101
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Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific. Mol Phylogenet Evol 2022; 173:107496. [PMID: 35569809 DOI: 10.1016/j.ympev.2022.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.
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102
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Miller JP, Delicado D, García-Guerrero F, Ramos MA. Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae). Mol Phylogenet Evol 2022; 173:107524. [DOI: 10.1016/j.ympev.2022.107524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/31/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
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103
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Hancock ZB, Lehmberg ES, Blackmon H. Phylogenetics in Space: How Continuous Spatial Structure Impacts Tree Inference. Mol Phylogenet Evol 2022; 173:107505. [PMID: 35577296 DOI: 10.1016/j.ympev.2022.107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent - what we call the "missing z-axis". In this article, we review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. We illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. We find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by utilizing our results to suggest how researchers can identify spatial structure in phylogenetic datasets.
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104
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Somoza-Valdeolmillos E, Gómez-Moliner BJ, Caro A, Chueca LJ, Martínez-Ortí A, Puente AI, Madeira MJ. Molecular phylogeny of the genus Chondrina (Gastropoda, Panpulmonata, Chondrinidae) in the Iberian Peninsula. Mol Phylogenet Evol 2022; 172:107480. [PMID: 35452839 DOI: 10.1016/j.ympev.2022.107480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022]
Abstract
Chondrina Reichenbach, 1828 is a highly diverse genus of terrestrial molluscs currently including 44 species with about 28 subspecific taxa. It is distributed through North Africa, central and southern Europe, from Portugal in the West to the Caucasus and Asia Minor in the East. Approximately 70% of the species are endemic to the Iberian Peninsula constituting its main center of speciation with 34 species. This genus includes many microendemic taxa, some of them not yet described, confined to limestone habitats (being strictly rock-dwelling species). They are distributed on rocky outcrops up to 2000 m.a.s.l. It is a genus of conical-fusiform snails that differ mainly in shell characters and in the number and position of teeth in their aperture. So far, molecular studies on Chondrina have been based exclusively on the mitochondrial Cytochrome Oxidase subunit I region (COI). These studies gave a first view of the phylogeny of the genus but many inner nodes were not statistically supported. The main objective of the study is to obtain a better understanding of the phylogeny and systematics of the genus Chondrina on the Iberian Peninsula, using multilocus molecular analysis. Partial sequences of the COI and 16S rRNA genes, as well as of the nuclear Internal Transcribed Spacer 1 (ITS1-5.8S) and Internal Transcribed Spacer 2 (5.8S-ITS2-28S) were obtained from individuals of all the extant Chondrina species known from the Iberian Peninsula. In addition to this, the newly obtained COI sequences were combined with those previously published in the GenBank. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods. The reconstructed phylogenies showed high values of support for more recent branches and basal nodes. Moreover, molecular species delimitation allowed to better definethe studied species and check the presence of new taxa.
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Affiliation(s)
- Eder Somoza-Valdeolmillos
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain.
| | - Benjamín J Gómez-Moliner
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
| | - Amaia Caro
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
| | - Luis J Chueca
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Alberto Martínez-Ortí
- Museu Valencià d'Història Natural, Apto. 8460, E-46018, Valencia and Universitat de València, Faculty of Pharmacy, Parasitology Departament, Burjassot, Valencia, (Spain)
| | - Ana I Puente
- University of the Basque Country (UPV/EHU), Faculty of Science and Technology, Department of Zoology and Animal Cell Biology: Barrio Sarriena s/n, 48015 Leioa, Spain
| | - María J Madeira
- University of the Basque Country (UPV/EHU), Faculty of Pharmacy, Department of Zoology and Animal Cell Biology: Paseo de la Universidad, 7. 01006 Vitoria-Gasteiz, Spain; Biodiversity Research Group CIEA Lucio Lascaray, Avda. Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Álava, Spain
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105
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Segovia NI, González-Wevar CA, Naretto J, Rosenfeld S, Brickle P, Hüne M, Bernal V, Haye PA, Poulin E. The right tool for the right question: contrasting biogeographic patterns in the notothenioid fish Harpagifer spp. along the Magellan Province. Proc Biol Sci 2022; 289:20212738. [PMID: 35382596 PMCID: PMC8984805 DOI: 10.1098/rspb.2021.2738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Molecular-based analysis has become a fundamental tool to understand the role of Quaternary glacial episodes. In the Magellan Province in southern South America, ice covering during the last glacial maximum (20 ka) radically altered the landscape/seascape, speciation rates and distribution of species. For the notothenioid fishes of the genus Harpagifer, in the area are described two nominal species. Nevertheless, this genus recently colonized South America from Antarctica, providing a short time for speciation processes. Combining DNA sequences and genotyping-by-sequencing SNPs, we evaluated the role of Quaternary glaciations over the patterns of genetic structure in Harpagifer across its distribution in the Magellan Province. DNA sequences showed low phylogeographic structure, with shared and dominant haplotypes between nominal species, suggesting a single evolutionary unit. SNPs identified contrastingly two groups in Patagonia and a third well-differentiated group in the Falkland/Malvinas Islands with limited and asymmetric gene flow. Linking the information of different markers allowed us to infer the relevance of postglacial colonization mediated by the general oceanographic circulation patterns. Contrasting rough- and fine-scale genetic patterns highlights the relevance of combined methodologies for species delimitation, which, depending on the question to be addressed, allows discrimination among phylogeographic structure, discarding incipient speciation, and contemporary spatial differentiation processes.
