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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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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; 39:771-784. [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] [MESH Headings] [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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3
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Wang MZ, Wu J, Zhang SL, Mao LM, Ohi-Toma T, Takano A, Zhang YH, Cameron KM, Li P. Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity. Cladistics 2024; 40:135-156. [PMID: 37983640 DOI: 10.1111/cla.12565] [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: 12/14/2022] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.
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Affiliation(s)
- Mei-Zhen Wang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jing Wu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Sheng-Lu Zhang
- Plant Quarantine Station of Lin'an District, Hangzhou, 311300, Zhejiang, China
| | - Li-Mi Mao
- Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, China
| | - Tetsuo Ohi-Toma
- Nature Fieldwork Center, Okayama University of Science, Okayama, 700-0005, Japan
| | - Atsuko Takano
- Museum of Nature and Human Activities, Hyogo 6 chome, Yayoigaoka, Sanda, Hyogo, 669-1546, Japan
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Kenneth M Cameron
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
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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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5
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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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6
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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [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: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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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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8
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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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9
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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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10
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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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11
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Hernández-Díaz YQ, Solis F, Beltrán-López RG, Benítez HA, Díaz-Jaimes P, Paulay G. Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics. PeerJ 2023; 11:e15655. [PMID: 37483979 PMCID: PMC10358340 DOI: 10.7717/peerj.15655] [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: 02/02/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
Ophiothrix angulata (Say, 1825) is one of the most common and well-known ophiuroids in the Western Atlantic, with a wide geographic and bathymetric range. The taxonomy of this species has been controversial for a century because of its high morphological variability. Here we integrate information from DNA sequence data, color patterns, and geometric morphometrics to assess species delimitation and geographic differentiation in O. angulata. We found three deeply divergent mtDNA-COI clades (K2P 17.0-27.9%). ITS2 nuclear gene and geometric morphometrics of dorsal and ventral arm plates differentiate one of these lineages, as do integrative species delineation analyses, making this a confirmed candidate species.
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Affiliation(s)
- Yoalli Quetzalli Hernández-Díaz
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Unidad Multidisciplinaria de Docencia e Investigación - Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Yucatán, México
| | - Francisco Solis
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosa G. Beltrán-López
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Hugo A. Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Universidad Católica del Maule, Talca, Chile
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Gustav Paulay
- Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America
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12
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Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives. BIOLOGY 2023; 12:biology12020288. [PMID: 36829565 PMCID: PMC9953438 DOI: 10.3390/biology12020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the 'Wettstein tesseract') led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov.
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13
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Joffard N, Buatois B, Arnal V, Véla E, Montgelard C, Schatz B. Delimiting species in the taxonomically challenging orchid section Pseudophrys: Bayesian analyses of genetic and phenotypic data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1058550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accurate species delimitation is critical for biodiversity conservation. Integrative taxonomy has been advocated for a long time, yet tools allowing true integration of genetic and phenotypic data have been developed quite recently and applied to few models, especially in plants. In this study, we investigated species boundaries within a group of twelve Pseudophrys taxa from France by analyzing genetic, morphometric and chemical (i.e., floral scents) data in a Bayesian framework using the program integrated Bayesian Phylogenetics and Phylogeography (iBPP). We found that these twelve taxa were merged into four species when only genetic data were used, while most formally described species were recognized as such when only phenotypic (either morphometric or chemical) data were used. The result of the iBPP analysis performed on both genetic and phenotypic data supports the proposal to merge Ophrys bilunulata and O. marmorata on the one hand, and O. funerea and O. zonata on the other hand. Our results show that phenotypic data are particularly informative in the section Pseudophrys and that their integration in a model-based method significantly improves the accuracy of species delimitation. We are convinced that the integrative taxonomic approach proposed in this study holds great promise to conduct taxonomic revisions in other orchid groups.
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14
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Barrett CF, Santee MV, Fama NM, Freudenstein JV, Simon SJ, Sinn BT. Lineage and role in integrative taxonomy of a heterotrophic orchid complex. Mol Ecol 2022; 31:4762-4781. [PMID: 35837745 PMCID: PMC9452484 DOI: 10.1111/mec.16617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Mathilda V. Santee
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Nicole M. Fama
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - John V. Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Rd., Columbus, Ohio, USA 43212
| | - Sandra J. Simon
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, USA
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, USA
- Department of Botany and Ecology, University of Latvia, Jelgavas iela 1, Riga, LV-1004, Latvia
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15
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Sidharthan C, Roy P, Narayanan S, Karanth KP. A widespread commensal loses its identity: suggested taxonomic revision for Indotyphlops braminus (Scolecophidia: Typhlopidae) based on molecular data. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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16
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The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives. PLANTS 2022; 11:plants11141878. [PMID: 35890512 PMCID: PMC9319895 DOI: 10.3390/plants11141878] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022]
Abstract
Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein’s morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an ‘integrative taxonomy’ fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz’s “Unified Species Concept”.
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17
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Zhao Z, Oosthuizen J, Heideman N. How many species does the
Psammobates tentorius
(tent tortoise) species complex (Reptilia, Testudinidae) comprise? A taxonomic solution potentially applicable to species complexes. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Jaco Oosthuizen
- School of Pathology University of the Free Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
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19
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Perez MF, Bonatelli IAS, Romeiro-Brito M, Franco FF, Taylor NP, Zappi DC, Moraes EM. Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system. Mol Ecol Resour 2021; 22:1016-1028. [PMID: 34669256 DOI: 10.1111/1755-0998.13534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 11/26/2022]
Abstract
Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.
