. griseodurus Lloyd, Poria incarnata Pers., Pseudoantrodia B.K. Cui, Y.Y. Chen & Shun Liu, Pseudofomitopsis B.K. Cui & Shun Liu, Ranadivia Zmitr., Rhizoporia Audet, Rhodofomes Kotl. & Pouzar, Rhodofomitopsis B.K. Cui, M.L. Han & Y.C. Dai, Rhodofomitopsis pseudofeei B.K. Cui & Shun Liu, R. roseomagna Nogueira-Melo, A.M.S. Soares & Gibertoni, Rubellofomes B.K. Cui, M.L. Han & Y.C. Dai, Subantrodia Audet, Trametes fulvirubida Corner, T. lignea Murrill, T. lusor Corner, T. pseudodochmia Corner, T. subalutacea Bourdot & Galzin, T. supermodesta Ryvarden & Iturr., T. tuberculata Bres., Tyromyces multipapillatus Corner, T. ochraceivinosus Corner, T. palmarum Murrill, T. singularis Corner, T. squamosellus Núñez & Ryvarden, Ungulidaedalea B.K. Cui, M.L. Han & Y.C. Dai. Lectotypes: Hexagonia sulcata Berk., Polyporus castaneae Bourdot & Galzin, Poria incarnata Pers., Trametes subalutacea Bourdot & Galzin, Ungulina substratosa Malençon. Neotypes: Agaricus soloniensis Dubois, Boletus pulvinus Pers. Citation: Spirin V, Runnel K, Vlasák J, Viner I, Barrett MD, Ryvarden L, Bernicchia A, Rivoire B, Ainsworth AM, Grebenc T, Cartabia M, Niemelä T, Larsson K-H, Miettinen O (2024). The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered. Studies in Mycology 107: 149-249. doi: 10.3114/sim.2024.107.03.
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Affiliation(s)
- V. Spirin
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - K. Runnel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - J. Vlasák
- Biology Centre, Academy of Sciences of the Czech Republic, Branišovská 31, CZ 37005, České Budějovice, Czech Republic
| | - I. Viner
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - M.D. Barrett
- Australian Tropical Herbarium, Sir Robert Norman Building, James Cook University Cairns Campus, McGregor Road, Smithfield, QLD 4878, Australia
| | - L. Ryvarden
- Institute of Biological Sciences, University of Oslo, P.O. Box 1045, Blindern, N-0316 Oslo, Norway
| | | | - B. Rivoire
- Société Linnéenne de Lyon, 33 rue Bossuet, 69006 Lyon, France
| | - A.M. Ainsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE UK
| | - T. Grebenc
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
| | | | - T. Niemelä
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
| | - K.-H. Larsson
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - O. Miettinen
- Botany Unit (Mycology), Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland
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16
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Sirsi S, Rodriguez D, Forstner MRJ. Using genome-wide data to ascertain taxonomic status and assess population genetic structure for Houston toads (Bufo [= Anaxyrus] houstonensis). Sci Rep 2024; 14:3306. [PMID: 38332325 PMCID: PMC10853240 DOI: 10.1038/s41598-024-53705-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/04/2024] [Indexed: 02/10/2024] Open
Abstract
The Houston toad (Bufo [= Anaxyrus] houstonensis) is an endangered amphibian with a small geographic range. Land-use changes have primarily driven decline in B. houstonensis with population supplementation predominant among efforts to reduce its current extinction risk. However, there has been historic uncertainty regarding the evolutionary and conservation significance of B. houstonensis. To this end, we used 1170 genome-wide nuclear DNA markers to examine phylogenetic relationships between our focal taxon, representatives of the Nearctic B. americanus group, and B. nebulifer, a sympatric Middle American species. Phylogenetic analyses indicate B. houstonensis is a taxon that is distinct from B. americanus. We corroborated such genetic distinctiveness with an admixture analysis that provided support for recent reproductive isolation between B. americanus and B. houstonensis. However, ABBA-BABA tests for ancient admixture indicated historic gene flow between Nearctic species while no signal of historic gene flow was detected between Nearctic and Middle-American species. We used an admixture analysis to recognize four Management Units (MU) based on observed genetic differentiation within B. houstonensis and recommend captive propagation, population supplementation, and habitat restoration efforts specific to each MU. Our results re-affirm the evolutionary novelty of an endangered relict.
