1
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Sato S, Derkarabetian S, Lord A, Giribet G. An ultraconserved element probe set for velvet worms (Onychophora). Mol Phylogenet Evol 2024; 197:108115. [PMID: 38810901 DOI: 10.1016/j.ympev.2024.108115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/04/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families - Peripatopsidae and Peripatidae - and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ∼ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics.
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Affiliation(s)
- Shoyo Sato
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, 2100 Copenhagen, Denmark(1).
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; San Diego Natural History Museum, Department of Entomology, San Diego, CA, USA(1)
| | - Arianna Lord
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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2
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Unmack PJ, Adams M, Hammer MP, Johnson JB, Gruber B, Gilles A, Young M, Georges A. Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.
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Affiliation(s)
- Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Mark Adams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Department of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Jerald B Johnson
- Department of Biology, Brigham Young University, Provo, UT, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Bernd Gruber
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - André Gilles
- UMR 1467 RECOVER, Aix Marseille Univ, INRAE, Centre St Charles, 3 place Victor Hugo, Marseille, France
| | - Matthew Young
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
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3
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Alda F, Ludt WB, Elías DJ, McMahan CD, Chakrabarty P. Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree. Genome Biol Evol 2021; 13:evab161. [PMID: 34272856 PMCID: PMC8369075 DOI: 10.1093/gbe/evab161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.
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Affiliation(s)
- Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Tennessee, USA
| | - William B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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4
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Diversification and geological history of the Liolaemus ornatus group (Squamata: Iguania) of Argentina including the recognition of a new species. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Cicero C, Mason NA, Benedict L, Rising JD. Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows ( Aimophila and Peucaea, Passerellidae). PeerJ 2020; 8:e9249. [PMID: 32596039 PMCID: PMC7307569 DOI: 10.7717/peerj.9249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Nicholas A Mason
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America.,Current affiliation: Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Lauryn Benedict
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States of America
| | - James D Rising
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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6
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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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7
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Adams RH, Castoe TA. Probabilistic Species Tree Distances: Implementing the Multispecies Coalescent to Compare Species Trees Within the Same Model-Based Framework Used to Estimate Them. Syst Biol 2020; 69:194-207. [PMID: 31086978 DOI: 10.1093/sysbio/syz031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 05/02/2019] [Indexed: 11/14/2022] Open
Abstract
Despite the ubiquitous use of statistical models for phylogenomic and population genomic inferences, this model-based rigor is rarely applied to post hoc comparison of trees. In a recent study, Garba et al. derived new methods for measuring the distance between two gene trees computed as the difference in their site pattern probability distributions. Unlike traditional metrics that compare trees solely in terms of geometry, these measures consider gene trees and associated parameters as probabilistic models that can be compared using standard information theoretic approaches. Consequently, probabilistic measures of phylogenetic tree distance can be far more informative than simply comparisons of topology and/or branch lengths alone. However, in their current form, these distance measures are not suitable for the comparison of species tree models in the presence of gene tree heterogeneity. Here, we demonstrate an approach for how the theory of Garba et al. (2018), which is based on gene tree distances, can be extended naturally to the comparison of species tree models. Multispecies coalescent (MSC) models parameterize the discrete probability distribution of gene trees conditioned upon a species tree with a particular topology and set of divergence times (in coalescent units), and thus provide a framework for measuring distances between species tree models in terms of their corresponding gene tree topology probabilities. We describe the computation of probabilistic species tree distances in the context of standard MSC models, which assume complete genetic isolation postspeciation, as well as recent theoretical extensions to the MSC in the form of network-based MSC models that relax this assumption and permit hybridization among taxa. We demonstrate these metrics using simulations and empirical species tree estimates and discuss both the benefits and limitations of these approaches. We make our species tree distance approach available as an R package called pSTDistanceR, for open use by the community.
