201
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New Approaches for Inferring Phylogenies in the Presence of Paralogs. Trends Genet 2021; 37:174-187. [DOI: 10.1016/j.tig.2020.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022]
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202
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Neretina AN, Karabanov DP, Sacherova V, Kotov AA. Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere. PeerJ 2021; 9:e10804. [PMID: 33585083 PMCID: PMC7860113 DOI: 10.7717/peerj.10804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 02/05/2023] Open
Abstract
Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
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Affiliation(s)
- Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- I.D. Papanin Institute for Biology of Inland Waters, Borok, Yaroslavl State, Russia
| | | | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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203
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204
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Zhu T, Yang Z. Complexity of the simplest species tree problem. Mol Biol Evol 2021; 38:3993-4009. [PMID: 33492385 PMCID: PMC8382899 DOI: 10.1093/molbev/msab009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 02/06/2023] Open
Abstract
The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here, we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood, and maximum likelihood. We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case, major differences exist among the methods. Full-likelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes,whereas these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation.
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Affiliation(s)
- Tianqi Zhu
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Ziheng Yang
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.,Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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205
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Zapelloni F, Pons J, Jurado-Rivera JA, Jaume D, Juan C. Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano. Sci Rep 2021; 11:366. [PMID: 33431936 PMCID: PMC7801522 DOI: 10.1038/s41598-020-79620-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Species diversification in ancient lakes has enabled essential insights into evolutionary theory as they embody an evolutionary microcosm compared to continental terrestrial habitats. We have studied the high-altitude amphipods of the Andes Altiplano using mitogenomic, nuclear ribosomal and single-copy nuclear gene sequences obtained from 36 Hyalella genomic libraries, focusing on species of the Lake Titicaca and other water bodies of the Altiplano northern plateau. Results show that early Miocene South American lineages have recently (late Pliocene or early Pleistocene) diversified in the Andes with a striking morphological convergence among lineages. This pattern is consistent with the ecological opportunities (access to unoccupied resources, initial relaxed selection on ecologically-significant traits and low competition) offered by the lacustrine habitats established after the Andean uplift.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain
| | - José A Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7'5, 07122, Palma de Mallorca, Balearic Islands, Spain.
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/ Miquel Marquès 21, 07190, Esporles, Balearic Islands, Spain.
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206
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Tamar K, Els J, Kornilios P, Soorae P, Tarroso P, Thanou E, Pereira J, Shah JN, Elhassan EEM, Aguhob JC, Badaam SF, Eltayeb MM, Pusey R, Papenfuss TJ, Macey JR, Carranza S. The demise of a wonder: Evolutionary history and conservation assessments of the Wonder Gecko Teratoscincus keyserlingii (Gekkota, Sphaerodactylidae) in Arabia. PLoS One 2021; 16:e0244150. [PMID: 33411750 PMCID: PMC7790289 DOI: 10.1371/journal.pone.0244150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/03/2020] [Indexed: 11/19/2022] Open
Abstract
Effective biodiversity conservation planning starts with genetic characterization within and among focal populations, in order to understand the likely impact of threats for ensuring the long-term viability of a species. The Wonder Gecko, Teratoscincus keyserlingii, is one of nine members of the genus. This species is distributed in Iran, Afghanistan, and Pakistan, with a small isolated population in the United Arab Emirates (UAE), where it is classified nationally as Critically Endangered. Within its Arabian range, anthropogenic activity is directly linked to the species’ decline, with highly localised and severely fragmented populations. Here we describe the evolutionary history of Teratoscincus, by reconstructing its phylogenetic relationships and estimating its divergence times and ancestral biogeography. For conservation implications of T. keyserlingii we evaluate the genetic structure of the Arabian population using genomic data. This study supports the monophyly of most species and reveals considerable intraspecific variability in T. microlepis and T. keyserlingii, which necessitate broad systematic revisions. The UAE population of T. keyserlingii likely arrived from southern Iran during the Pleistocene and no internal structure was recovered within, implying a single population status. Regional conservation of T. keyserlingii requires improved land management and natural habitat restoration in the species’ present distribution, and expansion of current protected areas, or establishment of new areas with suitable habitat for the species, mostly in northern Abu Dhabi Emirate.
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Affiliation(s)
- Karin Tamar
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
- * E-mail: (KT); (SC)
| | - Johannes Els
- Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Panagiotis Kornilios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
- The Molecular Ecology Backshop, G. Lekka, Loutraki, Greece
| | | | - Pedro Tarroso
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - Evanthia Thanou
- The Molecular Ecology Backshop, G. Lekka, Loutraki, Greece
- Section of Animal Biology, Department of Biology, School of Natural Sciences, University of Patras, Patras, Greece
| | - John Pereira
- Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Junid Nazeer Shah
- Natural Resource Conservation Section, Environment Department, Dubai Municipality, Dubai, United Arab Emirates
| | | | - Jeruel Cabadonga Aguhob
- Natural Resource Conservation Section, Environment Department, Dubai Municipality, Dubai, United Arab Emirates
| | - Saoud Faisal Badaam
- Natural Resource Conservation Section, Environment Department, Dubai Municipality, Dubai, United Arab Emirates
| | - Mohamed Mustafa Eltayeb
- Natural Resource Conservation Section, Environment Department, Dubai Municipality, Dubai, United Arab Emirates
| | | | - Theodore J. Papenfuss
- Museum of Vertebrate Zoology, Valley Life Sciences Building, University of California, Berkeley, CA, United States of America
| | - J. Robert Macey
- Peralta Genomics Institute, Chancellor’s Office, Peralta Community College District, Oakland, CA, United States of America
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
- * E-mail: (KT); (SC)
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207
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Jiang X, Edwards SV, Liu L. The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets. Syst Biol 2021; 69:795-812. [PMID: 32011711 PMCID: PMC7302055 DOI: 10.1093/sysbio/syaa008] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/30/2022] Open
Abstract
A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models. Although conducted on reduced data sets due to computational constraints, Bayesian model validation and comparison both strongly favor the MSC over concatenation across all data sets; the concatenation assumption of congruent gene trees rarely holds for phylogenomic data sets with more than 10 loci. Thus, for large phylogenomic data sets, model comparisons are expected to consistently and more strongly favor the coalescent model over the concatenation model. We also found that loci rejecting the MSC have little effect on species tree estimation. Our study reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference. [Bayes factor; Bayesian model validation; coalescent prior; congruent gene trees; independent prior; Metazoa; posterior predictive simulation.]
