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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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2
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Marcionetti A, Bertrand JAM, Cortesi F, Donati GFA, Heim S, Huyghe F, Kochzius M, Pellissier L, Salamin N. Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex. Mol Ecol 2024; 33:e17347. [PMID: 38624248 DOI: 10.1111/mec.17347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Laboratoire Génome et Développement Des Plantes (UMR 5096 UPVD/CNRS), University of Perpignan via Domitia, Perpignan, France
| | - Fabio Cortesi
- School of the Environment and Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giulia F A Donati
- EAWAG Swiss Federal Institute of Aquatic Science & Technology, Dübendorf, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Sara Heim
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Filip Huyghe
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Marc Kochzius
- Marine Biology - Ecology, Evolution and Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental System Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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3
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Lo YY, Cheng RC, Lin CP. Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan. PLoS One 2024; 19:e0301776. [PMID: 38722906 PMCID: PMC11081396 DOI: 10.1371/journal.pone.0301776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 05/13/2024] Open
Abstract
An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.
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Affiliation(s)
- Ying-Yuan Lo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Wild Animals Division, Biodiversity Research Institute, Nantou, Taiwan
| | - Ren-Chung Cheng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Research Center for Global Change Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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4
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Sgarlata GM, Rasolondraibe E, Salmona J, Le Pors B, Ralantoharijaona T, Rakotonanahary A, Jan F, Manzi S, Iribar A, Zaonarivelo JR, Volasoa Andriaholinirina N, Rasoloharijaona S, Chikhi L. The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species. Mol Phylogenet Evol 2024; 193:107997. [PMID: 38128795 DOI: 10.1016/j.ympev.2023.107997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.
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Affiliation(s)
| | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Jordi Salmona
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Barbara Le Pors
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, 201 Antsiranana, Madagascar.
| | | | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
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5
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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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6
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Hubert N, Phillips JD, Hanner RH. Delimiting Species with Single-Locus DNA Sequences. Methods Mol Biol 2024; 2744:53-76. [PMID: 38683311 DOI: 10.1007/978-1-0716-3581-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.
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Affiliation(s)
- Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France.
| | - Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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7
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Sánchez KI, Diaz Huesa EG, Breitman MF, Avila LJ, Sites JW, Morando M. Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade). Syst Biol 2023; 72:739-752. [PMID: 37097104 DOI: 10.1093/sysbio/syad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Emilce G Diaz Huesa
- Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEAus-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - María F Breitman
- Department of Biology and Environmental Science, Auburn University at Montgomery, Montgomery, 36117, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology, Austin Peay State University, Clarksville, 37044, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Puerto Madryn, U9120ACD, Argentina
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Tiley GP, Flouri T, Jiao X, Poelstra JW, Xu B, Zhu T, Rannala B, Yoder AD, Yang Z. Estimation of species divergence times in presence of cross-species gene flow. Syst Biol 2023; 72:820-836. [PMID: 36961245 PMCID: PMC10405360 DOI: 10.1093/sysbio/syad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].
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Affiliation(s)
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen, Guangdong, China
| | | | - Bo Xu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
- Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
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9
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Brandt S, Sole C, Lyle R. The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa. Mol Phylogenet Evol 2023; 184:107798. [PMID: 37094612 DOI: 10.1016/j.ympev.2023.107798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.