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Affiliation(s)
- Richard H Adams
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
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8
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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]
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9
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Abdala CS, Aguilar-Kirigin AJ, Semhan RV, Bulacios Arroyo AL, Valdes J, Paz MM, Gutiérrez Poblete R, Valladares Faundez P, Langstroth R, Aparicio J. Description and phylogeny of a new species of Liolaemus (Iguania: Liolaemidae) endemic to the south of the Plurinational State of Bolivia. PLoS One 2019; 14:e0225815. [PMID: 31790476 PMCID: PMC6886809 DOI: 10.1371/journal.pone.0225815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/12/2019] [Indexed: 11/19/2022] Open
Abstract
The Liolaemus montanus group is a diverse group of lizards that ranges from central Peru to southwestern Mendoza, Argentina, including much of the Plurinational State of Bolivia ("Bolivia") and Chile. The species of this group mainly inhabit high elevation areas with cold temperatures. In the last years, several species of this group have been described, mostly in Argentina and Chile. In Bolivia, there are at least thirteen valid species belonging to the L. montanus group. In this study, we describe a new species of the L. montanus group with a marked endemism in the Cordillera de Sama of the Tarija Department, Bolivia, and a combination of unique character states that allows its formal description as a new species. The phylogenetic relationships based on analysis of 159 morphological characters suggest that it belongs to the L. montanus group, and that it is closest to Liolaemus pulcherrimus, which is found allopatrically in a small area of the Jujuy Province, Argentina. The multivariate analyses of 66 morphological characters support the phylogenetic relationships. Statistical analyses of inter-species comparisons of morphological characters are not considered the only methods due to the non-independence of some characters states among species; thus, a phylogenetic analysis is recommended. The detailed revision of specimens of the L. montanus group held in the collections of Bolivia is filling major geographic gaps and improving our understanding of the phylogenetic and biogeographic relationships of this widely distributed group of South American lizards.
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Affiliation(s)
- Cristian Simón Abdala
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET)—Unidad Ejecutora Lillo (UEL), San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo (IML), Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Alvaro J. Aguilar-Kirigin
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Romina Valeria Semhan
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET)—Unidad Ejecutora Lillo (UEL), San Miguel de Tucumán, Argentina
| | - Ana Lucia Bulacios Arroyo
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET)—Unidad Ejecutora Lillo (UEL), San Miguel de Tucumán, Argentina
| | - Julián Valdes
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET)—Unidad Ejecutora Lillo (UEL), San Miguel de Tucumán, Argentina
- Cátedra Genética Evolutiva, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Marcos Maximiliano Paz
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET)—Unidad Ejecutora Lillo (UEL), San Miguel de Tucumán, Argentina
| | | | - Pablo Valladares Faundez
- Laboratorio de Zoología Integrativa, Departamento de Biología, Facultad de Ciencias, Universidad de Tarapacá, Arica, Chile
| | - Robert Langstroth
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - James Aparicio
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
- Museo Nacional de Historia Natural (MNHN), Cota Cota (Ovidio Suárez), La Paz, Bolivia
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10
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Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
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Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Life Science, Jilin Agricultural University, Changchun, China.
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11
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Nguyen HN, Lu CW, Chu JH, Grismer LL, Hung CM, Lin SM. Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation. Mol Ecol 2018; 28:772-784. [PMID: 30580492 DOI: 10.1111/mec.14985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022]
Abstract
Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
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Affiliation(s)
- Hung N Nguyen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Zoology, Southern Institute of Ecology, Vietnam Academia of Science and Technology, Ho Chi Minh City, Vietnam.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Wei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Si-Min Lin
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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12
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Sousa-Santos C, Jesus TF, Fernandes C, Robalo JI, Coelho MM. Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data. Mol Phylogenet Evol 2018; 133:263-285. [PMID: 30583043 DOI: 10.1016/j.ympev.2018.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 01/05/2023]
Abstract
The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.