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Affiliation(s)
- Xiaodong Jiang
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Liang Liu
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA.,Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602, USA
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208
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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209
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Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
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210
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Garavello JC, Ramirez JL, Oliveira AKD, Britski HA, Birindelli JLO, Galetti Jr PM. Integrative taxonomy reveals a new species of Neotropical headstanding fish in genus Schizodon (Characiformes: Anostomidae). NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Schizodon encompasses approximately 15 species of Neotropical headstanding fishes. Integrative taxonomy, combining molecular and morphometric analyses with traditional taxonomic methods, was used to investigate Schizodon vittatus and its potential new sister species. Molecular differences between the two species in the barcode are greater than intra-specific variation recovered in species of Schizodon, and the two species represent distinct lineages for approximately one million years. The two species are morphologically very similar, and the meristic data showed great overlap. Morphometric analyses also showed overlap among the putative species but indicated differences in caudal-peduncle depth, orbital diameter, and length of anal-fin rays. Color pattern seems to provide a clear diagnostic feature for the two species. Schizodon vittatus usually has four dark brown transversal bars on body, and its sister species has three conspicuous bars, with the fourth, if present, inconspicuous and dorsal to the lateral line. Schizodon vittatus is redescribed based on the type and recently collected specimens, its type locality is revisited, and its known distribution restricted to the Araguaia and Tocantins drainages. The new species, sister to S. vittatus, distributed in the Xingu and Tapajós drainages, is described. A key for the identification of the Amazon clade species of Schizodon is provided.
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211
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First insight into cryptic diversity of a Caucasian subterranean amphipod of the genus Niphargus (Crustacea: Amphipoda: Niphargidae). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2020.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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212
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Le T, Sy A, Molloy EK, Zhang Q, Rao S, Warnow T. Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2-15. [PMID: 32750844 DOI: 10.1109/tcbb.2020.2990867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Incremental tree building (INC) is a new phylogeny estimation method that has been proven to be absolute fast converging under standard sequence evolution models. A variant of INC, called Constrained-INC, is designed for use in divide-and-conquer pipelines for phylogeny estimation where a set of species is divided into disjoint subsets, trees are computed on the subsets using a selected base method, and then the subset trees are combined together. We evaluate the accuracy of INC and Constrained-INC for gene tree and species tree estimation on simulated datasets, and compare it to similar pipelines using NJMerge (another method that merges disjoint trees). For gene tree estimation, we find that INC has very poor accuracy in comparison to standard methods, and even Constrained-INC(using maximum likelihood methods to compute constraint trees) does not match the accuracy of the better maximum likelihood methods. Results for species trees are somewhat different, with Constrained-INC coming close to the accuracy of the best species tree estimation methods, while being much faster; furthermore, using Constrained-INC allows species tree estimation methods to scale to large datasets within limited computational resources. Overall, this study exposes the benefits and limitations of divide-and-conquer strategies for large-scale phylogenetic tree estimation.
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213
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Koch H, DeGiorgio M. Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure. Genome Biol Evol 2020; 12:3977-3995. [PMID: 32022857 PMCID: PMC7061232 DOI: 10.1093/gbe/evaa022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 11/12/2022] Open
Abstract
Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI's performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.
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Affiliation(s)
- Hillary Koch
- Department of Statistics, Pennsylvania State University
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University
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214
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Miranda LS, Prestes BO, Aleixo A. Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.
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Affiliation(s)
- Leonardo S Miranda
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Ciências da Terra e Ecologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Bernardo O Prestes
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
| | - Alexandre Aleixo
- Programa de Pós-graduação em Zoologia – Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, PA, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, Brazil
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215
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Puntambekar S, Newhouse R, San-Miguel J, Chauhan R, Vernaz G, Willis T, Wayland MT, Umrania Y, Miska EA, Prabakaran S. Evolutionary divergence of novel open reading frames in cichlids speciation. Sci Rep 2020; 10:21570. [PMID: 33299045 PMCID: PMC7726158 DOI: 10.1038/s41598-020-78555-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/26/2020] [Indexed: 01/02/2023] Open
Abstract
Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al. analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.
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Affiliation(s)
- Shraddha Puntambekar
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Rachel Newhouse
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Jaime San-Miguel
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Ruchi Chauhan
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Grégoire Vernaz
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Thomas Willis
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Matthew T Wayland
- Department of Zoology, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Yagnesh Umrania
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Sudhakaran Prabakaran
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India.
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
- St. Edmund's College, University of Cambridge, Cambridge, CB3 0BN, UK.
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216
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Systematics and geographical distribution of Galba species, a group of cryptic and worldwide freshwater snails. Mol Phylogenet Evol 2020; 157:107035. [PMID: 33285288 DOI: 10.1016/j.ympev.2020.107035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/18/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Cryptic species can present a significant challenge to the application of systematic and biogeographic principles, especially if they are invasive or transmit parasites or pathogens. Detecting cryptic species requires a pluralistic approach in which molecular markers facilitate the detection of coherent taxonomic units that can then be analyzed using various traits (e.g., internal morphology) and crosses. In asexual or self-fertilizing species, the latter criteria are of limited use. We studied a group of cryptic freshwater snails (genus Galba) from the family Lymnaeidae that have invaded almost all continents, reproducing mainly by self-fertilization and transmitting liver flukes to humans and livestock. We aim to clarify the systematics, distribution, and phylogeny of these species with an integrative approach that includes morphology, molecular markers, wide-scale sampling across America, and data retrieved from GenBank (to include Old World samples). Our phylogenetic analysis suggests that the genus Galba originated ca. 22 Myr ago and today comprises six species or species complexes. Four of them show an elongated-shell cryptic phenotype and exhibit wide variation in their genetic diversity, geographic distribution, and invasiveness. The remaining two species have more geographically restricted distributions and exhibit a globose-shell cryptic phenotype, most likely phylogenetically derived from the elongated one. We emphasize that no Galba species should be identified without molecular markers. We also discuss several hypotheses that can explain the origin of cryptic species in Galba, such as convergence and morphological stasis.
