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Schield DR, Brown CE, Shakya SB, Calabrese GM, Safran RJ, Sheldon FH. Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci. Mol Phylogenet Evol 2024; 197:108111. [PMID: 38801965 DOI: 10.1016/j.ympev.2024.108111] [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: 02/09/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/29/2024]
Abstract
Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting - a relatively rare nest construction phenotype in birds - was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA; Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | - Clare E Brown
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Subir B Shakya
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Gina M Calabrese
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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2
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Sánchez Reyes LL, McTavish EJ, O’Meara B. DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life. Syst Biol 2024; 73:470-485. [PMID: 38507308 PMCID: PMC11282365 DOI: 10.1093/sysbio/syae015] [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: 06/22/2022] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
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Affiliation(s)
- Luna L Sánchez Reyes
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Emily Jane McTavish
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
| | - Brian O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
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Jiang C, Kang H, Zhou Y, Zhu W, Zhao X, Mohamed N, Li B. Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes). Life (Basel) 2024; 14:881. [PMID: 39063634 PMCID: PMC11278119 DOI: 10.3390/life14070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.
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Affiliation(s)
- Chuan Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Hui Kang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Yang Zhou
- BGI Research, Shenzhen 518083, China;
- BGI Research, Wuhan 430074, China
| | - Wenwen Zhu
- School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Xilong Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Nassoro Mohamed
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Bo Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin 150040, 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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Imfeld TS, Barker FK. Passerine sister clade comparisons reveal variable macroevolutionary outcomes of interhemispheric dispersal. J Evol Biol 2024; 37:37-50. [PMID: 38285655 DOI: 10.1093/jeb/voad001] [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: 04/14/2023] [Revised: 09/18/2023] [Accepted: 11/04/2023] [Indexed: 01/31/2024]
Abstract
Dispersal events offer a unique window into macroevolutionary processes, especially with respect to the effects of competition on diversification. Empirical studies testing alternative predictions of competitive effects are often limited in either geographic or phylogenetic scale. Here, we tested some of these hypotheses by comparing an assemblage of 16 oscine passerine clades, representing independent dispersal events into the Western Hemisphere, to their sister clades in the Eastern Hemisphere. We also compared the diversity of this assemblage of clades to an older, incumbent passerine clade in the Western Hemisphere, the suboscines. Specifically, we tested for ecological opportunity and incumbency-mediated constraints by analysis of clade-specific morphological disparities and rates of evolution relative to dispersal history. While there was no consistent outcome of oscine dispersal and macroevolution in the Western Hemisphere relative to their Eastern Hemisphere sister groups, most clades supported a role for ecological opportunity or incumbency effects, and such effects were better explained by differences in species accumulation than by differences in rates of trait evolution or colonization timing. This general pattern was not evident when comparing the entire oscine assemblage of the Western Hemisphere to the incumbent suboscine radiation; oscines and suboscines occupy comparable regions of functional trait diversity and, despite higher rates of trait evolution in oscines, these observations were consistent with simulated null expectations. This result suggests that oscine and suboscine assemblages may have evolved in relative isolation for a significant fraction of their history.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, CO, United States
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- Bell Museum, University of Minnesota, St. Paul, MN, United States
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DeRaad DA, McCullough JM, DeCicco LH, Hime PM, Joseph L, Andersen MJ, Moyle RG. Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers. Mol Ecol 2023; 32:4844-4862. [PMID: 37515525 DOI: 10.1111/mec.17080] [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: 12/28/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/31/2023]
Abstract
Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome-wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome-wide gene trees. Meanwhile, a lack of inter-species shared ancestry, non-significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome-wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other 'great speciator' taxa across the Indo-Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.
