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Yan Y, da Fonseca RR, Rahbek C, Borregaard MK, Davis CC. A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia. Mol Phylogenet Evol 2024; 196:108089. [PMID: 38679302 DOI: 10.1016/j.ympev.2024.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
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Affiliation(s)
- Yujing Yan
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Silkwood Park campus, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA
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2
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Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
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Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
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3
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Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024; 22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary. RESULTS Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression. CONCLUSIONS Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
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Affiliation(s)
- Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Zang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shaoyuan Wu
- Jiangsu International Joint Center of Genomics, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China
| | - Sergei V Drovetski
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20004, USA
- Present address: U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, MD, 20708, USA
| | - Gang Liu
- Chinese Academy of Forestry, Institute of Ecological Conservation and Restoration, Beijing, 100091, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takema Saitoh
- Yamashina Institute for Ornithology, Abiko, Chiba, Japan
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden.
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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5
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Zhao YJ, Liu J, Yin GS, Gong X. Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications. BMC PLANT BIOLOGY 2023; 23:303. [PMID: 37280518 DOI: 10.1186/s12870-023-04323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/29/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data. RESULTS Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127-128 genes, including 82-83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset. CONCLUSION These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.
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Affiliation(s)
- Yu-Juan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming, Yunnan, 650201, China
| | - Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming, Yunnan, 650201, China
| | - Gen-Shen Yin
- Institute of Agriculture and Life Sciences, Kunming University, Kunming, 650214, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan Key Laboratory for Wild Plant Resources, Kunming, Yunnan, 650201, China.
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6
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Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
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7
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Almeida SC, Neiva J, Sousa F, Martins N, Cox CJ, Melo-Ferreira J, Guiry MD, Serrão EA, Pearson GA. A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation. Mol Ecol 2022; 31:4797-4817. [PMID: 35869812 DOI: 10.1111/mec.16623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/27/2022]
Abstract
Geologically recent radiations can shed light on speciation processes, but incomplete lineage sorting and introgressive gene flow render accurate evolutionary reconstruction and interpretation challenging. Independently evolving metapopulations of low dispersal taxa may provide an additional level of phylogeographic information, given sufficiently broad sampling and genome-wide sequencing. Evolution in the marine brown algal genus Fucus in the south-eastern North Atlantic was shaped by Quaternary climate-driven range shifts. Over this timescale, divergence and speciation occurred against a background of expansion-contraction cycles from multiple refugia, together with mating-system shifts from outcrossing (dioecy) to selfing hermaphroditism. We tested the hypothesis that peripheral isolation of range edge (dioecious) F. vesiculosus led to parapatric speciation and radiation of hermaphrodite lineages. Species tree methods using 876 single-copy nuclear genes and extensive geographic coverage produced conflicting topologies with respect to geographic clades of F. vesiculosus. All methods, however, revealed a new and early diverging hermaphrodite species, Fucus macroguiryi sp. nov. Both the multispecies coalescent and polymorphism-aware models (in contrast to concatenation) support sequential paraphyly in F. vesiculosus resulting from distinct evolutionary processes. Our results support (1) peripheral isolation of the southern F. vesiculosus clade prior to parapatric speciation and radiation of hermaphrodite lineages-a "low-latitude species pump". (2) Directional introgressive gene flow into F. vesiculosus around the present-day secondary contact zone (sympatric-allopatric boundary) between dioecious/hermaphrodite lineages as hermaphrodites expanded northwards, supported by concordance analysis and statistical tests of introgression. (3) Species boundaries in the extensive sympatric range are probably maintained by reproductive system (selfing in hermaphrodites) and reinforcement.
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Affiliation(s)
- Susana C Almeida
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - João Neiva
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Filipe Sousa
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Neusa Martins
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Cymon J Cox
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - José Melo-Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, R. Padre Armando Quintas, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Michael D Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Ester A Serrão
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Gareth A Pearson
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
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8
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Gatesy J, Springer MS. Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves. Genes (Basel) 2022; 13:1167. [PMID: 35885951 PMCID: PMC9324441 DOI: 10.3390/genes13071167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous−Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species−tree inference.
