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Yu D, DU S, Wei X, Zhu J, Ding Y, Hu F, Liu M, Zhang F. Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola). Mol Phylogenet Evol 2024; 200:108169. [PMID: 39121953 DOI: 10.1016/j.ympev.2024.108169] [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: 02/23/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.
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Affiliation(s)
- Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shiyu DU
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiping Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jie Zhu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yinhuan Ding
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Nanjing 212400, China.
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen MF, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G. Complexity of avian evolution revealed by family-level genomes. Nature 2024; 629:851-860. [PMID: 38560995 PMCID: PMC11111414 DOI: 10.1038/s41586-024-07323-1] [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: 04/25/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
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Affiliation(s)
- Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | - David A Duchêne
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Qi Fang
- BGI Research, Shenzhen, China
| | - Yuan Deng
- BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Santiago Claramunt
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Jacqueline M T Nguyen
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Julia Haag
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Guangji Chen
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongsheng Gao
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Yulong Xie
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zijian Huang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhen Cao
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Zhi Yan
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bent Lindow
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Jon Fjeldså
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rute R da Fonseca
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Bedong, Malaysia
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, UK
- ELKH-DE Reproductive Strategies Research Group, University of Debrecen, Debrecen, Hungary
| | - Jonathan David Kennedy
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hart Reeve
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andras Liker
- HUN-REN-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | | | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Carsten Rahbek
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Ecology, Peking University, Beijing, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Tandy Warnow
- University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Durham, NC, USA
| | | | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- BGI Research, Wuhan, China.
- Villum Center for Biodiversity Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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3
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Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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4
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Rodríguez-Machado S, Elías DJ, McMahan CD, Gruszkiewicz-Tolli A, Piller KR, Chakrabarty P. Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements. Mol Phylogenet Evol 2024; 190:107965. [PMID: 37977500 DOI: 10.1016/j.ympev.2023.107965] [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: 07/07/2023] [Revised: 10/18/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.
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Affiliation(s)
- Sheila Rodríguez-Machado
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States; Field Museum of Natural History, Chicago, IL 60605, United States
| | - Caleb D McMahan
- Field Museum of Natural History, Chicago, IL 60605, United States
| | - Anna Gruszkiewicz-Tolli
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Kyle R Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
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5
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Venice F, Spina F, Davolos D, Ghignone S, Varese GC. The genomes of Scedosporium between environmental challenges and opportunism. IMA Fungus 2023; 14:25. [PMID: 38049914 PMCID: PMC10694956 DOI: 10.1186/s43008-023-00128-3] [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: 01/27/2023] [Accepted: 11/05/2023] [Indexed: 12/06/2023] Open
Abstract
Emerging fungal pathogens are a global challenge for humankind. Many efforts have been made to understand the mechanisms underlying pathogenicity in bacteria, and OMICs techniques are largely responsible for those advancements. By contrast, our limited understanding of opportunism and antifungal resistance is preventing us from identifying, limiting and interpreting the emergence of fungal pathogens. The genus Scedosporium (Microascaceae) includes fungi with high tolerance to environmental pollution, whilst some species can be considered major human pathogens, such as Scedosporium apiospermum and Scedosporium boydii. However, unlike other fungal pathogens, little is known about the genome evolution of these organisms. We sequenced two novel genomes of Scedosporium aurantiacum and Scedosporium minutisporum isolated from extreme, strongly anthropized environments. We compared all the available Scedosporium and Microascaceae genomes, that we systematically annotated and characterized ex novo in most cases. The genomes in this family were integrated in a Phylum-level comparison to infer the presence of putative, shared genomic traits in filamentous ascomycetes with pathogenic potential. The analysis included the genomes of 100 environmental and clinical fungi, revealing poor evolutionary convergence of putative pathogenicity traits. By contrast, several features in Microascaceae and Scedosporium were detected that might have a dual role in responding to environmental challenges and allowing colonization of the human body, including chitin, melanin and other cell wall related genes, proteases, glutaredoxins and magnesium transporters. We found these gene families to be impacted by expansions, orthologous transposon insertions, and point mutations. With RNA-seq, we demonstrated that most of these anciently impacted genomic features responded to the stress imposed by an antifungal compound (voriconazole) in the two environmental strains S. aurantiacum MUT6114 and S. minutisporum MUT6113. Therefore, the present genomics and transcriptomics investigation stands on the edge between stress resistance and pathogenic potential, to elucidate whether fungi were pre-adapted to infect humans. We highlight the strengths and limitations of genomics applied to opportunistic human pathogens, the multifactoriality of pathogenicity and resistance to drugs, and suggest a scenario where pressures other than anthropic contributed to forge filamentous human pathogens.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Federica Spina
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy
| | - Domenico Davolos
- Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements (DIT), INAIL, Research Area, Via R. Ferruzzi 38/40, 00143, Rome, Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP), SS Turin-National Research Council (CNR), Viale Mattioli 25, 10125, Turin, Italy
| | - Giovanna Cristina Varese
- Department of Life Sciences and System Biology, University of Turin, Viale Mattioli 25, 10125, Turin, Italy.