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Affiliation(s)
- Devon A DeRaad
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Robert G Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
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Carotti E, Tittarelli E, Canapa A, Biscotti MA, Carducci F, Barucca M. LTR Retroelements and Bird Adaptation to Arid Environments. Int J Mol Sci 2023; 24:ijms24076332. [PMID: 37047324 PMCID: PMC10094322 DOI: 10.3390/ijms24076332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
TEs are known to be among the main drivers in genome evolution, leading to the generation of evolutionary advantages that favor the success of organisms. The aim of this work was to investigate the TE landscape in bird genomes to look for a possible relationship between the amount of specific TE types and environmental changes that characterized the Oligocene era in Australia. Therefore, the mobilome of 29 bird species, belonging to a total of 11 orders, was analyzed. Our results confirmed that LINE retroelements are not predominant in all species of this evolutionary lineage and highlighted an LTR retroelement dominance in species with an Australian-related evolutionary history. The bird LTR retroelement expansion might have happened in response to the Earth’s dramatic climate changes that occurred about 30 Mya, followed by a progressive aridification across most of Australian landmasses. Therefore, in birds, LTR retroelement burst might have represented an evolutionary advantage in the adaptation to arid/drought environments.
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8
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Steell EM, Nguyen JMT, Benson RBJ, Field DJ. Comparative anatomy of the passerine carpometacarpus helps illuminate the early fossil record of crown Passeriformes. J Anat 2023; 242:495-509. [PMID: 36070480 PMCID: PMC9919509 DOI: 10.1111/joa.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
The hyper-diverse clade Passeriformes (crown group passerines) comprises over half of extant bird diversity, yet disproportionately few studies have targeted passerine comparative anatomy on a broad phylogenetic scale. This general lack of research attention hinders efforts to interpret the passerine fossil record and obscures patterns of morphological evolution across one of the most diverse clades of extant vertebrates. Numerous potentially important crown passeriform fossils have proven challenging to place phylogenetically, due in part to a paucity of phylogenetically informative characters from across the passerine skeleton. Here, we present a detailed analysis of the morphology of extant passerine carpometacarpi, which are relatively abundant components of the passerine fossil record. We sampled >70% of extant family-level passerine clades (132 extant species) as well as several fossils from the Oligocene of Europe and scored them for 54 phylogenetically informative carpometacarpus characters optimised on a recently published phylogenomic scaffold. We document a considerable amount of previously undescribed morphological variation among passerine carpometacarpi, and, despite high levels of homoplasy, our results support the presence of representatives of both crown Passeri and crown Tyranni in Europe during the Oligocene.
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Affiliation(s)
| | - Jacqueline M T Nguyen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.,College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Museum of Zoology, University of Cambridge, Cambridge, UK
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Joakim RL, Irham M, Haryoko T, Rowe KMC, Dalimunthe Y, Anita S, Achmadi AS, McGuire JA, Perkins S, Bowie RCK. Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia. Anim Microbiome 2023; 5:4. [PMID: 36647179 PMCID: PMC9841722 DOI: 10.1186/s42523-022-00219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition. RESULTS The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae. CONCLUSIONS While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.
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Affiliation(s)
- Rachael L. Joakim
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA ,grid.241963.b0000 0001 2152 1081Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA ,grid.241963.b0000 0001 2152 1081The Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 USA
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Karen M. C. Rowe
- grid.436717.00000 0004 0500 6540Sciences Department, Museums Victoria, Carlton, VIC Australia ,grid.1008.90000 0001 2179 088XBioSciences Department, University of Melbourne, Parkville, VIC Australia
| | - Yohanna Dalimunthe
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Jimmy A. McGuire
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
| | - Susan Perkins
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA
| | - Rauri C. K. Bowie
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
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10
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Marcaigh FÓ, Kelly DJ, O’connell DP, Analuddin K, Karya A, Mccloughan J, Tolan E, Lawless N, Marples NM. Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Birds of the Indo-Pacific have provided biologists with many foundationalinsights. This study presents evidence for strong phylogeographic structure in two sunbird species from the heart of this region, the olive-backed sunbird, Cinnyris jugularis, and the black sunbird, Leptocoma aspasia. We assessed population divergence using morphological, plumage, bioacoustic and molecular data (mitochondrial ND2/ND3). Our findings indicate that the olive-backed sunbird should be recognized as multiple species, because birds from Sulawesi and the Sahul Shelf are closely related to each other, but widely separated from those in other regions. In addition, we provide evidence for an endemic species on the Wakatobi Islands, an archipelago of deep-sea islands off south-east Sulawesi. That a small bird could exhibit a range all the way from Sulawesi to Australia, while diverging on a small archipelago within this range, illustrates the complex interplay between dispersal and speciation. Our black sunbird genetic data also suggest unrecognized population structure, despite relatively weak plumage divergence. Black sunbirds in Sulawesi are likely to be a separate species from those in New Guinea, with a mean genetic distance of 9.1%. Current taxonomy suggests these sunbird species transcend classic biogeographic barriers, but our results suggest that these barriers are not easily bypassed.