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Affiliation(s)
- 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, CA 92521, USA;
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9
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Wang Y, Ruhsam M, Milne R, Graham SW, Li J, Tao T, Zhang Y, Mao K. Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae). Mol Phylogenet Evol 2022; 172:107485. [PMID: 35452840 DOI: 10.1016/j.ympev.2022.107485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/26/2022] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Inferring accurate biogeographic history of plant taxa with an East Asia (EA)-North America (NA) is usually hindered by conflicting phylogenies and a poor fossil record. The current distribution of Chamaecyparis (false cypress; Cupressaceae) with four species in EA, and one each in western and eastern NA, and its relatively rich fossil record, make it an excellent model for studying the EA-NA disjunction. Here we reconstruct phylogenomic relationships within Chamaecyparis using > 1400 homologous nuclear and 61 plastid genes. Our phylogenomic analyses using concatenated and coalescent approaches revealed strong cytonuclear discordance and conflicting topologies between nuclear gene trees. Incomplete lineage sorting (ILS) and hybridization are possible explanations of conflict; however, our coalescent analyses and simulations suggest that ILS is the major contributor to the observed phylogenetic discrepancies. Based on a well-resolved species tree and four fossil calibrations, the crown lineage of Chamaecyparis is estimated to have originated in the upper Cretaceous, followed by diversification events in the early and middle Paleogene. Ancestral area reconstructions suggest that Chamaecyparis had an ancestral range spanning both EA and NA. Fossil records further indicate that this genus is a relict of the "boreotropical" flora, and that local extinctions of European species were caused by global cooling. Overall, our results unravel a complex evolutionary history of a Paleogene relict conifer genus, which may have involved ILS, hybridization and the extinction of local species.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Science, School of Biological Science, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Tongzhou Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yujiao Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China; College of Science, Tibet University, Lhasa 850000, Xizang Autonomous Region, PR China.
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10
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. SCIENCE ADVANCES 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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11
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Kim A, Rosenberg NA, Degnan JH. Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. Mol Biol Evol 2021; 37:1480-1494. [PMID: 31860090 DOI: 10.1093/molbev/msz305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecies coalescent are considered. A ranked tree depicts not only the topological relationship among gene lineages, as an unranked tree does, but also the sequence in which the lineages coalesce. In this article, we study how the parameters of a species tree simulated under a constant-rate birth-death process can affect the probability that the species tree lies in the anomaly zone. We find that with more than five taxa, it is possible for species trees to have both anomalous unranked and ranked gene trees. The probability of being in either type of anomaly zone increases with more taxa. The probability of anomalous gene trees also increases with higher speciation rates. We observe that the probabilities of unranked anomaly zones are higher and grow much faster than those of ranked anomaly zones as the speciation rate increases. Our simulation shows that the most probable ranked gene tree is likely to have the same unranked topology as the species tree. We design the software PRANC, which computes probabilities of ranked gene tree topologies given a species tree under the coalescent model.
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Affiliation(s)
- Anastasiia Kim
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM
| | | | - James H Degnan
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM
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12
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Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae). Proc Biol Sci 2020; 287:20202102. [PMID: 33290680 PMCID: PMC7739936 DOI: 10.1098/rspb.2020.2102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/13/2020] [Indexed: 11/12/2022] Open
Abstract
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Carl R. Hutter
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L. Wood
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA 92505, USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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13
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Morales-Briones DF, Kadereit G, Tefarikis DT, Moore MJ, Smith SA, Brockington SF, Timoneda A, Yim WC, Cushman JC, Yang Y. Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l. Syst Biol 2020; 70:219-235. [PMID: 32785686 PMCID: PMC7875436 DOI: 10.1093/sysbio/syaa066] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/01/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022] Open
Abstract
Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
| | - Gudrun Kadereit
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Delphine T Tefarikis
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, 119 Woodland Street, Oberlin, OH 44074-1097, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge CB2 3EA, UK
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89577, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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14
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Dai C, Dong F, Yang X. Morphotypes or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves, Timaliidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University) Ministry of Education Guilin China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology Guangxi Normal University Guilin China
- School of Biological Sciences Guizhou Normal College Guiyang China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
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15
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Abstract
Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.