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Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [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: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
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Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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7
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Yan H, Hu Z, Thomas GWC, Edwards SV, Sackton TB, Liu JS. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance. Mol Biol Evol 2023; 40:msad195. [PMID: 37665177 PMCID: PMC10540510 DOI: 10.1093/molbev/msad195] [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: 12/23/2022] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023] Open
Abstract
An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
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Affiliation(s)
- Han Yan
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
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8
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Nickles GR, Oestereicher B, Keller NP, Drott M. Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Res 2023; 51:7220-7235. [PMID: 37427794 PMCID: PMC10415135 DOI: 10.1093/nar/gkad573] [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: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Milton T Drott
- USDA-ARS Cereal Disease Lab (CDL), St. Paul, MN 55108, USA
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9
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Titus-McQuillan JE, Nanni AV, McIntyre LM, Rogers RL. Estimating transcriptome complexities across eukaryotes. BMC Genomics 2023; 24:254. [PMID: 37170194 PMCID: PMC10173493 DOI: 10.1186/s12864-023-09326-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable lack of correspondence" between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study, we use a set of complexity metrics that allow for evaluating changes in complexity using TranD. RESULTS We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity varies. In this study, we define three metrics - TpG, EpT, and EpG- to quantify the transcriptome's complexity that encapsulates the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of orthologs and novel genes in transcript model analysis. Effective Exon Number (EEN) issued to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel gene differences in complexity for orthologs and whole-transcriptome analyses are biased towards low-complexity genes with few exons and few alternative transcripts. CONCLUSIONS With our metric analyses, we are able to quantify changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity.
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Affiliation(s)
- James E Titus-McQuillan
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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10
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Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
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11
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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12
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Ottenburghs J, Honka J, Heikkinen ME, Madsen J, Müskens GJDM, Ellegren H. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evol 2023; 23:2. [PMID: 36658479 PMCID: PMC9854053 DOI: 10.1186/s12862-023-02103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus). RESULTS First, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree. CONCLUSIONS The evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.
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Affiliation(s)
- Jente Ottenburghs
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.
| | - Johanna Honka
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Marja E. Heikkinen
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Jesper Madsen
- grid.7048.b0000 0001 1956 2722Department of Ecoscience, Aarhus University, C. F. Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Gerhard J. D. M. Müskens
- grid.4818.50000 0001 0791 5666Team Animal Ecology, Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3A, 6708 PB Wageningen, The Netherlands
| | - Hans Ellegren
- grid.8993.b0000 0004 1936 9457Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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Cueva D, Bravo GA, Silveira LF. Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager). PLoS One 2022; 17:e0270892. [PMID: 36197923 PMCID: PMC9534438 DOI: 10.1371/journal.pone.0270892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and βF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.