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Affiliation(s)
- Fionn Ó Marcaigh
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Darren P O’connell
- School of Biology and Environmental Science, University College Dublin , Dublin D04 N2E5 , Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Jennifer Mccloughan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Ellen Tolan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Naomi Lawless
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
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11
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [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: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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12
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Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [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: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
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13
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Salter JF, Hosner PA, Tsai WLE, McCormack JE, Braun EL, Kimball RT, Brumfield RT, Faircloth BC. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Mol Phylogenet Evol 2022; 175:107559. [PMID: 35803448 DOI: 10.1016/j.ympev.2022.107559] [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: 11/15/2021] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/22/2023]
Abstract
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
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Affiliation(s)
- Jessie F Salter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| | - Peter A Hosner
- Natural History Museum of Denmark, Center for Global Mountain Biodiversity, and Center for Macroecology, Evolution, and Climate, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Florida, Gainesville, FL, USA
| | - Whitney L E Tsai
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA
| | - John E McCormack
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA; Biology Department, Occidental College, Los Angeles, CA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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14
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Kubovčiak J, Schmiedová L, Albrecht T, Těšický M, Tomášek O, Kauzálová T, Kreisinger J. Within-community variation of interspecific divergence patterns in passerine gut microbiota. Ecol Evol 2022; 12:e9071. [PMID: 35813907 PMCID: PMC9251858 DOI: 10.1002/ece3.9071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.
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Affiliation(s)
- Jan Kubovčiak
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Lucie Schmiedová
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Tereza Kauzálová
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
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15
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McCullough JM, Oliveros C, Benz BW, Zenil-Ferguson R, Cracraft J, Moyle RG, Andersen MJ. Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine radiation Corvides. Syst Biol 2022; 71:1423-1439. [PMID: 35703981 DOI: 10.1093/sysbio/syac044] [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: 11/12/2021] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers-specifically isolated island systems and Wallace's Line-we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.
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Affiliation(s)
- Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Carl Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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16
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Lombardo G, Migliore NR, Colombo G, Capodiferro MR, Formenti G, Caprioli M, Moroni E, Caporali L, Lancioni H, Secomandi S, Gallo GR, Costanzo A, Romano A, Garofalo M, Cereda C, Carelli V, Gillespie L, Liu Y, Kiat Y, Marzal A, López-Calderón C, Balbontín J, Mousseau TA, Matyjasiak P, Møller AP, Semino O, Ambrosini R, Alquati AB, Rubolini D, Ferretti L, Achilli A, Gianfranceschi L, Olivieri A, Torroni A. The Mitogenome Relationships and Phylogeography of Barn Swallows (Hirundo rustica). Mol Biol Evol 2022; 39:6591937. [PMID: 35617136 PMCID: PMC9174979 DOI: 10.1093/molbev/msac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (< 20 kya) back migration to Asia took place. The exception to the haplogroup subspecies specificity is represented by the sedentary Levantine H. r. transitiva that extensively shares haplogroup A with the migratory European H. r. rustica and, to a lesser extent, haplogroup B with the Egyptian H. r. savignii. Our data indicate that rustica and transitiva most likely derive from a sedentary Levantine population source that split at the end of the Younger Dryas (11.7 kya). Since then, however, transitiva received genetic inputs from and admixed with both the closely related rustica and the adjacent savignii. Demographic analyses confirm this species' strong link with climate fluctuations and human activities making it an excellent indicator for monitoring and assessing the impact of current global changes on wildlife.