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Affiliation(s)
- Shannon Brandt
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Catherine Sole
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Robin Lyle
- Agricultural Research Council - Plant Health and Protection, Biosystematics, Roodeplaat, Pretoria, South Africa
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10
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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11
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Dietz L, Eberle J, Mayer C, Kukowka S, Bohacz C, Baur H, Espeland M, Huber BA, Hutter C, Mengual X, Peters RS, Vences M, Wesener T, Willmott K, Misof B, Niehuis O, Ahrens D. Standardized nuclear markers improve and homogenize species delimitation in Metazoa. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Paris‐Lodron‐University Salzburg Austria
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Sandra Kukowka
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Hannes Baur
- Naturhistorisches Museum Bern/Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Marianne Espeland
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Bernhard A. Huber
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Carl Hutter
- Museum of Natural Sciences and Department of Biological Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Ximo Mengual
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Ralph S. Peters
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Miguel Vences
- Technische Universität Braunschweig Braunschweig Germany
| | - Thomas Wesener
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Keith Willmott
- Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert‐Ludwigs‐Universität Freiburg Freiburg im Breisgau Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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12
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Daniels SR, Busschau T, Gullacksen G, Marais H, Gouws G, Barnes A. Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
AbstractWe examined the systematics of a ubiquitously distributed southern African freshwater crab, Potamonautes sidneyi s.l. species complex. Specimens were subjected to DNA sequence analyses of two mitochondrial loci (16S rRNA + COI). We applied three species delimitations methods (ASAP, bGMYC and bPTP) to test their utility in delineating species boundaries in Potamonautes and three additional Afrotropical genera (Liberonautes, Nesonautes and Seychellum). The combined mtDNA dataset retrieved five clades. Clade 1 comprised of P. barbarai, clade 2 comprised of specimens from the interior of the Great Karoo Basin, sister to P. sidneyi s.s. in clade 3. Clade 4 was confined to Eswatini and the Mpumalanga Province of South Africa, and sister to clade 5 that comprised P. danielsi. The three species delimitation methods either over- or underestimated the number of species. Phylogenetically, specimens from the Great Karoo Basin (clade 2) were equidistant to P. sidneyi s.s. and P. perlatus, while the Eswatini and Mpumalanga specimens (clade 4) were sister to P. danielsi. Clades 2 and 4 are herein described as P. karooensis sp. nov. and P. valles sp. nov., respectively.
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Affiliation(s)
- Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | - Theo Busschau
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | | | - Hannes Marais
- Mpumalanga Tourism and Parks Agency, Aquatic Unit , Lydenburg, 1120 , South Africa
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity , Private Bag 1015, Makhanda, 6140 , South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
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13
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Chou MH, Chu IH, Lau D, Huang JP. Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: a case study on. INVERTEBR SYST 2022. [DOI: 10.1071/is22011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alpha taxonomy is fundamental for many biological fields. Delineation of the species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets, and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialisation, and further corroborate that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can occur at a small geographic scale, even in a winged insect like tiger beetles. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered. ZooBank LSID: urn:lsid:zoobank.org:pub:9DEC1432-365C-4872-8D06-73B95F30624F
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14
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Chambers EA, Marshall TL, Hillis DM. The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation. Syst Biol 2022:6673165. [PMID: 35993885 DOI: 10.1093/sysbio/syac056] [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: 01/23/2022] [Revised: 06/17/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and L. gentilis, we examined a ∼700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and L. elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA.,Department of Environmental Science, Policy, and Management, The University of California Berkeley, Berkeley CA 94720 USA
| | - Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin TX 78712 USA
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15
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Young MK, Smith R, Pilgrim KL, Isaak DJ, McKelvey KS, Parkes S, Egge J, Schwartz MK. A Molecular Taxonomy of Cottus in western North America. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Michael K. Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Rebecca Smith
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Kristine L. Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Daniel J. Isaak
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Kevin S. McKelvey
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
| | - Sharon Parkes
- USDA Forest Service, Rocky Mountain Research Station, 322 East Front Street Suite 401, Boise, ID 83702
| | - Jacob Egge
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802
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16
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Hancock ZB, Lehmberg ES, Blackmon H. Phylogenetics in Space: How Continuous Spatial Structure Impacts Tree Inference. Mol Phylogenet Evol 2022; 173:107505. [PMID: 35577296 DOI: 10.1016/j.ympev.2022.107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent - what we call the "missing z-axis". In this article, we review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. We illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. We find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by utilizing our results to suggest how researchers can identify spatial structure in phylogenetic datasets.
