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Sánchez KI, Diaz Huesa EG, Breitman MF, Avila LJ, Sites JW, Morando M. Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade). Syst Biol 2023; 72:739-752. [PMID: 37097104 DOI: 10.1093/sysbio/syad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Emilce G Diaz Huesa
- Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEAus-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - María F Breitman
- Department of Biology and Environmental Science, Auburn University at Montgomery, Montgomery, 36117, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology, Austin Peay State University, Clarksville, 37044, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, U9120ACD, Argentina
- Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Puerto Madryn, U9120ACD, Argentina
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2
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Schütte A, Stüben PE, Astrin JJ. Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea). Biodivers Data J 2023; 11:e96438. [PMID: 38357418 PMCID: PMC10865102 DOI: 10.3897/bdj.11.e96438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/08/2022] [Indexed: 01/25/2023] Open
Abstract
The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.
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Affiliation(s)
- André Schütte
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
| | - Peter E Stüben
- Curculio Institute, Mönchengladbach, Germany Curculio Institute Mönchengladbach Germany
| | - Jonas J Astrin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
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3
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Edwards DL, Avila LJ, Martinez L, Sites JW, Morando M. Environmental correlates of phenotypic evolution in ecologically diverse
Liolaemus
lizards. Ecol Evol 2022; 12:e9009. [PMID: 35784059 PMCID: PMC9201750 DOI: 10.1002/ece3.9009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/02/2022] [Indexed: 01/02/2023] Open
Abstract
Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus, one of the most ecologically diverse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive diversification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26‐taxon dataset for the Liolaemus gracilis species group, representing much of the ecological diversity represented within Liolaemus and used environmental data to characterize how environments occupied by species' relate to phenotypic evolution. Our analyses, explicitly accounting for phylogenetic uncertainty, suggest diversification in phenotypic traits toward the present, with body shape evolution rapidly evolving in this group. Body shape evolution correlates with the occupation of different structural habitats indicated by vegetation axes suggesting species have adapted for maximal locomotory performance in these habitats. Our results also imply that the effects of phylogenetic uncertainty and model misspecification may be more extensive on univariate, relative to multivariate analyses of evolutionary correlations, which is an important consideration in analyzing data from rapidly radiating adaptive radiations.
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Affiliation(s)
- Danielle L. Edwards
- The Department of Life & Environmental Sciences University of California Merced California USA
| | - Luciano J. Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET) Puerto Madryn Argentina
| | - Lorena Martinez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET) Puerto Madryn Argentina
- Vigo Spain
| | - Jack W. Sites
- Department of Biology and M.L. Bean Life Science Museum Brigham Young University (BYU) Provo Utah USA
- Trenton Kentucky USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC‐CONICET) Puerto Madryn Argentina
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4
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Genetic structure, diversity and distribution of a threatened lizard affected by widespread habitat fragmentation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01408-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
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6
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Grummer JA, Avila LJ, Morando MM, Leaché AD. Four Species Linked by Three Hybrid Zones: Two Instances of Repeated Hybridization in One Species Group (Genus Liolaemus). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.624109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hybridization is an evolutionary process that can generate diverse outcomes, such as reinforcing species boundaries, generating new species, or facilitating the introgression of locally-adapted alleles into new genomic backgrounds. Liolaemus is a highly diverse clade of South American lizards with ~260 species and as many as ten new species are described each year. Previous Liolaemus studies have detected gene flow and introgression among species using phylogenetic network methods and/or through comparisons of nuclear and mitochondrial DNA patterns, yet no study has systematically studied hybrid zones between Liolaemus species. Here, we compared three hybrid zones between four species in the Liolaemus fitzingerii group of lizards in Central Argentina where two species, L. melanops and L. xanthoviridis, each hybridize with two other species (L. shehuen and L. fitzingerii). We sampled three transects that were each ~120 km in length and sequenced both mitochondrial and genome-wide SNP data for 267 individuals. In our analyses of nuclear DNA, we also compared bi-allelic SNPs to phased alleles (50 bp RAD loci). Population structure analyses confirmed that boundaries separating species are sharp, and all clines are <65 km wide. Cline center estimates were consistent between SNPs and phased alleles, but cline width estimates were significantly different with the SNPs producing wider estimates. The mitochondrial clines are narrower and shifted 4–20 km southward in comparison to the nuclear clines in all three hybrid zones, indicating that either each of the species has sex-biased dispersal (males northward or females southward), the population densities are unequal, or that the hybrid zones are moving north over time. These comparisons indicate that some patterns of hybridization are similar across hybrid zones (mtDNA clines all narrower and shifted to the south), whereas cline width is variable. Hybridization in the L. fitzingerii group is common and geographically localized; further studies are needed to investigate whether hybrid zones act as hard species boundaries or promoters of speciation through processes such as reinforcement. Nonetheless, this study provides insights into both biotic and abiotic mechanisms helping to maintain species boundaries within the speciose Liolaemus system.
