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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [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: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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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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3
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Koochekian N, Ascanio A, Farleigh K, Card DC, Schield DR, Castoe TA, Jezkova T. A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles. Gigascience 2022; 11:giab098. [PMID: 35134927 PMCID: PMC8848323 DOI: 10.1093/gigascience/giab098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/27/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding of macroevolutionary processes. Here, we introduce the genome of the desert horned lizard, Phrynosoma platyrhinos, an iguanid lizard occupying extreme desert conditions of the American southwest. We conduct analysis of the chromosomal structure and composition of this species and compare these features across genomes of 12 other reptiles (5 species of lizards, 3 snakes, 3 turtles, and 1 bird). FINDINGS The desert horned lizard genome was sequenced using Illumina paired-end reads and assembled and scaffolded using Dovetail Genomics Hi-C and Chicago long-range contact data. The resulting genome assembly has a total length of 1,901.85 Mb, scaffold N50 length of 273.213 Mb, and includes 5,294 scaffolds. The chromosome-level assembly is composed of 6 macrochromosomes and 11 microchromosomes. A total of 20,764 genes were annotated in the assembly. GC content and gene density are higher for microchromosomes than macrochromosomes, while repeat element distributions show the opposite trend. Pathway analyses provide preliminary evidence that microchromosome and macrochromosome gene content are functionally distinct. Synteny analysis indicates that large microchromosome blocks are conserved among closely related species, whereas macrochromosomes show evidence of frequent fusion and fission events among reptiles, even between closely related species. CONCLUSIONS Our results demonstrate dynamic karyotypic evolution across Reptilia, with frequent inferred splits, fusions, and rearrangements that have resulted in shuffling of chromosomal blocks between macrochromosomes and microchromosomes. Our analyses also provide new evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.
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Affiliation(s)
| | - Alfredo Ascanio
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Daren C Card
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, OH 45056, USA
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4
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Finger N, Farleigh K, Bracken JT, Leaché AD, François O, Yang Z, Flouri T, Charran T, Jezkova T, Williams DA, Blair C. Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US. Genome Biol Evol 2021; 14:6443127. [PMID: 34849831 PMCID: PMC8735750 DOI: 10.1093/gbe/evab260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/03/2022] Open
Abstract
The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.
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Affiliation(s)
- Nicholas Finger
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Jason T Bracken
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
| | - Olivier François
- Faculty of Medicine, University Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, La Tronche, F38706, France 38000
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tristan Charran
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Dean A Williams
- Department of Biology, Texas Christian University, 2800 S University Dr, Fort Worth, TX, 76129, USA
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA.,Biology PhD Program, CUNY Graduate Center, 365 5th Ave, New York, NY, 10016, USA
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Joel A, Linde JRN, Comanns P, Emonts C, Weissbach M, Flecks M, Rödder D. Phylogenetic and morphological influence on habitat choice in moisture-harvesting horned lizards ( Phrynosoma spp.). Ecol Evol 2021; 11:14146-14161. [PMID: 34707847 PMCID: PMC8525137 DOI: 10.1002/ece3.8132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022] Open
Abstract
In previous studies, the superhydrophilic skin of moisture-harvesting lizards has been linked to the morphological traits of the lizards' integument, that is, the occurrence of honeycomb-shaped microstructures. Interestingly, these structures can also cover the skin of lizards inhabiting wet habitats. We therefore tested the influence of the microstructures' main features on the habitat choice and wettability in the genus Phrynosoma. The genus Phrynosoma comprises moisture-harvesting species as well as nonspecialists. Lizards of this genus inhabit large areas of North America with diverse climatic conditions. Remarkably, the differences in the manifestation of microstructures are just as versatile as their surroundings. The phylogeny of the lizards as well as the depth of their ventral microstructures, though independent of each other, correlated with the precipitation in their respective habitat. All other morphological traits, as well as the skin's wettability itself, could not predict the habitat of Phrynosoma species. Hence, it is unlikely that the microstructure influences the wettability, at least directly. Hence, we presume an indirect influence for the following reasons: (a) As the ventral side cannot get wet by rain, but the belly could easily interact with a wet surface, the microstructure might facilitate water absorption from wet soil following precipitation. (b) We found the number of dorsal microstructures to be linked to the occurrence of silt in the habitat. In our study, we observed scales being heavily contaminated, most likely with a mixture of dead skin (after shedding) and silt. As many lizards burrow themselves or even shovel sand onto their backs, deploying the substrate might be a mechanism to increase the skin's wettability.