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17
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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18
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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19
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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20
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Carstens BC, Smith ML, Duckett DJ, Fonseca EM, Thomé MTC. Assessing model adequacy leads to more robust phylogeographic inference. Trends Ecol Evol 2022; 37:402-410. [PMID: 35027224 DOI: 10.1016/j.tree.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
Phylogeographic studies base inferences on large data sets and complex demographic models, but these models are applied in ways that could mislead researchers and compromise their inference. Researchers face three challenges associated with the use of models: (i) 'model selection', or the identification of an appropriate model for analysis; (ii) 'evaluation of analytical results', or the interpretation of the biological significance of the resulting parameter estimates, delimitations, and topologies; and (iii) 'model evaluation', or the use of statistical approaches to assess the fit of the model to the data. The field collectively invests most of its energy in point (ii) without considering the other points; we argue that attention to points (i) and (iii) is essential to phylogeographic inference.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA.
| | - Megan L Smith
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Drew J Duckett
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
| | - Emanuel M Fonseca
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
| | - M Tereza C Thomé
- Department of Evolution, Ecology, and Organismal Biology at The Ohio State University, Columbus, OH, USA
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21
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Zhao Z, Oosthuizen J, Heideman N. How many species does the
Psammobates tentorius
(tent tortoise) species complex (Reptilia, Testudinidae) comprise? A taxonomic solution potentially applicable to species complexes. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Jaco Oosthuizen
- School of Pathology University of the Free Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
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22
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Unmack PJ, Adams M, Hammer MP, Johnson JB, Gruber B, Gilles A, Young M, Georges A. Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.
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Affiliation(s)
- Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Mark Adams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Jerald B Johnson
- Department of Biology, Brigham Young University, Provo, UT, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Bernd Gruber
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - André Gilles
- UMR 1467 RECOVER, Aix Marseille Univ, INRAE, Centre St Charles, 3 place Victor Hugo, Marseille, France
| | - Matthew Young
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
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23
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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24
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Leaché AD, Davis HR, Singhal S, Fujita MK, Lahti ME, Zamudio KR. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.678110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.
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25
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Ottenlips MV, Mansfield DH, Buerki S, Feist MAE, Downie SR, Dodsworth S, Forest F, Plunkett GM, Smith JF. Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex. AMERICAN JOURNAL OF BOTANY 2021; 108:1217-1233. [PMID: 34105148 PMCID: PMC8362113 DOI: 10.1002/ajb2.1676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/26/2021] [Indexed: 05/29/2023]
Abstract
PREMISE Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.
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Affiliation(s)
| | | | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
| | | | - Stephen R. Downie
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Steven Dodsworth
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
- School of Life SciencesUniversity of BedfordshireLutonLU1 3JUUK
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
| | - Gregory M. Plunkett
- Cullman Program for Molecular SystematicsNew York Botanical Garden2900 Southern BoulevardBronxNY10458USA
| | - James F. Smith
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
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26
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Bamberger S, Xu J, Hausdorf B. Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete. Syst Biol 2021; 71:439-460. [PMID: 34181027 DOI: 10.1093/sysbio/syab050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023] Open
Abstract
Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3-9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.
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Affiliation(s)
- Sonja Bamberger
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Jie Xu
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
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27
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Wikramanayake SA, Wikramanayake ED, Pallewatta N, Leaché AD. Integration of genetic structure into conservation of an endangered, endemic lizard,
Ceratophora aspera
: A case study from Sri Lanka. Biotropica 2021. [DOI: 10.1111/btp.12970] [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]
Affiliation(s)
- Shanelle A. Wikramanayake
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
| | | | - Nirmalie Pallewatta
- Department of Zoology and Environment Science Faculty of Science University of Colombo Colombo Sri Lanka
| | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
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28
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Kim D, Bauer BH, Near TJ. Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae). Syst Biol 2021; 71:273-285. [PMID: 33944950 DOI: 10.1093/sysbio/syab029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/14/2022] Open
Abstract
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between non-sister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.
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Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Bruce H Bauer
- David A. Etnier Ichthyological Collection, 515 Hesler Biology Building, University of Tennessee, Knoxville, TN 37996, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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29
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Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
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Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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30
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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31
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Sánchez KI, Avila LJ, Sites JW, Morando M. An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini). Mol Phylogenet Evol 2021; 157:107046. [PMID: 33421613 DOI: 10.1016/j.ympev.2020.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/07/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina.