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Affiliation(s)
- Diego Cueva
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- * E-mail:
| | - Gustavo A. Bravo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Abstract
Insular woodiness (IW)-the evolutionary transition from herbaceousness toward woodiness on islands-is one of the most iconic features of island floras. Since pioneering work by Darwin and Wallace, a number of drivers of IW have been proposed, such as 1) competition for sunlight requiring plants with taller and stronger woody stems and 2) drought favoring woodiness to safeguard root-to-shoot water transport. Alternatively, IW may be the indirect result of increased lifespan related to 3) a favorable aseasonal climate and/or 4) a lack of large native herbivores. However, information on the occurrence of IW is fragmented, hampering tests of these potential drivers. Here, we identify 1,097 insular woody species on 375 islands and infer at least 175 evolutionary transitions on 31 archipelagos, concentrated in six angiosperm families. Structural equation models reveal that the insular woody species richness on oceanic islands correlates with a favorable aseasonal climate, followed by increased drought and island isolation (approximating competition). When continental islands are also included, reduced herbivory pressure by large native mammals, increased drought, and island isolation are most relevant. Our results illustrate different trajectories leading to rampant convergent evolution toward IW and further emphasize archipelagos as natural laboratories of evolution, where similar abiotic or biotic conditions replicated evolution of similar traits.
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15
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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16
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Berbel-Filho WM, Pacheco G, Tatarenkov A, Lira MG, Garcia de Leaniz C, Rodríguez López CM, Lima SMQ, Consuegra S. Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias. Mol Phylogenet Evol 2022; 177:107617. [PMID: 36038055 DOI: 10.1016/j.ympev.2022.107617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 10/15/2022]
Abstract
Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on the evolutionary relationships within the killifish genus Kryptolebias. In addition, we tested for evidence of past introgression in the genus given the multiple reports of undergoing hybridization between its members. Our mtDNA phylogeny generally agreed with the relationships previously proposed for the genus. However, our reconstruction based on nuclear DNA revealed an unknown lineage - Kryptolebias sp. 'ESP' - as the sister group of the self-fertilizing mangrove killifishes, K. marmoratus and K. hermaphroditus. All individuals sequenced of Kryptolebias sp. 'ESP' had the same mtDNA haplotype commonly observed in K. hermaphroditus, demonstrating a clear case of mito-nuclear discordance. Our analysis further confirmed extensive history of introgression between Kryptolebias sp. 'ESP' and K. hermaphroditus. Population genomics analyses indicate no current gene flow between the two lineages, despite their current sympatry and history of introgression. We also confirmed introgression between other species pairs in the genus that have been recently reported to form hybrid zones. Overall, our study provides a phylogenomic reconstruction covering most of the Kryptolebias species, reveals a new lineage hidden in a case of mito-nuclear discordance, and provides evidence of multiple events of ancestral introgression in the genus. These findings underscore the importance of investigating different genomic information in a phylogenetic framework, particularly in taxa where introgression is common as in the sexually diverse mangrove killifishes.
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Affiliation(s)
- Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, USA(1); Department of Biosciences, College of Science, Swansea University, Swansea, UK.
| | - George Pacheco
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Mateus G Lira
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | | | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
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17
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Doyle JJ. Cell types as species: Exploring a metaphor. FRONTIERS IN PLANT SCIENCE 2022; 13:868565. [PMID: 36072310 PMCID: PMC9444152 DOI: 10.3389/fpls.2022.868565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/29/2022] [Indexed: 06/05/2023]
Abstract
The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
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Affiliation(s)
- Jeff J. Doyle
- Section of Plant Biology and Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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18
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Xiong H, Wang D, Shao C, Yang X, Yang J, Ma T, Davis CC, Liu L, Xi Z. Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication. Syst Biol 2022; 71:1348-1361. [PMID: 35689633 PMCID: PMC9558847 DOI: 10.1093/sysbio/syac040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]
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Affiliation(s)
- Haifeng Xiong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Danying Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chen Shao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialin Yang
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Böhnert T, Luebert F, Merklinger FF, Harpke D, Stoll A, Schneider JV, Blattner FR, Quandt D, Weigend M. Plant migration under long-lasting hyperaridity - phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth. THE NEW PHYTOLOGIST 2022; 234:1863-1875. [PMID: 35274308 DOI: 10.1111/nph.18082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The post-Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae). We analyze phylogenetic relationships and historical biogeography by using next-generation sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas. Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene. We show that NGS combined with near-comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases.