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7
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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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8
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Moraes SDS, Murillo‐Ramos L, Machado PA, Ghanavi HR, Magaldi LM, Silva‐Brandão KL, Kato MJ, Freitas AVL, Wahlberg N. A double‐edged sword: Unrecognized cryptic diversity and taxonomic impediment in
Eois
(Lepidoptera, Geometridae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simeão de Souza Moraes
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
- Department of Biology Lund University Lund Sweden
| | - Leidys Murillo‐Ramos
- Department of Biology Lund University Lund Sweden
- Departamento de Biología Universidad de Sucre Sincelejo Colombia
| | - Patrícia A. Machado
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Luiza M. Magaldi
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Massuo J. Kato
- Laboratório de Química de Produtos Naturais Instituto de Química Universidade de São Paulo São Paulo Brazil
| | - André V. L. Freitas
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
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9
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Sánchez KI, Avila LJ, Sites JW, Morando M. An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini). Mol Phylogenet Evol 2021; 157:107046. [PMID: 33421613 DOI: 10.1016/j.ympev.2020.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/07/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina.
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT 84602, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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10
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Verheye ML, D’Udekem D’Acoz C. Integrative taxonomy of giant crested Eusirus in the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.
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Affiliation(s)
- Marie L Verheye
- Royal Belgian Institute of Natural Sciences, O.D. Nature, Rue Vautier, Brussels, Belgium
- Université de Liège, Laboratoire d’Océanologie, Quartier Agora, Allée du 6 Août, Liège, Belgium
| | - Cédric D’Udekem D’Acoz
- Royal Belgian Institute of Natural Sciences, O.D. Nature, Rue Vautier, Brussels, Belgium
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11
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Galuszynski NC, Potts AJ. Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa? PeerJ 2020; 8:e10045. [PMID: 33024648 PMCID: PMC7519721 DOI: 10.7717/peerj.10045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/20/2022] Open
Abstract
Aim The evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)-and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR. Location The CFR, located along the southern Cape of South Africa. Methods Published phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not. Results Phylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries. Main conclusions The evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts and test novel hypotheses pertaining to the distribution of genetic diversity among CFR plant taxa. Additionally, the resolution at which CoEs are mapped should be refined, which may provide a valuable tool for future conservation planning and the development of precautionary guidelines for the translocation of genetic material during species reintroductions and commercial cultivation of Cape endemic crops. Thus, to answer the question 'Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?'-yes, CoEs do appear to be an important tool for Cape phylogeographers. However, the data is limited and more plant phylogeography work is needed in the CFR.
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Affiliation(s)
| | - Alastair J Potts
- Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
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12
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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13
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Urtubey E, Stuessy TF, Justel JI, Nicola MV. Phylogeography and palaeomodelling of Duseniella patagonica (Barnadesioideae), an early-diverging member of Asteraceae endemic to the Argentinean Monte and Patagonia. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractWe performed an integrated phylogeographical and palaeoclimatic study of an early-diverging member of Asteraceae, Duseniella patagonica, endemic to Argentina. Chloroplast and nuclear markers were sequenced from 106 individuals belonging to 20 populations throughout the species range. We analysed genetic spatial distribution, diversity and structure, tested for range expansion, estimated divergence times, reconstructed ancestral areas and modelled present and past species distributions based on climatic data. Duseniella diverged from its sister genera during the Late/Middle Miocene. Its ancestral area included southern Monte plus eastern and central Patagonia. A vicariant event separated Monte and Patagonian clades during the Plio-Pleistocene. This would have involved unfavourable climate, soil, elevation, volcanism and/or other geomorphological processes between 40 and 43.5°S, in the sourroundings of the Somuncura plateau. Each clade possesses its own haplotypes and nucleotypes. Two populations, one in southern Monte and the other in eastern Patagonia, contain the highest diversity and exclusive haplotypes, representing hypothetical ancestral refugia. Northern Monte and southern Patagonian populations show low to null genetic diversity, being the most recently colonized areas. Climatic models indicate that winter temperature influenced the distribution of Duseniella, with an increase in probability of occurrence during colder periods, thus enabling diversification during glacial episodes.
