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de Miranda GS, Kulkarni SS, Tagliatela J, Baker CM, Giupponi APL, Labarque FM, Gavish-Regev E, Rix MG, Carvalho LS, Fusari LM, Harvey MS, Wood HM, Sharma PP. The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi). Syst Biol 2024; 73:495-505. [PMID: 38733598 DOI: 10.1093/sysbio/syae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 02/20/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024] Open
Abstract
Asymmetrical rates of cladogenesis and extinction abound in the tree of life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits but is survived by a single living species, Paracharon caecusHansen (1921), that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa," and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy.
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Affiliation(s)
- Gustavo S de Miranda
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC 20560, USA
| | - Siddharth S Kulkarni
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Jéssica Tagliatela
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, Campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Paulo, Brazil
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Alessandro P L Giupponi
- Lab. de Carrapatos e outros Vetores Ápteros LAC - CAVAISC; IOC - FIOCRUZ, Rio de Janeiro, Brazil
| | - Facundo M Labarque
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, Campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Paulo, Brazil
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Michael G Rix
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia
| | - Leonardo S Carvalho
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, 64808-605 Floriano, PI, Brazil
| | - Lívia Maria Fusari
- Departamento de Hidrobiologia, Universidade Federal de São Carlos, campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Paulo, Brazil
| | - Mark S Harvey
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC 20560, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
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2
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Primov KD, Burdick DR, Lemer S, Forsman ZH, Combosch DJ. Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia. Sci Rep 2024; 14:17107. [PMID: 39048606 PMCID: PMC11269739 DOI: 10.1038/s41598-024-67992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.
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Affiliation(s)
- Karim D Primov
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - David R Burdick
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
| | - Sarah Lemer
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
| | - Zac H Forsman
- King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - David J Combosch
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU, USA
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3
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Asar Y, Sauquet H, Ho SYW. Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution. Syst Biol 2023; 72:1337-1356. [PMID: 37695237 PMCID: PMC10924723 DOI: 10.1093/sysbio/syad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023] Open
Abstract
Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.
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Affiliation(s)
- Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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4
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Wang Y, Yang Y, Kong L, Sasaki T, Li Q. Phylogenomic resolution of Imparidentia (Mollusca: Bivalvia) diversification through mitochondrial genomes. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:326-336. [PMID: 37637250 PMCID: PMC10449738 DOI: 10.1007/s42995-023-00178-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/25/2023] [Indexed: 08/29/2023]
Abstract
Despite significant advances in the phylogenomics of bivalves over the past decade, the higher-level phylogeny of Imparidentia (a superorder of Heterodonta) remains elusive. Here, a total of five new mitochondrial sequences (Chama asperella, Chama limbula, Chama dunkeri, Barnea manilensis and Ctena divergens) was added to provide resolution in nodes that required additional study. Although the monophyly of Lucinida remains less clear, the results revealed the overall backbone of the Imparidentia tree and the monophyly of Imparidentia. Likewise, most relationships among the five major Imparidentia lineages-Lucinida, Cardiida, Adapedonta, Myida and Venerida-were addressed with a well-supported topology. Basal relationships of Imparidentia recovered Lucinidae as the sister group to all remaining imparidentian taxa. Thyasiridae is a sister group to other imparidentian bivalves (except Lucinidae species) which is split into Cardiida, Adapedonta and the divergent clade of Neoheterodontei. Neoheterodontei was comprised of Venerida and Myida, the former of which now also contains Chamidae as the sister group to all the remaining venerid taxa. Moreover, molecular divergence times were inferred by calibrating nine nodes in the Imparidentia tree of life by extinct taxa. The origin of these major clades ranged from Ordovician to Permian with the diversification through the Palaeozoic to Mesozoic. Overall, the results obtained in this study demonstrate a better-resolved Imparidentia phylogeny based on mitochondrial genomes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00178-x.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237 China
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Barord GJ, Combosch DJ, Giribet G, Landman N, Lemer S, Veloso J, Ward PD. Three new species of Nautilus Linnaeus, 1758 (Mollusca, Cephalopoda) from the Coral Sea and South Pacific. Zookeys 2023; 1143:51-69. [DOI: 10.3897/zookeys.1143.84427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Nautiloids are a charismatic group of marine molluscs best known for their rich fossil record, but today they are restricted to a handful of species in the family Nautilidae from around the Coral Triangle. Recent genetic work has shown a disconnect between traditional species, originally defined on shell characters, but now with new findings from genetic structure of various Nautilus populations. Here, three new species of Nautilus from the Coral Sea and South Pacific region are formally named using observations of shell and soft anatomical data augmented by genetic information: N. samoaensissp. nov. (from American Samoa), N. vitiensissp. nov. (from Fiji), and N. vanuatuensissp. nov. (from Vanuatu). The formal naming of these three species is timely considering the new and recently published information on genetic structure, geographic occurrence, and new morphological characters, including color patterns of shell and soft part morphology of hood, and will aid in managing these possibly endangered animals. As recently proposed from genetic analyses, there is a strong geographic component affecting taxonomy, with the new species coming from larger island groups that are separated by at least 200 km of deep water (greater than 800 m) from other Nautilus populations and potential habitats. Nautilid shells implode at depths greater than 800 m and depth therefore acts as a biogeographical barrier separating these species. This isolation, coupled with the unique, endemic species in each locale, are important considerations for the conservation management of the extant Nautilus species and populations.