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Affiliation(s)
- Evan S Forsythe
- Department of Biology, Colorado State University
- School of Plant Sciences, University of Arizona
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16
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova P, Panova M, Mikhailova NA, Granovitch AI. Proteomic similarity of the Littorinid snails in the evolutionary context. PeerJ 2020; 8:e8546. [PMID: 32095363 PMCID: PMC7024583 DOI: 10.7717/peerj.8546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/10/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. METHODS Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation. RESULTS Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.
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Affiliation(s)
- Arina L. Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina A. Varfolomeeva
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Arseniy A. Lobov
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Polina Tikanova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Department of Marine Sciences, Tjärnö, University of Gothenburg, Sweden
| | - Natalia A. Mikhailova
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
- Centre of Cell Technologies, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Andrei I. Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia
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17
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Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets. J Hered 2019; 111:147-168. [DOI: 10.1093/jhered/esz076] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - Erin K Molloy
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
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18
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Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV. Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone. Syst Biol 2019; 68:937-955. [PMID: 31135914 PMCID: PMC6857515 DOI: 10.1093/sysbio/syz019] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2019] [Accepted: 04/09/2019] [Indexed: 01/17/2023] Open
Abstract
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
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Affiliation(s)
- Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Timothy B Sackton
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Michele Clamp
- Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Department of Ornithology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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19
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Ballesteros JA, Sharma PP. A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error. Syst Biol 2019; 68:896-917. [DOI: 10.1093/sysbio/syz011] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 02/10/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractHorseshoe crabs (Xiphosura) are traditionally regarded as sister group to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We re-evaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic data set to date, expanding outgroup sampling, and including data from whole genome sequencing projects. In spite of uncertainty in the placement of some arachnid clades, all analyses show Xiphosura consistently nested within Arachnida as the sister group to Ricinulei (hooded tick spiders). It is apparent that the radiation of arachnids is an old one and occurred over a brief period of time, resulting in several consecutive short internodes, and thus is a potential case for the confounding effects of incomplete lineage sorting (ILS). We simulated coalescent gene trees to explore the effects of increasing levels of ILS on the placement of horseshoe crabs. In addition, common sources of systematic error were evaluated, as well as the effects of fast-evolving partitions and the dynamics of problematic long branch orders. Our results indicated that the placement of horseshoe crabs cannot be explained by missing data, compositional biases, saturation, or ILS. Interrogation of the phylogenetic signal showed that the majority of loci favor the derived placement of Xiphosura over a monophyletic Arachnida. Our analyses support the inference that horseshoe crabs represent a group of aquatic arachnids, comparable to aquatic mites, breaking a long-standing paradigm in chelicerate evolution and altering previous interpretations of the ancestral transition to the terrestrial habitat. Future studies testing chelicerate relationships should approach the task with a sampling strategy where the monophyly of Arachnida is not held as the premise.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Hubka V, Barrs V, Dudová Z, Sklenář F, Kubátová A, Matsuzawa T, Yaguchi T, Horie Y, Nováková A, Frisvad J, Talbot J, Kolařík M. Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization. PERSOONIA 2018; 41:142-174. [PMID: 30728603 PMCID: PMC6344812 DOI: 10.3767/persoonia.2018.41.08] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized by DNA sequencing of four to six loci. Biological compatibilities were tested within and between major phylogenetic clades, and ascospore morphology was characterised. Species delimitation methods based on the multispecies coalescent model (MSC) supported recognition of ten species including one new species. Four species are confirmed opportunistic pathogens; A. udagawae followed by A. felis and A. pseudoviridinutans are known from opportunistic human infections, while A. felis followed by A. udagawae and A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently described human-pathogenic species A. parafelis and A. pseudofelis are synonymized with A. felis and an epitype is designated for A. udagawae. Intraspecific mating assay showed that only a few of the heterothallic species can readily generate sexual morphs in vitro. Interspecific mating assays revealed that five different species combinations were biologically compatible. Hybrid ascospores had atypical surface ornamentation and significantly different dimensions compared to parental species. This suggests that species limits in the AVSC are maintained by both pre- and post-zygotic barriers and these species display a great potential for rapid adaptation and modulation of virulence. This study highlights that a sufficient number of strains representing genetic diversity within a species is essential for meaningful species boundaries delimitation in cryptic species complexes. MSC-based delimitation methods are robust and suitable tools for evaluation of boundaries between these species.