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Affiliation(s)
- N I Segovia
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - C A González-Wevar
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile.,Instituto de Ciencias Marinas y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.,Centro de Investigación en Dinámicas de Ecosistemas de Altas Latitudes (Fondap IDEAL), Universidad Austral de Chile
| | - J Naretto
- Costa Humboldt, Puerto Varas, Los Lagos, Chile
| | - S Rosenfeld
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Laboratorio de Ecosistemas Antárticos y sub-Antárticos, Universidad de Magallanes, Chile
| | - P Brickle
- South Atlantic Environmental Research Institute (SAERI), PO Box 609, Stanley Cottage, Port Stanley, Falkland Islands, UK
| | - M Hüne
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Centro de Investigación para la Conservación de los Ecosistemas Australes (ICEA), Punta Arenas, Chile
| | - V Bernal
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - P A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile
| | - E Poulin
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
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106
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Ji Y, Yang J, Landis JB, Wang S, Jin L, Xie P, Liu H, Yang JB, Yi TS. Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:832034. [PMID: 35444671 PMCID: PMC9014178 DOI: 10.3389/fpls.2022.832034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.
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Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jin Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jacob B. Landis
- Section of Plant Biology and the L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Pingxuan Xie
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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107
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Dissecting a Geographical Colourful Tapestry: Phylogeography of the Colour Polymorphic Spider Gasteracantha cancriformis. J ZOOL SYST EVOL RES 2022. [DOI: 10.1155/2022/8112945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Species with large distributions provide unique opportunities to test how geography has influenced biotic diversification. In this work, we aimed to explore the effect of geographic barriers on the distribution of the phenotypic and genetic variation of a spider species that is widespread in continental and insular America. We obtained an alignment of the mitochondrial locus Cytochrome Oxidase I (COI) for 408 individuals across the geographic range of Gasteracantha cancriformis. We used phylogenetics, population genetics, and morphology to explore the genetic and phenotypic variation of this species. We found five genetically differentiated and geographically structured populations. Three of them are distributed in continental America, separated by the Andes mountains, and two are in the Caribbean and Galapagos Islands. Some of these geographic clades shared haplotypes between them, which may be a consequence of dispersal. We detected at least 20 phenotypes of G. cancriformis, some of which were exclusive to a geographic region, while others occurred in multiple regions. We did not observe well-defined morphological differences across male genitalia. This evidence suggests that G. cancriformis is a widespread species with high phenotypic variation that should be explored in more depth.
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108
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Voss RS. An Annotated Checklist of Recent Opossums (Mammalia: Didelphidae). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.455.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
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109
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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110
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Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence. PLoS One 2022; 17:e0263764. [PMID: 35358210 PMCID: PMC8970393 DOI: 10.1371/journal.pone.0263764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
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111
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Chornelia A, Lu J, Hughes AC. How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.854509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.
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112
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Girard MG, Davis MP, Baldwin CC, Dettaï A, Martin RP, Smith WL. Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements. JOURNAL OF FISH BIOLOGY 2022; 100:793-810. [PMID: 35137410 DOI: 10.1111/jfb.14997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.
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Affiliation(s)
- Matthew G Girard
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthew P Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Agnès Dettaï
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, FRA
| | - Rene P Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - W Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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113
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Ciaccio E, Debray A, Hedin M. Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. Zookeys 2022; 1086:163-204. [PMID: 35221748 PMCID: PMC8873193 DOI: 10.3897/zookeys.1086.77190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Hypochilus is a relictual lineage of Nearctic spiders distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in Hypochilus has been challenging, and conserved morphology coupled with extreme genetic divergence has led to uncertain species limits in some complexes. Here, Hypochilus interspecies relationships have been reconstructed and cryptic speciation more critically evaluated using a combination of ultraconserved elements, mitochondrial CO1 by-catch, and morphology. Phylogenomic data strongly support the monophyly of regional clades and support a ((California, Appalachia), southern Rocky Mountains) topology. In Appalachia, five species are resolved as four lineages (H.thorelli Marx, 1888 and H.coylei Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved. The Appalachian species H.pococki Platnick, 1987 is recovered as monophyletic but is highly genetically structured at the nuclear level. While algorithmic analyses of nuclear data indicate many species (e.g., all H.pococki populations as species), male morphology instead reveals striking stasis. Within the California clade, nuclear and mitochondrial lineages of H.petrunkevitchi Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with H.bernardino Catley, 1994 nested within H.petrunkevitchi and sister to the southernmost basin populations. Combining nuclear, mitochondrial, geographical, and morphological evidence a new species from the Tule River and Cedar Creek drainages is described, Hypochilusxomotesp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.