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT 84602, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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32
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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33
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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34
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Mussmann SM, Douglas MR, Oakey DD, Douglas ME. Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem. Ecol Evol 2020; 10:10798-10817. [PMID: 33072297 PMCID: PMC7548178 DOI: 10.1002/ece3.6736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
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Affiliation(s)
- Steven M. Mussmann
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - David D. Oakey
- School of Life SciencesArizona State UniversityTempeAZUSA
- Present address:
Arizona State Veteran HomePhoenixAZUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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35
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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36
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Poelstra JW, Salmona J, Tiley GP, Schüßler D, Blanco MB, Andriambeloson JB, Bouchez O, Campbell CR, Etter PD, Hohenlohe PA, Hunnicutt KE, Iribar A, Johnson EA, Kappeler PM, Larsen PA, Manzi S, Ralison JM, Randrianambinina B, Rasoloarison RM, Rasolofoson DW, Stahlke AR, Weisrock DW, Williams RC, Chikhi L, Louis EE, Radespiel U, Yoder AD. Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent. Syst Biol 2020; 70:203-218. [PMID: 32642760 DOI: 10.1093/sysbio/syaa053] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/13/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mouse lemur diversity in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for two pairs of sister lineages that include three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among the two pairs of lineages. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported-a result that is particularly striking when using the genealogical discordance index (gdi). Nonsister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated relaxed-clock estimates. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case. [Cryptic species; effective population size; microendemism; multispecies coalescent; speciation; species delimitation.].
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Affiliation(s)
| | - Jordi Salmona
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Dominik Schüßler
- Research Group Ecology and Environmental Education, Department of Biology, University of Hildesheim, Universitaetsplatz 1, 31141 Hildesheim, Germany
| | - Marina B Blanco
- Department of Biology, Duke University, Durham, NC 27708, USA.,Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - Jean B Andriambeloson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo 101, Madagascar
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - C Ryan Campbell
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Kelsie E Hunnicutt
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Amaia Iribar
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Peter M Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 6, 37077 Göttingen, Germany
| | - Peter A Larsen
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Sophie Manzi
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - JosÉ M Ralison
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo 101, Madagascar
| | - Blanchard Randrianambinina
- Groupe d'Etude et de Recherche sur les Primates de Madagascar (GERP), BP 779, Antananarivo 101, Madagascar.,Faculté des Sciences, University of Mahajanga, Mahajanga, Madagascar
| | - Rodin M Rasoloarison
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 6, 37077 Göttingen, Germany
| | - David W Rasolofoson
- Groupe d'Etude et de Recherche sur les Primates de Madagascar (GERP), BP 779, Antananarivo 101, Madagascar
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - Rachel C Williams
- Department of Biology, Duke University, Durham, NC 27708, USA.,Duke Lemur Center, Duke University, Durham, NC 27705, USA
| | - LounÈs Chikhi
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany Jelmer Poelstra, Jordi Salmona, George P. Tiley are the joint first authors. Ute Radespiel and Anne D. Yoder are the joint senior authors
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
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37
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Hausdorf B, Hennig C. Species delimitation and geography. Mol Ecol Resour 2020; 20:950-960. [DOI: 10.1111/1755-0998.13184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Bernhard Hausdorf
- Zoological Museum Center of Natural History University of Hamburg Hamburg Germany
| | - Christian Hennig
- Dipartimento di Scienze Statistiche “Paolo Fortunati” Università di Bologna Bologna Italy
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38
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Barley AJ, Diesmos AC, Siler CD, Martinez CM, Brown RM. Taxonomic Revision of Philippine Sun Skinks (Reptilia: Squamata: Scincidae: Eutropis), and Descriptions of Eight New Species. HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00009.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Biology, University of Hawai‘i, Honolulu, HI 96822, USA
| | | | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
| | | | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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39
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Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
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40
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Freitas ES, Miller AH, Reynolds RG, Siler CD. A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar. Mol Phylogenet Evol 2020; 146:106754. [PMID: 32028030 DOI: 10.1016/j.ympev.2020.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphological data, we examine lineage diversification in a cryptic radiation of Riopa skinks in Myanmar. Four species of Riopa skinks are currently recognized from Myanmar based on morphological traits, but the boundaries between three of these species, R. anguina, R. lineolata, and R. popae, are not well-defined. We find high levels of genetic diversity within these three species. Our analyses suggest that they may comprise as many as 12 independently evolving lineages, highlighting the extent to which species diversity in the region is underestimated. However, quantitative trait data suggest that these lineages have not differentiated morphologically, possibly indicating that this cryptic radiation represents non-adaptive evolution, although additional data is needed to corroborate this.