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Affiliation(s)
- V. Hubka
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - V. Barrs
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - Z. Dudová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - A. Kubátová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague 2, Czech Republic
| | - T. Matsuzawa
- University of Nagasaki, 1-1-1 Manabino, Nagayo-cho, Nishi-Sonogi-gun, Nagasaki 851-2195, Japan
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Y. Horie
- Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - J.J. Talbot
- Sydney School of Veterinary Science, Faculty of Science, and Marie Bashir Institute of Infectious Diseases & Biosecurity, University of Sydney, Camperdown, NSW, Australia
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i, Vídeňská 1083, 142 20 Prague 4, Czech Republic
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21
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González Marín A, Olave M, Avila LJ, Sites JW, Morando M. Evidence of body size and shape stasis driven by selection in Patagonian lizards of the Phymaturus patagonicus clade (Squamata: Liolaemini). Mol Phylogenet Evol 2018; 129:226-241. [DOI: 10.1016/j.ympev.2018.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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22
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Shekhar S, Roch S, Mirarab S. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1738-1747. [PMID: 28976320 DOI: 10.1109/tcbb.2017.2757930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted gene tree topologies is ASTRAL. In this paper, we derive theoretical sample complexity results for the number of genes required by ASTRAL to guarantee reconstruction of the correct species tree with high probability. We also validate those theoretical bounds in a simulation study. Our results indicate that ASTRAL requires gene trees to reconstruct the species tree correctly with high probability where is the number of species and is the length of the shortest branch in the species tree. Our simulations, some under the anomaly zone, show trends consistent with the theoretical bounds and also provide some practical insights on the conditions where ASTRAL works well.
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Olave M, Avila LJ, Sites JW, Morando M. Hybridization could be a common phenomenon within the highly diverse lizard genus
Liolaemus. J Evol Biol 2018; 31:893-903. [DOI: 10.1111/jeb.13273] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Melisa Olave
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
- Department of Biology University of Konstanz Konstanz Germany
| | - Luciano J. Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum Brigham Young University (BYU) Provo UT USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales– Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
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24
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Species limits in the Morelet’s Alligator lizard (Anguidae: Gerrhonotinae). Mol Phylogenet Evol 2018; 120:16-27. [DOI: 10.1016/j.ympev.2017.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 11/22/2022]
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25
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Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes. Syst Biol 2018; 66:881-895. [PMID: 28334176 DOI: 10.1093/sysbio/syx038] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022] Open
Abstract
Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].
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Affiliation(s)
- Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Fernando Alda
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - William B Ludt
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Caleb D Mcmahan
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,The Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - James S Albert
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Laurie Sorenson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
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Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han KL, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL. Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling. Syst Biol 2018; 66:857-879. [PMID: 28369655 DOI: 10.1093/sysbio/syx041] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/22/2017] [Indexed: 01/27/2023] Open
Abstract
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Akanksha Pandey
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL 32607, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA
| | - Shannon J Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | | | - Christopher J Huddleston
- Collections Program, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Sarah Kingston
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution-MRC 163, PO Box 37012, Washington, DC 20013-7012, USA.,Bowdoin College, Department of Biology and Coastal Studies Center, 6500 College Station, Brunwick, ME 04011, USA
| | - Ben D Marks
- Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Kathleen J Miglia
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - William S Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University 15 of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK 73072, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.,Genetics Institute, University of Florida, Gainesville, FL 32607, USA
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Liu P, Xu L, Xu SL, Martínez A, Chen H, Cheng D, Dumont HJ, Han BP, Fontaneto D. Species and hybrids in the genus Diaphanosoma Fischer, 1850 (Crustacea: Branchiopoda: Cladocera). Mol Phylogenet Evol 2017; 118:369-378. [PMID: 29107154 DOI: 10.1016/j.ympev.2017.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 01/22/2023]
Abstract
Cladocerans are well-studied planktonic crustaceans, especially those of the genus Daphnia in which interesting evolutionary questions have been addressed on speciation processes. The aim of the present study is to demonstrate that other genera of cladocerans show similar levels of cryptic diversity, intraspecific gene flow, and thus become useful model systems for comparison. In order to do so, we chose the genus Diaphanosoma, widespread in tropical and temperate areas. We started with a survey of species diversity in the genus Diaphanosoma in Asia using a morphological approach, then obtained sequences from a mitochondrial and a nuclear marker from multiple individuals of different species, performed tests on DNA taxonomy and molecular phylogenies, and assessed the role of hybridization in explaining the cases of mitonuclear discordance. The results are that cryptic diversity occurs in Diaphanosoma, and mitonuclear discordance was found in about 6% of the sequenced animals. Past hybridization is supported as the most likely explanation for the discordance: no evidence was found of first generation hybrids with heterozygous sequences. Our analysis on patterns of genetic diversity in Diaphanosoma supports similarities and differences with what is known in Daphnia.