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217
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations. Proc Natl Acad Sci U S A 2020; 117:32509-32518. [PMID: 33277432 DOI: 10.1073/pnas.2001018117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second-largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this, we generated genome-wide sequence data for >700 individuals of seven codistributed plants from Lower Guinea in Central Africa. We inferred species' evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors, including climate, soil, and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging, and more emphasis is needed on species ecology to better conserve TRFs worldwide.
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218
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De La Harpe M, Paris M, Hess J, Barfuss MHJ, Serrano-Serrano ML, Ghatak A, Chaturvedi P, Weckwerth W, Till W, Salamin N, Wai CM, Ming R, Lexer C. Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation. PLANT, CELL & ENVIRONMENT 2020; 43:2987-3001. [PMID: 32677061 DOI: 10.1111/pce.13847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/28/2020] [Accepted: 07/05/2020] [Indexed: 05/24/2023]
Abstract
The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by shifts in several adaptive traits or "key innovations" including the transition from C3 to CAM photosynthesis associated with xeric (heat/drought) adaptation. We used phylogenomic approaches, complemented by differential gene expression (RNA-seq) and targeted metabolite profiling, to address the mechanisms of C3 /CAM evolution in the extremely species-rich bromeliad genus, Tillandsia, and related taxa. Evolutionary analyses of whole-genome sequencing and RNA-seq data suggest that evolution of CAM is associated with coincident changes to different pathways mediating xeric adaptation in this group. At the molecular level, C3 /CAM shifts were accompanied by gene expansion of XAP5 CIRCADIAN TIMEKEEPER homologs, a regulator involved in sugar- and light-dependent regulation of growth and development. Our analyses also support the re-programming of abscisic acid-related gene expression via differential expression of ABF2/ABF3 transcription factor homologs, and adaptive sequence evolution of an ENO2/LOS2 enolase homolog, effectively tying carbohydrate flux to abscisic acid-mediated abiotic stress response. By pinpointing different regulators of overlapping molecular responses, our results suggest plausible mechanistic explanations for the repeated evolution of correlated adaptive traits seen in a textbook example of an adaptive radiation.
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Affiliation(s)
- Marylaure De La Harpe
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland
| | - Margot Paris
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Michael Harald Johannes Barfuss
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | | | - Arindam Ghatak
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology (MOSYS), Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Nicolas Salamin
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ching Man Wai
- Department of Horticulture, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Ray Ming
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christian Lexer
- Department of Botany and Biodiversity Research, Division of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland
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219
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Garrido-Benavent I, Pérez-Ortega S, de Los Ríos A, Mayrhofer H, Fernández-Mendoza F. Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica. Mol Phylogenet Evol 2020; 155:107020. [PMID: 33242583 DOI: 10.1016/j.ympev.2020.107020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/07/2020] [Accepted: 11/17/2020] [Indexed: 11/25/2022]
Abstract
Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth's continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through "mountain-hopping" during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.
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Affiliation(s)
- Isaac Garrido-Benavent
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Serrano 115 dpdo, E-28045 Madrid, Spain; Institute of Plant Sciences, Karl-Franzens-Universität Graz, Graz A-8010, Austria.
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Serrano 115 dpdo, E-28045 Madrid, Spain
| | - Helmut Mayrhofer
- Institute of Plant Sciences, Karl-Franzens-Universität Graz, Graz A-8010, Austria
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220
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Pons J, Campión D, Chiozzi G, Ettwein A, Grangé J, Kajtoch Ł, Mazgajski TD, Rakovic M, Winkler H, Fuchs J. Phylogeography of a widespread Palaearctic forest bird species: The White‐backed Woodpecker (Aves, Picidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean‐Marc Pons
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
| | - David Campión
- Área de Biodiversidad, Biodibertsitate Arloa, Padre Adoain Pamplona‐Iruñea Spain
| | | | | | | | - Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences Kraków Poland
| | | | | | - Hans Winkler
- Department of Integrative Biology and Evolution Konrad Lorenz‐Institute of Ethology Vienna Austria
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
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221
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Degueldre F, Mardulyn P, Kuhn A, Pinel A, Karaman C, Lebas C, Schifani E, Bračko G, Wagner HC, Kiran K, Borowiec L, Passera L, Abril S, Espadaler X, Aron S. Evolutionary history of inquiline social parasitism in Plagiolepis ants. Mol Phylogenet Evol 2020; 155:107016. [PMID: 33242582 DOI: 10.1016/j.ympev.2020.107016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 11/29/2022]
Abstract
Social parasitism, i.e. the parasitic dependence of a social species on another free-living social species, is one of the most intriguing phenomena in social insects. It has evolved to various levels, the most extreme form being inquiline social parasites which have lost the worker caste, and produce only male and female sexual offspring that are reared by the host worker force. The inquiline syndrome has been reported in 4 species within the ant genus Plagiolepis, in Europe. Whether inquiline social parasitism evolved once or multiple times within the genus remains however unknown. To address this question, we generated data for 5 inquiline social parasites - 3 species previously described and 2 unidentified species - and their free-living hosts from Europe, and we inferred their phylogenetic relationships. We tested Emery's rule, which predicts that inquiline social parasites and their hosts are close relatives. Our results show that inquiline parasitism evolved independently at least 5 times in the genus. Furthermore, we found that all inquilines were associated with one of the descendants of their most related free-living species, suggesting sympatric speciation is the main process leading to the emergence of the parasitic species, consistent with the stricter version of Emery's rule.
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Affiliation(s)
- Félicien Degueldre
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium.