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Affiliation(s)
- Erik Ciaccio
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America.,Department of Entomology, Plant Pathology and Nematology, University of Idaho, Idaho, USA University of Idaho Idaho United States of America
| | - Andrew Debray
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America.,Nano PharmaSolutions Inc., San Diego, California, USA Nano PharmaSolutions Inc. San Diego United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America
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114
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Dissanayake DSB, Holleley CE, Sumner J, Melville J, Georges A. Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance. Ecol Evol 2022; 12:e8627. [PMID: 35342559 PMCID: PMC8928872 DOI: 10.1002/ece3.8627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/07/2022] Open
Abstract
Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning-subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three-lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well-supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re-evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.
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Affiliation(s)
- Duminda S. B. Dissanayake
- Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
- Australian National Wildlife CollectionCSIROCanberraAustralian Capital TerritoryAustralia
| | - Clare E. Holleley
- Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
- Australian National Wildlife CollectionCSIROCanberraAustralian Capital TerritoryAustralia
| | - Joanna Sumner
- Department of SciencesMuseums VictoriaCarlton GardensVictoriaAustralia
| | - Jane Melville
- Department of SciencesMuseums VictoriaCarlton GardensVictoriaAustralia
| | - Arthur Georges
- Institute for Applied EcologyUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
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115
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Campbell EO, MacDonald ZG, Gage EV, Gage RV, Sperling FAH. Genomics and ecological modelling clarify species integrity in a confusing group of butterflies. Mol Ecol 2022; 31:2400-2417. [PMID: 35212068 DOI: 10.1111/mec.16407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/30/2022]
Abstract
Recent advances in both genomics and ecological modelling present new, multidisciplinary opportunities for resolving species boundaries and understanding the mechanisms that maintain their integrity in regions of contact. Here, we use a combination of high-throughput DNA sequencing and ecological niche modelling to resolve species boundaries and niche divergence within the Speyeria atlantis-hesperis (Lepidoptera: Nymphalidae) complex, a confusing group of North American butterflies. This complex is notorious for its muddled species delimitations, morphological ambiguity, and extensive mito-nuclear discordance. Our admixture and multispecies coalescent-based analyses of single nucleotide polymorphisms identified substantial divergences between S. atlantis and S. hesperis in areas of contact, as well as between distinct northern and southern lineages within S. hesperis. Our results also provide evidence of past introgression relating to another species, S. zerene, which previous work has shown to be more distantly related to the S. atlantis-hesperis complex. We then used ecological models to predict habitat suitability for each of the three recovered genomic lineages in the S. atlantis-hesperis complex and assess their pairwise niche divergence. These analyses resolved that these three lineages are significantly diverged in their respective niches and are not separated by discontinuities in suitable habitat that might present barriers to gene flow. We therefore infer that ecologically-mediated selection resulting in disparate habitat associations is a principal mechanism reinforcing their genomic integrity. Overall, our results unambiguously support significant evolutionary and ecological divergence between the northern and southern lineages of S. hesperis, sufficient to recognize the southern evolutionary lineage as a distinct species, called S. nausicaa based on taxonomic priority.
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Affiliation(s)
- E O Campbell
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Z G MacDonald
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada.,Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - E V Gage
- Texas Museum of Entomology, Pipe Creek, TX, U.S.A
| | | | - F A H Sperling
- Department of Biological Sciences, Biosciences Centre, University of Alberta, Edmonton, AB, Canada
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116
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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117
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Landscape Genetics and Species Delimitation in the Andean Palm Rocket Frog (Aromobatidae, Rheobates). J ZOOL SYST EVOL RES 2022. [DOI: 10.1155/2022/6774225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by processes such as vicariance or local adaptation. Previous phylogenetic work on the palm rocket frog (Anura: Aromobatidae: Rheobates spp.), endemic to midelevation forests of Colombia, suggested that valleys were important in promoting divergence between lineages. In this study, we first evaluated previous hypotheses of species-level diversity, then fitted an isolation-with-migration (IM) historical demographic model, and tested two landscape genetic models to explain genetic divergence within Rheobates: isolation by distance and isolation by environment. The data consisted of two mitochondrial and four nuclear genes from 24 samples covering most of the geographic range of the genus. Species delimitation by Bayesian Phylogenetics and Phylogeography recovered five highly divergent genetic lineages within Rheobates, among which few to no migrants are exchanged according to IM. We found that isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role in driving the genetic divergence within this frog genus. Thus, genetic divergence in Rheobates may be driven more by variation among the local environments where these frogs live rather than by geographic distance.