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Affiliation(s)
- C Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - T F Jesus
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisbon, Portugal(2).
| | - C Fernandes
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
| | - J I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - M M Coelho
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
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13
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Esquerré D, Brennan IG, Catullo RA, Torres‐Pérez F, Keogh JS. How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae). Evolution 2018; 73:214-230. [DOI: 10.1111/evo.13657] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/04/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Renee A. Catullo
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
- School of Science & Health and Hawkesbury Institute for the EnvironmentWestern Sydney University 2751 Perth New South Wales Australia
| | - Fernando Torres‐Pérez
- Instituto de BiologíaPontificia Universidad Católica de Valparaíso 2950 Valparaíso Chile
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
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14
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González Marín A, Olave M, Avila LJ, Sites JW, Morando M. Evidence of body size and shape stasis driven by selection in Patagonian lizards of the Phymaturus patagonicus clade (Squamata: Liolaemini). Mol Phylogenet Evol 2018; 129:226-241. [DOI: 10.1016/j.ympev.2018.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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15
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Amador L, Parada A, D'Elía G, Guayasamin JM. Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae). PeerJ 2018; 6:e5856. [PMID: 30402351 PMCID: PMC6215445 DOI: 10.7717/peerj.5856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/02/2018] [Indexed: 11/20/2022] Open
Abstract
The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.
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Affiliation(s)
- Luis Amador
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Departamento de Investigación Científica, Universidad Laica Vicente Rocafuerte de Guayaquil, Guayaquil, Ecuador
| | - Andrés Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan M Guayasamin
- Instituto BIÓSFERA-USFQ, Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Centro de Investigación de la Biodiversidad y Cambio Climático, Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias del Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
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16
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Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Mol Phylogenet Evol 2018; 129:214-225. [PMID: 30189319 DOI: 10.1016/j.ympev.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022]
Abstract
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux. The number of species has increased from 23 to 51 over the last thirty years, predominately within three of the nine genera (Lampropeltis, Pantherophis, Pituophis). The remaining six depauperate genera (Arizona, Bogertophis, Cemophora, Pseudelaphe, Rhinocheilus, and Senticolis) have been poorly represented in phylogenetic studies. To estimate evolutionary relationships and determine if the dichotomy in depauperate and speciose genera within Lampropeltini is a function of taxon sampling or truly represents the lineage diversity, we estimated the phylogeny of this group using nuclear and mitochondrial loci in a concatenated and coalescent framework with the largest sampling of the six depauperate genera to date. In addition, we estimated the divergence dates among the genera to assess whether the instability of Lampropeltini phylogenetic relationships is due to an adaptive radiation. While some nodes still remain unresolved, the generic-level relationships we recovered agree with those of a recent next-generation study that used a much larger set of loci for fewer individuals. We also tested two putative species, Arizona pacata and Pseudelaphe phaescens, for the first time phylogenetically and find evidence that they are distinct lineages. Overall, we find that the taxonomic and genetic diversity are not correlated in Lampropeltini and that representing putative diversity in phylogenies will lead to a better estimate of evolutionary histories, especially in groups with complex radiations.
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17
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Kuang T, Tornabene L, Li J, Jiang J, Chakrabarty P, Sparks JS, Naylor GJP, Li C. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Mol Phylogenet Evol 2018; 128:192-202. [PMID: 30036699 DOI: 10.1016/j.ympev.2018.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 11/30/2022]
Abstract
The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.
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Affiliation(s)
- Ting Kuang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jingyan Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Prosanta Chakrabarty
- Louisiana State University, Museum of Natural Science, Department of Biological Sciences, Baton Rouge, LA 70803, USA
| | - John S Sparks
- American Museum of Natural History, Central Park West at 79th Street, NY, NY 10024, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China.
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18
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Adams RH, Schield DR, Card DC, Castoe TA. Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation. Syst Biol 2018; 67:1076-1090. [DOI: 10.1093/sysbio/syy034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/05/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Richard H Adams
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA
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19
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Espeland M, Breinholt J, Willmott KR, Warren AD, Vila R, Toussaint EF, Maunsell SC, Aduse-Poku K, Talavera G, Eastwood R, Jarzyna MA, Guralnick R, Lohman DJ, Pierce NE, Kawahara AY. A Comprehensive and Dated Phylogenomic Analysis of Butterflies. Curr Biol 2018; 28:770-778.e5. [DOI: 10.1016/j.cub.2018.01.061] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/21/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
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20
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Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers. Mol Phylogenet Evol 2018; 120:158-169. [DOI: 10.1016/j.ympev.2017.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/07/2017] [Accepted: 11/27/2017] [Indexed: 11/18/2022]
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21
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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.