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Affiliation(s)
- Estrella Urtubey
- Instituto de Botánica Darwinion, Provincia de Buenos Aires, Argentina
| | - Tod Falor Stuessy
- Herbarium and Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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14
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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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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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16
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The enigmatic Leiosaurae clade: Phylogeography, species delimitation, phylogeny and historical biogeography of its southernmost species. Mol Phylogenet Evol 2019; 144:106725. [PMID: 31884086 DOI: 10.1016/j.ympev.2019.106725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
The clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and understanding of their evolutionary histories. Here, we use data collected over 9 years to study the phylogenetic history, genetic diversity, and biogeographic history of almost all the southernmost species of Leiosaurae (except P. nigroigulus), including: Leiosaurus bellii, Diplolaemus darwinii, D. bibronii, D. sexcinctus and D. leopardinus. We use a fragment of the mitochondrial cytochrome-b gene to resolve general phylogeographic patterns, and add another mitochondrial gene and eight nuclear genes to perform species delimitation and phylogenetic analyses associated with divergence times. We found evidence for three putative new species-level taxa within L. bellii and five within Diplolaemus species, indicating high levels of geographic structure. We use a time-calibrated phylogeny to estimate ranges of ancestral distributions and to generate new hypotheses about their historical biogeography.
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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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Esquerré D, Ramírez-Álvarez D, Pavón-Vázquez CJ, Troncoso-Palacios J, Garín CF, Keogh JS, Leaché AD. Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Mol Phylogenet Evol 2019; 139:106524. [DOI: 10.1016/j.ympev.2019.106524] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
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19
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Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Mol Phylogenet Evol 2019; 139:106549. [DOI: 10.1016/j.ympev.2019.106549] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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20
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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21
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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Nicola MV, Johnson LA, Pozner R. Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae). Mol Phylogenet Evol 2019; 136:164-182. [PMID: 30858079 DOI: 10.1016/j.ympev.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022]
Abstract
Congruence among different sources of data is highly desirable in phylogenetic analyses. However, plastid and nuclear DNA may record different evolutionary processes such that incongruence among results from these sources can help unravel complex evolutionary histories. That is the case of Nassauvia subgenus Strongyloma (Asteraceae), a taxon with five putative species distributed in the southern Andes and Patagonian steppe. Morphometric and phylogeographic information cast doubt on the integrity of its species, and previous molecular data even questioned the monophyly of the subgenus. We tested those questions using plastid and nuclear DNA sequences by the application of different methods such as phylogenetic trees, networks, a test of genealogical sorting, an analysis of population structure, calibration of the trees, and hybridization test, assembling non-synchronous incongruent results at subgenus and species levels in a single reconstruction. The integration of our molecular analyses and previous taxonomic, morphological, and molecular studies support subgenus Strongyloma as a monophyletic group. However, the topology of the nuclear trees and the evidence of polyploids within subgenus Nassauvia, suggest a hypothetical origin and initial radiation of Nassauvia related to an ancient hybridization event that occurred around 17-6.3 Myr ago near the Andes in west-central Patagonia. Plastid data suggest a recent diversification within subgenus Strongyloma, at most 9.8 Myr ago, towards the Patagonian steppe east of the Andes. These processes cause phylogenies to deviate from the species tree since each putative species lack exclusive ancestry. The non-monophyly of its species using both plastid and nuclear data is caused mainly by incomplete lineage sorting occurred since the Miocene. The final uplift of the Andes and Pliocene-Pleistocene glacial-interglacial and its consequences on the landscape and climate structured the genetic composition of this group of plants in the Patagonian steppe. The molecular data presented here agree with previous morphological studies, in that the five putative species typically accepted in this subgenus are not independent taxa. This study emphasizes that adding more than one sequence per species, not combining data with dissimilar inheritance patterns without first performed incongruence tests, exploring data through different methodologies, considering the timing of events, and searching for the causes of poorly resolved and/or incongruent phylogenies help to reveal complex biological underlying processes, which might otherwise remain hidden.
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Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina.