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Affiliation(s)
| | | | | | | | | | - Morris Flecks
- Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
| | - Dennis Rödder
- Zoologisches Forschungsmuseum Alexander KoenigBonnGermany
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6
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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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7
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Gómez-Benitez A, Sherbrooke WC, Granados-González G, Suárez-Varón G, Pérez-Pérez A, López-Moreno AE, Hernández-Gallegos O. BLOOD-SQUIRT OCCURRENCE IN THE MEXICAN PLATEAU HORNED LIZARD (PHRYNOSOMA ORBICULARE). SOUTHWEST NAT 2021. [DOI: 10.1894/0038-4909-65.1.50] [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)
- Aldo Gómez-Benitez
- Laboratorio de Herpetología, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (AGB, GSV, APP, AELM, OHG)
| | - Wade C. Sherbrooke
- Southwestern Research Station, American Museum of Natural History, Portal, AZ 85632 (WCS)
| | - Gisela Granados-González
- Laboratorio de Morfofisiología de la Reproducción, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (GGG)
| | - Gabriel Suárez-Varón
- Laboratorio de Herpetología, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (AGB, GSV, APP, AELM, OHG)
| | - Ailed Pérez-Pérez
- Laboratorio de Herpetología, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (AGB, GSV, APP, AELM, OHG)
| | - Ana Esthela López-Moreno
- Laboratorio de Herpetología, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (AGB, GSV, APP, AELM, OHG)
| | - Oswaldo Hernández-Gallegos
- Laboratorio de Herpetología, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, CP 50000, México (AGB, GSV, APP, AELM, OHG)
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8
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Portik DM, Wiens JJ. Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Syst Biol 2020; 70:440-462. [PMID: 32797207 DOI: 10.1093/sysbio/syaa064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/14/2022] Open
Abstract
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.,California Academy of Sciences, San Francisco, CA 94118, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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9
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Morando M, Olave M, Avila LJ, Sites JW, Leaché AD. Phylogenomic data resolve higher-level relationships within South American Liolaemus lizards. Mol Phylogenet Evol 2020; 147:106781. [PMID: 32147573 DOI: 10.1016/j.ympev.2020.106781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 12/30/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Phylogenomic approaches now generate hundreds of loci representative of the whole genome that can be used for phylogenetic analyses. The South American lizard genus Liolaemus is the most species-rich vertebrate radiation from temperate zones (more than 265 described species), yet most higher-level phylogenetic relationships within Liolaemus remain poorly resolved. In this study, we used 584 nuclear loci collected using targeted sequenced capture to estimate the phylogenetic relationships among 26 species representing the two subgenera within Liolaemus (Eulaemus + Liolaemus), and all major groups within Eulaemus. Previous molecular and morphological-based phylogenetic analyses of Eulaemus based on a limited number of characters resolved few higher-level relationships, although one point of agreement is that the early divergence within Eulaemus corresponds to the lineomaculatus section, followed by the diversification of eight main clades that are strongly supported and recognized. Liolaemus probably experienced relatively rapid divergences during parts of its evolutionary history, and a phylogenomic approach was used to resolve the relationships among the major groups. The new analyses presented here support the division of Liolaemus into two subgenera, and resolve relationships among many of the major clades of Eulaemus with strong support. A Bayesian divergence dating analysis using 44 protein-coding genes provides an estimation of the split of the two Liolaemus subgenera of approximately 19,7 ma (95% HPD = 16,94-23,04), while diversification within Eulaemus started at 15,05 ma (95% HPD = 12,94 - 17,59) among the L. lineomaculatus and the L. montanus series by Mid Miocene. A novel phylogenetic network analyses for SNP data identified two hybridizing edges among different groups of Eulaemus at different points in time. Having a solid phylogenetic hypothesis of the main Eulaemus clades opens new opportunities to test a variety of macroevolutionary questions for this unique radiation.
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Affiliation(s)
- Mariana Morando
- Instituto para el Estudio de los Ecosistemas Continentales Patagónicos (IPEEC-CONICET), Argentina. Boulevard Almirante G. Brown 2915, U9120-ACD Puerto Madryn, Chubut, Argentina; Universidad Nacional de la Patagonia San Juan Bosco, Sede Puerto Madryn, Boulevard Almirante Brown 3700, U9120ACD Puerto Madryn, Chubut, Argentina.