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Affiliation(s)
- Gianluca Lombardo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Manuela Caprioli
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Elisabetta Moroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Simona Secomandi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Guido Roberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alessandra Costanzo
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Romano
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy.,Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40139 Bologna, Italy
| | - Lauren Gillespie
- Department of Academic Education, Central Community College, Columbus, NE 68601, USA
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yosef Kiat
- Israeli Bird Ringing Center (IBRC), Israel Ornithological Center, Tel Aviv, Israel
| | - Alfonso Marzal
- Department of Zoology, University of Extremadura, 06071 Badajoz, Spain
| | - Cosme López-Calderón
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, 41092 Seville, Spain
| | - Javier Balbontín
- Department of Zoology, University of Seville, 41012 Seville, Spain
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Piotr Matyjasiak
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Bonisoli Alquati
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA 91767, USA
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
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17
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de Raad J, Päckert M, Irestedt M, Janke A, Kryukov AP, Martens J, Red'kin YA, Sun Y, Töpfer T, Schleuning M, Neuschulz EL, Nilsson MA. Speciation and population divergence in a mutualistic seed dispersing bird. Commun Biol 2022; 5:429. [PMID: 35534538 PMCID: PMC9085801 DOI: 10.1038/s42003-022-03364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds. Genomic and phylogeographic analyses indicate that resource-specialization did not play a major role in the diversification and speciation of seed dispersing nutcrackers
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Affiliation(s)
- Jordi de Raad
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Russian Academy of Sciences, Stoletiya Avenue 159, 690022, Vladivostok, Russia
| | - Jochen Martens
- Institut für Organismische und Molekulare Evolutionsbiologie (iomE), Johannes Gutenberg-Universität Mainz, 55099, Mainz, Germany
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 2, 125009, Moscow, Russia
| | - Yuehua Sun
- Institute of Zoology, Chinese Academy of Sciences, CN-100101, Beijing, PR China
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Adenauerallee 127, 53113, Bonn, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.
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18
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Pavón-Vázquez CJ, Esquerré D, Fitch AJ, Maryan B, Doughty P, Donnellan SC, Scott Keogh J. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Mol Phylogenet Evol 2022; 173:107516. [DOI: 10.1016/j.ympev.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
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19
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Spottiswoode CN, Tong W, Jamie GA, Stryjewski KF, DaCosta JM, Kuras ER, Green A, Hamama S, Taylor IG, Moya C, Sorenson MD. Genetic architecture facilitates then constrains adaptation in a host-parasite coevolutionary arms race. Proc Natl Acad Sci U S A 2022; 119:e2121752119. [PMID: 35412865 PMCID: PMC9170059 DOI: 10.1073/pnas.2121752119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022] Open
Abstract
In coevolutionary arms races, interacting species impose selection on each other, generating reciprocal adaptations and counter adaptations. This process is typically enhanced by genetic recombination and heterozygosity, but these sources of evolutionary novelty may be secondarily lost when uniparental inheritance evolves to ensure the integrity of sex-linked adaptations. We demonstrate that host-specific egg mimicry in the African cuckoo finch Anomalospiza imberbis is maternally inherited, confirming the validity of an almost century-old hypothesis. We further show that maternal inheritance not only underpins the mimicry of different host species but also additional mimetic diversification that approximates the range of polymorphic egg “signatures” that have evolved within host species as an escalated defense against parasitism. Thus, maternal inheritance has enabled the evolution and maintenance of nested levels of mimetic specialization in a single parasitic species. However, maternal inheritance and the lack of sexual recombination likely disadvantage cuckoo finches by stifling further adaptation in the ongoing arms races with their individual hosts, which we show have retained biparental inheritance of egg phenotypes. The inability to generate novel genetic combinations likely prevents cuckoo finches from mimicking certain host phenotypes that are currently favored by selection (e.g., the olive-green colored eggs laid by some tawny-flanked prinia, Prinia subflava, females). This illustrates an important cost of coding coevolved adaptations on the nonrecombining sex chromosome, which may impede further coevolutionary change by effectively reversing the advantages of sexual reproduction in antagonistic coevolution proposed by the Red Queen hypothesis.