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexandre Kuhn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Amélie Pinel
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Celal Karaman
- Trakya University, Faculty of Science, Department of Biology, Balkan Campus, 22030 Edirne, Turkey
| | | | - Enrico Schifani
- Department of Chemistry, Life Sciences & Environmental Sustainability, Parco Area delle Scienze, 11/a, University of Parma, I-43124 Parma, Italy
| | - Gregor Bračko
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Herbert C Wagner
- ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria
| | - Kadri Kiran
- Trakya University, Faculty of Science, Department of Biology, Balkan Campus, 22030 Edirne, Turkey
| | - Lech Borowiec
- Department of Biodiversity and Evolutionary Taxonomy, University of Wrocław, Wrocław, Poland
| | - Luc Passera
- Université Paul Sabatier de Toulouse, France
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, M. Aurèlia Campmany, 69, 17003 Girona, Spain
| | - Xavier Espadaler
- CREAF, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Serge Aron
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
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222
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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223
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Alves PV, Chambrier A, Luque JL, Scholz T. Integrative taxonomy reveals hidden cestode diversity in
Pimelodus
catfishes in the Neotropics. ZOOL SCR 2020. [DOI: 10.1111/zsc.12465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Philippe V. Alves
- Departamento de Parasitologia Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Alain Chambrier
- Department of Invertebrates Natural History Museum Geneva Switzerland
| | - José L. Luque
- Departamento de Parasitologia Animal Universidade Federal Rural do Rio de Janeiro Seropédica Brazil
| | - Tomáš Scholz
- Institute of Parasitology Biology Centre of the Academy of Sciences of the Czech Republic České Budějovice Czech Republic
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224
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A yeast living ancestor reveals the origin of genomic introgressions. Nature 2020; 587:420-425. [PMID: 33177709 DOI: 10.1038/s41586-020-2889-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/11/2020] [Indexed: 11/08/2022]
Abstract
Genome introgressions drive evolution across the animal1, plant2 and fungal3 kingdoms. Introgressions initiate from archaic admixtures followed by repeated backcrossing to one parental species. However, how introgressions arise in reproductively isolated species, such as yeast4, has remained unclear. Here we identify a clonal descendant of the ancestral yeast hybrid that founded the extant Saccharomyces cerevisiae Alpechin lineage5, which carries abundant Saccharomyces paradoxus introgressions. We show that this clonal descendant, hereafter defined as a 'living ancestor', retained the ancestral genome structure of the first-generation hybrid with contiguous S. cerevisiae and S. paradoxus subgenomes. The ancestral first-generation hybrid underwent catastrophic genomic instability through more than a hundred mitotic recombination events, mainly manifesting as homozygous genome blocks generated by loss of heterozygosity. These homozygous sequence blocks rescue hybrid fertility by restoring meiotic recombination and are the direct origins of the introgressions present in the Alpechin lineage. We suggest a plausible route for introgression evolution through the reconstruction of extinct stages and propose that genome instability allows hybrids to overcome reproductive isolation and enables introgressions to emerge.
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225
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Lovrenčić L, Bonassin L, Boštjančić LL, Podnar M, Jelić M, Klobučar G, Jaklič M, Slavevska-Stamenković V, Hinić J, Maguire I. New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications. BMC Evol Biol 2020; 20:146. [PMID: 33158414 PMCID: PMC7648294 DOI: 10.1186/s12862-020-01709-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Background Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups. Results Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units. Conclusions Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.
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Affiliation(s)
- Leona Lovrenčić
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Lena Bonassin
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Ljudevit Luka Boštjančić
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Martina Podnar
- Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Mišel Jelić
- Department of Natural Sciences, Varaždin City Museum, Franjevački trg 10, 42000, Varaždin, Croatia
| | - Göran Klobučar
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Martina Jaklič
- Center for Clinical Research, University Medical Centre Ljubljana, Zaloška 2, 1000, Ljubljana, Slovenia
| | - Valentina Slavevska-Stamenković
- Department of Invertebrates and Animal Ecology, Faculty of Natural Sciences and Mathematics, University "St. Cyril and Methodius", Arhimedova 3, 1000, Skopje, Republic of North Macedonia
| | - Jelena Hinić
- Department of Invertebrates and Animal Ecology, Faculty of Natural Sciences and Mathematics, University "St. Cyril and Methodius", Arhimedova 3, 1000, Skopje, Republic of North Macedonia
| | - Ivana Maguire
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
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226
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Zhang C, Scornavacca C, Molloy EK, Mirarab S. ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Mol Biol Evol 2020; 37:3292-3307. [PMID: 32886770 PMCID: PMC7751180 DOI: 10.1093/molbev/msaa139] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees. However, most of these methods, including the widely used ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. As a result, most phylogenomic studies have focused on single-copy genes and have discarded large parts of the data. Here, we first propose a measure of quartet similarity between single-copy and multicopy trees that accounts for orthology and paralogy. We then introduce a method called ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree that optimizes our quartet similarity measure using dynamic programing. By studying its performance on an extensive collection of simulated data sets and on real data sets, we show that ASTRAL-Pro is more accurate than alternative methods.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA
| | | | - Erin K Molloy
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA
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227
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Menezes L, Batalha‐Filho H, Garda AA, Napoli M. Tiny treefrogs in the Pleistocene: Phylogeography of
Dendropsophus oliveirai
in the Atlantic Forest and associated enclaves in northeastern Brazil. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lucas Menezes
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | - Henrique Batalha‐Filho
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis ‐ LAR Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Marcelo Napoli
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
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228
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Freitas TMB, Sales JBL, Sampaio I, Piorski NM, Weber LN. Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers. BRAZ J BIOL 2020; 81:855-866. [PMID: 33111926 DOI: 10.1590/1519-6984.225646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 05/04/2020] [Indexed: 11/22/2022] Open
Abstract
The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.