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Affiliation(s)
- Manolo F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
| | | | - Daniela C Zappi
- Programa de Pós Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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20
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Bray RA, Cutmore SC, Cribb TH. A paradigm for the recognition of cryptic trematode species in tropical Indo-west Pacific fishes: the problematic genus Preptetos (Trematoda: Lepocreadiidae). Int J Parasitol 2021; 52:169-203. [PMID: 34656610 DOI: 10.1016/j.ijpara.2021.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/30/2022]
Abstract
Molecular data have transformed approaches to trematode taxonomy by providing objective evidence for the delineation of species. However, although the data are objective, the interpretation of these data regarding species boundaries is subjective, especially when different markers conflict. Conserved markers can lead to an underestimation of richness and those used for finer species delineation have the capacity to inflate species recognition, perhaps unrealistically. Here we examine molecular and morphological evidence for species recognition in an especially confusing system, the lepocreadiid genus Preptetos Pritchard, 1960 in acanthuriform fishes of the tropical Indo-west Pacific. We consider species boundaries within this genus based on combined data (ITS2 and 28S rDNA; cox1 mtDNA and morphometrics) for substantial new collections. Delineation of species using only morphological data suggest fewer species than analysis of the sequence data; the latter suggests the presence of potential cryptic species and analysis of different markers suggests the presence of differing numbers of species. We conclude that an integrative interpretation creates the most satisfying taxonomic hypothesis. In the light of the new data, we have chosen and propose a model of trematode species recognition that demands reciprocal monophyly in the most discriminating available molecular marker plus distinction in morphology or host distribution. By invoking these criteria, we distinguish eight species in our new tropical Indo-west Pacific collections. Six of these are new (Preptetos allocaballeroi n. sp., Preptetos paracaballeroi n. sp., Preptetos pearsoni n. sp., Preptetos prudhoei n. sp., Preptetos quandamooka n. sp. and Preptetos zebravaranus n. sp.) and we continue to recognise Preptetos cannoni Barker, Bray & Cribb, 1993 and Preptetos laguncula Bray and Cribb, 1996. Notably; two of the new species, P. allocaballeroi n. sp. and P. paracaballeroi n. sp., are morphologically cryptic relative to each other. Our criteria lead us to recognise, as species, populations with unvarying morphology and similar host relationships but which may have a complex population structure over their range. In our view, this paradigm has the capacity to render tractable the interpretation of the species status of the huge trematode fauna of the tropical Indo-west Pacific.
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Affiliation(s)
- Rodney A Bray
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Scott C Cutmore
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
| | - Thomas H Cribb
- The University of Queensland, School of Biological Sciences, St Lucia, Queensland 4072, Australia
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21
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Unmack PJ, Adams M, Hammer MP, Johnson JB, Gruber B, Gilles A, Young M, Georges A. Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.
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Affiliation(s)
- Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Mark Adams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Jerald B Johnson
- Department of Biology, Brigham Young University, Provo, UT, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Bernd Gruber
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - André Gilles
- UMR 1467 RECOVER, Aix Marseille Univ, INRAE, Centre St Charles, 3 place Victor Hugo, Marseille, France
| | - Matthew Young
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
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22
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Prado JR, Knowles LL, Percequillo AR. A new species of South America marsh rat (Holochilus, Cricetidae) from northeastern Brazil. J Mammal 2021. [DOI: 10.1093/jmammal/gyab104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Marsh rats of the genus Holochilus are broadly distributed and inhabit several distinct environments throughout South America. As an enigmatic group with a somewhat uncertain taxonomy, the composition and names of taxa have shifted throughout history, including the boundaries of Holochilus sciureus, a species formerly distributed in the lowlands of the Guianas, Peru, Bolivia, and northern, central, and northeastern of Brazil. Based on a combination of morphological and morphometric traits, and genomic sequences, we redefined species boundaries and split this wide concept of H. sciureus into three separated species, including a redefined H. sciureus, the newly erected from synonymy H. nanus, and an unnamed taxon. We describe this unnamed species, and provide emended diagnoses for the two redefined species. The newly named taxon inhabits the northeastern part of Brazil and differs from the other congeners by a unique combination of phenotypic and genomic characters.
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Affiliation(s)
- Joyce R Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
| | - Alexandre R Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Piracicaba, SP, Brazil
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23
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Calderon MS, Bustamante DE, Gabrielson PW, Martone PT, Hind KR, Schipper SR, Mansilla A. Type specimen sequencing, multilocus analyses, and species delimitation methods recognize the cosmopolitan Corallina berteroi and establish the northern Japanese C. yendoi sp. nov. (Corallinaceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2021; 57:1659-1672. [PMID: 34310713 DOI: 10.1111/jpy.13202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
A partial rbcL sequence of the lectotype specimen of Corallina berteroi shows that it is the earliest available name for C. ferreyrae. Multilocus species delimitation analyses (ABGD, SPN, GMYC, bPTP, and BPP) using independent or concatenated COI, psbA, and rbcL sequences recognized one, two, or three species in this complex, but only with weak support for each species hypothesis. Conservatively, we recognize a single worldwide species in this complex of what appears to be multiple, evolving populations. Included in this species, besides C. ferreyrae, are C. caespitosa, the morphologically distinct C. melobesioides, and, based on a partial rbcL sequence of the holotype specimen, C. pinnatifolia. Corallina berteroi, not C. officinalis, is the cosmopolitan temperate species found thus far in the NE Atlantic, Mediterranean Sea, warm temperate NW Atlantic and NE Pacific, cold temperate SW Atlantic (Falkland Islands), cold and warm temperate SE Pacific, NW Pacific and southern Australia. Also proposed is C. yendoi sp. nov. from Hokkaido, Japan, which was recognized as distinct by 10 of the 13 species discrimination analyses, including the multilocus BPP.