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Affiliation(s)
- Shashwat Sirsi
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.
| | - David Rodriguez
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Michael R J Forstner
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
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17
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Dalapicolla J, Rodrigues do Prado J, Lacey Knowles L, Reis Percequillo A. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Mol Phylogenet Evol 2024; 191:107992. [PMID: 38092321 DOI: 10.1016/j.ympev.2023.107992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 12/01/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.
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Affiliation(s)
- Jeronymo Dalapicolla
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil; Instituto Tecnológico Vale, Belém, Pará, Brazil.
| | | | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, São Paulo, Brazil
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18
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Seesamut T, Oba Y, Jirapatrasilp P, Martinsson S, Lindström M, Erséus C, Panha S. Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855). Sci Rep 2024; 14:1753. [PMID: 38243053 PMCID: PMC10799051 DOI: 10.1038/s41598-024-52252-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.
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Affiliation(s)
- Teerapong Seesamut
- Department of Biology, Faculty of Science, Rangsit University, Pathumthani, 12000, Thailand
| | - Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai, 487-8501, Japan
| | - Parin Jirapatrasilp
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Svante Martinsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Göteborg, Sweden
| | - Maria Lindström
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Göteborg, Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Göteborg, Sweden.
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300, Thailand.
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19
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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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20
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Hubert N, Phillips JD, Hanner RH. Delimiting Species with Single-Locus DNA Sequences. Methods Mol Biol 2024; 2744:53-76. [PMID: 38683311 DOI: 10.1007/978-1-0716-3581-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.
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Affiliation(s)
- Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France.
| | - Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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21
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Pyron RA, Kakkera A, Beamer DA, O'Connell KA. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype. Mol Ecol 2024; 33:e17219. [PMID: 38015012 DOI: 10.1111/mec.17219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Anvith Kakkera
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia, USA
| | - David A Beamer
- Office of Research, Economic Development and Engagement, East Carolina University, Greenville, North Carolina, USA
| | - Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
- Deloitte Consulting LLP, Health and Data AI, Arlington, Virginia, USA
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22
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Chan KO, Mulcahy DG, Anuar S. The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex). Syst Biol 2023; 72:1209-1219. [PMID: 37478480 DOI: 10.1093/sysbio/syad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/19/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiates the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Daniel G Mulcahy
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Shahrul Anuar
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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23
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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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24
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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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25
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Muñoz-Ramírez CP, Colin N, Canales-Aguirre CB, Manosalva A, López-Rodríguez R, Sukumaran J, Górski K. Species tree analyses and speciation-based species delimitation support new species in the relict catfish family Diplomystidae and provide insights on recent glacial history in Patagonia. Mol Phylogenet Evol 2023; 189:107932. [PMID: 37751827 DOI: 10.1016/j.ympev.2023.107932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 09/28/2023]
Abstract
Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of Diplomystes as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species D. nahuelbutaensis is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: Diplomystes arratiae sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining D. nahuelbutaensis valid only for the Imperial Basin, and Diplomystes habitae sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNA-based taxonomy.
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Affiliation(s)
- Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - Nicole Colin
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristian B Canales-Aguirre
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio INVASAL, Concepción, Chile
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Chile
| | - Ruby López-Rodríguez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Konrad Górski
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile.
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26
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Wang WY, Yamada A. Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics. PeerJ 2023; 11:e16416. [PMID: 38025712 PMCID: PMC10657568 DOI: 10.7717/peerj.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.