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Affiliation(s)
- Claire N. Spottiswoode
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- FitzPatrick Institute of African Ornithology, Department of Science and Technology–National Research Foundation Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | - Wenfei Tong
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Gabriel A. Jamie
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- FitzPatrick Institute of African Ornithology, Department of Science and Technology–National Research Foundation Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Jeffrey M. DaCosta
- Department of Biology, Boston University, Boston, MA 02215
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Evan R. Kuras
- Department of Biology, Boston University, Boston, MA 02215
| | - Ailsa Green
- Chenga Farm, Choma, Southern Province, Zambia
| | - Silky Hamama
- Musumanene Farm, Choma, Southern Province, Zambia
| | | | - Collins Moya
- Musumanene Farm, Choma, Southern Province, Zambia
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20
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Pavón-Vázquez CJ, Brennan IG, Skeels A, Keogh JS. Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards. Evolution 2022; 76:476-495. [PMID: 34816437 DOI: 10.1111/evo.14403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 10/06/2021] [Accepted: 10/16/2021] [Indexed: 01/21/2023]
Abstract
How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,Current Address: Department of Biological Sciences, New York City College of Technology, City University of New York, Brooklyn, New York, 11201
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alexander Skeels
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, CH-8092, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, CH-8903, Switzerland
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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21
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Systematics and biogeography of the whistlers (Aves: Pachycephalidae) inferred from ultraconserved elements and ancestral area reconstruction. Mol Phylogenet Evol 2021; 168:107379. [PMID: 34965464 DOI: 10.1016/j.ympev.2021.107379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022]
Abstract
The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions' most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific.
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22
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Sigeman H, Strandh M, Proux-Wéra E, Kutschera VE, Ponnikas S, Zhang H, Lundberg M, Soler L, Bunikis I, Tarka M, Hasselquist D, Nystedt B, Westerdahl H, Hansson B. Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration. Mol Biol Evol 2021; 38:5275-5291. [PMID: 34542640 PMCID: PMC8662655 DOI: 10.1093/molbev/msab277] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Ma formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Maria Strandh
- Department of Biology, Lund University, Lund, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
| | - Maja Tarka
- Department of Biology, Lund University, Lund, Sweden
| | | | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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23
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Chen D, Hosner PA, Dittmann DL, O'Neill JP, Birks SM, Braun EL, Kimball RT. Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements. BMC Ecol Evol 2021; 21:209. [PMID: 34809586 PMCID: PMC8609756 DOI: 10.1186/s12862-021-01935-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results. RESULTS In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different "gene shopping" schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree. CONCLUSIONS We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL, USA
- Natural History Museum of Denmark and Center for Global Mountain Biodiversity, University of Copenhagen, Copenhagen, Denmark
| | - Donna L Dittmann
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - John P O'Neill
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Sharon M Birks
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
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24
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DeRaad DA, Manthey JD, Ostrow EN, DeCicco LH, Andersen MJ, Hosner PA, Shult HT, Joseph L, Dumbacher JP, Moyle RG. Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves. Mol Phylogenet Evol 2021; 166:107333. [PMID: 34688879 DOI: 10.1016/j.ympev.2021.107333] [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: 07/29/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022]
Abstract
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.
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Affiliation(s)
- Devon A DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Joseph D Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Emily N Ostrow
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87106, USA
| | - Peter A Hosner
- Natural History Museum of Denmark and Center for Global Mountain Biodiversity, University of Copenhagen, Copenhagen, Denmark
| | - Hannah T Shult
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT 2601, Australia
| | - John P Dumbacher
- California Academy of Sciences, Golden Gate Park, San Francisco, CA 94118, USA
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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25
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Duchêne DA, Mather N, Van Der Wal C, Ho SYW. Excluding loci with substitution saturation improves inferences from phylogenomic data. Syst Biol 2021; 71:676-689. [PMID: 34508605 PMCID: PMC9016599 DOI: 10.1093/sysbio/syab075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.]