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Affiliation(s)
- Tim Böhnert
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
| | - Federico Luebert
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
- Facultad de Ciencias Agronómicas and Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, 8820000, Santiago, Chile
| | - Felix F Merklinger
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
- Sukkulenten-Sammlung Zürich/Grün Stadt Zürich, 8002, Zürich, Switzerland
| | - Dörte Harpke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, 1720256, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de la Serena, 1720170, La Serena, Chile
| | - Julio V Schneider
- Botany and Molecular Evolution and Entomology III, Senckenberg Research Institute and Natural History Museum, Frankfurt, 60325, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Maximilian Weigend
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
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20
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Feng S, Bai M, Rivas-González I, Li C, Liu S, Tong Y, Yang H, Chen G, Xie D, Sears KE, Franco LM, Gaitan-Espitia JD, Nespolo RF, Johnson WE, Yang H, Brandies PA, Hogg CJ, Belov K, Renfree MB, Helgen KM, Boomsma JJ, Schierup MH, Zhang G. Incomplete lineage sorting and phenotypic evolution in marsupials. Cell 2022; 185:1646-1660.e18. [PMID: 35447073 PMCID: PMC9200472 DOI: 10.1016/j.cell.2022.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022]
Abstract
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
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Affiliation(s)
- Shaohong Feng
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Agriculture, Ningxia University, Yinchuan 750021, China; College of Plant Protection, Hebei Agricultural University, Baoding 071001, China
| | | | - Cai Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yijie Tong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China; Hainan Yazhou Bay Seed Lab, Building 1, No. 7 Yiju Road, Yazhou District, Sanya, Hainan 572024, China
| | - Haidong Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duo Xie
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lida M Franco
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, Colombia
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remont Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Parice A Brandies
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacobus J Boomsma
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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21
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Lagomarsino LP, Frankel L, Uribe-Convers S, Antonelli A, Muchhala N. Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation. ANNALS OF BOTANY 2022; 129:723-736. [PMID: 35363863 PMCID: PMC9113290 DOI: 10.1093/aob/mcac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/24/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
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Affiliation(s)
- Laura P Lagomarsino
- Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Lauren Frankel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Simon Uribe-Convers
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Science, University of Oxford, Oxford, UK
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
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22
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Sanderson MJ, Búrquez A, Copetti D, McMahon MM, Zeng Y, Wojciechowski MF. Origin and diversification of the saguaro cactus (Carnegiea gigantea): a within-species phylogenomic analysis. Syst Biol 2022; 71:1178-1194. [PMID: 35244183 DOI: 10.1093/sysbio/syac017] [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: 03/25/2020] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects post-glacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.