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Affiliation(s)
- Wendy Y. Wang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Aiki Yamada
- Systematic Zoology Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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27
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Gretgrix LJ, Decker O, Green PT, Köhler F, Moussalli A, Murphy NP. Genetic diversity of a short-ranged endemic terrestrial snail. Ecol Evol 2023; 13:e10785. [PMID: 38034337 PMCID: PMC10684984 DOI: 10.1002/ece3.10785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
The factors that influence population structure and connectivity are unknown for most terrestrial invertebrates but are of particular interest both for understanding the impacts of disturbance and for determining accurate levels of biodiversity and local endemism. The main objective of this study was to determine the historical patterns of genetic differentiation and contemporary gene flow in the terrestrial snail, Austrochloritis kosciuszkoensis (Shea & O. L. Griffiths, 2010). Snails were collected in the Mt Buffalo and Alpine National Parks in Victoria, in a bid to understand how populations of this species are connected both within continuous habitat and between adjacent, yet separate environments. Utilising both mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, the degree of population structure was determined within and between sites. Very high levels of genetic divergence were found between the Mt Buffalo and Alpine snails, with no evidence for genetic exchange detected between the two regions, indicating speciation has possibly occurred between the two regions. Our analyses of the combined mtDNA and nDNA (generated from SNPs) data have revealed patterns of genetic diversity that are consistent with a history of long-term isolation and limited connectivity. This history may be related to past cycles of changes to the climate over hundreds of thousands of years, which have, in part, caused the fragmentation of Australian forests. Within both regions, extremely limited gene flow between separate populations suggests that these land snails have very limited dispersal capabilities across existing landscape barriers, especially at Mt Buffalo: here, populations only 5 km apart from each other are genetically differentiated. The distinct genetic divergences and clearly reduced dispersal ability detected in this data explain the likely existence of at least two previously unnamed cryptic Austrochloritis species within a 30-50 km radius, and highlight the need for more concentrated efforts to understand population structure and gene flow in terrestrial invertebrates.
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Affiliation(s)
- Lachlan J. Gretgrix
- Department of Environment and Genetics, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Orsi Decker
- Department of Environment and Genetics, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
- Bavarian National ParkNationalparkverwaltung Bayerischer WaldGrafenauGermany
| | - Peter T. Green
- Department of Environment and Genetics, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | | | | | - Nicholas P. Murphy
- Department of Environment and Genetics, School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
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28
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Unmack PJ, Cook BD, Johnson JB, Hammer MP, Adams M. Phylogeography of a widespread Australian freshwater fish, western carp gudgeon (Eleotridae: Hypseleotris klunzingeri): Cryptic species, hybrid zones, and strong intra-specific divergences. Ecol Evol 2023; 13:e10682. [PMID: 37920767 PMCID: PMC10618717 DOI: 10.1002/ece3.10682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co-occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here, we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between-species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray-Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together, these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.
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Affiliation(s)
- Peter J Unmack
- Centre for Applied Water Science Institute for Applied Ecology, University of Canberra Canberra Australian Capital Territory Australia
| | - Benjamin D Cook
- Australian Rivers Institute, Griffith University Brisbane Queensland Australia
- frc environmental Wellington Point Queensland Australia
| | - Jerald B Johnson
- Evolutionary Ecology Laboratories, Department of Biology Brigham Young University Provo Utah USA
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory Darwin Northwest Territories Australia
| | - Mark Adams
- Evolutionary Biology Unit South Australian Museum Adelaide South Australia Australia
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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29
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Dufresnes C, Poyarkov N, Jablonski D. Acknowledging more biodiversity without more species. Proc Natl Acad Sci U S A 2023; 120:e2302424120. [PMID: 37748058 PMCID: PMC10556632 DOI: 10.1073/pnas.2302424120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets ("genomic taxonomy"), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research, College of Biology and Environment, Nanjing Forestry University, Nanjing210037, People’s Republic of China
| | - Nikolay Poyarkov
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi122000, Vietnam
- Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow119234, Russia
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava84215, Slovakia
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30
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Sánchez KI, Diaz Huesa EG, Breitman MF, Avila LJ, Sites JW, Morando M. Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade). Syst Biol 2023; 72:739-752. [PMID: 37097104 DOI: 10.1093/sysbio/syad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Emilce G Diaz Huesa
- Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEAus-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - María F Breitman
- Department of Biology and Environmental Science, Auburn University at Montgomery, Montgomery, 36117, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology, Austin Peay State University, Clarksville, 37044, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Puerto Madryn, U9120ACD, Argentina
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31
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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32
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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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33
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Calixto-Rojas M, Lira-Noriega A, Rubio-Godoy M, Pérez-Ponce de León G, Pinacho-Pinacho CD. Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty. Mol Phylogenet Evol 2023:107856. [PMID: 37327830 DOI: 10.1016/j.ympev.2023.107856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.