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Kolbasova G, Schmidt-Rhaesa A, Syomin V, Bredikhin D, Morozov T, Neretina T. Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Leiva C, Riesgo A, Combosch D, Arias MB, Giribet G, Downey R, Kenny NJ, Taboada S. Guiding marine protected area network design with comparative phylogeography and population genomics: An exemplary case from the Southern Ocean. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Carlos Leiva
- Marine Laboratory University of Guam Mangilao Guam USA
- Life Sciences Department The Natural History Museum London UK
| | - Ana Riesgo
- Life Sciences Department The Natural History Museum London UK
- Department of Biodiversity and Evolutionary Biology National Museum of Natural Sciences (CSIC) Madrid Spain
| | - David Combosch
- Marine Laboratory University of Guam Mangilao Guam USA
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts USA
| | - María Belén Arias
- Life Sciences Department The Natural History Museum London UK
- School of Life Sciences University of Essex Colchester Campus UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts USA
| | - Rachel Downey
- Fenner School of Environment and Society Australian National University Acton Australian Capital Territory Australia
| | - Nathan James Kenny
- Life Sciences Department The Natural History Museum London UK
- Department of Biochemistry University of Otago Dunedin New Zealand
| | - Sergi Taboada
- Life Sciences Department The Natural History Museum London UK
- Departamento de Biodiversidad, Ecología y Evolución Universidad Complutense de Madrid Madrid Spain
- Departamento de Ciencias de la Vida, Apdo. 20 Universidad de Alcalá Alcalá de Henares Spain
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8
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Quintero-Galvis JF, Saenz-Agudelo P, Amico GC, Vazquez S, Shafer ABA, Nespolo RF. Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae). Mol Phylogenet Evol 2022; 168:107405. [PMID: 35033671 DOI: 10.1016/j.ympev.2022.107405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/28/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022]
Abstract
Three orders represent the South American fauna of marsupials. Of these, Microbiotheria was until recently known as a monotypic genus with the only surviving species Dromiciops gliroides (monito del monte). The recent proposal of a new Dromiciops species (Dromiciops bicinovici), together with new information on the origin and diversification of living microbioterians has changed the prevailing paradigm around the evolutionary history of these emblematic marsupials. Here, we used a RADseq approach to test for evidence of admixture and past or current gene flow among both species of Dromiciops and evaluate the genetic structure within D. gliroides. We analyzed 127 samples of Dromiciops distributed across the known distribution range of both species. We also inferred the joint demographic history of these lineages, thus corroborating the status of D. bozinovici as a distinct species. Demographic history reconstruction indicated that D. bozinovici diverged from D. gliroides around 4my ago and has remained isolated and demographically stable ever since. In contrast, D. gliroides is subdivided into three subclades that experienced recent expansions and moderate gene flow among them (mostly from north to south). Furthermore, genetic distances among populations within D. gliroides were significantly correlated with geographic distances. These results suggest that some of the D. gliroides populations would have survived in glacial refuges, with posterior expansions after ice retreat. Our results have important implications for the systematics of the genus and have profound conservation consequences for the new species, especially considering the fragmentation level of the temperate rainforest.