| | - Melisa Olave
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Instituto Argentino de Investigaciones de Zonas Arídas, Consejo Nacional de Investigaciones Científicas y Técnicas (IADIZA-CONICET), 5500 Mendoza, Argentina
| | - Luciano J Avila
- Instituto para el Estudio de los Ecosistemas Continentales Patagónicos (IPEEC-CONICET), Argentina. Boulevard Almirante G. Brown 2915, U9120-ACD Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA(1)
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington 98195-1800, USA
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10
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Schmidt JO. Predator–Prey Battle of Ecological Icons: Horned Lizards (Phrynosoma spp.) and Harvester Ants (Pogonomyrmex spp.). COPEIA 2019. [DOI: 10.1643/cp-18-158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Justin O. Schmidt
- Southwestern Biological Institute, 1961 W. Brichta Drive, Tucson, Arizona 85745;
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11
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Catanach TA, Sweet AD, Nguyen NPD, Peery RM, Debevec AH, Thomer AK, Owings AC, Boyd BM, Katz AD, Soto-Adames FN, Allen JM. Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 2019; 7:e6142. [PMID: 30627489 PMCID: PMC6321758 DOI: 10.7717/peerj.6142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023] Open
Abstract
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye" prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
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Affiliation(s)
- Therese A. Catanach
- Ornithology Department, Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Andrew D. Sweet
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nam-phuong D. Nguyen
- Computer Science and Engineering, University of San Diego, California, La Jolla, CA, United States of America
| | - Rhiannon M. Peery
- Department of Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrew H. Debevec
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrea K. Thomer
- School of Information, University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Amanda C. Owings
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Bret M. Boyd
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Georga, Athens, GA, United States of America
| | - Aron D. Katz
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Felipe N. Soto-Adames
- Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States of America
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Julie M. Allen
- Biology Department, University of Nevada, Reno, Reno, NV, United States of America
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12
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Blair C, Bryson RW, Linkem CW, Lazcano D, Klicka J, McCormack JE. Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus). Mol Ecol Resour 2018; 19:349-365. [PMID: 30565862 DOI: 10.1111/1755-0998.12970] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 01/28/2023]
Abstract
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
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Affiliation(s)
- Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York.,Biology PhD Program, CUNY Graduate Center, New York, New York
| | - Robert W Bryson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington.,Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Charles W Linkem
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - David Lazcano
- Laboratorio de Herpetología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
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13
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Leaché AD, McElroy MT, Trinh A. A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma). Mol Ecol 2018; 27:2884-2895. [PMID: 29742301 DOI: 10.1111/mec.14715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022]
Abstract
Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, Phrynosoma cerroense and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The number of taxa recognized in the group has been reevaluated by herpetologists over 20 times during the last 180 years, and typically without the aid of explicit species delimitation methods, resulting in a turbulent taxonomy containing anywhere from one to seven taxa. In this study, we evaluate taxonomic trends through time by ranking 15 of these species delimitation models (SDMs) using coalescent analyses of nuclear loci and SNPs in a Bayesian model comparison framework. Species delimitation models containing more species were generally favoured by Bayesian model selection; however, several three-species models outperformed some four- and five-species SDMs, and the top-ranked model, which contained five species, outperformed all SDMs containing six species. Model performance peaked in the 1950s based on marginal likelihoods estimated from nuclear loci and SNPs. Not surprisingly, SDMs based on genetic data outperformed morphological taxonomies when using genetic data alone to evaluate models. The de novo estimation of population structure favours a three-population model that matches the currently recognized integrative taxonomy containing three species. We discuss why Bayesian model selection might favour models containing more species, and why recognizing more than three species might be warranted.
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Affiliation(s)
- Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - Matthew T McElroy
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - Anna Trinh
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
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14
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Blair C, Bryson RW. Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae:Phrynosoma). Mol Ecol Resour 2017; 17:1168-1182. [DOI: 10.1111/1755-0998.12658] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher Blair
- Department of Biological Sciences; New York City College of Technology; The City University of New York; 300 Jay Street Brooklyn NY 11201 USA
- Biology PhD Program; CUNY Graduate Center; 365 5th Avenue New York NY 10016 USA
| | - Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; 4331 Memorial Way Northeast Seattle WA 98195 USA
- Moore Laboratory of Zoology; Occidental College; Los Angeles CA 90041 USA
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15
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Powell GL, Russell AP, Jamniczky HA, Hallgrímsson B. Shape Variation in the Dermatocranium of the Greater Short-Horned Lizard Phrynosoma hernandesi (Reptilia: Squamata: Phrynosomatidae). Evol Biol 2016. [DOI: 10.1007/s11692-016-9403-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Leaché AD, Banbury BL, Linkem CW, de Oca ANM. Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)? BMC Evol Biol 2016; 16:63. [PMID: 27000803 PMCID: PMC4802581 DOI: 10.1186/s12862-016-0628-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/29/2016] [Indexed: 01/25/2023] Open
Abstract
Background Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. Results The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). Conclusions Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA
| | - Charles W Linkem
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México
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17
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Leaché AD, Banbury BL, Felsenstein J, de Oca ANM, Stamatakis A. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies. Syst Biol 2015; 64:1032-47. [PMID: 26227865 PMCID: PMC4604835 DOI: 10.1093/sysbio/syv053] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/24/2015] [Indexed: 01/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA;
| | - Barbara L Banbury
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Joseph Felsenstein
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Adrián Nieto-Montes de Oca
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México 04510, Distrito Federal, México
| | - Alexandros Stamatakis
- Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany; and Department of Informatics, Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
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