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Affiliation(s)
- Martha S Calderon
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile
| | - Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
- Department of Civil and Environmental Engineering (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
| | - Paul W Gabrielson
- Biology Department and Herbarium, Coker Hall CB 3280, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, 27599-3280, USA
| | - Patrick T Martone
- Botany Department & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Katharine R Hind
- Department of Biology, University of Victoria, PO Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Soren R Schipper
- Botany Department & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Andrés Mansilla
- Laboratorio de Ecosistemas Marinos Antárticos y Sub-antárticos (LEMAS), Universidad de Magallanes, Punta Arenas, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile
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24
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Frugone MJ, Cole TL, López ME, Clucas G, Matos‐Maraví P, Lois NA, Pistorius P, Bonadonna F, Trathan P, Polanowski A, Wienecke B, Raya‐Rey A, Pütz K, Steinfurth A, Bi K, Wang‐Claypool CY, Waters JM, Bowie RCK, Poulin E, Vianna JA. Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- María José Frugone
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de Chile Valdivia Chile
| | - Theresa L. Cole
- Department of Zoology University of Otago Dunedin New Zealand
- Department of Biology, Ecology and Evolution University of Copenhagen Copenhagen Denmark
| | - María Eugenia López
- Department of Aquatic Resources Swedish University of Agricultural Sciences Drottningholm Sweden
| | - Gemma Clucas
- Atkinson Center for a Sustainable Future Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Cornell University Ithaca NY USA
| | - Pável Matos‐Maraví
- Biology Centre of the Czech Academy of SciencesInstitute of Entomology České Budějovice Czech Republic
| | - Nicolás A. Lois
- Departamento de Ecología Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Ecología Genética y Evolución de Buenos AiresConsejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires Argentina
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology Department of Zoology Nelson Mandela University Port Elizabeth South Africa
| | | | | | | | | | - Andrea Raya‐Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC‐CONICET) Ushuaia Argentina
- Wildlife Conservation Society Bronx NY USA
- Instituto de Ciencias Polares, Ambiente y Recursos NaturalesUniversidad Nacional de Tierra del Fuego Ushuaia Argentina
| | | | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology University of Cape Town Rondebosch South Africa
- RSPB Centre for Conservation Science Cambridge UK
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Cynthia Y. Wang‐Claypool
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | | | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Elie Poulin
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
| | - Juliana A. Vianna
- Pontificia Universidad Católica de ChileCenter for Genome RegulationFacultad de Agronomía e Ingeniería ForestalDepartamento de Ecosistemas y Medio Ambiente Santiago Chile
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25
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Yang B, Zhang Z, Yang C, Wang Y, Orr MC, Hongbin W, Zhang AB. Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks. Syst Biol 2021; 71:690-705. [PMID: 34524452 DOI: 10.1093/sysbio/syab076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 09/08/2021] [Indexed: 11/14/2022] Open
Abstract
Integrative taxonomy is central to modern taxonomy and systematic biology, including behaviour, niche preference, distribution, morphological analysis and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network (MMNet)) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently-available alternative methods when tested with 10 independent datasets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species) and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy (>98%) in four datasets including closely related species from the same genus. The average accuracy of two modest sub-genomic (single nucleotide polymorphism) datasets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image versus gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multi-modal information for integrative taxonomy, such as image, audio, video, 3D scanning and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring and conservation of biodiversity.
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Affiliation(s)
- Bing Yang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Zhenxin Zhang
- The Key Laboratory of 3D Information Acquisition and Application, MOE, Capital Normal University, Beijing 100048, People's Republic of China.,Beijing Laboratory of Water Resources Security, Capital Normal University, Beijing 100048, People's Republic of China.,Base of the State Key Laboratory of Urban Environmental Process and Digital, Capital Normal University, Beijing 100048, People's Republic of China
| | - Caiqing Yang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Ying Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Wang Hongbin
- Museum of Forest Biodiversity, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
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26
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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27
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Leaché AD, Davis HR, Singhal S, Fujita MK, Lahti ME, Zamudio KR. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.678110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.
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28
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MacGuigan DJ, Hoagstrom CW, Domisch S, Hulsey CD, Near TJ. Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Sami Domisch
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - C. Darrin Hulsey
- Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Peabody Museum of Natural History Yale University New Haven CT USA
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29
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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30
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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31
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Gao Y, Zhang Y, Dietrich CH, Duan Y. Phylogenetic analyses and species delimitation of Nephotettix Matsumura (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida). Mol Phylogenet Evol 2021; 163:107240. [PMID: 34197900 DOI: 10.1016/j.ympev.2021.107240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/28/2022]
Abstract
There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
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33
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Esquerré D, Donnellan SC, Pavón-Vázquez CJ, Fenker J, Keogh JS. Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia). Mol Phylogenet Evol 2021; 161:107181. [PMID: 33892100 DOI: 10.1016/j.ympev.2021.107181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
| | | | - Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jéssica Fenker
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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34
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Colella JP, Frederick LM, Talbot SL, Cook JA. Extrinsically reinforced hybrid speciation within Holarctic ermine (
Mustela
spp.) produces an insular endemic. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- Biodiversity Institute University of Kansas Lawrence KS USA
| | - Lindsey M. Frederick
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- New Mexico Museum of Natural History and Science Albuquerque NM USA
| | | | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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35
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Cadenillas R, D'Elía G. The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae). Mol Phylogenet Evol 2021; 159:107111. [PMID: 33607277 DOI: 10.1016/j.ympev.2021.107111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.