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Affiliation(s)
- T M B Freitas
- Universidade Federal do Maranhão - UFMA, Departamento de Biologia, Laboratório de Ecologia e Sistemática de Peixes, Programa de Pós-graduação Bionorte, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, São Luís, MA, Brasil
| | - J B L Sales
- Universidade Federal do Pará - UFPA, Centro de Estudos Avançados da Biodiversidade - CEABIO, Programa de Pós-graduação em Ecologia Aquática e Pesca - PPGEAP, Grupo de Investigação Biológica Integrada - GIBI, Belém, PA, Brasil
| | - I Sampaio
- Universidade Federal do Pará - UFPA, Instituto de Estudos Costeiros - IECOS, Laboratório e Filogenomica e Bioinformatica, Programa de Pós-graduação Biologia Ambiental - PPBA, Grupo de Estudos em Genética e Filogenômica, Bragança, PA, Brasil
| | - N M Piorski
- Universidade Federal do Maranhão - UFMA, Departamento de Biologia, Laboratório de Ecologia e Sistemática de Peixes, Programa de Pós-graduação Bionorte, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, São Luís, MA, Brasil
| | - L N Weber
- Universidade Federal do Sul da Bahia - UFSB, Centro de Formação em Ciências Ambientais, Instituto Sosígenes Costa de Humanidades, Artes e Ciências, Departamento de Ciências Biológicas, Laboratório de Zoologia, Programa de Pós-graduação Bionorte, Grupo Biodiversidade da Fauna do Sul da Bahia, Porto Seguro, BA, Brasil
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229
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Nuñez JJ, Suárez-Villota EY, Quercia CA, Olivares AP, Sites JW. Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia. PeerJ 2020; 8:e9980. [PMID: 33083116 PMCID: PMC7546244 DOI: 10.7717/peerj.9980] [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: 03/24/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.
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Affiliation(s)
- José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Elkin Y Suárez-Villota
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Concepción, Región del Bio-Bío, Chile
| | - Camila A Quercia
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Angel P Olivares
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, UT, United States of America.,Current affiliation: Department of Biology, Austin Peay St University, Clarksville, TN, United States of America
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230
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García-Martínez RM, de Los Angeles Barriga-Sosa I, López B, Mejía O. "Colonization routes and demographic history of Chirostoma humboldtianum in the central Mexican plateau". JOURNAL OF FISH BIOLOGY 2020; 97:1039-1050. [PMID: 32658333 DOI: 10.1111/jfb.14462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico.
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Affiliation(s)
- Rosa María García-Martínez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Irene de Los Angeles Barriga-Sosa
- Laboratorio de Genética y Biología Molecular de la Planta Experimental de Producción Acuícola, Departamento de Hidrobiología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - Benjamín López
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Omar Mejía
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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231
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Bassitta M, Buades JM, Pérez‐Cembranos A, Pérez‐Mellado V, Terrasa B, Brown RP, Navarro P, Lluch J, Ortega J, Castro JA, Picornell A, Ramon C. Multilocus and morphological analysis of south‐eastern Iberian Wall lizards (Squamata,
Podarcis
). ZOOL SCR 2020. [DOI: 10.1111/zsc.12450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Bassitta
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Joana M. Buades
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | | | | | - Barbara Terrasa
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Richard P. Brown
- School of Biological & Environmental Sciences Liverpool John Moores University Liverpool United Kingdom
| | - Pilar Navarro
- Departamento de Zoología Facultad de Ciencias Biológicas Universitat de València Valencia Spain
| | - Javier Lluch
- Departamento de Zoología Facultad de Ciencias Biológicas Universitat de València Valencia Spain
| | - Jesús Ortega
- Evolutionary Ecology Unit Department of Biology Lund University Lund Sweden
| | - Jose A. Castro
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Antònia Picornell
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Cori Ramon
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
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232
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Chen J, Zeng YF, Zhang DY. Dispersal as a result of asymmetrical hybridization between two closely related oak species in China. Mol Phylogenet Evol 2020; 154:106964. [PMID: 32956798 DOI: 10.1016/j.ympev.2020.106964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022]
Abstract
Hybridization has played an important role in plant evolution. Less attention has been paid, however, to its role in dispersal. In this study, historical divergence and hybridization were investigated in two closely related Chinese oaks, Quercus mongolica and Q. liaotungensis, to estimate the role that hybridization played in their dispersal. We genotyped 27 Q. mongolica and Q. liaotungensis populations throughout the distributional range of the two oak species, using 14 single-copy nuclear genes and four noncoding chloroplast DNA regions. Bayesian cluster and population tree analyses indicated that there were three groups over all oak populations, namely, Q. mongolica, northwest-northern China (NW-NC) Q. liaotungensis, and northeastern China (NEC) Q. liaotungensis. Approximate Bayesian computation simulation supported an asymmetrical hybridization origin of NEC Q. liaotungensis, after a previous divergence between NW-NC Q. liaotungensis and Q. mongolica. IMa3 analyses suggested that Q. liaotungensis and Q. mongolica diverged in the NW-NC and NEC regions, respectively, and that NEC Q. liaotungensis arose from Q. mongolica, not from NW-NC Q. liaotungensis, and was greatly introgressed by NW-NC Q. liaotungensis. Oak populations in NW-NC and NEC regions held different chloroplast DNA haplotypes, and Q. liaotungensis in NEC shared most haplotypes with Q. mongolica populations, but none with NW-NC Q. liaotungensis populations, suggesting the maternal origin of NEC Q. liaotungensis from Q. mongolica. This study found clear signals of isolation divergence of Q. liaotungensis in NW-NC and Q. mongolica in NEC, and the results suggest that asymmetrical hybridization and introgression from Q. liaotungensis to Q. mongolica, mostly likely via pollen flow, facilitated Q. liaotungensis dispersal to NEC.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yan-Fei Zeng
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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233
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Cheng J, Xia L, Feijó A, Shenbrot GI, Wen Z, Ge D, Lu L, Yang Q. Phylogeny, taxonomic reassessment and ‘ecomorph’ relationship of the Orientallactaga sibirica complex (Rodentia: Dipodidae: Allactaginae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The ecological gradient–morphological variation (‘ecomorph’) relationship has long interested ecologists and evolutionary biologists, but it is applied far less frequently than genetic differentiation in cryptic species detection and species identification. With integrative methods, we revise taxonomic uncertainties in the Orientallactaga sibirica complex (OSC), with 298 sequence specimens and 469 voucher specimens from 138 localities covering nearly the entire distribution of the OSC. Phylogenetic relationships are assessed by Bayesian inference and maximum likelihood using two mitochondrial and nine nuclear genes. We use species-delimitation approaches to divide and validate the ‘candidate species’. We evaluate correlations between ecological divergence and phylogenetic splits, and visualize geographical patterns of morphological variation. The OSC is divided into four phylogenetic groups, the Ognevi, Altay, Bogda and Sibirica groups, and the OSC exhibits a significant ecomorph relationship and ecological divergence pattern. Morphological variations not only follow the general regularity under a large gradient of ecological factors, but are also closely related to the local environment/habitat. We suggest considering the comprehensive ecomorph relationship to identify species. Molecular analyses reveal that the OSC more easily forms deeply divergent lineages in the foothills and this differentiation depth may be related to mountain system size.
