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Ji J, Jackson DJ, Leaché AD, Yang Z. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks. Syst Biol 2023; 72:446-465. [PMID: 36504374 PMCID: PMC10275556 DOI: 10.1093/sysbio/syac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 10/25/2023] Open
Abstract
In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].
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Affiliation(s)
- Jiayi Ji
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Donavan J Jackson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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2
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Matsudaira K, Reichard UH, Ishida T, Malaivijitnond S. Introgression and mating patterns between white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) in a natural hybrid zone. PLoS One 2022; 17:e0264519. [PMID: 35358199 PMCID: PMC8970389 DOI: 10.1371/journal.pone.0264519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
Gibbons (Family Hylobatidae) are a suitable model for exploring hybridization in pair-living primates as several species form hybrid zones. In Khao Yai National Park, Thailand, white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) are distributed parapatrically and hybridize in a narrow zone. Their phenotypic characteristics suggest limited inter-species gene flow, although this has never been assessed. To uncover the history and degree of gene flow between the two species, we studied the genetic structure of gibbons in the hybrid zone by analyzing fecal DNA samples, phenotypic characteristics, vocalizations and individuals’ social status. We determined eight autosomal single nucleotide variant (SNV) loci, and mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes of 72 gibbons. We compared these markers with reference types of wild pureblood white-handed gibbons (n = 12) in Kaeng Krachan National Park and pureblood pileated gibbons (n = 4) in Khao Soi Dao Wildlife Sanctuary. Autosomal genotypic analyses confirmed the various levels of mixed ancestry for several adult gibbons with or without atypical phenotypic traits in Khao Yai National Park. In some other adult gibbons, the mixed ancestry was not detected in either autosomal SNVs or their phenotypic traits but the mtDNA. Both male and female adult hybrids formed reproductive units mainly with a phenotypic pureblood partner and many of them produced offspring. Taken together, our results suggest that once hybridization occurs, white-handed-pileated-gibbon hybrids can reproduce with either parental species and that the backcrossing and thus introgression may occur in successive generations, with no drastic changes in phenotypic appearance.
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Affiliation(s)
- Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Ulrich H. Reichard
- Department of Anthropology and Center for Ecology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
| | - Takafumi Ishida
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
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3
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Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA. Taxonomic and genetic assessment of captive White-Handed Gibbons ( Hylobateslar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. Zookeys 2022; 1076:25-41. [PMID: 34975272 PMCID: PMC8674214 DOI: 10.3897/zookeys.1076.73262] [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: 08/20/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobateslar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H.lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H.lar subspecies suggesting that these individuals belong to the H.larlar subspecies. In addition, two populations of H.l.lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H.lar.
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Affiliation(s)
- Millawati Gani
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Noor Azleen Mohd Kulaimi
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Chew Cheah Zheng
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Aida Nur Atiqah
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Nur Maisarah Abd Rahim
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia Universiti Putra Malaysia Serdang Malaysia
| | - Ahmad Azhar Mohammed
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
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4
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Markviriya D, Asensio N, Brockelman WY, Jeratthitikul E, Kongrit C. Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand. Primates 2021; 63:51-63. [PMID: 34716489 DOI: 10.1007/s10329-021-00958-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/17/2021] [Indexed: 10/20/2022]
Abstract
Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.
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Affiliation(s)
- Darunee Markviriya
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Norberto Asensio
- Faculty of Environment and Resource Studies, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,Department of Clinical and Health Psychology and Research Methodology, Faculty of Psychology, University of the Basque Country, 20018, Donostia, Gipuzkoa, Spain
| | - Warren Y Brockelman
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Chalita Kongrit
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand.