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Affiliation(s)
- Miguel Calixto-Rojas
- Doctorado en Ciencias, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Miguel Rubio-Godoy
- Instituto de Ecología, A.C., Red de Biología Evolutiva, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Gerardo Pérez-Ponce de León
- Escuela Nacional de Estudios Superiores unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Municipio de Ucú, Yucatán 97357, Mexico
| | - Carlos D Pinacho-Pinacho
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
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34
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Arantes ÍC, Vasconcellos MM, Smith ML, Garrick RC, Colli GR, Noonan BP. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Mol Phylogenet Evol 2023:107843. [PMID: 37286064 DOI: 10.1016/j.ympev.2023.107843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.
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Affiliation(s)
- Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
| | - Mariana M Vasconcellos
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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35
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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36
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Zhang W, Hu Y, Zhang S, Shao J. Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex. Mol Phylogenet Evol 2023:107840. [PMID: 37279815 DOI: 10.1016/j.ympev.2023.107840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; College of Life Sciences, Anqing Normal University, Anqing 246011, Anhui, China
| | - Yingfeng Hu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Siyu Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; Provincial Key Laboratory of Conservation and Utilization of Biological Resources, Wuhu 241000, Anhui, China.
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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Garrido-Benavent I, de Los Ríos A, Núñez-Zapata J, Ortiz-Álvarez R, Schultz M, Pérez-Ortega S. Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota). Mol Phylogenet Evol 2023:107829. [PMID: 37247701 DOI: 10.1016/j.ympev.2023.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/24/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.
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Affiliation(s)
- Isaac Garrido-Benavent
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València, C/ Doctor Moliner 50, E-46100-Burjassot, València, Spain; Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Serrano 115 dpdo, E-28045 Madrid, Spain.
| | - Jano Núñez-Zapata
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Rüdiger Ortiz-Álvarez
- Department of International Science, Spanish Federation of Science and Technology (FECYT), C/ Pintor Murillo 15, E-28100 Alcobendas, Madrid, Spain.
| | - Matthias Schultz
- Herbarium Hamburgense, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany.
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
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40
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Oswald CB, de Magalhães RF, Garcia PC, Santos FR, Neckel-Oliveira S. Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest. PeerJ 2023; 11:e15393. [PMID: 37250715 PMCID: PMC10225124 DOI: 10.7717/peerj.15393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Background The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.
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Affiliation(s)
- Caroline Batistim Oswald
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafael Félix de Magalhães
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Paulo C.A. Garcia
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Fabrício R. Santos
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Selvino Neckel-Oliveira
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Mera-Rodríguez D, Jourdan H, Ward PS, Shattuck S, Cover SP, Wilson EO, Rabeling C. Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics. Mol Phylogenet Evol 2023:107825. [PMID: 37244505 DOI: 10.1016/j.ympev.2023.107825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Studying the historical biogeography and life history transitions from eusocial colony life to social parasitism contributes to our understanding of the evolutionary mechanisms generating biodiversity in eusocial insects. The ants in the genus Myrmecia are a well-suited system for testing evolutionary hypotheses about how their species diversity was assembled through time because the genus is endemic to Australia with the single exception of the species M. apicalis inhabiting the Pacific Island of New Caledonia, and because at least one social parasite species exists in the genus. However, the evolutionary mechanisms underlying the disjunct biogeographic distribution of M. apicalis and the life history transition(s) to social parasitism remain unexplored. To study the biogeographic origin of the isolated, oceanic species M. apicalis and to reveal the origin and evolution of social parasitism in the genus, we reconstructed a comprehensive phylogeny of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements (UCEs) as molecular markers to generate a comprehensive molecular genetic dataset consisting of 2,287 loci per taxon on average for 66 out of the 93 known Myrmecia species as well as for the sister lineage Nothomyrmecia macrops and selected outgroups. Our time-calibrated phylogeny inferred that: (i) stem Myrmeciinae originated during the Paleocene ∼58 Ma ago; (ii) the current disjunct biogeographic distribution of M. apicalis was driven by long-distance dispersal from Australia to New Caledonia during the Miocene ∼14 Ma ago; (iii) the single social parasite species, M. inquilina, evolved directly from one of the two known host species, M. nigriceps, in sympatry via the intraspecific route of social parasite evolution; and (iv) 5 of the 9 previously established taxonomic species groups are non-monophyletic. We suggest minor changes to reconcile the molecular phylogenetic results with the taxonomic classification. Our study enhances our understanding of the evolution and biogeography of Australian bulldog ants, contributes to our knowledge about the evolution of social parasitism in ants, and provides a solid phylogenetic foundation for future inquiries into the biology, taxonomy, and classification of Myrmeciinae.