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Affiliation(s)
- Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Georgy I Shenbrot
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Changping District, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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234
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Mello B, Tao Q, Barba-Montoya J, Kumar S. Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour 2020; 21:122-136. [PMID: 32881388 DOI: 10.1111/1755-0998.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer-simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.
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Affiliation(s)
- Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Brazil.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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235
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An integrative approach assesses the intraspecific variations of Procamallanus ( Spirocamallanus) inopinatus, a common parasite in Neotropical freshwater fishes, and the phylogenetic patterns of Camallanidae. Parasitology 2020; 147:1752-1764. [PMID: 32921341 DOI: 10.1017/s0031182020001687] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Integrative taxonomy was used to evaluate two component populations of Procamallanus (Spirocamallanus) inopinatus in Brazil and the phylogeny Camallanidae. Parasite populations were collected in the characiform Anostomoides passionis from River Xingu (Amazon basin) and Megaleporinus elongatus from River Miranda (Paraguay basin). Morphology was analysed using light and scanning electron microscopy (SEM). Genetic characterization was based on partial sequences of the 18S and 28S rDNA, and COI mtDNA. Phylogenies were based on 18S and COI due to data availability. Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (PTP) and *BEAST were used for species delimitation and validation. SEM revealed for the first time the presence of minute denticles and pore-like structures surrounding the oral opening, phasmids in females and confirmed other important morphological aspects. Statistical comparison between the two-component populations indicated morphometric variations, especially among males. The different component population of P. (S.) inopinatus showed variable morphometry, but uniform morphology and were validated as conspecific by the GMYC, PTP and *BEAST. Some camallanid sequences in GenBank have incorrect taxonomic labelling. Host, environment and geographic aspects seem to be related to some lineages within Camallanidae; however, their real phylogenetic meanings are still unclear.
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236
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Molecular phylogeny and species delimitation of the genus Schizodon (Characiformes, Anostomidae). Mol Phylogenet Evol 2020; 153:106959. [PMID: 32920128 DOI: 10.1016/j.ympev.2020.106959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022]
Abstract
The genus Schizodon is part of a group of headstanders and relatives (Family Anostomidae) that are widespread and ecologically important fishes in South American rivers. Schizodon includes 15 nominal species but their taxonomy has been challenging due to paucity of decisive characters to diagnose species. We present new molecular data to assess species boundaries or molecular operational taxonomic units (MOTUs), and to infer phylogenetic relationships among species. Evidence from two mitochondrial and three nuclear genes was used in these analyses. Mitochondrial DNA data for 112 specimens (from 11 nominal species) supported 13 consensus MOTUs, six of which matched valid nominal species (Schizodon borellii, S. fasciatus, S. intermedius, S. isognathus, S. knerii and S. scotorhabdotus). The nominal species Schizodon vittatus, S. nasutus, and S. dissimilis were subdivided into two MOTUs each, revealing either cryptic species or strong population structuring. In contrast, S. platae and S. jacuiensis constituted a single MOTU, indicating a possible case of synonymy. Our phylogenetic analysis subdivided the genus Schizodon into two large clades that are compatible with observed color patterns and biogeographic distribution. The first clade includes species with three to four conspicuous dark vertical bars on the flanks that originated in the Amazonas region (S. borellii, S. dissimilis, S. intermedius, S. fasciatus, S. scotorhabdotus, S. vittatus, and a cryptic species, Schizodon aff. vittatus). The second clade includes species with a conspicuous dark caudal blotch on the caudal peduncle, with vertical bars absent or inconspicuous, with a biogeographic origin in the La Plata drainage (S. isognathus, S. jacuiensis, S. knerii, S. nasutus and S. platae). Our results reinforce the importance of using molecular analyses to accelerate the study of diversity, particularly in groups with a wide distribution, few variable meristic characters, and high morphological plasticity, which may hide still unknown or underestimated diversity.
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237
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Rengifo‐Correa L, Abad‐Franch F, Martínez‐Hernández F, Salazar‐Schettino PM, Téllez‐Rendón JL, Villalobos G, Morrone JJ. A biogeographic–ecological approach to disentangle reticulate evolution in the
Triatoma phyllosoma
species group (Heteroptera: Triatominae), vectors of Chagas disease. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12409] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Laura Rengifo‐Correa
- Departamento de Biología Evolutiva Facultad de Ciencias Museo de Zoología ‘Alfonso L. Herrera’Universidad Nacional Autónoma de México Mexico City Mexico
| | - Fernando Abad‐Franch
- Programa de Pós‐graduação em Medicina Tropical Núcleo de Medicina Tropical Facultade Medicina Universidade de Brasília Brasília Brazil
| | | | - Paz M. Salazar‐Schettino
- Laboratorio de Biología de Parásitos Departamento de Microbiología y Parasitología Facultad de Medicina Universidad Nacional Autónoma de México Mexico City Mexico
| | | | - Guiehdani Villalobos
- Departamento de Ecología de Agentes Patógenos Hospital General Dr. Manuel Gea González Mexico City Mexico
| | - Juan J. Morrone
- Departamento de Biología Evolutiva Facultad de Ciencias Museo de Zoología ‘Alfonso L. Herrera’Universidad Nacional Autónoma de México Mexico City Mexico
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238
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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239
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Doyle ED, Prates I, Sampaio I, Koiffmann C, Silva WA, Carnaval AC, Harris EE. Molecular phylogenetic inference of the howler monkey radiation (Primates: Alouatta). Primates 2020; 62:177-188. [PMID: 32876810 DOI: 10.1007/s10329-020-00854-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Howler monkeys (Alouatta), comprising between nine and 14 species and ranging from southern Mexico to northern Argentina, are the most widely distributed platyrrhines. Previous phylogenetic studies of howlers have used chromosomal and morphological characters and a limited number of molecular markers; however, branching patterns conflict between studies or remain unresolved. We performed a new phylogenetic analysis of Alouatta using both concatenated and coalescent-based species tree approaches based on 14 unlinked non-coding intergenic nuclear regions. Our taxon sampling included five of the seven South American species (Alouatta caraya, Alouatta belzebul, Alouatta guariba, Alouatta seniculus, Alouatta sara) and the two recognized species from Mesoamerica (Alouatta pigra, Alouatta palliata). Similarly to previous studies, our phylogenies supported a Mesoamerican clade and a South American clade. For the South American howlers, both methods recovered the Atlantic Forest endemic A. guariba as sister to all remaining South American species, albeit with moderate support. Moreover, we found no support for the previously proposed sister relationship between A. guariba and A. belzebul. For the first time, a clade composed of A. sara and A. caraya was identified. The relationships among the other South American howlers, however, were not fully supported. Our estimates for divergence times within Alouatta are generally older compared to estimates in earlier studies. However, they conform to recent studies proposing a Miocene age for the Isthmus of Panama and for the uplift of the northern Andes. Our results also point to an early genetic isolation of A. guariba in the Atlantic Forest, in agreement with the hypothesis of biotic exchange across South American rain forests in the Miocene. Collectively, these findings contribute to a better understanding of the diversification processes among howler monkey species; however, they also suggest that further comprehension of the evolutionary history of the Alouatta radiation will rely on broadened taxonomic, geographic, and genomic sampling.