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Affiliation(s)
- Richard Cadenillas
- Doctorado en Ciencias, Mención Ecología y Evolución, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile; Instituto de Paleontología, Universidad Nacional de Piura, Piura 20002, Peru.
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile.
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36
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Porto DS, Almeida EAB, Pennell MW. Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees. Syst Biol 2021; 70:295-306. [PMID: 32722788 PMCID: PMC7882150 DOI: 10.1093/sysbio/syaa059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022] Open
Abstract
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is a useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. [Apidae; entropy; morphological modules; phenotypic integration; phylogenetic information.].
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Affiliation(s)
- Diego S Porto
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061 USA
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
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37
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Rabiee M, Mirarab S. SODA: Multi-locus species delimitation using quartet frequencies. Bioinformatics 2021; 36:5623-5631. [PMID: 33555318 DOI: 10.1093/bioinformatics/btaa1010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 10/19/2020] [Accepted: 11/21/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in evolutionary computational biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years. RESULTS In this paper, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy. AVAILABILITY The code and data presented here are available on https://github.com/maryamrabiee/SODA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maryam Rabiee
- Computer Science and Engineering, University of California, San Diego, US
| | - Siavash Mirarab
- Electrical and Computer Engineering, University of California, San Diego, US
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38
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Sharkey MJ, Janzen DH, Hallwachs W, Chapman EG, Smith MA, Dapkey T, Brown A, Ratnasingham S, Naik S, Manjunath R, Perez K, Milton M, Hebert P, Shaw SR, Kittel RN, Solis MA, Metz MA, Goldstein PZ, Brown JW, Quicke DL, van Achterberg C, Brown BV, Burns JM. Minimalist revision and description of 403 new species in 11 subfamilies of Costa Rican braconid parasitoid wasps, including host records for 219 species. Zookeys 2021; 1013:1-665. [PMID: 34512087 PMCID: PMC8390796 DOI: 10.3897/zookeys.1013.55600] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Three new genera are described: Michener (Proteropinae), Bioalfa (Rogadinae), and Hermosomastax (Rogadinae). Keys are given for the New World genera of the following braconid subfamilies: Agathidinae, Braconinae, Cheloninae, Homolobinae, Hormiinae, Ichneutinae, Macrocentrinae, Orgilinae, Proteropinae, Rhysipolinae, and Rogadinae. In these subfamilies 416 species are described or redescribed. Most of the species have been reared and all but 13 are new to science. A consensus sequence of the COI barcodes possessed by each species is employed to diagnose the species, and this approach is justified in the introduction. Most descriptions consist of a lateral or dorsal image of the holotype, a diagnostic COI consensus barcode, the Barcode Index Number (BIN) code with a link to the Barcode of Life Database (BOLD), and the holotype specimen information required by the International Code of Zoological Nomenclature. The following species are treated and those lacking authorship are newly described here with authorship attributable to Sharkey except for the new species of Macrocentrinae which are by Sharkey & van Achterberg: AGATHIDINAE: Aerophiluspaulmarshi, Mesocoelusdavidsmithi, Neothlipsisbobkulai, Plesiocoelusvanachterbergi, Pneumagathiserythrogastra (Cameron, 1905), Therophilusbobwhartoni, T.donaldquickei, T.gracewoodae, T.maetoi, T.montywoodi, T.penteadodiasae, Zacremnopsbrianbrowni, Z.coatlicue Sharkey, 1990, Zacremnopscressoni (Cameron, 1887), Z.ekchuah Sharkey, 1990, Z.josefernandezi, Zelomorphasarahmeierottoae. BRACONINAE: