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Oliver PM, Prasetya AM, Tedeschi LG, Fenker J, Ellis RJ, Doughty P, Moritz C. Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia. PeerJ 2020; 8:e7971. [PMID: 32025362 PMCID: PMC6991128 DOI: 10.7717/peerj.7971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022] Open
Abstract
For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
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Affiliation(s)
- Paul M Oliver
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, South Brisbane, QLD, Australia.,Biodiversity and Geosciences Programme, Queensland Museum, Brisbane, QLD, Australia
| | - Audrey Miranda Prasetya
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Jessica Fenker
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Ryan J Ellis
- Terrestrial Zoology, Western Australian Museum, Welshpool, WA, Australia.,Biologic Environmental Survey, East Perth, WA, Australia
| | - Paul Doughty
- Terrestrial Zoology, Western Australian Museum, Welshpool, WA, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
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Parks MB, Wickett NJ, Alverson AJ. Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta). Mol Biol Evol 2019; 35:80-93. [PMID: 29040712 PMCID: PMC5850769 DOI: 10.1093/molbev/msx268] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
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Affiliation(s)
- Matthew B Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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Ashman LG, Bragg JG, Doughty P, Hutchinson MN, Bank S, Matzke NJ, Oliver P, Moritz C. Diversification across biomes in a continental lizard radiation. Evolution 2018; 72:1553-1569. [PMID: 29972238 DOI: 10.1111/evo.13541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/23/2022]
Abstract
Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.
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Affiliation(s)
- L G Ashman
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - J G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Royal Botanic Garden, Sydney, NSW 2000, Australia
| | - P Doughty
- Department of Terrestrial Zoology, Western Australian Museum, Perth, WA 6016, Australia
| | - M N Hutchinson
- South Australian Museum, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
| | - S Bank
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen 37073, Germany
| | - N J Matzke
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - P Oliver
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, QLD 4101, Australia
| | - C Moritz
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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Hughes DF, Tolley KA, Behangana M, Lukwago W, Menegon M, Dehling JM, Stipala J, Tilbury CR, Khan AM, Kusamba C, Greenbaum E. Cryptic diversity in Rhampholeon boulengeri (Sauria: Chamaeleonidae), a pygmy chameleon from the Albertine Rift biodiversity hotspot. Mol Phylogenet Evol 2018; 122:125-141. [PMID: 29199108 PMCID: PMC6010225 DOI: 10.1016/j.ympev.2017.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 10/03/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R. boulengeri as a complex of at least six genetically distinct species. The spatiotemporal speciation patterns for these cryptic species conform to general biogeographic hypotheses supporting vicariance as the main factor behind patterns of divergence in the Albertine Rift, a biodiversity hotspot in Central Africa. However, we found that parapatric species and sister species inhabited adjacent habitats, but were found in largely non-overlapping elevational ranges in the Albertine Rift, suggesting that differentiation in elevation was also an important mode of divergence. The phylogeographic patterns recovered for the genus-level phylogeny provide additional evidence for speciation by isolation in forest refugia, and dating estimates indicated that the Miocene was a significant period for this diversification. Our results highlight the importance of investigating cryptic diversity in widespread species to improve understanding of diversification patterns in environmentally diverse regions such as the montane Afrotropics.
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Affiliation(s)
- Daniel F Hughes
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA.
| | - Krystal A Tolley
- South African National Biodiversity Institute, Private Bag X7, Claremont, Cape Town, South Africa; Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2000, Johannesburg, South Africa
| | - Mathias Behangana
- Department of Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Wilber Lukwago
- Department of Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Michele Menegon
- Tropical Biodiversity Section, MUSE - The Science Museum of Trento, Corso del Lavoro e della Scienza 3, Trento 38123, Italy
| | - J Maximilian Dehling
- Institut für Integrierte Naturwissenschaften, Abteilung Biologie, AG Zoologie, Universität Koblenz-Landau, Universitätsstraße 1, 56070 Koblenz, Germany
| | - Jan Stipala
- School of Biosciences, University of Exeter, Tremough Campus, Penryn, Cornwall TR10 9EZ, United Kingdom
| | - Colin R Tilbury
- Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - Arshad M Khan
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, Democratic Republic of the Congo
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
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Title PO, Rabosky DL. Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles. Syst Biol 2018; 66:843-856. [PMID: 27821703 DOI: 10.1093/sysbio/syw102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/27/2016] [Indexed: 01/03/2023] Open
Abstract
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 2017; 107:455-465. [DOI: 10.1016/j.ympev.2016.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022]
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