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, 4102 LSB, Brigham Young University, Provo, UT 84602, USA
| | - Raúl Pozner
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
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23
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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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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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25
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The True Identity of the New World Iguanid Lizard Liolaemus chillanensis Müller and Hellmich 1932 (Iguania: Liolaemidae) and Description of a New Species in the Liolaemus elongatus Group. Zool Stud 2018; 57:e22. [PMID: 31966262 DOI: 10.6620/zs.2018.57-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 04/19/2018] [Indexed: 11/18/2022]
Abstract
Jaime Troncoso-Palacios, Damien Esquerré, Félix A. Urra, Hugo A. Díaz, Carlos Castro-Pastene, and María Soledad Ruiz (2018) Liolaemus is a particularly species-rich radiation of New World iguanid lizards from southern South America. Thanks to intense systematic and taxonomic research, the knowledge on its species- level diversity has increased rapidly over the past several years. The L. elongatus species-complex has received considerable attention and a remarkable case is Liolaemus chillanensis, a name that has been used for two different species that are sympatric in Termas de Chillán, central Chile. Since the holotype is lost, we propose that the first step to identify the true L. chillanensis is through the analysis of the original description. Then we provide a morphological and molecular characterization of L. chillanensis based on topotypes and a description of the taxon previously confused with it.
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Lobo F, Barrasso DA, Paz M, Basso NG. Phylogenetic relationships within a patagonian clade of reptiles (Liolaemidae:Phymaturus) based on DNA sequences and morphology. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Lobo
- IBIGEO (Instituto de Bio y Geociencias del NOA); Facultad de Ciencias Naturales; Universidad Nacional de Salta and CONICET; Salta Argentina
| | - Diego A. Barrasso
- IDEAUS (Instituto de Diversidad y Evolución Austral-CONICET); Puerto Madryn Chubut Argentina
- Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia “San Juan Bosco” (UNPSJB); Puerto Madryn Chubut Argentina
| | - Marcos Paz
- UEL (Unidad Ejecutora Lillo-CONICET); S. M. de Tucumán Argentina
| | - Néstor G. Basso
- IDEAUS (Instituto de Diversidad y Evolución Austral-CONICET); Puerto Madryn Chubut Argentina
- Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia “San Juan Bosco” (UNPSJB); Puerto Madryn Chubut Argentina
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27
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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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28
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Portelli SN, Quinteros AS. Phylogeny, time divergence, and historical biogeography of the South American Liolaemus alticolor-bibronii group (Iguania: Liolaemidae). PeerJ 2018; 6:e4404. [PMID: 29479502 PMCID: PMC5824678 DOI: 10.7717/peerj.4404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/02/2018] [Indexed: 11/20/2022] Open
Abstract
The genus Liolaemus comprises more than 260 species and can be divided in two subgenera: Eulaemus and Liolaemus sensu stricto. In this paper, we present a phylogenetic analysis, divergence times, and ancestral distribution ranges of the Liolaemus alticolor-bibronii group (Liolaemus sensu stricto subgenus). We inferred a total evidence phylogeny combining molecular (Cytb and 12S genes) and morphological characters using Maximum Parsimony and Bayesian Inference. Divergence times were calculated using Bayesian MCMC with an uncorrelated lognormal distributed relaxed clock, calibrated with a fossil record. Ancestral ranges were estimated using the Dispersal-Extinction-Cladogenesis (DEC-Lagrange). Effects of some a priori parameters of DEC were also tested. Distribution ranged from central Perú to southern Argentina, including areas at sea level up to the high Andes. The L. alticolor-bibronii group was recovered as monophyletic, formed by two clades: L. walkeri and L. gracilis, the latter can be split in two groups. Additionally, many species candidates were recognized. We estimate that the L. alticolor-bibronii group diversified 14.5 Myr ago, during the Middle Miocene. Our results suggest that the ancestor of the Liolaemus alticolor-bibronii group was distributed in a wide area including Patagonia and Puna highlands. The speciation pattern follows the South-North Diversification Hypothesis, following the Andean uplift.