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Affiliation(s)
- David A Duchêne
- Centre for Evolutionary Hologenomics, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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26
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Oliveros CH, Andersen MJ, Moyle RG. A phylogeny of white-eyes based on ultraconserved elements. Mol Phylogenet Evol 2021; 164:107273. [PMID: 34333115 DOI: 10.1016/j.ympev.2021.107273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. Zosterops white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian family Zosteropidae. We used concatenated maximum likelihood and species tree methods and found strong support for seven clades of white-eyes and three clades within the species-rich Zosterops radiation.
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Affiliation(s)
- Carl H Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.
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27
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Vankan M, Ho SYW, Duchêne DA. Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. Syst Biol 2021; 71:490-500. [PMID: 34255084 PMCID: PMC8830059 DOI: 10.1093/sysbio/syab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
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Affiliation(s)
- Mezzalina Vankan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,Research School of Biology, Australian National University, ACT 2601, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - David A Duchêne
- Research School of Biology, Australian National University, ACT 2601, Australia.,Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
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28
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Smith BT, Mauck WM, Benz BW, Andersen MJ. Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets. Genome Biol Evol 2021; 12:1131-1147. [PMID: 32470111 PMCID: PMC7486955 DOI: 10.1093/gbe/evaa113] [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] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, New York, New York.,New York Genome Center, New York, New York
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico
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29
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Barker FK. A shift in taste. Science 2021; 373:154-155. [PMID: 34244394 DOI: 10.1126/science.abj6746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- F Keith Barker
- Department of Ecology, Evolution and Behavior and Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA.
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30
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Mitchell KJ, Hugall AF, Heiniger H, Joseph L, Oliver PM. Disparate origins for endemic bird taxa from the ‘Gondwana Rainforests’ of Central Eastern Australia. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Subtropical and temperate rainforests of Central Eastern Australia are some of the largest remaining fragments of their kind globally. The biota of these rainforests appears to comprise two broad biogeographical elements: a more ancient (Miocene or older) and typically upland temperate (‘Gondwanan’) element and a younger (Plio-Pleistocene) lowland tropical element. We present the first phylogenetic synthesis of the spatiotemporal origins for the eight bird taxa endemic to Central Eastern Australian Rainforests. At least five of these eight focal taxa show Plio-Pleistocene divergences from their respective northern sister taxa, consistent with origins driven by recent expansion and contraction of lowland rainforest. In contrast, two more strictly upland species, the rufous scrub-bird (Atrichornis rufescens) and the logrunner (Orthonyx temminckii), diverged from their nearest living relatives during the Miocene, suggesting potentially longer histories of persistence and more temperate origins. Finally, we did not recover reciprocal monophyly in mitogenomes from the two extant lyrebirds, Albert’s lyrebird (Menura alberti) and the superb lyrebird (Menura novaehollandiae). The disparate divergence ages recovered among all eight taxa are consistent with the biota of the Central Eastern Australian Rainforests comprising isolates either of younger age and tropical lowland origins or of older age and temperate upland origins.