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5
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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6
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Flouri T, Jiao X, Rannala B, Yang Z. A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis. Mol Biol Evol 2021; 37:1211-1223. [PMID: 31825513 PMCID: PMC7086182 DOI: 10.1093/molbev/msz296] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Davis, CA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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7
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Jiao X, Yang Z. Defining Species When There is Gene Flow. Syst Biol 2020; 70:108-119. [PMID: 32617579 DOI: 10.1093/sysbio/syaa052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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8
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Jiao X, Flouri T, Rannala B, Yang Z. The Impact of Cross-Species Gene Flow on Species Tree Estimation. Syst Biol 2020; 69:830-847. [DOI: 10.1093/sysbio/syaa001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Abstract
Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multilocus sequence data. Our results suggest that the majority-vote method based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambiae species complex constitute such an example of extreme impact of gene flow on species phylogeny. [IM; introgression; migration; MSci; multispecies coalescent; species tree.]
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Tomáš Flouri
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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9
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Hosoishi S, Ogata K. Cryptic Diversity in the Widespread Asian Ant Crematogaster rothneyi (Hymenoptera: Formicidae) Inferred from Morphological and Genetic Evidence. Zool Stud 2019; 58:e11. [PMID: 31966312 PMCID: PMC6778772 DOI: 10.6620/zs.2019.58-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2019] [Indexed: 11/18/2022]
Abstract
The myrmicine species Crematogaster rothneyi is one of the most widely distributed ants in Asia, but it has rarely been collected in the field. Its distribution range covers South and Southeast Asia, extending approximately 5,000 km from India in the west to Sulawesi in the east. Despite this wide distribution range, C. rothneyi has been treated as a single taxonomic species, and no combined morphological or molecular analysis has been conducted to assess whether any intraspecific variation exists. The sequence divergences of C. rothneyi populations, mainly obtained from Southeast Asia, were investigated by analyzing 387 bp and 175 bp sequences of the 12S ribosomal RNA and cytochrome c oxidase subunit (COI) genes, respectively. Phylogenetic analysis indicated that the C. rothneyi populations were separated into three groups: group I from Thailand and Cambodia, group II from Bangladesh and Myanmar, and group III from Krakatau and Sulawesi. Groups II and III were recovered as a single clade, sister to group I. The interspecific divergences were 7.3% to 8.5% for 12S and 14.5% to 23.3% for COI between most C. rothneyi specimens and Cambodian specimens, while divergence for 12S was 3.5% between Thai and Cambodian specimens. The Thai specimens are not morphologically differentiated, and are considered conspecific to C. rothneyi. We describe the Cambodian series as a new species, Crematogaster yaharai sp. nov., based on unique antennal morphology and mesosomal sculpture patterns with molecular evidence. Crematogaster rothneyi civa Forel, 1902 is synonymized under C. rothneyi. Crematogaster rothneyi is widespread and has sister species, suggesting recent diversification within the Indochinese Peninsula.
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Affiliation(s)
- Shingo Hosoishi
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
| | - Kazuo Ogata
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
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10
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Abstract
In humans, patterns of cranial variation mirror genetic diversity globally, implicating population history as a key driver of cranial disparity. Here, we demonstrate that the magnitude of genetic diversity within 12 extant ape taxa explains a large proportion of cranial shape variation. Taxa that are more genetically diverse tend to be more cranially diverse also. Our results suggest that neutral evolutionary processes such as mutation, genetic drift, and gene flow are reflected in both genetic and cranial diversity in apes. This work provides a perspective on intraspecific cranial variation in apes which has important implications for interpreting selective and developmental pressures on the cranium and for understanding shape variation in fossil hominin crania. Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.