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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
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22
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Chattopadhyay B, Garg KM, Gwee CY, Edwards SV, Rheindt FE. Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation. BMC Evol Biol 2017; 17:210. [PMID: 28863778 PMCID: PMC5580441 DOI: 10.1186/s12862-017-1047-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/10/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Pleistocene climatic fluctuations are known to be an engine of biotic diversification at higher latitudes, but their impact on highly diverse tropical areas such as the Andes remains less well-documented. Specifically, while periods of global cooling may have led to fragmentation and differentiation at colder latitudes, they may - at the same time - have led to connectivity among insular patches of montane tropical habitat with unknown consequences on diversification. In the present study we utilized ~5.5 kb of DNA sequence data from eight nuclear loci and one mitochondrial gene alongside diagnostic morphological and bioacoustic markers to test the effects of Pleistocene climatic fluctuations on diversification in a complex of Andean tyrant-flycatchers of the genus Elaenia. RESULTS Population genetic and phylogenetic approaches coupled with coalescent simulations demonstrated disparate levels of gene flow between the taxon chilensis and two parapatric Elaenia taxa predominantly during the last glacial period but not thereafter, possibly on account of downward shifts of montane forest habitat linking the populations of adjacent ridges. Additionally, morphological and bioacoustic analyses revealed a distinct pattern of character displacement in coloration and vocal traits between the two sympatric taxa albiceps and pallatangae, which were characterized by a lack of gene flow. CONCLUSION Our study demonstrates that global periods of cooling are likely to have facilitated gene flow among Andean montane Elaenia flycatchers that are more isolated from one another during warm interglacial periods such as the present era. We also identify a hitherto overlooked case of plumage and vocal character displacement, underpinning the complexities of gene flow patterns caused by Pleistocene climate change across the Andes.
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Affiliation(s)
- Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore.
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore.
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23
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Malaney JL, Demboski JR, Cook JA. Integrative species delimitation of the widespread North American jumping mice (Zapodinae). Mol Phylogenet Evol 2017; 114:137-152. [PMID: 28600183 DOI: 10.1016/j.ympev.2017.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023]
Abstract
Delimiting species can be challenging, but is a key step for the critical examination of evolutionary history and for prioritizing conservation efforts. Because systematic relationships are often determined iteratively using tests based on taxonomy, such methods can fail to detect cryptic variation and result in biased conclusions. Conversely, discovery-based approaches provide a powerful way to define operational taxonomic units and test species boundaries. We compare both approaches (taxonomy-based delimitation - TBD and discovery-based delimitation - DBD) within North American jumping mice (Zapodinae) using broad sampling, multilocus analyses, and ecological tests. This group diversified through the dynamic glacial-interglacial periods of the Quaternary and phylogeographic tests reveal 28 lineages that correspond poorly with current taxonomy (4 species, 32 nominal subspecies). However, neither the 4-species or 28-lineage hypotheses are optimal for species-level classification. Rather, information theoretic approaches (Bayes Factors) indicate a 15-species hypothesis is best for characterizing genetic variation in this group, with subsequent iterative pairwise ecological tests failing to confirm four species pairs. Taken together, evolutionary and ecological tests capture divergence among 11 putative species that, if upheld by additional tests, will lead to taxonomic revision and reevaluation of conservation plans.