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Affiliation(s)
- Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile; Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile
| | - Guillermo C Amico
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Soledad Vazquez
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Aaron B A Shafer
- Department of Forensic Science & Environmental Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia. Chile.
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9
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Erratum. Mol Ecol 2021; 30:6806. [PMID: 34676936 DOI: 10.1111/mec.16205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Significance of the suture line in cephalopod taxonomy revealed by 3D morphometrics in the modern nautilids Nautilus and Allonautilus. Sci Rep 2021; 11:17114. [PMID: 34429487 PMCID: PMC8384854 DOI: 10.1038/s41598-021-96611-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Assessing the taxonomic importance of the suture line in shelled cephalopods is a key to better understanding the diversity of this group in Earth history. Because fossils are subject to taphonomic artifacts, an in-depth knowledge of well-preserved modern organisms is needed as an important reference. Here, we examine the suture line morphology of all known species of the modern cephalopods Nautilus and Allonautilus. We applied computed tomography and geometric morphometrics to quantify the suture line morphology as well as the conch geometry and septal spacing. Results reveal that the suture line and conch geometry are useful in distinguishing species, while septal spacing is less useful. We also constructed cluster trees to illustrate the similarity among species. The tree based on conch geometry in middle ontogeny is nearly congruent with those previously reconstructed based on molecular data. In addition, different geographical populations of the same species of Nautilus separate out in this tree. This suggests that genetically distinct (i.e., geographically isolated) populations of Nautilus can also be distinguished using conch geometry. Our results are applicable to closely related fossil cephalopods (nautilids), but may not apply to more distantly related forms (ammonoids).
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11
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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12
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Song H, Sun LN, Wang HY, Zhang T. Nautilus pompilius. Trends Genet 2021; 38:107-108. [PMID: 34218958 DOI: 10.1016/j.tig.2021.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China.
| | - Li-Na Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hai-Yan Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China.
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13
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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America. Sci Rep 2021; 11:10752. [PMID: 34031525 PMCID: PMC8144384 DOI: 10.1038/s41598-021-90325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
Abstract
Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
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Ballesteros JA, Setton EVW, Santibáñez-López CE, Arango CP, Brenneis G, Brix S, Corbett KF, Cano-Sánchez E, Dandouch M, Dilly GF, Eleaume MP, Gainett G, Gallut C, McAtee S, McIntyre L, Moran AL, Moran R, López-González PJ, Scholtz G, Williamson C, Woods HA, Zehms JT, Wheeler WC, Sharma PP. Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes. Mol Biol Evol 2021; 38:686-701. [PMID: 32915961 PMCID: PMC7826184 DOI: 10.1093/molbev/msaa228] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | | | - Claudia P Arango
- Queensland Museum, Biodiversity Program, Brisbane, QLD, Australia
| | - Georg Brenneis
- Zoologisches Institut und Museum, Cytologie und Evolutionsbiologie, Universität Greifswald, Greifswald, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), c/o Biocenter Grindel (CeNak), Martin-Luther-King-Platz 3, Hamburg, Germany
| | - Kevin F Corbett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Esperanza Cano-Sánchez
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Merai Dandouch
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Geoffrey F Dilly
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Marc P Eleaume
- Départment Milieux et Peuplements Aquatiques, Muséum National d’Histoire Naturelle, Paris, France
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Cyril Gallut
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Concarneau, France
| | - Sean McAtee
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Lauren McIntyre
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Amy L Moran
- Department of Biology, University of Hawai’I at Mānoa, Honolulu, HI
| | - Randy Moran
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Gerhard Scholtz
- Institut für Biologie, Vergleichende Zoologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Clay Williamson
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
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15
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Garcia-Elfring A, Barrett RDH, Millien V. Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus). J Hered 2020; 110:684-695. [PMID: 31300816 DOI: 10.1093/jhered/esz045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.
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Affiliation(s)
- Alan Garcia-Elfring
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Rowan D H Barrett
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
| | - Virginie Millien
- Redpath Museum, McGill University, Montreal, QC, Canada.,Department of Biology, McGill University, Montreal, QC, Canada
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16
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Schwentner M, Giribet G, Combosch DJ, Timms BV. Genetic differentiation in mountain-dwelling clam shrimp, Paralimnadia (Crustacea : Branchiopoda : Spinicaudata), in eastern Australia. INVERTEBR SYST 2020. [DOI: 10.1071/is19027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.
