1
|
Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
Collapse
Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| |
Collapse
|
2
|
Edwards DL, Avila LJ, Martinez L, Sites JW, Morando M. Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards. Ecol Evol 2022; 12:e9009. [PMID: 35784059 PMCID: PMC9201750 DOI: 10.1002/ece3.9009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/02/2022] [Indexed: 01/02/2023] Open
Abstract
Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus, one of the most ecologically diverse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive diversification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26-taxon dataset for the Liolaemus gracilis species group, representing much of the ecological diversity represented within Liolaemus and used environmental data to characterize how environments occupied by species' relate to phenotypic evolution. Our analyses, explicitly accounting for phylogenetic uncertainty, suggest diversification in phenotypic traits toward the present, with body shape evolution rapidly evolving in this group. Body shape evolution correlates with the occupation of different structural habitats indicated by vegetation axes suggesting species have adapted for maximal locomotory performance in these habitats. Our results also imply that the effects of phylogenetic uncertainty and model misspecification may be more extensive on univariate, relative to multivariate analyses of evolutionary correlations, which is an important consideration in analyzing data from rapidly radiating adaptive radiations.
Collapse
Affiliation(s)
- Danielle L. Edwards
- The Department of Life & Environmental SciencesUniversity of CaliforniaMercedCaliforniaUSA
| | - Luciano J. Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET)Puerto MadrynArgentina
| | - Lorena Martinez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET)Puerto MadrynArgentina
- VigoSpain
| | - Jack W. Sites
- Department of Biology and M.L. Bean Life Science MuseumBrigham Young University (BYU)ProvoUtahUSA
- TrentonKentuckyUSA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET)Puerto MadrynArgentina
| |
Collapse
|
3
|
Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
Collapse
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| |
Collapse
|
4
|
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Diversification and Evolutionary Histories of Patagonian Steppe Lizards. NATURAL AND SOCIAL SCIENCES OF PATAGONIA 2020. [DOI: 10.1007/978-3-030-42752-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
7
|
The enigmatic Leiosaurae clade: Phylogeography, species delimitation, phylogeny and historical biogeography of its southernmost species. Mol Phylogenet Evol 2019; 144:106725. [PMID: 31884086 DOI: 10.1016/j.ympev.2019.106725] [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: 06/07/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
The clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and understanding of their evolutionary histories. Here, we use data collected over 9 years to study the phylogenetic history, genetic diversity, and biogeographic history of almost all the southernmost species of Leiosaurae (except P. nigroigulus), including: Leiosaurus bellii, Diplolaemus darwinii, D. bibronii, D. sexcinctus and D. leopardinus. We use a fragment of the mitochondrial cytochrome-b gene to resolve general phylogeographic patterns, and add another mitochondrial gene and eight nuclear genes to perform species delimitation and phylogenetic analyses associated with divergence times. We found evidence for three putative new species-level taxa within L. bellii and five within Diplolaemus species, indicating high levels of geographic structure. We use a time-calibrated phylogeny to estimate ranges of ancestral distributions and to generate new hypotheses about their historical biogeography.
Collapse
|
8
|
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]
|
9
|
Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
Collapse
Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| |
Collapse
|
10
|
Grummer JA, Morando MM, Avila LJ, Sites JW, Leaché AD. Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group. Mol Phylogenet Evol 2018; 125:243-254. [DOI: 10.1016/j.ympev.2018.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
|
11
|
Olave M, Avila LJ, Sites JW, Morando M. Hybridization could be a common phenomenon within the highly diverse lizard genus
Liolaemus. J Evol Biol 2018; 31:893-903. [DOI: 10.1111/jeb.13273] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Melisa Olave
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
- Department of Biology University of Konstanz Konstanz Germany
| | - Luciano J. Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum Brigham Young University (BYU) Provo UT USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
| |
Collapse
|
12
|
Walker JF, Yang Y, Feng T, Timoneda A, Mikenas J, Hutchison V, Edwards C, Wang N, Ahluwalia S, Olivieri J, Walker-Hale N, Majure LC, Puente R, Kadereit G, Lauterbach M, Eggli U, Flores-Olvera H, Ochoterena H, Brockington SF, Moore MJ, Smith SA. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales. AMERICAN JOURNAL OF BOTANY 2018; 105:446-462. [PMID: 29738076 DOI: 10.1002/ajb2.1069] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/04/2018] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. METHODS We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses. KEY RESULTS Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling. CONCLUSIONS Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.