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Affiliation(s)
- Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Alberto Búrquez
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721 USA
| | | | - Yichao Zeng
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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23
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Franco FF, Amaral DT, Bonatelli IAS, Romeiro-Brito M, Telhe MC, Moraes EM. Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992-2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
- Programa de Pós-graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto 14040-901, Brazil
| | - Isabel A. S. Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo 04021-001, Brazil;
| | - Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Milena Cardoso Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Evandro Marsola Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
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24
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Zeb U, Wang X, AzizUllah A, Fiaz S, Khan H, Ullah S, Ali H, Shahzad K. Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species. Saudi J Biol Sci 2022; 29:1618-1627. [PMID: 35280541 PMCID: PMC8913380 DOI: 10.1016/j.sjbs.2021.10.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/24/2021] [Accepted: 10/31/2021] [Indexed: 01/02/2023] Open
Abstract
Genus Pinus is a widely dispersed genus of conifer plants in the Northern Hemisphere. However, the inadequate accessibility of genomic knowledge limits our understanding of molecular phylogeny and evolution of Pinus species. In this study, the evolutionary features of complete plastid genome and the phylogeny of the Pinus genus were studied. A total of thirteen divergent hotspot regions (trnk-UUU, matK, trnQ-UUG, atpF, atpH, rpoC1, rpoC2, rpoB, ycf2, ycf1, trnD-GUC, trnY-GUA, and trnH-GUG) were identified that would be utilized as possible genetic markers for determination of phylogeny and population genetics analysis of Pinus species. Furthermore, seven genes (petD, psaI, psaM, matK, rps18, ycf1, and ycf2) with positive selection site in Pinus species were identified. Based on the whole genome this phylogenetic study showed that twenty-four Pinus species form a significant genealogical clade. Divergence time showed that the Pinus species originated about 100 million years ago (MYA) (95% HPD, 101.76.35–109.79 MYA), in lateral stages of Cretaceous. Moreover, two of the subgenera are consequently originated in 85.05 MYA (95% HPD, 81.04–88.02 MYA). This study provides a phylogenetic relationship and a chronological framework for the future study of the molecular evolution of the Pinus species.
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Affiliation(s)
- Umar Zeb
- Department of Biology, The University of Haripur, 22620, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, Shaanxi, China
- Corresponding authors.
| | | | - Sajid Fiaz
- Department of Plant Breeding anf Genetics, The University of Haripur, 22620 Haripur, Pakistan
- Corresponding authors.
| | - Hanif Khan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Shariat Ullah
- Department of Botany University of Malakand, Pakistan
| | - Habib Ali
- Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan
| | - Khurram Shahzad
- Department of Plant Breeding anf Genetics, The University of Haripur, 22620 Haripur, Pakistan
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25
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de Lima Ferreira P, Batista R, Andermann T, Groppo M, Bacon CD, Antonelli A. Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses. Mol Phylogenet Evol 2022; 169:107432. [DOI: 10.1016/j.ympev.2022.107432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022]
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26
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Abstract
Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.]
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27
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Smith ML, Hahn MW. The Frequency and Topology of Pseudoorthologs. Syst Biol 2021; 71:649-659. [PMID: 34951639 DOI: 10.1093/sysbio/syab097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/12/2022] Open
Abstract
Phylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, identifying orthologs is difficult because gene duplication can obscure relationships among genes. Researchers have been particularly concerned with the insidious effects of pseudoorthologs-duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. Because gene tree topologies of pseudoorthologs may differ from the species tree topology, they have often been invoked as the cause of counterintuitive results in phylogenetics. Despite these perceived problems, no previous work has calculated the probabilities of pseudoortholog topologies, or has been able to circumscribe the regions of parameter space in which pseudoorthologs are most likely to occur. Here, we introduce a model for calculating the probabilities and branch lengths of orthologs and pseudoorthologs, including concordant and discordant pseudoortholog topologies, on a rooted three-taxon species tree. We show that the probability of orthologs is high relative to the probability of pseudoorthologs across reasonable regions of parameter space. Furthermore, the probabilities of the two discordant topologies are equal and never exceed that of the concordant topology, generally being much lower. We describe the species tree topologies most prone to generating pseudoorthologs, finding that they are likely to present problems to phylogenetic inference irrespective of the presence of pseudoorthologs. Overall, our results suggest that pseudoorthologs are unlikely to mislead inferences of species relationships under the biological scenarios considered here.