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Affiliation(s)
- Daniela Mera-Rodríguez
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany.
| | - Hervé Jourdan
- Institute of Research for Development. Promenade Roger Laroque, Nouméa 98848, New Caledonia
| | - Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, CA 95616, United States of America
| | - Steven Shattuck
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Stefan P Cover
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Edward O Wilson
- Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America
| | - Christian Rabeling
- Social Insect Research Group, School of Life Sciences, Arizona State University. 550 E Orange St., Tempe, AZ 85281, United States of America; Department of Integrative Taxonomy of Insects, Institute of Biology, University of Hohenheim. Garbenstraße 30, 70599, Stuttgart, Germany; KomBioTa - Center for Biodiversity and Integrative Taxonomy, University of Hohenheim and State Museum of Natural History Stuttgart, Germany; Museum of Comparative Zoology, Harvard University. 26 Oxford Street, Cambridge, MA 02138, United States of America.
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Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
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Brandt S, Sole C, Lyle R. The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa. Mol Phylogenet Evol 2023; 184:107798. [PMID: 37094612 DOI: 10.1016/j.ympev.2023.107798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.
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Affiliation(s)
- Shannon Brandt
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Catherine Sole
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Robin Lyle
- Agricultural Research Council - Plant Health and Protection, Biosystematics, Roodeplaat, Pretoria, South Africa
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Yi H, Dong S, Yang L, Wang J, Kidner C, Kang M. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Mol Phylogenet Evol 2023; 184:107801. [PMID: 37088242 DOI: 10.1016/j.ympev.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Shiying Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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Whelan NV, Strong EE, Gladstone NS, Mays JW. Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Pateranantahala (Gastropoda, Polygyridae). Zookeys 2023; 1158:91-120. [PMID: 37234252 PMCID: PMC10208601 DOI: 10.3897/zookeys.1158.94152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/13/2023] [Indexed: 05/27/2023] Open
Abstract
Terrestrial gastropods are among the most imperiled groups of organisms on Earth. Many species have a complex taxonomic history, often including poorly defined subspecies, most of which have not been the focus of modern systematics research. Genomic tools, geometric morphometrics, and environmental niche modeling were used to assess the taxonomic status of Pateraclarkiinantahala (Clench & Banks, 1932), a subspecies of high conservation concern with a restricted range of approximately 3.3 km2 in North Carolina, USA. A genome-scale dataset was generated that included individuals with morphologies matching P.c.nantahala, P.c.clarkii, and one individual with an intermediate form between P.c.nantahala and P.c.clarkii that was initially hypothesized as a potential hybrid. Mitochondrial phylogenetics, nuclear species tree inference, and phylogenetic networks were used to assess relationships and gene flow. Differences in shell shape via geometric morphometrics and whether the environmental niches of the two subspecies were significantly different were also examined. Molecular analyses indicated an absence of gene flow among lineages of P.clarkii sensu lato. Analyses rejected our hypothesis that the intermediate shelled form represented a hybrid, but instead indicated that it was a distinct lineage. Environmental niche models indicated significant differences in environmental niche between P.c.clarkii and P.c.nantahala, and geometric morphometrics indicated that P.c.nantahala had a significantly different shell shape. Given multiple lines of evidence, species-level recognition of P.nantahala is warranted.
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Affiliation(s)
- Nathan V. Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, US Fish and Wildlife Service, 203 Swingle Hall, Auburn, Alabama, 36849, USAAuburn UniversityAuburnUnited States of America
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Ellen E. Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Nicholas S. Gladstone
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Jason W. Mays
- Asheville Ecological Services Field Office, United States Fish and Wildlife Service, 160 Zillicoa ST, Asheville, NC 28801, USAAsheville Ecological Services Field Office, United States Fish and Wildlife ServiceAshevilleUnited States of America
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Newton LG, Starrett J, Jochim EE, Bond JE. Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae). Ecol Evol 2023; 13:e10025. [PMID: 37122769 PMCID: PMC10133383 DOI: 10.1002/ece3.10025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.
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Affiliation(s)
- Lacie G. Newton
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - James Starrett
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Emma E. Jochim
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jason E. Bond
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex. BIOLOGY 2023; 12:biology12030418. [PMID: 36979110 PMCID: PMC10045763 DOI: 10.3390/biology12030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.