Collapse
Affiliation(s)
- Joseph F Walker
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Ning Wang
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Sonia Ahluwalia
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
- Institute of Computational and Mathematical Engineering (ICME), Stanford University, 475 Via Ortega, Suite B060, Stanford, CA, 94305-4042, USA
| | - Nathanael Walker-Hale
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, Wellington, 6012, New Zealand
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ, 85008, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Maximilian Lauterbach
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
- Institut für Molekulare und Organismische Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099, Mainz, Germany
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich / Grün Stadt Zürich, Mythenquai 88, CH-8002, Zürich, Switzerland
| | - Hilda Flores-Olvera
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | - Helga Ochoterena
- Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado, Postal 70-367, 04510, Mexico City, Mexico
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH, 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI, 48109-1048, USA
| |
Collapse
|
13
|
Mendes FK, Hahn MW. Why Concatenation Fails Near the Anomaly Zone. Syst Biol 2018; 67:158-169. [PMID: 28973673 DOI: 10.1093/sysbio/syx063] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/30/2017] [Indexed: 11/12/2022] Open
Abstract
Genome-scale sequencing has been of great benefit in recovering species trees but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge and has prompted the development of new strategies that can make the best use of available data. One such strategy-the concatenation of gene alignments-can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone-a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure cannot be easily predicted from the topology of the most common gene tree. We demonstrate that likelihood-based methods often fail in a region partially overlapping the anomaly zone, likely because of the lower relative cost of substitutions on discordant gene tree branches that are absent from the species tree. Our results confirm and extend previous reports on the performance of these methods applied to concatenated data from a rooted, asymmetric four-taxon species tree, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.
Collapse
Affiliation(s)
- Fábio K Mendes
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
14
|
Torres-Pérez F, Boric-Bargetto D, Rodríguez-Valenzuela E, Escobar C, Palma RE. Molecular phylogenetic analyses reveal the importance of taxon sampling in cryptic diversity: Liolaemus nigroviridis and L. monticola (Liolaeminae) as focal species. REVISTA CHILENA DE HISTORIA NATURAL 2017. [DOI: 10.1186/s40693-017-0068-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
15
|
Panzera A, Leaché AD, D'Elía G, Victoriano PF. Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data. PeerJ 2017; 5:e3941. [PMID: 29085750 PMCID: PMC5660876 DOI: 10.7717/peerj.3941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/27/2017] [Indexed: 01/19/2023] Open
Abstract
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.
Collapse
Affiliation(s)
- Alejandra Panzera
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Programa de Doctorado en Sistemática y Biodiversidad, Universidad de Concepción, Concepción, Chile
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States of America
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Pedro F Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| |
Collapse
|
16
|
The effects of Quaternary sea-level fluctuations on the evolutionary history of an endemic ground lizard (Tropidurus hygomi). ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
17
|
Olave M, Avila LJ, Sites JW, Morando M. Hidden diversity within the lizard genus Liolaemus: Genetic vs morphological divergence in the L. rothi complex (Squamata:Liolaeminae). Mol Phylogenet Evol 2017; 107:56-63. [DOI: 10.1016/j.ympev.2016.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/25/2016] [Accepted: 09/12/2016] [Indexed: 11/29/2022]
|
18
|
Veith M, Göçmen B, Sotiropoulos K, Kieren S, Godmann O, Steinfartz S. Seven at one blow: the origin of major lineages of the viviparous Lycian salamanders (Lyciasalamandra Veith and Steinfartz, 2004) was triggered by a single paleo-historic event. AMPHIBIA-REPTILIA 2016. [DOI: 10.1163/15685381-00003067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The number of tectonic and climatic events that are used to explain speciation processes in the eastern Mediterranean region is low compared to the western Mediterranean. Among them, the emergence of the mid-Aegean trench and the Messinian Salinity Crisis (MSC) often concurred with speciation time estimates that were inferred from molecular data. We here present a dated molecular phylogeny of Lyciasalamandra from Turkey and Greece based on ca. 4500 bp of the mitochondrial genome (3000 bp of three nuclear genes appeared to be completely inconclusive due to their extremely low degree of variation among taxa). Seven major lineages emerged simultaneously from a basal hard polytomy. A scenario that dates this polytomy to 12.3 and 10.2 million years ago, around the final emergence of the mid-Aegean trench, appears to be most plausible. The MSC can be made responsible for first intraspecific divergence events within L. luschani, L. fazilae and L. flavimembris. Further diversification can be explained by Pliocene and Pleistocene glaciations. Based on levels of molecular differentiation we suggest the recently described species L. arikani, L. irfani and L. yehudahi to be treated as subspecies of L. billae.