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Affiliation(s)
- Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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28
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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29
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Santos SHD, Peery RM, Miller JM, Dao A, Lyu FH, Li X, Li MH, Coltman DW. Ancient hybridization patterns between bighorn and thinhorn sheep. Mol Ecol 2021; 30:6273-6288. [PMID: 34845798 DOI: 10.1111/mec.16136] [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] [Received: 12/29/2020] [Revised: 07/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
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Affiliation(s)
- Sarah H D Santos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anh Dao
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Feng-Hua Lyu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Chinese Academy of Sciences (CAS), Beijing, China
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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30
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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31
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Simon S, Breeschoten T, Jansen HJ, Dirks RP, Schranz ME, Ros VID. Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control. G3 (BETHESDA, MD.) 2021; 11:jkab311. [PMID: 34557910 PMCID: PMC8527508 DOI: 10.1093/g3journal/jkab311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022]
Abstract
The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura, and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed on > 130 host plants, including several economically important crops. The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long-read data and Illumina short read), a high-quality genome assembly was achieved (N50 = 1.1 Mb). An official gene set (18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq datasets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression combined with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them Spodoptera-specific) upregulated during first- and third-instar larval stages for targeted pest-outbreak management. The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provide critical insights into the biology of this devastating polyphagous insect pest species worldwide. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Thijmen Breeschoten
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Hans J Jansen
- Future Genomics Technologies, Leiden, The Netherlands
| | - Ron P Dirks
- Future Genomics Technologies, Leiden, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Adams RH, Castoe TA, DeGiorgio M. PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. Bioinformatics 2021; 37:1923-1925. [PMID: 33051672 DOI: 10.1093/bioinformatics/btaa884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 09/16/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Here, we present PhyloWGA, an open source R package for conducting phylogenetic analysis and investigation of whole genome data. AVAILABILITYAND IMPLEMENTATION Available at Github (https://github.com/radamsRHA/PhyloWGA). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Richard H Adams
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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Alda F, Ludt WB, Elías DJ, McMahan CD, Chakrabarty P. Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree. Genome Biol Evol 2021; 13:evab161. [PMID: 34272856 PMCID: PMC8369075 DOI: 10.1093/gbe/evab161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.
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Affiliation(s)
- Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Tennessee, USA
| | - William B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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35
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Blasco-Costa I, Hayward A, Poulin R, Balbuena JA. Next-generation cophylogeny: unravelling eco-evolutionary processes. Trends Ecol Evol 2021; 36:907-918. [PMID: 34243958 DOI: 10.1016/j.tree.2021.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/19/2022]
Abstract
A fundamental question in evolutionary biology is how microevolutionary processes translate into species diversification. Cophylogeny provides an appropriate framework to address this for symbiotic associations, but historically has been primarily limited to unveiling patterns. We argue that it is essential to integrate advances from ecology and evolutionary biology into cophylogeny, to gain greater mechanistic insights and transform cophylogeny into a platform to advance understanding of interspecific interactions and diversification more widely. We discuss key directions, such as incorporating trait reconstruction and considering multiple scales of network organization, and highlight recent developments for implementation. A new quantitative framework is proposed to allow integration of relevant information, such as quantitative traits and assessment of the contribution of individual mechanisms to cophylogenetic patterns.
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Affiliation(s)
- Isabel Blasco-Costa
- Department of Invertebrates, Natural History Museum of Geneva, PO Box 6434, CH-1211 Geneva 6, Switzerland; Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, PO Box 6050, 9037 Tromsø, Norway.
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK
| | - Robert Poulin
- Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Juan A Balbuena
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, PO Box 22085, 46071 Valencia, Spain
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36
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Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
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Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
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37
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Kartavtsev YP. Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society. Animals (Basel) 2021; 11:1473. [PMID: 34065552 PMCID: PMC8160991 DOI: 10.3390/ani11051473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 01/27/2023] Open
Abstract
Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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38
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Congrains C, Zucchi RA, de Brito RA. Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae). Mol Phylogenet Evol 2021; 162:107200. [PMID: 33984467 DOI: 10.1016/j.ympev.2021.107200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 01/30/2021] [Accepted: 05/03/2021] [Indexed: 01/08/2023]
Abstract
New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.
