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Richmond JQ, McGuire JA, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Toffelmier E, Fisher RN, Wang IJ, Shaffer HB. Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii. J Hered 2023; 114:410-417. [PMID: 37195437 DOI: 10.1093/jhered/esad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/19/2023] [Indexed: 05/18/2023] Open
Abstract
Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville's horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.
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Affiliation(s)
- Jonathan Q Richmond
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Ian J Wang
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
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Firneno TJ, O’Neill JR, Itgen MW, Kihneman TA, Townsend JH, Fujita MK. Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance. Ecol Evol 2021; 11:12739-12753. [PMID: 34594535 PMCID: PMC8462145 DOI: 10.1002/ece3.8018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/24/2022] Open
Abstract
The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation-related actions.
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Affiliation(s)
- Thomas J. Firneno
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTXUSA
- Department of Biology, Amphibian and Reptile Diversity Research CenterUniversity of Texas at ArlingtonArlingtonTXUSA
| | | | | | | | - Josiah H. Townsend
- Department of BiologyIndiana University of PennsylvaniaIndianaPAUSA
- Departamento de Ambiente y DesarrolloCentro Zamorano de BiodiversidadEscuela Agrícola Panamericana ZamoranoMunicipalidad de San Antonio de OrienteFrancisco MorazánHonduras
| | - Matthew K. Fujita
- Department of BiologyUniversity of Texas at ArlingtonArlingtonTXUSA
- Department of Biology, Amphibian and Reptile Diversity Research CenterUniversity of Texas at ArlingtonArlingtonTXUSA
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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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R Oaks J, A Cobb K, N Minin V, D Leaché A. Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications. Syst Biol 2019; 68:681-697. [PMID: 30668834 PMCID: PMC6701458 DOI: 10.1093/sysbio/syz003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 11/29/2022] Open
Abstract
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro- and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here, we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.
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Affiliation(s)
- Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
- Correspondence to be sent to: Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA; E-mail:
| | - Kerry A Cobb
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Vladimir N Minin
- Department of Statistics, University of California, Irvine, CA 92697, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
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Esquerré D, Ramírez-Álvarez D, Pavón-Vázquez CJ, Troncoso-Palacios J, Garín CF, Keogh JS, Leaché AD. Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Mol Phylogenet Evol 2019; 139:106524. [DOI: 10.1016/j.ympev.2019.106524] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
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Kornilios P, Thanou E, Lymberakis P, Ilgaz Ç, Kumlutaş Y, Leaché A. A phylogenomic resolution for the taxonomy of Aegean green lizards. ZOOL SCR 2019. [DOI: 10.1111/zsc.12385] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Panagiotis Kornilios
- Department of Biology University of Washington Seattle WA USA
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra) Barcelona Spain
- The Molecular Ecology Backshop Loutraki Greece
| | - Evanthia Thanou
- Department of Biology University of Washington Seattle WA USA
- The Molecular Ecology Backshop Loutraki Greece
| | - Petros Lymberakis
- Natural History Museum of Crete University of Crete Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science Dokuz Eylül University Buca‐İzmir Turkey
- Research and Application Center for Fauna Flora Dokuz Eylul University Buca‐İzmir Turkey
| | - Adam Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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Tonzo V, Papadopoulou A, Ortego J. Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex. Mol Ecol 2019; 28:3869-3886. [DOI: 10.1111/mec.15189] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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Demos TC, Webala PW, Goodman SM, Kerbis Peterhans JC, Bartonjo M, Patterson BD. Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics. BMC Evol Biol 2019; 19:166. [PMID: 31434566 PMCID: PMC6704657 DOI: 10.1186/s12862-019-1485-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/19/2019] [Indexed: 11/24/2022] Open
Abstract
Background The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. Results We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. Conclusions Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution. Electronic supplementary material The online version of this article (10.1186/s12862-019-1485-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Terrence C Demos
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Steven M Goodman
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,Association Vahatra, BP 3972, 101, Antananarivo, Madagascar
| | - Julian C Kerbis Peterhans
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.,College of Professional Studies, Roosevelt University, Chicago, IL, 60605, USA
| | | | - Bruce D Patterson
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
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