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118
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Pyron RA, O’Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones. Ecol Evol 2022; 12:e8574. [PMID: 35222955 PMCID: PMC8848459 DOI: 10.1002/ece3.8574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/19/2022] Open
Abstract
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species-level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early-diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.
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Affiliation(s)
- Robert Alexander Pyron
- Department of Biological SciencesThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
- Division of Amphibians and ReptilesDepartment of Vertebrate ZoologyNational Museum of Natural History Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Kyle A. O’Connell
- Department of Biological SciencesThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
- Division of Amphibians and ReptilesDepartment of Vertebrate ZoologyNational Museum of Natural History Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
- Global Genome InitiativeNational Museum of Natural History Smithsonian InstitutionWashingtonDistrict of ColumbiaUSA
- Biomedical Data Science LabDeloitte Consulting LLPArlingtonVirginiaUSA
| | | | - Alan R. Lemmon
- Department of Scientific ComputingFlorida State UniversityTallahasseeFloridaUSA
| | - David A. Beamer
- Department of Natural SciencesNash Community CollegeRocky MountNorth CarolinaUSA
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119
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Amador L, Leaché AD, Victoriano PF, Hickerson MJ, D'Elía G. Genomic scale data shows that Parastacus nicoleti encompasses more than one species of burrowing continental crayfishes and that lineage divergence occurred with and without gene flow. Mol Phylogenet Evol 2022; 169:107443. [DOI: 10.1016/j.ympev.2022.107443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 10/19/2022]
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120
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Karameta E, Lymberakis P, Grillitsch H, Ilgaz Ç, Avci A, Kumlutaş Y, Candan K, Wagner P, Sfenthourakis S, Pafilis P, Poulakakis N. The story of a rock-star: multilocus phylogeny and species delimitation in the starred or roughtail rock agama, Laudakia stellio (Reptilia: Agamidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Situated at the junction of three continents, Europe, Asia and Africa, the Eastern Mediterranean is an ideal region to study the effects of palaeogeography, ecology and long human presence on animal evolution. Laudakia stellio (Squamata: Agamidae) is found across this region and offers an excellent opportunity for such studies. The high morphological variation across their range suggests that these lizards might represent a species complex. This is the first study exploring their evolutionary history, using molecular markers and individuals from all described subspecies. We employed the latest phylogenetic and species-delimitation methods to identify all distinct evolutionary lineages, their genetic variation and divergence times. The phenotypical diversity of L. stellio matches its genetic differentiation: almost all subspecies correspond to well-supported retrieved subclades and additional distinct lineages representing intermediate morphs have been retrieved. ‘Laudakia stellio’ represents three distinct evolutionary entities that diverged during the Plio-Pleistocene transition, which we propose as distinct species. One includes Greek and Turkish populations, as well as cryptic Anatolian lineages. The second comprises all other Near East populations and the third is endemic to Cyprus. Our results indicate a role of humans in shaping present distribution patterns, and highlight the importance of the Aegean, Anatolia and the Levant as glacial refugia and diversity hotspots.
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Affiliation(s)
- Emmanouela Karameta
- Section of Zoology and Marine Biology, Department of Biology, University of Athens, Panepistimioupolis, 15771 Athens, Greece
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
| | - Heinz Grillitsch
- Herpetological Collection, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
- Fauna and Flora Research Centre, Dokuz Eylül University, 35610 Buca- İzmir, Turkey
| | - Aziz Avci
- Department of Biology, Faculty of Science and Arts, Aydın Adnan Menderes University, Aydın, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
- Fauna and Flora Research Centre, Dokuz Eylül University, 35610 Buca- İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, 35160 Buca- İzmir, Turkey
| | | | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, University Campus, 2109 Aglantzia, Nicosia, Cyprus
| | - Panayiotis Pafilis
- Section of Zoology and Marine Biology, Department of Biology, University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, 71409 Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece
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121
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van Steenderen C, Sutton G. SPEDE‐sampler: an R Shiny application to assess how methodological choices and taxon‐sampling can affect Generalised Mixed Yule Coalescent (GMYC) output and interpretation. Mol Ecol Resour 2022; 22:2054-2069. [PMID: 35094502 PMCID: PMC9306842 DOI: 10.1111/1755-0998.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely used methods is the Generalized Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated data sets, where model assumptions are not violated. Here, we present a user‐friendly R Shiny application, ‘SPEDE‐sampler’ (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that (1) sample size, (2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and (3) singletons have on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it with GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE‐sampler, allowing for the further investigation of potential cryptic species or geographical substructuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program's workflow, and the variation that can arise when applying the GMYC model to empirical data sets. The R Shiny program is available for download at https://github.com/clarkevansteenderen/spede_sampler_R.