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Affiliation(s)
- Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Aryeh H Miller
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - R Graham Reynolds
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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41
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Chambers EA, Hillis DM. The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa. Syst Biol 2020; 69:184-193. [PMID: 31180508 DOI: 10.1093/sysbio/syz042] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/14/2022] Open
Abstract
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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42
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Duckett DJ, Pelletier TA, Carstens BC. Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP. PeerJ 2020; 8:e8271. [PMID: 31949994 PMCID: PMC6956792 DOI: 10.7717/peerj.8271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/22/2019] [Indexed: 11/20/2022] Open
Abstract
Phylogenetic estimation under the multispecies coalescent model (MSCM) assumes all incongruence among loci is caused by incomplete lineage sorting. Therefore, applying the MSCM to datasets that contain incongruence that is caused by other processes, such as gene flow, can lead to biased phylogeny estimates. To identify possible bias when using the MSCM, we present P2C2M.SNAPP. P2C2M.SNAPP is an R package that identifies model violations using posterior predictive simulation. P2C2M.SNAPP uses the posterior distribution of species trees output by the software package SNAPP to simulate posterior predictive datasets under the MSCM, and then uses summary statistics to compare either the empirical data or the posterior distribution to the posterior predictive distribution to identify model violations. In simulation testing, P2C2M.SNAPP correctly classified up to 83% of datasets (depending on the summary statistic used) as to whether or not they violated the MSCM model. P2C2M.SNAPP represents a user-friendly way for researchers to perform posterior predictive model checks when using the popular SNAPP phylogenetic estimation program. It is freely available as an R package, along with additional program details and tutorials.
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Affiliation(s)
- Drew J Duckett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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43
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Campillo LC, Barley AJ, Thomson RC. Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated? Syst Biol 2019; 69:708-721. [DOI: 10.1093/sysbio/syz072] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/06/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Abstract
A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]
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Affiliation(s)
- Luke C Campillo
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Anthony J Barley
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
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44
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Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions. mBio 2019; 10:mBio.01976-19. [PMID: 31772050 PMCID: PMC6879716 DOI: 10.1128/mbio.01976-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion of C. posadasii across South America through southeastern Mexico, Honduras, Guatemala, and Venezuela. Comparative phylogenomic analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the North American populations found in (i) Arizona and (ii) Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations of C. posadasii in Central America. Additionally, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck and shows a strong population structure. This analysis provides insight into potential for Coccidioides spp. to invade new regions.IMPORTANCE Valley Fever is a fungal disease caused by two species of fungi: Coccidioides immitis and C. posadasii These fungi are found throughout the arid regions of North and South America; however, our understanding of genetic diversity and disease in South America is limited. In this report, we analyze 10 new genomes of Coccidioides posadasii from regions bordering the Caribbean Sea. We show that these populations are distinct and that isolates from Venezuela are likely a result of a recent bottleneck. These data point to patterns that might be observed when investigating recently established populations.
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45
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Wagner F, Ott T, Zimmer C, Reichhart V, Vogt R, Oberprieler C. 'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae). THE NEW PHYTOLOGIST 2019; 223:2039-2053. [PMID: 30851196 DOI: 10.1111/nph.15784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Verena Reichhart
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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46
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Pinto BJ, Titus-McQuillan J, Daza JD, Gamble T. Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos. J Hered 2019; 110:523-534. [PMID: 30859222 DOI: 10.1093/jhered/esz015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN.,Milwaukee Public Museum, Milwaukee, WI
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47
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko. Mol Phylogenet Evol 2019; 133:54-66. [DOI: 10.1016/j.ympev.2018.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022]
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48
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Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol 2019; 132:219-231. [DOI: 10.1016/j.ympev.2018.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/09/2018] [Accepted: 12/09/2018] [Indexed: 12/15/2022]
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49
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50
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Mable BK. Conservation of adaptive potential and functional diversity: integrating old and new approaches. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1129-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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