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Affiliation(s)
- Ping Liu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Lei Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shao-Lin Xu
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Alejandro Martínez
- National Research Council of Italy, Institute of Ecosystem Study, Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
| | - Hua Chen
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Dan Cheng
- Jinan University, Department of Ecology, Guangzhou 510632, China
| | - Henri J Dumont
- Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Bo-Ping Han
- Jinan University, Department of Ecology, Guangzhou 510632, China.
| | - Diego Fontaneto
- National Research Council of Italy, Institute of Ecosystem Study, Largo Tonolli 50, I-28922 Verbania Pallanza, Italy
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Swain TD. Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference. Mol Phylogenet Evol 2017; 118:1-12. [PMID: 28919505 DOI: 10.1016/j.ympev.2017.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA.
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Affiliation(s)
- Timothy D Swain
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA.
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29
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Ochoa-Sánchez LE, Vinuesa P. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex. Front Microbiol 2017; 8:1548. [PMID: 28861062 PMCID: PMC5562727 DOI: 10.3389/fmicb.2017.01548] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.
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Affiliation(s)
- Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
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30
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Olave M, Avila LJ, Sites JW, Morando M. Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melisa Olave
- Patagonian Institute for the Study of Continental Ecosystems – The National Scientific and Technical Research Council (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
- Department of Biology University of Konstanz Konstanz Germany
| | - Luciano J. Avila
- Patagonian Institute for the Study of Continental Ecosystems – The National Scientific and Technical Research Council (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum Brigham Young University (BYU) Provo UT USA
| | - Mariana Morando
- Patagonian Institute for the Study of Continental Ecosystems – The National Scientific and Technical Research Council (IPEEC‐CONICET) Puerto Madryn Chubut Argentina
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31
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Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation. Mol Phylogenet Evol 2017; 116:13-24. [PMID: 28780022 DOI: 10.1016/j.ympev.2017.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/26/2017] [Accepted: 07/22/2017] [Indexed: 02/01/2023]
Abstract
Methods for inferring species trees from gene trees motivated by incomplete lineage sorting typically use either rooted gene trees to infer a rooted species tree, or use unrooted gene trees to infer an unrooted species tree, which is then typically rooted using one or more outgroups. Theoretically, however, it has been known since 2011 that it is possible to consistently infer the root of the species tree directly from unrooted gene trees without assuming an outgroup. Here, we use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees assuming the multispecies coalescent model. It is hoped that this approach will be useful in cases where an appropriate outgroup is difficult to find and gene trees do not follow a molecular clock. We use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees. This approach could also be useful when there is prior information that makes a small number of root locations plausible in an unrooted species tree.
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Perea S, Vukić J, Šanda R, Doadrio I. Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece. PLoS One 2016; 11:e0166292. [PMID: 27906993 PMCID: PMC5132402 DOI: 10.1371/journal.pone.0166292] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/26/2016] [Indexed: 11/18/2022] Open
Abstract
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese.
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Affiliation(s)
- Silvia Perea
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Václavské nám, Prague, Czech Republic
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Group, Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal, Madrid, Spain
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Sayyari E, Mirarab S. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. BMC Genomics 2016; 17:783. [PMID: 28185574 PMCID: PMC5123309 DOI: 10.1186/s12864-016-3098-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. Results We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. Conclusions We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3098-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Dr, La Jolla CA, 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego, 9500 Gilman Dr, La Jolla CA, 92093, USA.