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11
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Dalquen DA, Zhu T, Yang Z. Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species. Syst Biol 2018; 66:379-398. [PMID: 27486180 DOI: 10.1093/sysbio/syw063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 07/08/2016] [Indexed: 01/03/2023] Open
Abstract
We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Markov chain characterization of the genealogical process of coalescence and migration is used to integrate out the migration histories at each locus analytically, whereas Gaussian quadrature is used to integrate over the coalescent times on each genealogical tree numerically. This is an extension of our early implementation of the symmetrical isolation-with-migration model for three species to accommodate arbitrary loci with two or three sequences per locus and to allow asymmetrical migration rates. Our implementation can accommodate tens of thousands of loci, making it feasible to analyze genome-scale data sets to test for gene flow. We calculate the posterior probabilities of gene trees at individual loci to identify genomic regions that are likely to have been transferred between species due to gene flow. We conduct a simulation study to examine the statistical properties of the likelihood ratio test for gene flow between the two in-group species and of the ML estimates of model parameters such as the migration rate. Inclusion of data from a third out-group species is found to increase dramatically the power of the test and the precision of parameter estimation. We compiled and analyzed several genomic data sets from the Drosophila fruit flies. Our analyses suggest no migration from D. melanogaster to D. simulans, and a significant amount of gene flow from D. simulans to D. melanogaster, at the rate of ~0.02 migrant individuals per generation. We discuss the utility of the multispecies coalescent model for species tree estimation, accounting for incomplete lineage sorting and migration.
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Affiliation(s)
- Daniel A Dalquen
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Tianqi Zhu
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.,Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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12
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Schroeder L, von Cramon-Taubadel N. The evolution of hominoid cranial diversity: A quantitative genetic approach. Evolution 2017; 71:2634-2649. [DOI: 10.1111/evo.13361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/03/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Lauren Schroeder
- Department of Anthropology; University of Toronto Mississauga; Mississauga ON L5L 1C6 Canada
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
- Human Evolution Research Institute; University of Cape Town; Rondebosch 7701 South Africa
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
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13
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Patel RP, Wutke S, Lenz D, Mukherjee S, Ramakrishnan U, Veron G, Fickel J, Wilting A, Förster DW. Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes. J Hered 2017; 108:349-360. [PMID: 28498987 DOI: 10.1093/jhered/esx017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/21/2017] [Indexed: 01/02/2023] Open
Abstract
The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species' distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).
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Affiliation(s)
- Riddhi P Patel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Saskia Wutke
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Shomita Mukherjee
- Salim Ali Centre for Ornithology and Natural History, Coimbatore, India.,);National Centre for Biological Sciences, GKVK Campus, Bangalore, India
| | - Uma Ramakrishnan
- );National Centre for Biological Sciences, GKVK Campus, Bangalore, India
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, CP 51, Paris, France
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Andreas Wilting
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
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14
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Saha A, Johansen T, Hedeholm R, Nielsen EE, Westgaard JI, Hauser L, Planque B, Cadrin SX, Boje J. Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure. Evol Appl 2016; 10:77-90. [PMID: 28035237 PMCID: PMC5192944 DOI: 10.1111/eva.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/19/2016] [Indexed: 01/17/2023] Open
Abstract
Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group, "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.
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Affiliation(s)
- Atal Saha
- Tromsø Department Institute of Marine Research Tromsø Norway
| | - Torild Johansen
- Tromsø Department Institute of Marine Research Tromsø Norway
| | | | - Einar E Nielsen
- DTU Aqua - National Institute of Aquatic Resources Charlottenlund Denmark
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Benjamin Planque
- Tromsø Department Institute of Marine Research Tromsø Norway; Hjort Centre for Marine Ecosystem Dynamics Bergen Norway
| | - Steven X Cadrin
- School for Marine Science and Technology University of Massachusetts Darmouth Fairhaven MA USA
| | - Jesper Boje
- Greenland Institute of Natural Resources Nuuk Greenland; DTU Aqua - National Institute of Aquatic Resources Charlottenlund Denmark
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15
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16