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Sierra-Patev S, Min B, Naranjo-Ortiz M, Looney B, Konkel Z, Slot JC, Sakamoto Y, Steenwyk JL, Rokas A, Carro J, Camarero S, Ferreira P, Molpeceres G, Ruiz-Dueñas FJ, Serrano A, Henrissat B, Drula E, Hughes KW, Mata JL, Ishikawa NK, Vargas-Isla R, Ushijima S, Smith CA, Donoghue J, Ahrendt S, Andreopoulos W, He G, LaButti K, Lipzen A, Ng V, Riley R, Sandor L, Barry K, Martínez AT, Xiao Y, Gibbons JG, Terashima K, Grigoriev IV, Hibbett D. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A 2023; 120:e2214076120. [PMID: 36848567 PMCID: PMC10013852 DOI: 10.1073/pnas.2214076120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023] Open
Abstract
Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia-Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase (lecsl) and γ-glutamyl transpeptidase (leggt), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula. Paralogs of both genes that are unique to Lentinula (lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes. The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.
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Affiliation(s)
| | - Byoungnam Min
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Brian Looney
- Biology Department, Clark University, Worcester, MA01610
| | - Zachary Konkel
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Jason C. Slot
- Department of Plant Pathology, Ohio State University, Columbus, OH43210
| | - Yuichi Sakamoto
- Iwate Biotechnology Research Center, Kitakami, Iwate024-0003, Japan
| | - Jacob L. Steenwyk
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN37235
| | - Juan Carro
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, 50009Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza,50018Zaragoza, Spain
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Université13288, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques13009, Marseille, France
| | - Karen W. Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN37996
| | - Juan L. Mata
- Department of Biology, University of South Alabama, Mobile, AL36688
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, ManausAM 69067-375, Brazil
| | - Shuji Ushijima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Chris A. Smith
- Manaaki Whenua - Landcare Research, Auckland1072, New Zealand
| | - John Donoghue
- Northwest Mycological Consultants, Corvallis, OR97330
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Guifen He
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Laura Sandor
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas “Margarita Salas,” Consejo Superior de Investigaciones Científicas, MadridE-28040, Spain
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei430070, China
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA01003
| | - Kazuhisa Terashima
- The Tottori Mycological Institute, Japan Kinoko Research Center Foundation, Tottori689-1125, Japan
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA94720
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA01610
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49
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Gorring PS, Farrell BD. Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles. Mol Phylogenet Evol 2023; 184:107777. [PMID: 36990304 DOI: 10.1016/j.ympev.2023.107777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 02/18/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Plant-feeding beetle species are diverse and often individually highly variable. Accurate classifications can be difficult to establish yet are essential for study of evolutionary patterns and processes. Molecular data are key to further characterizing morphologically difficult groups and defining genus and species boundaries. Monochamus Dejean species are ecologically and economically significant, and in coniferous forests they vector the nematode that causes Pine Wilt Disease. This study uses nuclear and mitochondrial genes to test the monophyly and relationships of Monochamus and applies coalescent methods to further delimit the conifer-feeding species. Monochamus has also included approximately 120 Old World species associated with diverse angiosperm tree species. We sample from these additional morphologically diverse species to determine their placement in the Lamiini. Through supermatrix and coalescent methods, the higher-level relationships of Monochamus show that conifer-feeders are a monophyletic group that includes the type species and has split into Nearctic and Palearctic clades. Molecular dating indicates a single dispersal of conifer-feeders to North America over the second Bering Land Bridge circa 5.3 Ma. All other Monochamus sampled fall in different parts of the Lamiini tree. Small-bodied angiosperm-feeding Monochamus group with the monotypic genus Microgoes Casey. The African Monochamus subgenera sampled are distantly related to the conifer-feeding clade. The multispecies coalescent delimitation methods BPP and STACEY delimit 17 conifer-feeding Monochamus species for a total of 18 species, and supports the retention of all current species. An interrogation with nuclear gene allele phasing reveals that unphased data can be unreliable for accurate delimitations and divergence times. The delimited species are discussed with integrative evidence, highlighting real-world challenges in recognizing the completion of speciation trajectories.
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Affiliation(s)
- Patrick S Gorring
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St. Cambridge, MA, USA.
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St. Cambridge, MA, USA
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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