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Affiliation(s)
| | - Ivan Prates
- Department of Biology, City College of New York, New York, NY, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal Do Pará, Campus de Bragança, Belém, PA, Brazil
| | - Celia Koiffmann
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Wilson Araujo Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, NY, USA
- The Graduate Center, The City University of New York, New York, NY, USA
| | - Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, The City University of New York, New York, NY, USA.
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Möller M, Liu J, Li Y, Li JH, Ye LJ, Mill R, Thomas P, Li DZ, Gao LM. Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.). Mol Phylogenet Evol 2020; 153:106952. [PMID: 32889136 DOI: 10.1016/j.ympev.2020.106952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 07/19/2020] [Accepted: 08/28/2020] [Indexed: 12/24/2022]
Abstract
The genus Taxus (Taxaceae) consists of 16 genetically well-defined lineages that are predominantly distributed across the Northern hemisphere. We investigated its biogeographic origin and evolutionary history by sampling 13 chloroplast gene sequences, the nuclear internal transcribed spacers (ITS) and NEEDLY sequences for all 16 lineages. We applied Maximum Parsimony and Bayesian Inference analyses to infer their phylogenetic relationships, time-calibrated phylogenies using BEAST and inferred the ancestral area of occupancy with BioGeoBEARS. We found strong evidence for the hybrid origin of three lineages and dated these events to a rather narrow time window of 6.8-4.9 million years ago (Mya). The dated phylogenies inferred an Upper Cretaceous origin of the genus, with the extant lineages diversifying in North America much later during the Oligocene/early Miocene. Repeated migrations via the Bering land bridge to Eurasia and back were further inferred, with the return to North America as a possible result of vicariance. The diversification in Eurasia (from ~8 Mya onwards) coincided with the orogeny of the Hengduan Mountains, the intensification of the East Asian summer monsoon and the occupancy of ecological niches by lineages that experienced secondary contacts and hybridizations in the Hengduan Mountains and Qinling Mountain, especially around the Sichuan basin. We provide a hypothesis for the evolution of extant lineages of Taxus, a genus with an old and complex evolutionary history. The study highlights that the history of complex species can be unravelled with a careful dissection of phylogenetic signals.
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Affiliation(s)
- Michael Möller
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom.
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yan Li
- Institute of Alpine Economic Plants, Yunnan Academy of Agricultural Sciences, Lijiang, Yunnan 674100, China
| | - Jian-Hua Li
- Biology Department, Hope College, Holland, MI 49423, USA
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Robert Mill
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Philip Thomas
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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241
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Linscott TM, Weaver K, Morales V, Parent CE. Assessing species number and genetic diversity of the Mountainsnails (Oreohelicidae). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01302-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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242
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Dong F, Li SH, Chiu CC, Dong L, Yao CT, Yang XJ. Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Mol Phylogenet Evol 2020; 153:106941. [PMID: 32818596 DOI: 10.1016/j.ympev.2020.106941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chi-Cheng Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Endemic Species Research Institute, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan.
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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243
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Grond K, Bell KC, Demboski JR, Santos M, Sullivan JM, Hird SM. No evidence for phylosymbiosis in western chipmunk species. FEMS Microbiol Ecol 2020; 96:5626339. [PMID: 31730167 DOI: 10.1093/femsec/fiz182] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.
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Affiliation(s)
- Kirsten Grond
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA
| | - Kayce C Bell
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave, NW, Washington, DC, 20560, USA
| | - John R Demboski
- Zoology Department, Denver Museum of Nature & Science, 2001 Colorado Blvd, Denver, CO, 80205, USA
| | - Malia Santos
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Jack M Sullivan
- Department of Biological Sciences, University of Idaho, Life Sciences South 252, Moscow, ID, 83844, USA
| | - Sarah M Hird
- Department of Molecular & Cell Biology, University of Connecticut, 91 N Eagleville Rd, Storrs, CT, 06269, USA.,Institute of Systems Genomics, University of Connecticut, 67 N Eagleville Rd, Storrs, CT, 06269, USA
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244
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Leavitt DH, Hollingsworth BD, Fisher RN, Reeder TW. Introgression obscures lineage boundaries and phylogeographic history in the western banded gecko, Coleonyx variegatus (Squamata: Eublepharidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe geomorphological formation of the Baja California peninsula and the Gulf of California is a principal driver of diversification for the reptiles of North America’s warm deserts. The western banded gecko, Coleonyx variegatus, is distributed throughout the Mojave, Sonoran and Peninsular deserts. In this study we use multilocus sequence data to address deep phylogeographic structure within C. variegatus. Analyses of mtDNA data recover six divergent clades throughout the range of C. variegatus. Topology of the mtDNA gene tree suggests separate origins of peninsular populations with an older lineage in the south and a younger one in the north. In contrast, analyses of multilocus nuclear data provide support for four lineages, corresponding to the subspecies C. v. abbotti, C. v. peninsularis, C. v. sonoriensis and C. v. variegatus. Phylogenetic analyses of the nuclear data recover C. v. abbotti and C. v. peninsularis as a clade, indicating a single origin of the peninsular populations. Discordance between the nuclear and mtDNA data is largely the result of repeated episodes of mtDNA introgression that have obscured both lineage boundaries and biogeographic history. Dating analyses of the combined nuclear and mtDNA data suggest that the peninsular clade diverged from the continental group in the Late Miocene.