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Affiliation(s)
- C.J.M. van Steenderen
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
| | - G.F. Sutton
- Centre for Biological Control Department of Zoology and Entomology Rhodes University Grahamstown/Makhanda 6139 Eastern Cape South Africa
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122
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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123
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Carstens BC, Smith ML, Duckett DJ, Fonseca EM, Thomé MTC. Assessing model adequacy leads to more robust phylogeographic inference. Trends Ecol Evol 2022; 37:402-410. [PMID: 35027224 DOI: 10.1016/j.tree.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
Phylogeographic studies base inferences on large data sets and complex demographic models, but these models are applied in ways that could mislead researchers and compromise their inference. Researchers face three challenges associated with the use of models: (i) 'model selection', or the identification of an appropriate model for analysis; (ii) 'evaluation of analytical results', or the interpretation of the biological significance of the resulting parameter estimates, delimitations, and topologies; and (iii) 'model evaluation', or the use of statistical approaches to assess the fit of the model to the data. The field collectively invests most of its energy in point (ii) without considering the other points; we argue that attention to points (i) and (iii) is essential to phylogeographic inference.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA.
| | - Megan L Smith
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Drew J Duckett
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
| | - Emanuel M Fonseca
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
| | - M Tereza C Thomé
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
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125
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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126
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Zamora J, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S. Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Syst Evol 2022; 9:27-42. [PMID: 35978985 PMCID: PMC9355100 DOI: 10.3114/fuse.2022.09.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
A new genus named Dendrodacrys is proposed for a monophyletic group in Dacrymycetaceae, containing species with pulvinate to depressed basidiocarps, distinctly branched hymenial hyphidia, and up to 3-septate mature basidiospores. Four taxa in this group, occurring in Europe, are proposed as new species, viz. De. ciprense, De. concrescens, De. ellipsosporum, and De. oblongisporum, based both on morphological and DNA data (nrDNA, RPB1, RPB2, TEF-1α, 12S). These new species are all described in detail, illustrated, and compared with other published taxa that with which they can be confounded. The new combination De. paraphysatum is proposed after revising the type material of Dacrymyces paraphysatus, but other combinations or potentially new non-European species descriptions are postponed pending further studies of additional specimens. Citation: Zamora JC, Savchenko A, González-Cruz Á, Prieto-García F, Olariaga I, Ekman S (2022). Dendrodacrys: a new genus for species with branched hyphidia in Dacrymyces s.l., with the description of four new species. Fungal Systematics and Evolution9: 27–42. doi: 10.3114/fuse.2022.09.04
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Affiliation(s)
- J.C. Zamora
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
- Conservatoire et Jardin Botaniques de la Ville de Genève, Chemin de l’Impératrice 1, 1292 Chambésy-Genève, Switzerland
| | - A. Savchenko
- Institute of Ecology & Earth Sciences, University of Tartu, 51014 Tartu, Estonia
| | | | | | - I. Olariaga
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid, Spain
| | - S. Ekman
- Museum of Evolution, Uppsala University, Norbyvägen 16, 752 36 Uppsala, Sweden
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127
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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128
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Dufresnes C, Litvinchuk SN. Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology & Environment, Nanjing Forestry University, Nanjing, China
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biology, Dagestan State University, Makhachkala, Russia
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129
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do Amaral KB, Barragán-Barrera DC, Mesa-Gutiérrez RA, Farías-Curtidor N, Caballero Gaitán SJ, Méndez-Fernandez P, Santos MCO, Rinaldi C, Rinaldi R, Siciliano S, Martín V, Carrillo M, de Meirelles ACO, Franco-Trecu V, Fagundes NJR, Moreno IB, Lacey Knowles L, Amaral AR. Seascape Genetics of the Atlantic Spotted Dolphin (Stenella frontalis) Based on Mitochondrial DNA. J Hered 2021; 112:646-662. [PMID: 34453543 DOI: 10.1093/jhered/esab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study, we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.