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Affiliation(s)
- Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | - Roberto A Zucchi
- Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ, Universidade de São Paulo - USP, Piracicaba, SP, Brazil
| | - Reinaldo A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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39
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Montero-Mendieta S, De la Riva I, Irisarri I, Leonard JA, Webster MT, Vilà C. Phylogenomics and evolutionary history of Oreobates (Anura: Craugastoridae) Neotropical frogs along elevational gradients. Mol Phylogenet Evol 2021; 161:107167. [PMID: 33798672 DOI: 10.1016/j.ympev.2021.107167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Mountain ranges offer opportunities for understanding how species evolved and diversified across different environmental conditions. Neotropical frogs of the genus Oreobates (Anura: Craugastoridae) are adapted to highland and lowland habitats along the Andes, but many aspects of their evolution remain unknown. We studied their evolutionary history using ~18,000 exons enriched by targeted sequence-capture. Since capture success was very variable across samples, we evaluated to what degree differing data filtering produced robust inferences. The inferred evolutionary framework evidenced phylogenetic discordances among lowland species that can be explained by taxonomic misidentification or admixture of ancestral lineages. Highland species showed smaller effective populations than lowland frogs, probably due to greater habitat fragmentation in montane environments. Stronger genetic drift likely decreased the power of purifying selection and led to an increased proportion of nonsynonymous mutations in highland populations that could play an important role in their adaptation. Overall, our work sheds light on the evolutionary history and diversification of this group of Neotropical frogs along elevational gradients in the Andes as well as on their patterns of intraspecific diversity.
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Affiliation(s)
- Santiago Montero-Mendieta
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain.
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40
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Shen XX, Steenwyk JL, Rokas A. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Syst Biol 2021; 70:997-1014. [PMID: 33616672 DOI: 10.1093/sysbio/syab011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result in incongruent topologies, but the causes of this conflict can be difficult to characterize. We examined incongruence stemming from conflict between likelihood-based signal (quantified by the difference in gene-wise log likelihood score or ΔGLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or ΔGQS) for every gene in three phylogenomic studies in animals, fungi, and plants, which were chosen because their concatenation-based IQ-TREE (T1) and quartet-based ASTRAL (T2) phylogenies are known to produce eight conflicting internal branches (bipartitions). By comparing the types of phylogenetic signal for all genes in these three data matrices, we found that 30% - 36% of genes in each data matrix are inconsistent, that is, each of these genes has higher log likelihood score for T1 versus T2 (i.e., ΔGLS >0) whereas its T1 topology has lower quartet score than its T2 topology (i.e., ΔGQS <0) or vice versa. Comparison of inconsistent and consistent genes using a variety of metrics (e.g., evolutionary rate, gene tree topology, distribution of branch lengths, hidden paralogy, and gene tree discordance) showed that inconsistent genes are more likely to recover neither T1 nor T2 and have higher levels of gene tree discordance than consistent genes. Simulation analyses demonstrate that removal of inconsistent genes from datasets with low levels of incomplete lineage sorting (ILS) and low and medium levels of gene tree estimation error (GTEE) reduced incongruence and increased accuracy. In contrast, removal of inconsistent genes from datasets with medium and high ILS levels and high GTEE levels eliminated or extensively reduced incongruence, but the resulting congruent species phylogenies were not always topologically identical to the true species trees.
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Affiliation(s)
- Xing-Xing Shen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.,Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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41
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New Approaches for Inferring Phylogenies in the Presence of Paralogs. Trends Genet 2021; 37:174-187. [DOI: 10.1016/j.tig.2020.08.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022]
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42
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Jiang X, Edwards SV, Liu L. The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets. Syst Biol 2021; 69:795-812. [PMID: 32011711 PMCID: PMC7302055 DOI: 10.1093/sysbio/syaa008] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/30/2022] Open
Abstract
A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models. Although conducted on reduced data sets due to computational constraints, Bayesian model validation and comparison both strongly favor the MSC over concatenation across all data sets; the concatenation assumption of congruent gene trees rarely holds for phylogenomic data sets with more than 10 loci. Thus, for large phylogenomic data sets, model comparisons are expected to consistently and more strongly favor the coalescent model over the concatenation model. We also found that loci rejecting the MSC have little effect on species tree estimation. Our study reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference. [Bayes factor; Bayesian model validation; coalescent prior; congruent gene trees; independent prior; Metazoa; posterior predictive simulation.]