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Affiliation(s)
- Sabrina N. Portelli
- UNSa-CONICET, Instituto de Bio y Geociencias del NOA, Rosario de Lerma, Salta, Argentina
| | - Andrés S. Quinteros
- UNSa-CONICET, Instituto de Bio y Geociencias del NOA, Rosario de Lerma, Salta, Argentina
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Reaney AM, Saldarriaga-Córdoba M, Pincheira-Donoso D. Macroevolutionary diversification with limited niche disparity in a species-rich lineage of cold-climate lizards. BMC Evol Biol 2018; 18:16. [PMID: 29409440 PMCID: PMC5801843 DOI: 10.1186/s12862-018-1133-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Life diversifies via adaptive radiation when natural selection drives the evolution of ecologically distinct species mediated by their access to novel niche space, or via non-adaptive radiation when new species diversify while retaining ancestral niches. However, while cases of adaptive radiation are widely documented, examples of non-adaptively radiating lineages remain rarely observed. A prolific cold-climate lizard radiation from South America (Phymaturus), sister to a hyper-diverse adaptive radiation (Liolaemus), has extensively diversified phylogenetically and geographically, but with exceptionally minimal ecological and life-history diversification. This lineage, therefore, may offer unique opportunities to investigate the non-adaptive basis of diversification, and in combination with Liolaemus, to cover the whole spectrum of modes of diversification predicted by theory, from adaptive to non-adaptive. Using phylogenetic macroevolutionary modelling performed on a newly created 58-species molecular tree, we establish the tempo and mode of diversification in the Phymaturus radiation. RESULTS Lineage accumulation in Phymaturus opposes a density-dependent (or 'niche-filling') process of diversification. Concurrently, we found that body size diversification is better described by an Ornstein-Uhlenbeck evolutionary model, suggesting stabilizing selection as the mechanism underlying niche conservatism (i.e., maintaining two fundamental size peaks), and which has predominantly evolved around two major adaptive peaks on a 'Simpsonian' adaptive landscape. CONCLUSIONS Lineage diversification of the Phymaturus genus does not conform to an adaptive radiation, as it is characterised by a constant rate of species accumulation during the clade's history. Their strict habitat requirements (rocky outcrops), predominantly invariant herbivory, and especially the constant viviparous reproduction across species have likely limited their opportunities for adaptive diversifications throughout novel environments. This mode of diversification contrasts dramatically with its sister lineage Liolaemus, which geographically overlaps with Phymaturus, but exploits all possible microhabitats in these and other bioclimatic areas. Our study contributes importantly to consolidate these lizards (liolaemids) as promising model systems to investigate the entire spectrum of modes of species formations, from the adaptive to the non-adaptive extremes of the continuum.
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Affiliation(s)
- Ashley M. Reaney
- Laboratory of Evolutionary Ecology of Adaptations, School of Life Sciences, University of Lincoln, Brayford Campus, Lincoln, Lincolnshire LN6 7DL UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY UK
| | - Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago, Chile
| | - Daniel Pincheira-Donoso
- Laboratory of Evolutionary Ecology of Adaptations, School of Life Sciences, University of Lincoln, Brayford Campus, Lincoln, Lincolnshire LN6 7DL UK
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Torres-Pérez F, Boric-Bargetto D, Rodríguez-Valenzuela E, Escobar C, Palma RE. Molecular phylogenetic analyses reveal the importance of taxon sampling in cryptic diversity: Liolaemus nigroviridis and L. monticola (Liolaeminae) as focal species. REVISTA CHILENA DE HISTORIA NATURAL 2017. [DOI: 10.1186/s40693-017-0068-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Dagnino D, Minuto L, Casazza G. Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:1003-1011. [PMID: 28691341 DOI: 10.1111/plb.12600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision.
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Affiliation(s)
- D Dagnino
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
| | - L Minuto
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
| | - G Casazza
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
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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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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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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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Troncoso-Palacios J, Diaz HA, Puas GI, Riveros-Riffo E, Elorza AA. Two new Liolaemus lizards from the Andean highlands of Southern Chile (Squamata, Iguania, Liolaemidae). Zookeys 2016:121-146. [PMID: 27920609 PMCID: PMC5126550 DOI: 10.3897/zookeys.632.9528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 10/16/2016] [Indexed: 11/12/2022] Open
Abstract
Liolaemus is a diverse genus of lizards, subdivided into two subgenera: Liolaemus (sensu stricto) and Eulaemus, distributed mainly in Chile and Argentina. The Liolaemus elongatus-kriegi complex is the most diverse group within Liolaemus (sensu stricto), especially the species closely related to Liolaemus elongatus, which form a clade currently comprising nine species. Several Chilean species of this group have been recently described, mainly from volcanoes and poorly explored mountains. Here molecular and morphological evidence are provided for a new species of the Liolaemus elongatus clade, which is characterized by its small size and lack of dorsal pattern, unusual features for the species of this group of lizards. Additionally, the lack of precloacal pores in males of Liolaemus (sensu stricto) is a trait found in few species, which do not constitute a monophyletic group. A second new southern Chilean species is also described, without precloacal pores and supported by molecular phylogenetics to be related to Liolaemus villaricensis. Both new species were found in the same locality, near a lake located in a pre-Andean zone with Araucaria and Nothofagus forest. The two species are dedicated to prominent Lonkos (tribal chiefs) of the Mapuche and Pehuenche people: Janequeo and Leftraru. Additionally, the phylogenetic results suggest that Liolaemus lonquimayensis is a synonym of Liolaemus elongatus.