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Affiliation(s)
- Karina Bohrer do Amaral
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil
| | - Dalia C Barragán-Barrera
- Centro de Investigaciones Oceanográficas de Hidrográficas del Caribe CIOH-DIMAR, Barrio Bosque, Sector Manzanillo Escuela Naval de Cadetes "Almirante Padilla," Cartagena, Colombia.,Fundación Macuáticos Colombia, Colombia, Medellín, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | | | | | - Susana Josefina Caballero Gaitán
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | - Paula Méndez-Fernandez
- Observatoire PELAGIS, UMS 3462 La Rochelle Université / CNRS, Pôle Analytique, 5 allées de l'Océan, 17000 La Rochelle, France
| | - Marcos C Oliveira Santos
- Laboratório de Biologia da Conservação de Mamíferos Aquáticos (LABCMA), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, Sala 145-A, 05508-120 São Paulo, SP, Brazil
| | - Caroline Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Renato Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Salvatore Siciliano
- Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4.365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Vidal Martín
- Sociedad para el Estudio de Cetáceos del Archipélago Canario (SECAC), Casa de los Arroyo, Avda. Coll n.6, 35500 Arrecife, Lanzarote, Spain
| | - Manuel Carrillo
- Tenerife Conservación, C/Maya No. 8, La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Carolina O de Meirelles
- AQUASIS-Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Praia de Iparana, s/no, SESC Iparana, 61600-000 Caucaia, CE, Brazil
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul. Avenida Bento Gonçalves 9500, Prédio 43312, sala 113, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco III, Prédio 43312, 91501-970 Porto Alegre, RS, Brazil
| | - Ignacio Benites Moreno
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Campus Litoral Norte, Universidade Federal do Rio Grande do Sul, Avenida Tramandaí, 976, Imbé, Rio Grande do Sul, 95625-000, Brazil
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI
| | - Ana Rita Amaral
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024
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130
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Esselstyn JA, Achmadi AS, Handika H, Swanson MT, Giarla TC, Rowe KC. Fourteen New, Endemic Species of Shrew (Genus Crocidura) from Sulawesi Reveal a Spectacular Island Radiation. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.454.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, West Java, Indonesia
| | - Heru Handika
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | - Mark T. Swanson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | | | - Kevin C. Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
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131
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Jorna J, Linde JB, Searle PC, Jackson AC, Nielsen M, Nate MS, Saxton NA, Grewe F, Herrera‐Campos MDLA, Spjut RW, Wu H, Ho B, Lumbsch HT, Leavitt SD. Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi. Ecol Evol 2021; 11:18615-18632. [PMID: 35003697 PMCID: PMC8717302 DOI: 10.1002/ece3.8467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022] Open
Abstract
Species delimitation among closely related species is challenging because traditional phenotype-based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single-locus and genome-scale data consisting of (a) single-locus species delimitation analysis using ASAP, (b) maximum likelihood-based phylogenetic tree inference, (c) genome-scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross-validate results between genome-scale and single-locus datasets, differently sampled subsets of genomic data and to control for population-level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro-endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.
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Affiliation(s)
- Jesse Jorna
- Department of BiologyBrigham Young UniversityProvoUtahUSA
| | | | | | | | | | | | | | - Felix Grewe
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | | | | | - Huini Wu
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Brian Ho
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Steven D. Leavitt
- Department of BiologyBrigham Young UniversityProvoUtahUSA
- Monte L. Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
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132
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Bourke BP, Justi SA, Caicedo-Quiroga L, Pecor DB, Wilkerson RC, Linton YM. Phylogenetic analysis of the Neotropical Albitarsis Complex based on mitogenome data. Parasit Vectors 2021; 14:589. [PMID: 34838107 PMCID: PMC8627034 DOI: 10.1186/s13071-021-05090-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Some of the most important malaria vectors in South America belong to the Albitarsis Complex (Culicidae; Anophelinae; Anopheles). Understanding the origin, nature, and geographical distribution of species diversity in this important complex has important implications for vector incrimination, control, and management, and for modelling future responses to climate change, deforestation, and human population expansion. This study attempts to further explore species diversity and evolutionary history in the Albitarsis Complex by undertaking a characterization and phylogenetic analysis of the mitogenome of all 10 putative taxa in the Albitarsis Complex. METHODS Mitogenome assembly and annotation allowed for feature comparison among Albitarsis Complex and Anopheles species. Selection analysis was conducted across all 13 protein-coding genes. Maximum likelihood and Bayesian inference methods were used to construct gene and species trees, respectively. Bayesian methods were also used to jointly estimate species delimitation and species trees. RESULTS Gene composition and order were conserved across species within the complex. Unique signatures of positive selection were detected in two species-Anopheles janconnae and An. albitarsis G-which may have played a role in the recent and rapid diversification of the complex. The COI gene phylogeny does not fully recover the mitogenome phylogeny, and a multispecies coalescent-based phylogeny shows that considerable uncertainty exists through much of the mitogenome species tree. The origin of divergence in the complex dates to the Pliocene/Pleistocene boundary, and divergence within the distinct northern South American clade is estimated at approximately 1 million years ago. Neither the phylogenetic trees nor the delimitation approach rejected the 10-species hypothesis, although the analyses could not exclude the possibility that four putative species with scant a priori support (An. albitarsis G, An. albitarsis H, An. albitarsis I, and An. albitarsis J), represent population-level, rather than species-level, splits. CONCLUSION The lack of resolution in much of the species tree and the limitations of the delimitation analysis warrant future studies on the complex using genome-wide data and the inclusion of additional specimens, particularly from two putative species, An. albitarsis I and An. albitarsis J.