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34
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Uricchio LH, Warnow T, Rosenberg NA. An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. BMC Bioinformatics 2016; 17:417. [PMID: 28185570 PMCID: PMC5123308 DOI: 10.1186/s12859-016-1266-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify “sufficiently large”. Results Using the multispecies coalescent model, we report a general analytical upper bound on the number of gene trees n required such that with probability q, each bipartition of a species tree is represented at least once in a set of n random gene trees. This bound employs a formula that is straightforward to compute, depends only on the minimum internal branch length of the species tree and the number of taxa, and applies irrespective of the species tree topology. Using simulations, we investigate numerical properties of the bound as well as its accuracy under the multispecies coalescent. Conclusions Our results are helpful for conservatively bounding the number of gene trees required by the ASTRAL inference method, and the approach has potential to be extended to bound other properties of gene tree sets under the model.
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35
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Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA 02138 USA
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36
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Suh A. The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. ZOOL SCR 2016. [DOI: 10.1111/zsc.12213] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University SE ‐ 752 36 Uppsala Sweden
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37
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Linkem CW, Minin VN, Leaché AD. Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae). Syst Biol 2016; 65:465-77. [PMID: 26738927 PMCID: PMC6383586 DOI: 10.1093/sysbio/syw001] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/29/2015] [Indexed: 01/28/2023] Open
Abstract
The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.
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Affiliation(s)
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle WA; Department of Statistics, University of Washington, Seattle WA
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle WA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
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38
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Sayyari E, Mirarab S. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol 2016; 33:1654-68. [PMID: 27189547 PMCID: PMC4915361 DOI: 10.1093/molbev/msw079] [Citation(s) in RCA: 442] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the MSC to compute (1) the local posterior probability (PP) that the branch is in the species tree and (2) the length of the branch in coalescent units. We evaluate the precision and recall of the local PP on a wide set of simulated and biological datasets, and show that it has very high precision and improved recall compared with multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene tree estimation error is low, but are underestimated when gene tree estimation error increases. Computation of both the branch length and local PP is implemented as new features in ASTRAL.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego
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39
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Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure. Theor Popul Biol 2016; 110:12-24. [PMID: 27086043 DOI: 10.1016/j.tpb.2016.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 12/22/2015] [Accepted: 02/05/2016] [Indexed: 11/21/2022]
Abstract
In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure.
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40
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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41
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Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL. Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Syst Biol 2016; 65:612-27. [DOI: 10.1093/sysbio/syw014] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
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42
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Zhang L, Wu W, Yan HF, Ge XJ. Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales. Evol Bioinform Online 2016; 11:81-91. [PMID: 26819541 PMCID: PMC4718149 DOI: 10.4137/ebo.s22448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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43
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Mol Phylogenet Evol 2016; 94:447-62. [DOI: 10.1016/j.ympev.2015.10.027] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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44
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Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT. Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes). Mol Biol Evol 2015; 33:1110-25. [PMID: 26715628 DOI: 10.1093/molbev/msv347] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconciliation methods, across five thresholds of missing data. Results of maximum likelihood and quartet analyses were similar, well resolved, and demonstrated increasing support with increasing matrix size and sparseness. Conversely, gene tree reconciliation produced unexpected relationships when we included all informative loci, with certain taxa placed toward the root compared with other approaches. Inspection of these taxa identified a prevalence of short average contigs, which potentially biased gene tree inference and caused erroneous results in gene tree reconciliation. This suggests that the more problematic missing data in gene tree-based analyses are partial sequences rather than entire missing sequences from locus alignments. Limiting gene tree reconciliation to the most informative loci solved this problem, producing well-supported topologies congruent with concatenation and quartet methods. Collectively, our analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera (Lerwa, Melanoperdix) not sampled in previous molecular phylogenetic studies.