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Affiliation(s)
- Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA; Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA.
| | - Joseph A Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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24
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Medina CD, Avila LJ, Sites JW, Morando M. Phylogeographic history of Patagonian lizards of theLiolaemus elongatuscomplex (Iguania: Liolaemini) based on mitochondrial and nuclear DNA sequences. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cintia Débora Medina
- Grupo de Herpetología Patagónica; Instituto para el Estudio de los Ecosistemas Patagónicos; IPEEC-CONICET; Puerto Madryn Chubut Argentina
| | - Luciano Javier Avila
- Grupo de Herpetología Patagónica; Instituto para el Estudio de los Ecosistemas Patagónicos; IPEEC-CONICET; Puerto Madryn Chubut Argentina
| | - Jack Walter Sites
- Biology Department and Bean Life Science Museum; Brigham Young University; Provo UT USA
| | - Mariana Morando
- Grupo de Herpetología Patagónica; Instituto para el Estudio de los Ecosistemas Patagónicos; IPEEC-CONICET; Puerto Madryn Chubut Argentina
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25
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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]
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26
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Tarvin RD, Powell EA, Santos JC, Ron SR, Cannatella DC. The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs. Mol Phylogenet Evol 2017; 109:283-295. [PMID: 28089841 DOI: 10.1016/j.ympev.2016.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/30/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023]
Abstract
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.
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Affiliation(s)
- Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States.
| | - Emily A Powell
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States; Department of Biology, University of Miami, Miami, FL, United States
| | - Juan C Santos
- Department of Biology, Brigham Young University, Provo, UT, United States; Department of Biological Sciences, St. John's University, Queens, NY, United States
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX, United States
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27
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Zhao L, Li X, Zhang N, Zhang SD, Yi TS, Ma H, Guo ZH, Li DZ. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol Phylogenet Evol 2016; 105:166-176. [DOI: 10.1016/j.ympev.2016.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/06/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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28
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Harrington S, Reeder TW. Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification. J Evol Biol 2016; 30:313-325. [DOI: 10.1111/jeb.13004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/24/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S. Harrington
- Department of Biology; San Diego State University; San Diego CA USA
- Department of Biology; University of California; Riverside CA USA
| | - T. W. Reeder
- Department of Biology; San Diego State University; San Diego CA USA
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29
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Gaubert P, Njiokou F, Ngua G, Afiademanyo K, Dufour S, Malekani J, Bi SG, Tougard C, Olayemi A, Danquah E, Djagoun CAMS, Kaleme P, Mololo CN, Stanley W, Luo SJ, Antunes A. Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification. Mol Ecol 2016; 25:5975-5993. [PMID: 27862533 DOI: 10.1111/mec.13886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 01/03/2023]
Abstract
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, BP 812, Yaoundé, Cameroon
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE), Barrio Ukomba, S/N, Bata, Equatorial Guinea
| | - Komlan Afiademanyo
- Département de Zoologie et de Biologie Animale, Université de Lomé, BP 1515, Lomé, Togo
| | | | - Jean Malekani
- Department of Biology, University of Kinshasa, PO Box 218, Kinshasa XI, Democratic Republic of Congo
| | - Sery Gonedelé Bi
- Laboratoire de Génétique, Université Félix Houphouët Boigny d'Abidjan-Cocody, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005, Ile-Ife, Nigeria
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 LEA-FSA, Cotonou, Benin
| | - Prince Kaleme
- Laboratoire de Mammalogie, Département de Biologie, Centre de Recherches en Sciences Naturelles (CRSN) - Lwiro, DS (Dépêche Spéciale) Bukavu, Democratic Republic of Congo.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Casimir Nebesse Mololo
- Université de Kisangani, Faculté des Sciences, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - William Stanley
- Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
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Rocha S, Perera A, Bunbury N, Kaiser-Bunbury CN, Harris DJ. Speciation history and species-delimitation within the Seychelles Bronze geckos,Ailuronyxspp.: molecular and morphological evidence. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sara Rocha
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Campus Lagoas-Marcosende; 36310 Vigo Spain
| | - Ana Perera
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
| | - Nancy Bunbury
- Seychelles Islands Foundation; La Ciotat Building; Mont Fleuri PO Box 853 Victoria, Mahé Seychelles
| | | | - David J. Harris
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
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31
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Aguilar C, Wood PL, Belk MC, Duff MH, Sites JW. Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cesar Aguilar