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Affiliation(s)
- Jaime Troncoso-Palacios
- Programa de Fisiologia y Biofisica, Instituto de Ciencias Biomedicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Hugo A Diaz
- Departamento de Ciencias Ecologicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile; Departamento de Ciencias Biologicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa 11735, Santiago, Chile
| | - German I Puas
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
| | - Edvin Riveros-Riffo
- Red de Observadores de Aves y Vida Silvestre de Chile, Julio Prado 1144 Dpto. 31, Providencia, Chile
| | - Alvaro A Elorza
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
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Troncoso-Palacios J, Elorza AA, Puas GI, Alfaro-Pardo E. A new species of Liolaemus related to L. nigroviridis from the Andean highlands of Central Chile (Iguania, Liolaemidae). Zookeys 2016:91-114. [PMID: 26877688 PMCID: PMC4740823 DOI: 10.3897/zookeys.555.6011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/26/2015] [Indexed: 11/12/2022] Open
Abstract
The Liolaemusnigroviridis group is a clade of highland lizards endemic to Chile. These species are distributed from northern to central Chile, and currently there are no cases of sympatric distribution. This study describes a new species, Liolaemusuniformissp. n., from this group, and provides a detailed morphological characterization and mitochondrial phylogeny using cytochrome-b. Liolaemusuniformis was found in sympatry with Liolaemusnigroviridis but noticeably differed in size, scalation, and markedly in the color pattern, without sexual dichromatism. This new species has probably been confused with Liolaemusmonticola and Liolaemusbellii, both of which do not belong to the nigroviridis group. The taxonomic issues of this group that remain uncertain are also discussed.
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Affiliation(s)
- Jaime Troncoso-Palacios
- Programa de Fisiologia y Biofisica, Instituto de Ciencias Biomedicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alvaro A Elorza
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
| | - German I Puas
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
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Trickey JS, Thiel M, Waters JM. Transoceanic dispersal and cryptic diversity in a cosmopolitan rafting nudibranch. INVERTEBR SYST 2016. [DOI: 10.1071/is15052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within the Pacific Ocean. Low genetic divergences within each lineage suggest that rafting can mediate dispersal across transoceanic scales. A third, highly divergent, lineage was detected in a single Indonesian specimen. Broadly concordant phylogeographic relationships were detected for the nuclear ITS1 region, with distinct tropical versus antitropical lineages observed. The substantial genetic divergences and largely allopatric distributions observed among the F. pinnata lineages suggest that they represent a species complex.
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Breitman MF, Bonino MF, Sites JW, Avila LJ, Morando M. Morphological Variation, Niche Divergence, and Phylogeography of Lizards of the Liolaemus lineomaculatus Section (Liolaemini) from Southern Patagonia. HERPETOLOGICAL MONOGRAPHS 2015. [DOI: 10.1655/herpmonographs-d-14-00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- M. Florencia Breitman
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Marcelo F. Bonino
- INIBIOMA (CONICET-UNCOMA), Laboratorio de Fotobiología, Centro Regional Universitario Bariloche, Quintral 1250, 8400, Bariloche, Río Negro, Argentina
| | - Jack W. Sites
- Brigham Young University, Life Sciences Building, Biology Department, Provo, UT 84602, USA
| | - Luciano J. Avila
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
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39
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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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40
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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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Troncoso-Palacios J, Díaz HA, Esquerré D, Urra FA. Two new species of the Liolaemuselongatus-kriegi complex (Iguania, Liolaemidae) from Andean highlands of southern Chile. Zookeys 2015:83-109. [PMID: 25987873 PMCID: PMC4432242 DOI: 10.3897/zookeys.500.8725] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/18/2015] [Indexed: 11/26/2022] Open
Abstract
The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemusbuergeri and Liolaemuskriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of Liolaemuskriegi was recently recognized as an undescribed taxon called “Liolaemus sp. A” based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: Liolaemusscorialissp. n. and Liolaemuszabalaisp. n., previously considered Liolaemusbuergeri and “Liolaemuskriegi/Liolaemus sp. A” respectively. Additionally, we identified another population of Liolaemusscorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemusscorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemuszabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of Liolaemusneuquensis in Chile from a museum specimen from La Mula Lagoon.