Braconalejandromarini, B.alejandromasisi, B.alexamasisae, B.andresmarini, B.andrewwalshi, B.anniapicadoae, B.anniemoriceae, B.barryhammeli, B.bernardoespinozai, B.carlossanabriai, B.chanchini, B.christophervallei, B.erasmocoronadoi, B.eugeniephillipsae, B.federicomatarritai, B.frankjoycei, B.gerardovegai, B.germanvegai, B.isidrochaconi, B.jimlewisi, B.josejaramilloi, B.juanjoseoviedoi, B.juliodiazi, B.luzmariaromeroae, B.manuelzumbadoi, B.marialuisariasae, B.mariamartachavarriae, B.mariorivasi, B.melissaespinozae, B.nelsonzamorai, B.nicklaphami, B.ninamasisae, B.oliverwalshi, B.paulamarinae, B.rafamoralesi, B.robertofernandezi, B.rogerblancoi, B.ronaldzunigai, B.sigifredomarini, B.tihisiaboshartae, B.wilberthbrizuelai, Digonogastramontylloydi, D.montywoodi, D.motohasegawai, D.natwheelwrighti, D.nickgrishini. CHELONINAE: Adeliusadrianguadamuzi, A.gauldi Shimbori & Shaw, 2019, A.janzeni Shimbori & Shaw, 2019, Ascogastergloriasihezarae, A.grettelvegae, A.guillermopereirai, A.gustavoecheverrii, A.katyvandusenae, A.luisdiegogomezi, Chelonusalejandrozaldivari, C.gustavogutierrezi, C.gustavoinduni, C.harryramirezi, C.hartmanguidoi, C.hazelcambroneroae, C.iangauldi, C.isidrochaconi, C.janecheverriae, C.jeffmilleri, C.jennyphillipsae, C.jeremydewaardi, C.jessiehillae, C.jesusugaldei, C.jimlewisi, C.jimmilleri, C.jimwhitfieldi, C.johanvalerioi, C.johnburnsi, C.johnnoyesi, C.jorgebaltodanoi, C.jorgehernandezi, C.josealfredohernandezi, C.josefernandeztrianai, C.josehernandezcortesi, C.josemanuelperezi, C.josephinerodriguezae, C.juanmatai, C.junkoshimurae, C.kateperezae, C.luciariosae, C.luzmariaromeroae, C.manuelpereirai, C.manuelzumbadoi, C.marianopereirai, C.maribellealvarezae, C.markmetzi, C.markshawi, C.martajimenezae, C.mayrabonillae, C.meganmiltonae, C.melaniamunozae, C.michaelstroudi, C.michellevanderbankae, C.mingfangi, C.minorcarmonai, C.monikaspringerae, C.moniquegilbertae, C.motohasegawai, C.nataliaivanovae, C.nelsonzamorai, C.normwoodleyi, C.osvaldoespinozai, C.pamelacastilloae, C.paulgoldsteini, C.paulhansoni, C.paulheberti, C.petronariosae, C.ramyamanjunathae, C.randallgarciai, C.rebeccakittelae, C.robertoespinozai, C.robertofernandezi, C.rocioecheverriae, C.rodrigogamezi, C.ronaldzunigai, C.rosibelelizondoae, C.rostermoragai, C.ruthfrancoae, C.scottmilleri, C.scottshawi, C.sergioriosi, C.sigifredomarini, C.stevearonsoni, C.stevestroudi, C.sujeevanratnasinghami, C.sureshnaiki, C.torbjornekremi, C.yeimycedenoae, Leptodrepanaalexisae, L.erasmocoronadoi, L.felipechavarriai, L.freddyquesadai, L.gilbertfuentesi, L.manuelriosi, Phanerotomaalmasolisae, P.alvaroherrerai, P.anacordobae, P.anamariamongeae, P.andydeansi, P.angelagonzalezae, P.angelsolisi, P.barryhammeli, P.bernardoespinozai, P.calixtomoragai, P.carolinacanoae, P.christerhanssoni, P.christhompsoni, P.davesmithi, P.davidduthiei, P.dirksteinkei, P.donquickei, P.duniagarciae, P.duvalierbricenoi, P.eddysanchezi, P.eldarayae, P.eliethcantillanoae, P.jenopappi, Pseudophanerotomaalanflemingi, Ps.albanjimenezi, Ps.alejandromarini, Ps.alexsmithi, Ps.allisonbrownae, Ps.bobrobbinsi. HOMOLOBINAE: Exasticolusjennyphillipsae, E.randallgarciai, E.robertofernandezi, E.sigifredomarini, E.tomlewinsoni. HORMIINAE: Hormiusanamariamongeae, H.angelsolisi, H.anniapicadoae, H.arthurchapmani, H.barryhammeli, H.carmenretanae, H.carloswalkeri, H.cesarsuarezi, H.danbrooksi, H.eddysanchezi, H.erikframstadi, H.georgedavisi, H.grettelvegae, H.gustavoinduni, H.hartmanguidoi, H.hectoraritai, H.hesiquiobenitezi, H.irenecanasae, H.isidrochaconi, H.jaygallegosi, H.jimbeachi, H.jimlewisi, H.joelcracrafti, H.johanvalerioi, H.johnburleyi, H.joncoddingtoni, H.jorgecarvajali, H.juanmatai, H.manuelzumbadoi, H.mercedesfosterae, H.modonnellyae, H.nelsonzamorai, H.pamelacastilloae, H.raycypessi, H.ritacolwellae, H.robcolwelli, H.rogerblancosegurai, H.ronaldzunigai, H.russchapmani, H.virginiaferrisae, H.warrenbrighami, H.willsflowersi. ICHNEUTINAE: Oligoneuruskriskrishtalkai, O.jorgejimenezi, Paroligoneuruselainehoaglandae, P.julianhumphriesi, P.mikeiviei. MACROCENTRINAE: Austrozelejorgecampabadali, A.jorgesoberoni, Dolichozelegravitarsis (Muesebeck, 