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Osada N. Genetic diversity in humans and non-human primates and its evolutionary consequences. Genes Genet Syst 2016; 90:133-45. [PMID: 26510568 DOI: 10.1266/ggs.90.133] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity is a key parameter in population genetics and is important for understanding the process of evolution and for the development of appropriate conservation strategies. Recent advances in sequencing technology have enabled the measurement of genetic diversity of various organisms at the nucleotide level and on a genome-wide scale, yielding more precise estimates than were previously achievable. In this review, I have compiled and summarized the estimates of genetic diversity in humans and non-human primates based on recent genome-wide studies. Although studies on population genetics demonstrated fluctuations in population sizes over time, general patterns have emerged. As shown previously, genetic diversity in humans is one of the lowest among primates; however, certain other primate species exhibit genetic diversity that is comparable to or even lower than that in humans. There exists greater than 10-fold variation in genetic diversity among primate species, and I found weak correlation with species fecundity but not with body or propagule size. I further discuss the potential evolutionary consequences of population size decline on the evolution of primate species. The level of genetic diversity negatively correlates with the ratio of non-synonymous to synonymous polymorphisms in a population, suggesting that proportionally greater numbers of slightly deleterious mutations segregate in small rather than large populations. Although population size decline is likely to promote the fixation of slightly deleterious mutations, there are molecular mechanisms, such as compensatory mutations at various molecular levels, which may prevent fitness decline at the population level. The effects of slightly deleterious mutations from theoretical and empirical studies and their relevance to conservation biology are also discussed in this review.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics
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17
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Roos C. Phylogeny and Classification of Gibbons (Hylobatidae). DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-5614-2_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. Genetics 2015; 200:295-308. [PMID: 25769979 DOI: 10.1534/genetics.115.174425] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022] Open
Abstract
Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.
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Baicharoen S, Miyabe-Nishiwaki T, Arsaithamkul V, Hirai Y, Duangsa-ard K, Siriaroonrat B, Domae H, Srikulnath K, Koga A, Hirai H. Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes. PLoS One 2014; 9:e109151. [PMID: 25290445 PMCID: PMC4188616 DOI: 10.1371/journal.pone.0109151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/29/2014] [Indexed: 01/05/2023] Open
Abstract
Recently, we discovered that alpha satellite DNA has unique and genus-specific localizations on the chromosomes of small apes. This study describes the details of alpha satellite localization in the genera Nomascus and Hylobates and explores their usefulness in distinguishing parental genome sets in hybrids between these genera. Fluorescence in situ hybridization was used to establish diagnostic criteria of alpha satellite DNA markers in discriminating small ape genomes. In particular we established the genus specificity of alpha satellite distribution in three species of light-cheeked gibbons (Nomascus leucogenys, N. siki, and N. gabriellae) in comparison to that of Hylobates lar. Then we determined the localization of alpha satellite DNA in a hybrid individual which resulted from a cross between these two genera. In Nomascus the alpha satellite DNA blocks were located at the centromere, telomere, and four interstitial regions. In Hylobates detectable amounts of alpha satellite DNA were seen only at centromeric regions. The differences in alpha satellite DNA locations between Nomascus and Hylobates allowed us to easily distinguish the parental chromosomal sets in the genome of intergeneric hybrid individuals found in Thai and Japanese zoos. Our study illustrates how molecular cytogenetic markers can serve as diagnostic tools to identify the origin of individuals. These molecular tools can aid zoos, captive breeding programs and conservation efforts in managing small apes species. Discovering more information on alpha satellite distribution is also an opportunity to examine phylogenetic and evolutionary questions that are still controversial in small apes.
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Affiliation(s)
- Sudarath Baicharoen
- Bioscience Program, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Visit Arsaithamkul
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Boripat Siriaroonrat
- Conservation, Research and Education Division, Zoological Park Organization, Bangkok, Thailand
| | | | - Kornsorn Srikulnath
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- * E-mail:
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20
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Kutschera VE, Bidon T, Hailer F, Rodi JL, Fain SR, Janke A. Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol Biol Evol 2014; 31:2004-17. [PMID: 24903145 PMCID: PMC4104321 DOI: 10.1093/molbev/msu186] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
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Affiliation(s)
- Verena E Kutschera
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Julia L Rodi
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Steven R Fain
- National Fish and Wildlife Forensic Laboratory, Ashland, OR
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyInstitute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
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