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Affiliation(s)
- Jaime Troncoso-Palacios
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Hugo A Díaz
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile ; Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Damien Esquerré
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Felix A Urra
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile ; Programa de Farmacología Molecular y Clínica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
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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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43
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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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44
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Reynolds RG, Puente-Rolón AR, Platenberg R, Tyler RK, Tolson PJ, Revell LJ. Large divergence and low diversity suggest genetically informed conservation strategies for the endangered Virgin Islands Boa (Chilabothrus monensis). Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2015.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Out of the deep: Cryptic speciation in a Neotropical gecko (Squamata, Phyllodactylidae) revealed by species delimitation methods. Mol Phylogenet Evol 2014; 80:113-24. [DOI: 10.1016/j.ympev.2014.07.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/21/2014] [Accepted: 07/29/2014] [Indexed: 11/23/2022]
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Nicola MV, Sede SM, Pozner R, Johnson LA. Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe. Ecol Evol 2014; 4:4270-86. [PMID: 25540689 PMCID: PMC4267866 DOI: 10.1002/ece3.1268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/04/2014] [Indexed: 11/22/2022] Open
Abstract
The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central-western and south-eastern Patagonia, consistent with long-term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.
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Affiliation(s)
- Marcela V Nicola
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Silvana M Sede
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Raúl Pozner
- Instituto de Botánica Darwinion C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina
| | - Leigh A Johnson
- Department of Biology and Bean Life Science Museum, Brigham Young University 4102 LSB, Provo, Utah, 84602, USA
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47
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Medina CD, Avila LJ, Sites JW, Morando M. Multilocus phylogeography of the Patagonian lizard complexLiolaemus kriegi(Iguania: Liolaemini). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cintia D. Medina
- Grupo de Herpetología Patagónica; CENPAT-CONICET; Boul. Almt. G. Brown U2915ACD Puerto Madryn Chubut Argentina
| | - Luciano J. Avila
- Grupo de Herpetología Patagónica; CENPAT-CONICET; Boul. Almt. G. Brown U2915ACD Puerto Madryn Chubut Argentina
| | - Jack W. Sites
- Biology Department; and Bean Life Science Museum; Brigham Young University; 695 WIDB Provo UT 84602 USA
| | - Mariana Morando
- Grupo de Herpetología Patagónica; CENPAT-CONICET; Boul. Almt. G. Brown U2915ACD Puerto Madryn Chubut Argentina
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48
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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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49
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Morando M, Medina CD, Avila LJ, Perez CHF, Buxton A, Sites JW. Molecular phylogeny of the New World gecko genusHomonota(Squamata: Phyllodactylidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12052] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariana Morando
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas; Boulevard Almirante Brown 2915 U9120ACD Puerto Madryn Chubut Argentina
| | - Cintia D. Medina
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas; Boulevard Almirante Brown 2915 U9120ACD Puerto Madryn Chubut Argentina
| | - Luciano J. Avila
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas; Boulevard Almirante Brown 2915 U9120ACD Puerto Madryn Chubut Argentina
| | - Cristian H. F. Perez
- Centro Nacional Patagónico - Consejo Nacional de Investigaciones Científicas y Técnicas; Boulevard Almirante Brown 2915 U9120ACD Puerto Madryn Chubut Argentina
| | - Amy Buxton
- Department of Biology and Bean Life Science Museum, 401 WIDB; Brigham Young University; Provo UT 84602 USA
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum, 401 WIDB; Brigham Young University; Provo UT 84602 USA
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50
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Diedericks G, Daniels SR. Ain’t no mountain high enough, ain’t no valley low enough? Phylogeography of the rupicolous Cape girdled lizard (Cordylus cordylus) reveals a generalist pattern. Mol Phylogenet Evol 2014; 71:234-48. [DOI: 10.1016/j.ympev.2013.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/11/2013] [Accepted: 10/18/2013] [Indexed: 10/26/2022]
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