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Affiliation(s)
- Xiaodong Jiang
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Liang Liu
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA.,Institute of Bioinformatics, University of Georgia, 120 Green Street, Athens, GA 30602, USA
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Lopes F, Oliveira LR, Kessler A, Beux Y, Crespo E, Cárdenas-Alayza S, Majluf P, Sepúlveda M, Brownell RL, Franco-Trecu V, Páez-Rosas D, Chaves J, Loch C, Robertson BC, Acevedo-Whitehouse K, Elorriaga-Verplancken FR, Kirkman SP, Peart CR, Wolf JBW, Bonatto SL. Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere. Syst Biol 2020; 70:786-802. [PMID: 33367817 DOI: 10.1093/sysbio/syaa099] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].
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Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
| | - Larissa R Oliveira
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil.,GEMARS, Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, 95560-000 Torres, RS, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Enrique Crespo
- Centro Nacional Patagónico - CENPAT, CONICET, Puerto Madryn, Argentina
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Robert L Brownell
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, NOAA, La Jolla, USA
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | | | - Stephen P Kirkman
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Claire R Peart
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Jochen B W Wolf
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
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44
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Bossert S, Murray EA, Pauly A, Chernyshov K, Brady SG, Danforth BN. Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees. Syst Biol 2020; 70:803-821. [PMID: 33367855 DOI: 10.1093/sysbio/syaa097] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 11/12/2022] Open
Abstract
Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree, and RAxML. We study their performance in the phylogenomic framework of $>$800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus Pseudapis, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (ModelFinder program). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for Pseudapis s. l. and map the distribution of distinct morphological features of the group. [ASTRAL; Bees; concordance; gene tree estimation error; IQ-Tree; MrBayes, Nomiinae; PhyloBayes; RAxML; phylogenomics; stemminess].
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Elizabeth A Murray
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Alain Pauly
- O.D. Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium
| | - Kyrylo Chernyshov
- College of Arts and Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
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45
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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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46
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Blair C, Ané C. Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data. Syst Biol 2020; 69:593-601. [PMID: 31432090 DOI: 10.1093/sysbio/syz056] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/15/2019] [Indexed: 11/14/2022] Open
Abstract
Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.
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Affiliation(s)
- Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin - Madison, 1300 University Ave, Madison, WI 53706, USA
- Department of Statistics, University of Wisconsin - Madison, 1300 University Ave, Madison, WI 53706, USA
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47
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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48
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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Straub SCK, Boutte J, Fishbein M, Livshultz T. Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11400. [PMID: 33304663 PMCID: PMC7705337 DOI: 10.1002/aps3.11400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/12/2020] [Indexed: 05/07/2023]
Abstract
PREMISE Apocynaceae is the 10th largest flowering plant family and a focus for study of plant-insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non-model taxa, such as Apocynaceae. METHODS Transcriptomes were used to design probes for targeted sequencing of putatively single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. RESULTS From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single-nucleotide polymorphisms with potential for use in population-level studies. DISCUSSION Community use of this Hyb-Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
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Affiliation(s)
- Shannon C. K. Straub
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Julien Boutte
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology, and EvolutionOklahoma State University301 Physical SciencesStillwaterOklahoma74078USA
| | - Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental Sciences and the Academy of Natural SciencesDrexel University1900 Benjamin Franklin ParkwayPhiladelphiaPennsylvania19103USA
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50
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Bocalini F, Bolívar-Leguizamón SD, Silveira LF, Bravo GA. Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest. Mol Phylogenet Evol 2020; 154:106973. [PMID: 33059067 DOI: 10.1016/j.ympev.2020.106973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/08/2020] [Accepted: 09/28/2020] [Indexed: 11/30/2022]
Abstract
The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.
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Affiliation(s)
- Fernanda Bocalini
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Departamento de Zoologia do Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | | | - Luís F Silveira
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil
| | - Gustavo A Bravo
- Museu de Zoologia da Universidade de São Paulo, 04263-000 Ipiranga, São Paulo, SP, Brazil; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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