1938), D.josefernandeztrianai, D.josephinerodriguezae, Hymenochaoniakalevikulli, H.kateperezae, H.katherinebaillieae, H.katherineellisonae, H.katyvandusenae, H.kazumifukunagae, H.keithlangdoni, H.keithwillmotti, H.kenjinishidai, H.kimberleysheldonae, H.krisnorvigae, H.lilianamadrigalae, H.lizlangleyae, Macrocentrusfredsingeri, M.geoffbarnardi, M.gregburtoni, M.gretchendailyae, M.grettelvegae, M.gustavogutierrezi, M.hannahjamesae, M.harisridhari, M.hillaryrosnerae, M.hiroshikidonoi, M.iangauldi, M.jennyphillipsae, M.jesseausubeli, M.jessemaysharkae, M.jimwhitfieldi, M.johnbrowni, M.johnburnsi, M.jonathanfranzeni, M.jonathanrosenbergi, M.jorgebaltodanoi, M.lucianocapelli. ORGILINAE: Orgilusamyrossmanae, O.carrolyoonae, O.christhompsoni, O.christinemcmahonae, O.dianalipscombae, O.ebbenielsoni, O.elizabethpennisiae, O.evertlindquisti, O.genestoermeri, O.jamesriegeri, O.jeanmillerae, O.jeffmilleri, O.jerrypowelli, O.jimtiedjei, O.johnlundbergi, O.johnpipolyi, O.jorgellorentei, O.larryspearsi, O.marlinricei, O.mellissaespinozae, O.mikesmithi, O.normplatnicki, O.peterrauchi, O.richardprimacki, O.sandraberriosae, O.sarahmirandae, O.scottmilleri, O.scottmorii, Stantoniabillalleni, S.brookejarvisae, S.donwilsoni, S.erikabjorstromae, S.garywolfi, S.henrikekmani, S.luismirandai, S.miriamzunzae, S.quentinwheeleri, S.robinkazmierae, S.ruthtifferae. PROTEROPINAE: Hebichneutestricolor Sharkey & Wharton, 1994, Proteropsiangauldi, P.vickifunkae, Michenercharlesi. RHYSIPOLINAE: Pseudorhysipolisluisfonsecai, P. mailyngonzalezaeRhysipolisjulioquirosi. ROGADINAE: Aleiodesadrianaradulovae, A.adrianforsythi, A.agnespeelleae, A.alaneaglei, A.alanflemingi, A.alanhalevii, A.alejandromasisi, A.alessandracallejae, A.alexsmithi, A.alfonsopescadori, A.alisundermieri, A.almasolisae, A.alvarougaldei, A.alvaroumanai, A.angelsolisi, A.annhowdenae, A.bobandersoni, A.carolinagodoyae, A.charlieobrieni, A.davefurthi, A.donwhiteheadi, A.doylemckeyi, A.frankhovorei, A.henryhowdeni, A.inga Shimbori & Shaw, 2020, A.johnchemsaki, A.johnkingsolveri, A.gonodontovorus Shimbori & Shaw, 2020, A.manuelzumbadoi, A.mayrabonillae, A.michelledsouzae, A.mikeiviei, A.normwoodleyi, A.pammitchellae, A.pauljohnsoni, A.rosewarnerae, A.steveashei, A.terryerwini, A.willsflowersi, Bioalfapedroleoni, B.alvarougaldei, B.rodrigogamezi, Choreborogasandydeansi, C.eladiocastroi, C.felipechavarriai, C.frankjoycei, Clinocentrusandywarreni, Cl.angelsolisi, Cystomastaxalexhausmanni, Cy.angelagonzalezae, Cy.ayaigarashiae, Hermosomastaxclavifemorus Quicke sp. nov., Heterogamusdonstonei, Pseudoyeliconesbernsweeneyi, Stiropiusbencrairi, S.berndkerni, S.edgargutierrezi, S.edwilsoni, S.ehakernae, Triraphisbillfreelandi, T.billmclarneyi, T.billripplei, T.bobandersoni, T.bobrobbinsi, T.bradzlotnicki, T.brianbrowni, T.brianlaueri, T.briannestjacquesae, T.camilocamargoi, T.carlosherrerai, T.carolinepalmerae, T.charlesmorrisi, T.chigiybinellae, T.christerhanssoni, T.christhompsoni, T.conniebarlowae, T.craigsimonsi, T.defectus Valerio, 2015, T.danielhubi, T.davidduthiei, T.davidwahli, T.federicomatarritai, T.ferrisjabri, T.mariobozai, T.martindohrni, T.matssegnestami, T.mehrdadhajibabaei, T.ollieflinti, T.tildalauerae, Yeliconesdirksteinkei, Y.markmetzi, Y.monserrathvargasae, Y.tricolor Quicke, 1996. Y.woldai Quicke, 1996. The following new combinations are proposed: Neothlipsissmithi (Ashmead), new combination for Microdussmithi Ashmead, 1894; Neothlipsispygmaeus (Enderlein), new combination for Microduspygmaeus Enderlein, 1920; Neothlipsisunicinctus (Ashmead), new combination for Microdusunicinctus Ashmead, 1894; Therophilusanomalus (Bortoni and Penteado-Dias) new combination for Plesiocoelusanomalus Bortoni and Penteado-Dias, 2015; Aerophilusareolatus (Bortoni and Penteado-Dias) new combination for Plesiocoelusareolatus Bortoni and Penteado-Dias, 2015; Pneumagathiserythrogastra (Cameron) new combination for Agathiserythrogastra Cameron, 1905. Dolichozelecitreitarsis (Enderlein), new combination for Paniscozelecitreitarsis Enderlein, 1920. Dolichozelefuscivertex (Enderlein) new combination for Paniscozelefuscivertex Enderlein, 1920. Finally, Bassusbrooksi Sharkey, 1998 is synonymized with Agathiserythrogastra Cameron, 1905; Paniscozelegriseipes Enderlein, 1920 is synonymized with Dolichozelekoebelei Viereck, 1911; Paniscozelecarinifrons Enderlein, 1920 is synonymized with Dolichozelefuscivertex (Enderlein, 1920); and Paniscozelenigricauda Enderlein,1920 is synonymized with Dolichozelequaestor (Fabricius, 1804). (originally described as Ophionquaestor Fabricius, 1804).