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
- Departamento de Herpetologia; Museo de Historia Natural de San Marcos (MUSM); Av. Arenales 1256, Jesus Maria Lima Peru
- Facultad de Ciencias Biologicas; Instituto de Ciencias Biologicas Antonio Raimondi; Universidad Nacional Mayor de San Marcos; Lima Peru
| | - Perry L. Wood
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mark C. Belk
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mike H. Duff
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
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32
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Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches. Sci Rep 2016; 6:22262. [PMID: 26915968 PMCID: PMC4768097 DOI: 10.1038/srep22262] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
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Ogilvie HA, Heled J, Xie D, Drummond AJ. Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods. Syst Biol 2016; 65:381-96. [PMID: 26821913 PMCID: PMC4851174 DOI: 10.1093/sysbio/syv118] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/07/2015] [Indexed: 01/02/2023] Open
Abstract
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common genealogical history, thereby equating gene coalescence with species divergence. The multispecies coalescent is supported by previous studies which found that its predicted distributions fit empirical data, and that concatenation is not a consistent estimator of the species tree. *BEAST, a fully Bayesian implementation of the multispecies coalescent, is popular but computationally intensive, so the increasing size of phylogenetic data sets is both a computational challenge and an opportunity for better systematics. Using simulation studies, we characterize the scaling behavior of *BEAST, and enable quantitative prediction of the impact increasing the number of loci has on both computational performance and statistical accuracy. Follow-up simulations over a wide range of parameters show that the statistical performance of *BEAST relative to concatenation improves both as branch length is reduced and as the number of loci is increased. Finally, using simulations based on estimated parameters from two phylogenomic data sets, we compare the performance of a range of species tree and concatenation methods to show that using *BEAST with tens of loci can be preferable to using concatenation with thousands of loci. Our results provide insight into the practicalities of Bayesian species tree estimation, the number of loci required to obtain a given level of accuracy and the situations in which supermatrix or summary methods will be outperformed by the fully Bayesian multispecies coalescent.
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Affiliation(s)
- Huw A Ogilvie
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
| | - Joseph Heled
- Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Dong Xie
- Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Alexei J Drummond
- Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
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34
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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
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35
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Konowalik K, Wagner F, Tomasello S, Vogt R, Oberprieler C. Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting. Mol Phylogenet Evol 2015; 92:308-28. [DOI: 10.1016/j.ympev.2015.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 12/23/2022]
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36
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Ruane S, Raxworthy CJ, Lemmon AR, Lemmon EM, Burbrink FT. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evol Biol 2015; 15:221. [PMID: 26459325 PMCID: PMC4603904 DOI: 10.1186/s12862-015-0503-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. METHODS Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. RESULTS Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. CONCLUSIONS Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees.
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Affiliation(s)
- Sara Ruane
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Alan R Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Biology Department, College of Staten Island/CUNY, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.
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Extreme food-plant specialisation in Megabombus bumblebees as a product of long tongues combined with short nesting seasons. PLoS One 2015; 10:e0132358. [PMID: 26267382 PMCID: PMC4534414 DOI: 10.1371/journal.pone.0132358] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/14/2015] [Indexed: 12/21/2022] Open
Abstract
Megabombus bumblebees have unusually long tongues and are generally more specialised than other bumblebees in their choice of food plants. The phylogeny of Megabombus bumblebees shows that speciation was concentrated in two periods. Speciation in the first period (ca 4.25–1.5 Ma) is associated with the late rise of the Hengduan Mountains at the eastern end of the Qinghai-Tibetan plateau. Speciation in the second period (1.2–0.3 Ma) is associated with climatic cooling in the northern forests. The most extreme food-specialist species belong to the second period, which may point to climate as a factor in specialisation. These extreme specialist species occur either in the far north (Bombus consobrinus), or at high elevations (Bombus gerstaeckeri), in situations where long tongues coincide with the shortest nesting seasons. Species with the longest tongues but occurring further south (even at high elevations) use a broader range of food plants.