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Affiliation(s)
| | - Bradford D Hollingsworth
- San Diego State University, San Diego, CA, USA
- San Diego Natural History Museum, El Prado, San Diego, CA, USA
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245
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Yan P, Pan T, Wu G, Kang X, Ali I, Zhou W, Li J, Wu X, Zhang B. Species Delimitation and Evolutionary History of Tree Frogs in the Hyla chinensis Group (Hylidae, Amphibian). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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246
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Yourdkhani S, Rhodes JA. Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance. Bull Math Biol 2020; 82:97. [PMID: 32676801 DOI: 10.1007/s11538-020-00773-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022]
Abstract
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these weights, and shown to exactly fit the same tree topology, but with edge weights rescaled by certain factors dependent on the associated split size. These distances are analogs for metric trees of similar ones recently introduced for topological trees that are based on induced unweighted rooted triples and quartets. The distances introduced here lead to new statistically consistent methods of inferring a metric species tree from a collection of topological gene trees generated under the multispecies coalescent model of incomplete lineage sorting. Simulations provide insight into their potential.
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Affiliation(s)
- Samaneh Yourdkhani
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, 99775, USA
| | - John A Rhodes
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, 99775, USA.
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247
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Marin J, Achaz G, Crombach A, Lambert A. The genomic view of diversification. J Evol Biol 2020; 33:1387-1404. [PMID: 32654283 DOI: 10.1111/jeb.13677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/11/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The process of species diversification is traditionally summarized by a single tree, the species tree, whose reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Here, we argue that instead of seeing these conflicts as nuisances, we can exploit them to inform the diversification process itself. We adopt a gene-based view of diversification to model the ubiquitous presence of gene flow between diverging lineages, one of the most important processes explaining disagreements among gene trees. We propose a new framework for modelling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees inherent to the standard view, as embodied in a popular model known as the multispecies coalescent (MSC). We implement this framework in two alternative models called the gene-based diversification models (GBD): (a) GBD-forward following all evolving genomes through time and (b) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose an inference method based on differences between gene trees. Applied to two empirical data sets prone to gene flow, we find better support for the GBD-backward model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.
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Affiliation(s)
- Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France
| | - Guillaume Achaz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Inria, Lyon Antenne La Doua, Villeurbanne, France.,INSA-Lyon, LIRIS, UMR 5205, Université de Lyon, Villeurbanne, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), CNRS UMR 8001, Sorbonne Université, Paris, France
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248
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Huang J, Flouri T, Yang Z. A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model. Mol Biol Evol 2020; 37:3211-3224. [DOI: 10.1093/molbev/msaa166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
AbstractWe use computer simulation to examine the information content in multilocus data sets for inference under the multispecies coalescent model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes, and cross-species introgression probabilities), species tree estimation, and species delimitation based on Bayesian comparison of delimitation models. We found that the number of loci is the most influential factor for almost all inference problems examined. Although the number of sequences per species does not appear to be important to species tree estimation, it is very influential to species delimitation. Increasing the number of sites and the per-site mutation rate both increase the mutation rate for the whole locus and these have the same effect on estimation of parameters, but the sequence length has a greater effect than the per-site mutation rate for species tree estimation. We discuss the computational costs when the data size increases and provide guidelines concerning the subsampling of genomic data to enable the application of full-likelihood methods of inference.
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Affiliation(s)
- Jun Huang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Mathematics, Beijing Jiaotong University, Beijing, P.R. China
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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249
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Palmerín‐Serrano PN, Tavera J, Espinoza E, Angulo A, Martínez‐Gómez JE, González‐Acosta AF, Domínguez‐Domínguez O. Evolutionary history of the reef fish
Anisotremus interruptus
(Perciformes: Haemulidae) throughout the Tropical Eastern Pacific. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paola Nallely Palmerín‐Serrano
- Programa Institucional de Maestría en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - Jose Tavera
- Laboratorio de Ictiología Departamento de Biología Universidad del Valle Cali Colombia
| | - Eduardo Espinoza
- Investigación Marina Aplicada Parque Nacional Galápagos “Charles Darwin” Puerto Ayora Isla Santa Cruz Ecuador
| | - Arturo Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología Universidad de Costa Rica San Pedro de Montes de Oca San José Costa Rica
- Laboratorio de Ictiología Departamento de Zoología e Botánica Universidad Estadual Paulista “Julio de MesquitaFilho” São José do Rio Preto São Paul Brazil
| | - Juan E. Martínez‐Gómez
- Instituto de Ecología A. C. (INECOL)Red de Interacciones Multitróficas Xalapa Veracruz México
| | - Adrián F. González‐Acosta
- Instituto Politécnico NacionalCentro Interdisciplinario de Ciencias Marinas (CICIMAR)Pesquerías y Biología Marina La Paz México
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de México Morelia Michoacán México
- Instituto Nacional de BiodiversidadColección de Peces Quito Ecuador
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250
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Stoltz M, Baeumer B, Bouckaert R, Fox C, Hiscott G, Bryant D. Bayesian Inference of Species Trees using Diffusion Models. Syst Biol 2020; 70:145-161. [PMID: 33005955 DOI: 10.1093/sysbio/syaa051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we call Snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybean SNP data demonstrates that the models implemented in Snapp and Snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP data set sampled from 399 fresh water turtles in 41 populations. [Bayesian inference; diffusion models; multi-species coalescent; SNP data; species trees; spectral methods.].
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Affiliation(s)
- Marnus Stoltz
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Boris Baeumer
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland 1142, New Zealand
| | - Colin Fox
- Department of Physics, University of Otago, Dunedin 9054, New Zealand
| | - Gordon Hiscott
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
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