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Affiliation(s)
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia
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45
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Degnan JH, Rhodes JA. There are no caterpillars in a wicked forest. Theor Popul Biol 2015; 105:17-23. [DOI: 10.1016/j.tpb.2015.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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46
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Suh A, Smeds L, Ellegren H. The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds. PLoS Biol 2015; 13:e1002224. [PMID: 26284513 PMCID: PMC4540587 DOI: 10.1371/journal.pbio.1002224] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/10/2015] [Indexed: 12/18/2022] Open
Abstract
The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree. A study of ancient genetic variation reveals genomic evidence for near-simultaneous speciation at the base of Neoaves (a group containing most modern birds), which temporally coincides with the mass extinction of nonavian dinosaurs and archaic birds. The rise of modern birds began after the mass extinction of nonavian dinosaurs and archaic birds at the Cretaceous-Paleogene (K-Pg) boundary, about 66 million years ago. This coincides with the super-rapid adaptive radiation of Neoaves (a group that contains most modern birds), which has been difficult to resolve even with whole genome sequences. We reconstructed the genealogical fates of thousands of rare genomic changes (insertions of selfish mobile elements called retrotransposons), a third of which were found to be affected by a phenomenon known as incomplete lineage sorting (ILS), namely a persistence of polymorphisms across multiple successive speciation events. Astoundingly, we found that near the K-Pg boundary, speciation events were accompanied by extreme levels of ILS, suggesting a near-simultaneous, star-like diversification process that appears plausible in the context of instantaneous niche availability that must have followed the K-Pg mass extinction. Our genome-scale results provide a population genomic explanation as to why some species radiations may be more complex than a fully bifurcating tree of life. We suggest that, under such circumstances, ILS bears witness to the biological limitation of phylogenetic resolution.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
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47
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Bayzid MS, Mirarab S, Boussau B, Warnow T. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. PLoS One 2015; 10:e0129183. [PMID: 26086579 PMCID: PMC4472720 DOI: 10.1371/journal.pone.0129183] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/05/2015] [Indexed: 11/19/2022] Open
Abstract
Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity. Coalescent-based methods have been developed to estimate species trees, many of which operate by combining estimated gene trees, and so are called "summary methods". Because summary methods are generally fast (and much faster than more complicated coalescent-based methods that co-estimate gene trees and species trees), they have become very popular techniques for estimating species trees from multiple loci. However, recent studies have established that summary methods can have reduced accuracy in the presence of gene tree estimation error, and also that many biological datasets have substantial gene tree estimation error, so that summary methods may not be highly accurate in biologically realistic conditions. Mirarab et al. (Science 2014) presented the "statistical binning" technique to improve gene tree estimation in multi-locus analyses, and showed that it improved the accuracy of MP-EST, one of the most popular coalescent-based summary methods. Statistical binning, which uses a simple heuristic to evaluate "combinability" and then uses the larger sets of genes to re-calculate gene trees, has good empirical performance, but using statistical binning within a phylogenomic pipeline does not have the desirable property of being statistically consistent. We show that weighting the re-calculated gene trees by the bin sizes makes statistical binning statistically consistent under the multispecies coalescent, and maintains the good empirical performance. Thus, "weighted statistical binning" enables highly accurate genome-scale species tree estimation, and is also statistically consistent under the multi-species coalescent model. New data used in this study are available at DOI: http://dx.doi.org/10.6084/m9.figshare.1411146, and the software is available at https://github.com/smirarab/binning.
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Affiliation(s)
| | - Siavash Mirarab
- Department of Computer Science, University of Texas at Austin, Austin, Texas, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyons, France
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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48
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Heyduk K, Trapnell DW, Barrett CF, Leebens-Mack J. Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12551] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | | | - Craig F. Barrett
- Department of Biological Sciences; California State University; Los Angeles CA 90032 USA
| | - Jim Leebens-Mack
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
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49
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Liu L, Xi Z, Wu S, Davis CC, Edwards SV. Estimating phylogenetic trees from genome-scale data. Ann N Y Acad Sci 2015; 1360:36-53. [DOI: 10.1111/nyas.12747] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liang Liu
- Department of Statistics; University of Georgia; Athens Georgia
- Institute of Bioinformatics; University of Georgia; Athens Georgia
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology & Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences; Tianjin Medical University; Tianjin China
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
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50
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Brunkard JO, Runkel AM, Zambryski PC. Evolution. Comment on "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity". Science 2015; 347:621. [PMID: 25657240 DOI: 10.1126/science.1255437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Sayou et al. (Reports, 7 February 2014, p. 645) proposed a new model for evolution of transcription factors without gene duplication, using LEAFY as an archetype. Their proposal contradicts the evolutionary history of plants and ignores evidence that LEAFY evolves through gene duplications. Within their data set, we identified a moss with multiple LEAFY orthologs, which contests their model and supports that LEAFY evolves through duplications.
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Affiliation(s)
- Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Anne M Runkel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Patricia C Zambryski
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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