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Affiliation(s)
- Michael J. Sharkey
- The Hymenoptera Institute, 116 Franklin Ave., Redlands, CA, 92373, USAThe Hymenoptera InstituteRedlandsUnited States of America
| | - Daniel H. Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USAUniversity of PennsylvaniaPhiladelphiaUnited States of America
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USAUniversity of PennsylvaniaPhiladelphiaUnited States of America
| | - Eric G. Chapman
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USAUniversity of KentuckyLexingtonUnited States of America
| | - M. Alex Smith
- Department of Integrative Biology, University of Guelph and Biodiversity Institute of Ontario, Guelph, CanadaUniversity of GuelphGuelphCanada
| | - Tanya Dapkey
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Allison Brown
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Sujeevan Ratnasingham
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Suresh Naik
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Ramya Manjunath
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Kate Perez
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Megan Milton
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Paul Hebert
- Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USAAcademy of Natural SciencesPhiladelphiaUnited States of America
| | - Scott R. Shaw
- Department of Ecosystem Science, University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071, USAUniversity of WyomingLaramieUnited States of America
| | - Rebecca N. Kittel
- Museum Wiesbaden, Hessisches Landesmuseum für Kunst und Natur, Friedrich-Ebert-Allee 2, 65185 Wiesbaden, GermanyHessisches Landesmuseum für Kunst und NaturWiesbadenGermany
| | - M. Alma Solis
- Systematic Entomology Laboratory, Beltsville Agriculture Research Center, Agricultural Research Service, U.S. Department of Agriculture, c/o National Museum Natural History, MRC 168, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USAU.S. Department of AgricultureWashingtonUnited States of America
| | - Mark A. Metz
- Systematic Entomology Laboratory, Beltsville Agriculture Research Center, Agricultural Research Service, U.S. Department of Agriculture, c/o National Museum Natural History, MRC 168, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USAU.S. Department of AgricultureWashingtonUnited States of America
| | - Paul Z. Goldstein
- Systematic Entomology Laboratory, Beltsville Agriculture Research Center, Agricultural Research Service, U.S. Department of Agriculture, c/o National Museum Natural History, MRC 168, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USAU.S. Department of AgricultureWashingtonUnited States of America
| | - John W. Brown
- Division of Entomology, PO Box 37012 12. National Museum of Natural History E515 MRC127, Washington, DC 20013-7012, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
| | - Donald L.J. Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University, Bangkok, ThailandNational Museum of Natural HistoryWashingtonUnited States of America
| | - C. van Achterberg
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The NetherlandsChulalongkorn UniversityBangkokThailand
| | - Brian V. Brown
- Department of Entomology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, USANaturalis Biodiversity CenterLeidenNetherlands
| | - John M. Burns
- Division of Entomology, PO Box 37012 12. National Museum of Natural History E515 MRC127, Washington, DC 20013-7012, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
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Sánchez KI, Avila LJ, Sites JW, Morando M. An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini). Mol Phylogenet Evol 2021; 157:107046. [PMID: 33421613 DOI: 10.1016/j.ympev.2020.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/07/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
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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), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina.
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT 84602, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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Richmond JQ, Ota H, Grismer LL, Fisher RN. Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction methods to infer shifts in ecology. We show evidence of multidirectional spread from a centre of origin in western Micronesia, and that the phyletic diversity of the group is derived from a putative habitat specialist that survives in the littoral zone. This species is composed of paraphyletic lineages that represent stages or possible endpoints in the continuum toward speciation. Several descendant species have transitioned to either strand or interior forest habitat, but only on remote islands with depauperate terrestrial faunas. Our results suggest that the atrocostata group might be in the early phases of a Wilsonian taxon cycle and that the capacity to tolerate salt stress has promoted dispersal and colonization of remote oceanic islands. Divergence itself, however, is largely driven by geographical isolation rather than shifts in ecology.
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Affiliation(s)
| | - Hidetoshi Ota
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, CA, USA
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Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M. Repositories for Taxonomic Data: Where We Are and What is Missing. Syst Biol 2020; 69:1231-1253. [PMID: 32298457 PMCID: PMC7584136 DOI: 10.1093/sysbio/syaa026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/05/2022] Open
Abstract
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].
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Affiliation(s)
- Aurélien Miralles
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Teddy Bruy
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Katherine Wolcott
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mark D Scherz
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Biology, Universität Konstanz, Universitätstraße 10, 78464 Konstanz, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bank Beszteri
- Department of Phycology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Center of Excellence in Plant Sciences (CEPLAS), Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674 Köln, Germany
| | - Janine Felden
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobenerstraße 8, 28359 Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Birgit Gemeinholzer
- Department of Systematic Botany, Justus Liebig University Gießen, Heinrich-Buff Ring 38, 35392 Giessen, Germany
| | - Frank Glaw
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Oliver Hawlitschek
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Scientific Infrastructure, Centrum für Naturkunde (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ivaylo Kostadinov
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Center of Biotechnology (CeBiTec), Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Jasmin Renz
- Zooplankton Research Group, DZMB – Senckenberg am Meer, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Nataliya Rybalka
- Department of Experimental Phycology and Culture Collection of Algae, University Göttingen, Nikolausberger-Weg 18, 37073 Göttingen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Tanja Weibulat
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Gießen, Heinrich-Buff Ring 26, 35392 Giessen, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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42
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Alström P, van Linschooten J, Donald PF, Sundev G, Mohammadi Z, Ghorbani F, Shafaeipour A, van den Berg A, Robb M, Aliabadian M, Wei C, Lei F, Oxelman B, Olsson U. Multiple species delimitation approaches applied to the avian lark genus Alaudala. Mol Phylogenet Evol 2020; 154:106994. [PMID: 33250446 DOI: 10.1016/j.ympev.2020.106994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.
