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Alanzi AAR, Degnan JH. Statistical inconsistency of the unrooted minimize deep coalescence criterion. PLoS One 2021; 16:e0251107. [PMID: 33970931 PMCID: PMC8109837 DOI: 10.1371/journal.pone.0251107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.
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Affiliation(s)
- Ayed A. R. Alanzi
- Mathematics Department, College of Science and Human Studies of Hotat Sudair, Majmaah University, Majmaah, Saudi Arabia
| | - James H. Degnan
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, United States of America
- * E-mail:
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Koch H, DeGiorgio M. Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure. Genome Biol Evol 2020; 12:3977-3995. [PMID: 32022857 PMCID: PMC7061232 DOI: 10.1093/gbe/evaa022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 11/12/2022] Open
Abstract
Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI's performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.
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Affiliation(s)
- Hillary Koch
- Department of Statistics, Pennsylvania State University
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University
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Gernandt DS, Aguirre Dugua X, Vázquez-Lobo A, Willyard A, Moreno Letelier A, Pérez de la Rosa JA, Piñero D, Liston A. Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes. AMERICAN JOURNAL OF BOTANY 2018; 105:711-725. [PMID: 29683492 DOI: 10.1002/ajb2.1052] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/24/2018] [Indexed: 05/04/2023]
Abstract
PREMISE OF THE STUDY Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.
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Affiliation(s)
- David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Xitlali Aguirre Dugua
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Alejandra Vázquez-Lobo
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Col. Chamilpa, Cuernavaca, Morelos, 62209, Mexico
| | - Ann Willyard
- Biology Department, Hendrix College, Conway, Arkansas, 72032, USA
| | - Alejandra Moreno Letelier
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Jorge A Pérez de la Rosa
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Instituto de Botánica, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, 45510, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Aaron Liston
- Department of Botany and Plant Pathology, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
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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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Abstract
Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1 We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.
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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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Stadler T, Degnan JH, Rosenberg NA. Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times? Syst Biol 2016; 65:628-39. [PMID: 26968785 PMCID: PMC4911941 DOI: 10.1093/sysbio/syw019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 03/01/2016] [Indexed: 11/13/2022] Open
Abstract
Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth-death and multispecies coalescent model can explain the difference in empirical trees and birth-death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion.
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Affiliation(s)
- Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - James H Degnan
- Department of Mathematics and Statistics, University of New Mexico, 311 Terrace NE, Albuquerque, NM, 87131, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA; and
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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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Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R. Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. FRONTIERS IN PLANT SCIENCE 2016; 7:484. [PMID: 27148310 PMCID: PMC4838605 DOI: 10.3389/fpls.2016.00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/25/2016] [Indexed: 05/20/2023]
Abstract
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats - climate change, white pine blister rust, mountain pine beetle, and fire exclusion - and it is suffering significant mortality range-wide, prompting the tree to be listed as 'globally endangered' by the International Union for Conservation of Nature and 'endangered' by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
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Affiliation(s)
- John V. Syring
- Department of Biology, Linfield College, McMinnvilleOR, USA
- *Correspondence: John V. Syring,
| | - Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, CorvallisOR, USA
| | - Tara N. Jennings
- Department of Botany and Plant Pathology, Oregon State University, CorvallisOR, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, StorrsCT, USA
| | - Camille Scelfo-Dalbey
- Jack Baskin School of Engineering, University of California, Santa Cruz, Santa CruzCA, USA
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, CorvallisOR, USA
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Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae). Mol Ecol Resour 2015; 16:1124-35. [DOI: 10.1111/1755-0998.12487] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
| | - Aaron Liston
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Vojtěch Zeisek
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| | - Kenneth Oberlander
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Kevin Weitemier
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Shannon C. K. Straub
- Department of Biology; Hobart and William Smith Colleges; 213 Eaton Hall Geneva NY 14456 USA
| | - Richard C. Cronn
- USDA Forest Service; Pacific Northwest Research Station; 3200 SW Jefferson Way Corvallis OR 97331 USA
| | - Léanne L. Dreyer
- Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Jan Suda
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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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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13
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Subramaniyan V, Venkatachalam R. Analysis of E and NS proteins of dengue serotypes and identification of active binding sites for drug molecule. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2015. [DOI: 10.1016/s2222-1808(15)60852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Jockusch EL, Martínez-Solano I, Timpe EK. The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps). Syst Biol 2014; 64:66-83. [DOI: 10.1093/sysbio/syu078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Elizabeth L. Jockusch
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Iñigo Martínez-Solano
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Elizabeth K. Timpe
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, U-3043, Storrs, CT 06269-3043, USA; and 2CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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