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Affiliation(s)
- Brian P Bourke
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA.
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA.
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA.
| | - Silvia A Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
| | - David B Pecor
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
| | - Richard C Wilkerson
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, MRC-534, 4210 Silver Hill Rd., Suitland, MD, 20746, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History, 10th St NE & Constitution Ave NE, Washington, DC, 20002, USA
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133
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Finger N, Farleigh K, Bracken JT, Leaché AD, François O, Yang Z, Flouri T, Charran T, Jezkova T, Williams DA, Blair C. Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US. Genome Biol Evol 2021; 14:6443127. [PMID: 34849831 PMCID: PMC8735750 DOI: 10.1093/gbe/evab260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/03/2022] Open
Abstract
The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.
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Affiliation(s)
- Nicholas Finger
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Jason T Bracken
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
| | - Olivier François
- Faculty of Medicine, University Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, La Tronche, F38706, France 38000
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tristan Charran
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Dean A Williams
- Department of Biology, Texas Christian University, 2800 S University Dr, Fort Worth, TX, 76129, USA
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA.,Biology PhD Program, CUNY Graduate Center, 365 5th Ave, New York, NY, 10016, USA
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134
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Smart U, Ingrasci MJ, Sarker GC, Lalremsanga H, Murphy RW, Ota H, Tu MC, Shouche Y, Orlov NL, Smith EN. A comprehensive appraisal of evolutionary diversity in venomous Asian coralsnakes of the genus
Sinomicrurus
(Serpentes: Elapidae) using Bayesian coalescent inference and supervised machine learning. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Utpal Smart
- Center for Human Identification University of North Texas Health Science Center Fort Worth Texas USA
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Matthew J. Ingrasci
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | - Goutam C. Sarker
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
| | | | - Robert W. Murphy
- Royal Ontario Museum Centre for Biodiversity and Conservation Biology Toronto ON Canada
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Kunming China
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences Museum of Nature and Human Activities University of Hyogo Sanda Japan
| | - Ming Chung Tu
- Department of Life Sciences National Taiwan Normal University Taipei City Taiwan
| | - Yogesh Shouche
- National Centre for Microbial ResourceNational Center for Cell Science Pune India
| | - Nikolai L. Orlov
- Zoological Institute Russian Academy of SciencesSaint Petersburg Russia
| | - Eric N. Smith
- Department of Biology The Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington Texas USA
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135
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DNA barcoding in Dorcadionini (Coleoptera, Cerambycidae) uncovers mitochondrial-morphological discordance and the hybridogenic origin of several subspecies. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00531-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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136
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Goulding TC, Khalil M, Tan SH, Cumming RA, Dayrat B. Global diversification and evolutionary history of onchidiid slugs (Gastropoda, Pulmonata). Mol Phylogenet Evol 2021; 168:107360. [PMID: 34793980 DOI: 10.1016/j.ympev.2021.107360] [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: 06/05/2021] [Revised: 09/29/2021] [Accepted: 11/09/2021] [Indexed: 12/24/2022]
Abstract
Many marine species are specialized to specific parts of a habitat. In a mangrove forest, for instance, species may be restricted to the mud surface, the roots and trunks of mangrove trees, or rotting logs, which can be regarded as distinct microhabitats. Shifts to new microhabitats may be an important driver of sympatric speciation. However, the evolutionary history of these shifts is still poorly understood in most groups of marine organisms, because it requires a well-supported phylogeny with relatively complete taxon sampling. Onchidiid slugs are an ideal case study for the evolutionary history of habitat and microhabitat shifts because onchidiid species are specialized to different tidal zones and microhabitats in mangrove forests and rocky shores, and the taxonomy of the family in the Indo-West Pacific has been recently revised in a series of monographs. Here, DNA sequences for onchidiid species from the North and East Pacific, the Caribbean, and the Atlantic are used to reconstruct phylogenetic relationships among Onchidella species, and are combined with new data for Indo-West Pacific species to reconstruct a global phylogeny of the family. The phylogenetic relationships of onchidiid slugs are reconstructed based on three mitochondrial markers (COI, 12S, 16S) and three nuclear markers (28S, ITS2, H3) and nearly complete taxon sampling (all 13 genera and 62 of the 67 species). The highly-supported phylogeny presented here suggests that ancestral onchidiids most likely lived in the rocky intertidal, and that a lineage restricted to the tropical Indo-West Pacific colonized new habitats, including mudflats, mangrove forests, and high-elevation rainforests. Many onchidiid species in the Indo-West Pacific diverged during the Miocene, around the same time that a high diversity of mangrove plants appears in the fossil record, while divergence among Onchidella species occurred earlier, likely beginning in the Eocene. It is demonstrated that ecological specialization to microhabitats underlies the divergence between onchidiid genera, as well as the diversification through sympatric speciation in the genera Wallaconchis and Platevindex. The geographic distributions of onchidiid species also indicate that allopatric speciation played a key role in the diversification of several genera, especially Onchidella and Peronia. The evolutionary history of several morphological traits (penial gland, rectal gland, dorsal eyes, intestinal loops) is examined in relation to habitat and microhabitat evolutionary transitions and that the rectal gland of onchidiids is an adaptation to high intertidal and terrestrial habitats.