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Medina CD, Avila LJ, Sites JW, Morando M. Molecular Phylogeny of the Liolaemus kriegi Complex (Iguania, Liolaemini). HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-13-00083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Cintia D. Medina
- Grupo de Herpetología Patagónica, CENPAT-CONICET, Boulevard Almirante Brown 2915 U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Luciano J. Avila
- Grupo de Herpetología Patagónica, CENPAT-CONICET, Boulevard Almirante Brown 2915 U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Jack W. Sites
- Biology Department and Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| | - Mariana Morando
- Grupo de Herpetología Patagónica, CENPAT-CONICET, Boulevard Almirante Brown 2915 U9120ACD, Puerto Madryn, Chubut, Argentina
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Bagley JC, Alda F, Breitman MF, Bermingham E, van den Berghe EP, Johnson JB. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). PLoS One 2015; 10:e0121139. [PMID: 25849959 PMCID: PMC4388586 DOI: 10.1371/journal.pone.0121139] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 02/10/2015] [Indexed: 12/20/2022] Open
Abstract
Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.
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Affiliation(s)
- Justin C. Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- * E-mail:
| | - Fernando Alda
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - M. Florencia Breitman
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- Centro Nacional Patagónico (CENPAT-CONICET), U9120ACD, Puerto Madryn, Chubut, Argentina
| | | | - Eric P. van den Berghe
- Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Zamorano University, Tegucigalpa, Honduras
| | - Jerald B. Johnson
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
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Olave M, Avila LJ, Sites JW, Morando M. Model-based approach to test hard polytomies in theEulaemusclade of the most diverse South American lizard genusLiolaemus(Liolaemini, Squamata). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12231] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melisa Olave
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
| | - Luciano J. Avila
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; LSB; Brigham Young University; ZC: 84602 Provo UT USA
| | - Mariana Morando
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Argentina
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Meyer BS, Matschiner M, Salzburger W. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach. Mol Phylogenet Evol 2015; 83:56-71. [PMID: 25433288 PMCID: PMC4334724 DOI: 10.1016/j.ympev.2014.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 11/14/2022]
Abstract
The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12-16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the 'H-lineage', which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the 'H-lineage', as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the 'H-lineage' received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
| | - Michael Matschiner
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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Šmíd J, Moravec J, Kratochvíl L, Nasher AK, Mazuch T, Gvoždík V, Carranza S. Multilocus phylogeny and taxonomic revision of theHemidactylus robustusspecies group (Reptilia, Gekkonidae) with descriptions of three new species from Yemen and Ethiopia. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2014.996264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Lambert SM, Reeder TW, Wiens JJ. When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny. Mol Phylogenet Evol 2014; 82 Pt A:146-55. [PMID: 25315885 DOI: 10.1016/j.ympev.2014.10.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/09/2014] [Accepted: 10/02/2014] [Indexed: 02/03/2023]
Abstract
Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, andsuggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling.
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Affiliation(s)
- Shea M Lambert
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
| | - Tod W Reeder
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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Maia-Carvalho B, Gonçalves H, Ferrand N, Martínez-Solano I. Multilocus assessment of phylogenetic relationships in Alytes (Anura, Alytidae). Mol Phylogenet Evol 2014; 79:270-8. [DOI: 10.1016/j.ympev.2014.05.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
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A time-calibrated, multi-locus phylogeny of piranhas and pacus (Characiformes: Serrasalmidae) and a comparison of species tree methods. Mol Phylogenet Evol 2014; 81:242-57. [PMID: 25261120 DOI: 10.1016/j.ympev.2014.06.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 12/13/2022]
Abstract
The phylogeny of piranhas, pacus, and relatives (family Serrasalmidae) was inferred on the basis of DNA sequences from eleven gene fragments that include the mitochondrial control region plus 10 nuclear genes (two exons and eight introns). The new data were obtained for a representative sampling of 53 specimens, collected from all major South American rivers, accounting for over 40% of the valid species and all genera excluding Utiaritichthys. Two fossil calibration points and relaxed-clock Bayesian analyses were used to estimate the timing of diversification. The new multilocus dataset also is used to compare several species-tree approaches against the results obtained using the concatenated alignment analyzed under maximum likelihood and Bayesian inference. Individual gene trees showed substantial topological discordance, but analyses based on concatenation and Bayesian and maximum likelihood-based species trees approaches converged onto a single phylogeny. The resulting phylogenetic hypothesis is robust and supports a division of the family into three major clades, consistent with previous results based on mitochondrial DNA alone. The earliest branching event separated a "pacu" clade (Colossoma, Mylossoma and Piaractus) from the rest of the family in the Late Cretaceous (over 68 Ma). The other two clades, that contain most of the diversity, are formed by the "true piranhas" (Metynnis, Pygopristis, Pygocentrus, Pristobrycon, Catoprion, and Serrasalmus) and the Myleus-like pacus (the Myleus clade). The "true" piranha clade originated during the Eocene (∼53 Ma) but the most recent diversification of flesh-eating piranhas within the genera Serrasalmus and Pygocentrus did not start until the Miocene (∼17 Ma). A comparison of species tree approaches indicates that most methods tested are consistent with results obtained by concatenation, suggesting that the gene-tree incongruence observed is mild and will not produce misleading results under simple concatenation analysis. Non-monophyly of several genera (Pristobrycon, Tometes, Myloplus, Mylesinus) and putative species (Serrasalmus rhombeus) was obtained, suggesting that further study of this family is necessary.