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17
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Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat Commun 2019; 10:4201. [PMID: 31519986 PMCID: PMC6744486 DOI: 10.1038/s41467-019-12133-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species. Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.
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18
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Voskarides K, Dweep H, Chrysostomou C. Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes. Hum Genomics 2019; 13:26. [PMID: 31174607 PMCID: PMC6555970 DOI: 10.1186/s40246-019-0210-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023] Open
Abstract
Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. The availability of animal genomes permitted comparison of gene content of genomes of 24 vertebrate species that evolved through adaptive radiation (representing high evolutionary rate) and of 20 vertebrate species that are considered as living fossils (representing a slow evolutionary rate or evolutionary stasis). Mammals, birds, reptiles, and bony fishes were included in the analysis. Pathway analysis was performed for genes found to be specific in adaptive radiation or evolutionary stasis respectively. Pathway analysis revealed that DNA repair and cellular response to DNA damage are important (false discovery rate = 8.35 × 10−5; 7.15 × 10−6, respectively) for species evolved through adaptive radiation. This was confirmed by further genetic in silico analysis (p = 5.30 × 10−3). Nucleotide excision repair and base excision repair were the most significant pathways. Additionally, the number of DNA repair genes was found to be linearly related to the genome size and the protein number (proteome) of the 44 animals analyzed (p < 1.00 × 10−4), this being compatible with Drake’s rule. This is the first study where radiated and living fossil species have been genetically compared. Evidence has been found that cancer-related genes have a special role in radiated species. Linear association of the number of DNA repair genes with the species genome size has also been revealed. These comparative genetics results can support the idea of punctuated equilibrium evolution.
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19
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Yacobucci MM. Postmortem transport in fossil and modern shelled cephalopods. PeerJ 2018; 6:e5909. [PMID: 30515355 PMCID: PMC6266924 DOI: 10.7717/peerj.5909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
The chambered shells of cephalopod mollusks, such as modern Nautilus and fossil ammonoids, have the potential to float after death, which could result in significant postmortem transport of shells away from living habitats. Such transport would call into question these clades' documented biogeographic distributions and therefore the many (paleo)biological interpretations based on them. It is therefore imperative to better constrain the likelihood and extent of postmortem transport in modern and fossil cephalopods. Here, I combine the results of classic experiments on postmortem buoyancy with datasets on cephalopod shell form to determine that only those shells with relatively high inflation are likely to float for a significant interval after death and therefore potentially experience postmortem transport. Most ammonoid cephalopods have shell forms making postmortem transport unlikely. Data on shell forms and geographic ranges of early Late Cretaceous cephalopod genera demonstrate that even genera with shell forms conducive to postmortem buoyancy do not, in fact, show artificially inflated biogeographic ranges relative to genera with non-buoyant morphologies. Finally, georeferenced locality data for living nautilid specimens and dead drift shells indicate that most species have relatively small geographic ranges and experience limited drift. Nautilus pompilius is the exception, with a broad Indo-Pacific range and drift shells found far from known living populations. Given the similarity of N. pompilius to other nautilids in its morphology and ecology, it seems unlikely that this species would have a significantly different postmortem fate than its close relatives. Rather, it is suggested that drift shells along the east African coast may indicate the existence of modern (or recently extirpated) living populations of nautilus in the western Indian Ocean, which has implications for the conservation of these cephalopods.
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Affiliation(s)
- Margaret M. Yacobucci
- Department of Geology, Bowling Green State University, Bowling Green, OH, United States of America
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20
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Beichman AC, Huerta-Sanchez E, Lohmueller KE. Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062431] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.
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Affiliation(s)
- Annabel C. Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
| | - Emilia Huerta-Sanchez
- Department of Molecular and Cell Biology, University of California, Merced, California 95343, USA
- Current affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program in Bioinformatics and Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
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21
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Abdelkrim J, Aznar-Cormano L, Fedosov AE, Kantor YI, Lozouet P, Phuong MA, Zaharias P, Puillandre N. Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea). Mol Biol Evol 2018; 35:2355-2374. [DOI: 10.1093/molbev/msy144] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jawad Abdelkrim
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Laetitia Aznar-Cormano
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Yuri I Kantor
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Pierre Lozouet
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue Buffon, 75005 Paris, France
| | - Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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