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Affiliation(s)
- Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jip van Linschooten
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Paul F Donald
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, P.O. Box 537, Ulaanbaatar 210646a, Ulaanbaatar, Mongolia
| | - Zeinolabedin Mohammadi
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Fatemeh Ghorbani
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Arya Shafaeipour
- Department of Biology, Faculty of Science, Yasouj University, Yasouj, Iran
| | - Arnoud van den Berg
- The Sound Approach, c/o Duinlustparkweg 98, 2082 EG Santpoort-Zuid, the Netherlands
| | - Magnus Robb
- The Sound Approach, c/o Rua Dr Pedro Almeida Lima 6, 2710-122 Sintra, Portugal
| | - Mansour Aliabadian
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Chentao Wei
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bengt Oxelman
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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43
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Liu T, Chen J, Jiang L, Qiao G. Phylogeny and species reassessment of
Hyalopterus
(Aphididae, Aphidinae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tongyi Liu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
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44
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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45
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Gu J, Jiang B, Wang H, Wei T, Lin L, Huang Y, Huang J. Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence. PLoS One 2020; 15:e0237882. [PMID: 32845927 PMCID: PMC7449498 DOI: 10.1371/journal.pone.0237882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.
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Affiliation(s)
- Jingxiao Gu
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Bing Jiang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
| | - Haojie Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People’s Republic of China
| | - Tao Wei
- Tanxi Street Agency, Liunan Subdistrict, Liuzhou, Guangxi, People’s Republic of China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, People’s Republic of China
| | - Jianhua Huang
- Key Laboratory of Insect Evolution and Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, Hunan, People’s Republic of China
- Key Laboratory of Cultivation and Protection for Non–Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, People’s Republic of China
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46
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Orchid-pollinator network in Euro-Mediterranean region: What we know, what we think we know, and what remains to be done. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2020. [DOI: 10.1016/j.actao.2020.103605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Zhang CY, Ling Low S, Song YG, Nurainas, Kozlowski G, Li L, Zhou SS, Tan YH, Cao GL, Zhou Z, Meng HH, Li J. Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae). Mol Phylogenet Evol 2020; 152:106918. [PMID: 32738292 DOI: 10.1016/j.ympev.2020.106918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.
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Affiliation(s)
- Can-Yu Zhang
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shook Ling Low
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yi-Gang Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Nurainas
- Department of Biology, Faculty of Math. & Nat. Sci. Andalas University, Padang 25163, West Sumatra, Indonesia
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Shi-Shun Zhou
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Guan-Long Cao
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar.
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China.
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48
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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49
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Colston TJ, Kulkarni P, Jetz W, Pyron RA. Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs). BMC Evol Biol 2020; 20:81. [PMID: 32650718 PMCID: PMC7350713 DOI: 10.1186/s12862-020-01642-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
Background The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with statistical and machine learning algorithms to present a phylogenetically informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species. Results In contrast to other terrestrial vertebrates and their own diversity in the fossil record, the recent extant lineages of turtles and crocodilians have not experienced any global mass extinctions or lineage-wide shifts in diversification rate or body-size evolution over time. We predict threat statuses for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened turtles and crocodilians in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies. Conclusions Extant turtles and crocodilians maintain unique, conserved morphologies which make them globally recognizable. Many species are threatened due to exploitation and global change. We use taxonomically complete, dated molecular phylogenies and various approaches to produce a comprehensive assessment of threat status and evolutionary distinctiveness of both groups. Neither group exhibits significant overall shifts in diversification rate or body-size evolution, or any signature of global mass extinctions in recent, extant lineages. However, the most evolutionarily distinct species tend to be the most threatened, and species richness and extinction risk are centered in areas of high anthropogenic disturbance, particularly South and Southeast Asia. Range size is the strongest predictor of threat, and a disproportionate amount of evolutionary diversity is at risk of imminent extinction.
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Affiliation(s)
- Timothy J Colston
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA. .,Present address: Department of Biological Science, Florida State University, Tallahassee, FL, 32304, USA.
| | | | - Walter Jetz
- Center for Biodiversity and Global Change, Yale University, New Haven, CT, 06511, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
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50
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Kolb AW, Brandt CR. Genomic nucleotide-based distance analysis for delimiting old world monkey derived herpes simplex virus species. BMC Genomics 2020; 21:436. [PMID: 32590937 PMCID: PMC7318535 DOI: 10.1186/s12864-020-06847-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Herpes simplex viruses form a genus within the alphaherpesvirus subfamily, with three identified viral species isolated from Old World monkeys (OWM); Macacine alphaherpesvirus 1 (McHV-1; herpes B), Cercopithecine alphaherpesvirus 2 (SA8), and Papiine alphaherpesvirus 2 (PaHV-2; herpes papio). Herpes B is endemic to macaques, while PaHV-2 and SA8 appear endemic to baboons. All three viruses are genetically and antigenically similar, with SA8 and PaHV-2 thought to be avirulent in humans, while herpes B is a biosafety level 4 pathogen. Recently, next-generation sequencing (NGS) has resulted in an increased number of published OWM herpes simplex genomes, allowing an encompassing phylogenetic analysis. RESULTS In this study, phylogenetic networks, in conjunction with a genome-based genetic distance cutoff method were used to examine 27 OWM monkey herpes simplex isolates. Genome-based genetic distances were calculated, resulting in distances between lion and pig-tailed simplex viruses themselves, and versus herpes B core strains that were higher than those between PaHV-2 and SA8 (approximately 14 and 10% respectively). The species distance cutoff was determined to be 8.94%, with the method recovering separate species status for PaHV-2 and SA8 and showed that lion and pig-tailed simplex viruses (vs core herpes B strains) were well over the distance species cutoff. CONCLUSIONS We propose designating lion and pig-tailed simplex viruses as separate, individual viral species, and that this may be the first identification of viral cryptic species.
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Affiliation(s)
- Aaron W Kolb
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave, Madison, WI, 53706, USA.
| | - Curtis R Brandt
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave, Madison, WI, 53706, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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