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Jockusch EL, Martínez-Solano I, Timpe EK. The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps). Syst Biol 2014; 64:66-83. [DOI: 10.1093/sysbio/syu078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elizabeth L. Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Iñigo Martínez-Solano
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Elizabeth K. Timpe
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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Farrington HL, Lawson LP, Clark CM, Petren K. The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape. Evolution 2014; 68:2932-44. [PMID: 24976076 DOI: 10.1111/evo.12484] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 06/13/2014] [Indexed: 11/27/2022]
Abstract
Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species-trees recovered seven major finch clades: ground, tree, vegetarian, Cocos Island, grey and green warbler finches, and a distinct clade of sharp-beaked ground finches (Geospiza cf. difficilis) basal to all ground and tree finches. The ground and tree finch clades lack species-level phylogenetic structure. Interisland gene flow and interspecies introgression vary geographically in predictable ways. First, several species exhibit concordant patterns of population divergence across the channel separating the Galápagos platform islands from the separate volcanic province of northern islands. Second, peripheral islands have more admixed populations while central islands maintain more distinct species boundaries. This landscape perspective highlights a likely role for isolation of peripheral populations in initial divergence, and demonstrates that peripheral populations may maintain genetic diversity through outbreeding during the initial stages of speciation.
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Affiliation(s)
- Heather L Farrington
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, 45221; North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601
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Altermann S, Leavitt SD, Goward T, Nelsen MP, Lumbsch HT. How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS One 2014; 9:e97556. [PMID: 24831224 PMCID: PMC4022584 DOI: 10.1371/journal.pone.0097556] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 11/19/2022] Open
Abstract
The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon L. columbiana (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative Letharia lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate Letharia species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc ΔK statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘L. lupina’ and L. vulpina, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘L. lucida’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other L. columbiana s.l. populations with the two sorediate genetic clusters.
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Affiliation(s)
- Susanne Altermann
- Biology Department, Whitman College, Walla Walla, Washington, United States of America
| | - Steven D. Leavitt
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
| | - Trevor Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew P. Nelsen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
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Olave M, Avila LJ, Sites JW, Morando M. Multilocus phylogeny of the widely distributed South American lizard cladeEulaemus(Liolaemini,Liolaemus). ZOOL SCR 2014. [DOI: 10.1111/zsc.12053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Melisa Olave
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Chubut Argentina
| | - Luciano J. Avila
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Chubut Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; 401 WIDB ZC: 84602 Provo Utah USA
| | - Mariana Morando
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas (CENPAT-CONICET); Boulevard Almirante Brown 2915 ZC: U9120ACD Puerto Madryn Chubut Argentina
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50
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DeGiorgio M, Syring J, Eckert AJ, Liston A, Cronn R, Neale DB, Rosenberg NA. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol Biol 2014; 14:67. [PMID: 24678701 PMCID: PMC4021425 DOI: 10.1186/1471-2148-14-67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/10/2014] [Indexed: 12/26/2022] Open
Abstract
Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.
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Affiliation(s)
- Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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