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Affiliation(s)
- Tricia C Goulding
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Munawar Khalil
- Department of Marine Science, Universitas Malikussaleh, Reuleut Main Campus, Kecamatan Muara Batu, North Aceh, Aceh 24355, Indonesia
| | - Shau Hwai Tan
- Centre for Marine and Coastal Studies, Universiti Sains Malaysia, 11800 Minden Penang, Malaysia; Marine Science Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden Penang, Malaysia
| | - Rebecca A Cumming
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Benoît Dayrat
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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137
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Mirarab S, Nakhleh L, Warnow T. Multispecies Coalescent: Theory and Applications in Phylogenetics. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-095340] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Species tree estimation is a basic part of many biological research projects, ranging from answering basic evolutionary questions (e.g., how did a group of species adapt to their environments?) to addressing questions in functional biology. Yet, species tree estimation is very challenging, due to processes such as incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, and hybridization, which can make gene trees differ from each other and from the overall evolutionary history of the species. Over the last 10–20 years, there has been tremendous growth in methods and mathematical theory for estimating species trees and phylogenetic networks, and some of these methods are now in wide use. In this survey, we provide an overview of the current state of the art, identify the limitations of existing methods and theory, and propose additional research problems and directions.
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Affiliation(s)
- Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, La Jolla, California 92093, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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138
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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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139
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Chou MH, Tseng WZ, Sang YD, Morgan B, De Vivo M, Kuan YH, Wang LJ, Chen WY, Huang JP. Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.
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Affiliation(s)
- Ming-Hsun Chou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Zhe Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yao-De Sang
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei-Yun Chen
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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140
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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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141
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Ellepola G, Herath J, Manamendra-Arachchi K, Wijayathilaka N, Senevirathne G, Pethiyagoda R, Meegaskumbura M. Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae). PLoS One 2021; 16:e0258594. [PMID: 34665841 PMCID: PMC8525734 DOI: 10.1371/journal.pone.0258594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.
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Affiliation(s)
- Gajaba Ellepola
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
- Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Jayampathi Herath
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
| | | | - Nayana Wijayathilaka
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Gayani Senevirathne
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Rohan Pethiyagoda
- Ichthyology Section, Australian Museum, Sydney, New South Wales, Australia
| | - Madhava Meegaskumbura
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
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142
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Ortego J, Knowles LL. Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization. Mol Ecol 2021; 31:296-312. [PMID: 34651368 DOI: 10.1111/mec.16225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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143
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Santos Rampasso A, O'Grady PM. Standardized terminology and visual atlas of the external morphology and terminalia for the genus Scaptomyza (Diptera: Drosophilidae). Fly (Austin) 2021; 16:37-61. [PMID: 34641736 PMCID: PMC8525988 DOI: 10.1080/19336934.2021.1969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The genus Scaptomyza is one of the two Drosophilidae genera with Hawaiian endemic species. This genus is an excellent model for biogeographic studies since it is distributed throughout the majority of continents, including continental islands, the Hawaiian Islands, and many other remote oceanic islands. This genus currently comprises 273 described species, 148 of which are endemic to the Hawaiian Islands. However, most descriptions were published before efforts to standardizing the morphological terminology across the Diptera were made in the 1980’s. Since research groups developed their own set of terminologies independently, without considering homologies, multiple terms have been used to refer to the same characters. This is especially true for the male terminalia, which have remarkable modifications within the family Drosophilidae. We reviewed the Scaptomyza literature, in addition to other studies across the Drosophilidae and Diptera, compiled the English synonyms, and provided a visual atlas of each body part, indicating how to recognize the morphological characters. The goal of the present study is to facilitate species identification and propose preferred terms to be adopted for future Scaptomyza descriptions.
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144
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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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145
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Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
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Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
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146
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DNA Barcode is Efficient for Identifying Bat Species. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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147
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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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148
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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149
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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150
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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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