Collapse
Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | - Bayram Göçmen
- Zoology Section, Department of Biology, Faculty of Science, Ege University, 35100 Bornova, İzmir, Turkey
| | - Konstantinos Sotiropoulos
- Department of Biological Applications & Technologies, University of Ioannina, 45110 Ioannina, Greece
| | - Sarah Kieren
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | | | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| |
Collapse
|
19
|
Morando M, Olave M, Avila LJ, Baker E, Sites JW. Molecular Phylogeny of the Lizard Clade Leiosaurae Endemic to Southern South America. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Mariana Morando
- Centro Nacional Patagónico – Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, ZC: U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Melisa Olave
- Centro Nacional Patagónico – Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, ZC: U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Luciano J. Avila
- Centro Nacional Patagónico – Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, ZC: U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Eric Baker
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| |
Collapse
|
20
|
Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol 2015; 25:306-23. [PMID: 26363411 DOI: 10.1111/mec.13385] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/31/2015] [Accepted: 09/04/2015] [Indexed: 02/03/2023]
Abstract
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus cowlesi and Aspidoscelis inornata, for which previous research has linked mutations in the melanocortin-1 receptor gene (Mc1r) to blanched coloration. We sampled populations both on and off the dunes and used a custom sequence capture assay based on probed fosmid libraries to obtain >50 kb of sequence around Mc1r and hundreds of other random genomic locations. We then used model-based statistical inference methods to describe the demographic and adaptive history characterizing the colonization of White Sands. We identified a number of similarities between the two focal species, including strong evidence of selection in the blanched populations in the Mc1r region. We also found important differences between the species, suggesting different colonization times, different genetic architecture underlying the blanched phenotype and different ages of the beneficial alleles. Finally, the beneficial allele is dominant in S. cowlesi and recessive in A. inornata, allowing for a rare empirical test of theoretically expected patterns of selective sweeps under these differing models.
Collapse
Affiliation(s)
- Stefan Laurent
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Susanne P Pfeifer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matthew L Settles
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Kayla M Hardwick
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA
| | - Louise Ormond
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Vitor C Sousa
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, CH-3012, Berne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Erica Bree Rosenblum
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.,Department of Environmental Sciences, Policy & Management, Berkeley, CA, 94720, USA
| |
Collapse
|
21
|
Aguilar C, Stark MR, Arroyo JA, Standing MD, Rios S, Washburn T, Sites JW. Placental morphology in two sympatric Andean lizards of the genusLiolaemus(Reptilia: Liolaemidae). J Morphol 2015. [DOI: 10.1002/jmor.20412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- César Aguilar
- Department of Biology and Bean Life Science Museum; Brigham Young University (BYU); Provo Utah 84602
- Departamento de Herpetologia; Museo De Historia Natural De San Marcos (MUSM); Av. Arenales 1256 Jesus María Lima Perú
- Instituto de Ciencias Biologicas Antonio Raimondi, Department of Zoology, Facultad De Ciencias Biologicas, Universidad Nacional Mayor De San Marcos; Lima Perú
| | - Michael R. Stark
- Department of Physiology and Developmental Biology; BYU; Provo Utah 84602
| | - Juan A. Arroyo
- Department of Physiology and Developmental Biology; BYU; Provo Utah 84602
| | | | - Shary Rios
- Departamento de Herpetologia; Museo De Historia Natural De San Marcos (MUSM); Av. Arenales 1256 Jesus María Lima Perú
| | - Trevor Washburn
- Department of Physiology and Developmental Biology; BYU; Provo Utah 84602
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum; Brigham Young University (BYU); Provo Utah 84602
| |
Collapse
|
22
|
Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga. BMC Evol Biol 2015; 15:94. [PMID: 26001787 PMCID: PMC4494643 DOI: 10.1186/s12862-015-0368-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards. Results Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River. Conclusions The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0368-3) contains supplementary material, which is available to authorized users.
Collapse
|