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Affiliation(s)
- Kieren J Mitchell
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide, SA, Australia
| | - Andrew F Hugall
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia
| | - Holly Heiniger
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide, SA, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT, Australia
| | - Paul M Oliver
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD, Australia
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31
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Campana MG, Corvelo A, Shelton J, Callicrate TE, Bunting KL, Riley-Gillis B, Wos F, DeGrazia J, Jarvis ED, Fleischer RC. Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapōlā'au and the Hawai'i 'amakihi. J Hered 2021; 111:21-32. [PMID: 31723957 DOI: 10.1093/jhered/esz057] [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: 03/04/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The Hawai'ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes involved in bill morphology phenotypes in 2 honeycreepers: the 'akiapōlā'au (Hemignathus wilsoni) and the Hawai'i 'amakihi (Chlorodrepanis virens). The 'akiapōlā'au is an endangered island endemic, filling the "woodpecker" niche by using a unique bill morphology, while the Hawai'i 'amakihi is a dietary generalist common on the islands of Hawai'i and Maui. We de novo sequenced the 'akiapōlā'au genome and compared it to the previously sequenced 'amakihi genome. The 'akiapōlā'au is far less heterozygous and has a smaller effective population size than the 'amakihi, which matches expectations due to its smaller census population and restricted ecological niche. Our investigation revealed genomic islands of divergence, which may be involved in the honeycreeper radiation. Within these islands of divergence, we identified candidate genes (including DLK1, FOXB1, KIF6, MAML3, PHF20, RBP1, and TIMM17A) that may play a role in honeycreeper adaptations. The gene DLK1, previously shown to influence Darwin's finch bill size, may be related to honeycreeper bill morphology evolution, while the functions of the other candidates remain unknown.
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Affiliation(s)
- Michael G Campana
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC
| | | | | | - Taylor E Callicrate
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC.,Species Conservation Toolkit Initiative, Chicago Zoological Society, Brookfield, IL
| | | | | | - Frank Wos
- New York Genome Center, New York, NY
| | | | - Erich D Jarvis
- The Rockefeller University, New York, NY.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC
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Toussaint EFA, White LT, Shaverdo H, Lam A, Surbakti S, Panjaitan R, Sumoked B, von Rintelen T, Sagata K, Balke M. New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline. BMC Ecol Evol 2021; 21:51. [PMID: 33823805 PMCID: PMC8022562 DOI: 10.1186/s12862-021-01764-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea's location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated. RESULTS We inferred a comprehensive dated molecular phylogeny of endemic diving beetles to test historical hypotheses pertaining to the evolution of the New Guinean biota. We used geospatial analysis techniques to compare our phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species ( https://arcg.is/189zmz ). Our divergence time estimations indicate a crown age (early diversification) for New Guinea Exocelina beetles in the mid-Miocene ca. 17 Ma, when the New Guinean orogeny was at an early stage. Geographic and geological ancestral state reconstructions suggest an origin of Exocelina ancestors on the eastern part of the New Guinean central range on basement rocks (with a shared affinity with the Australian Plate). Our results do not support the hypothesis of ancestors migrating to the northern margin of the Australian Plate from Pacific terranes that incrementally accreted to New Guinea over time. However, our analyses support to some extent a scenario in which Exocelina ancestors would have been able to colonize back and forth between the amalgamated Australian and Pacific terranes from the Miocene onwards. Our reconstructions also do not support an origin on ultramafic or ophiolite rocks that have been colonized much later in the evolution of the radiation. Macroevolutionary analyses do not support the hypothesis of heterogeneous diversification rates throughout the evolution of this radiation, suggesting instead a continuous slowdown in speciation. CONCLUSIONS Overall, our geospatial analysis approach to investigate the links between the location and evolution of New Guinea's biota with the underlying geology sheds a new light on the patterns and processes of lineage diversification in this exceedingly diverse region of the planet.
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Affiliation(s)
| | - Lloyd T White
- GeoQuEST Research Centre, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Helena Shaverdo
- Naturhistorisches Museum Wien, Burgring 7, 1010, Vienna, Austria
| | - Athena Lam
- SNSB-Zoologische Staatssammlung München, Munich, Germany
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Suriani Surbakti
- Department of Biology, Universitas Cenderawasih (UNCEN), Waena, Papua, Indonesia
| | - Rawati Panjaitan
- Department of Biology, Faculty of Sciences and Mathematics, State University of Papua (UNIPA), Jalan Gunung Salju Amban, Manokwari, 98314, West Papua, Indonesia
| | - Bob Sumoked
- Walian 2, Tomohon Selatan, 95439, N Sulawesi, Indonesia
| | - Thomas von Rintelen
- Museum Für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Katayo Sagata
- University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany.
- Department of Entomology, SNSB-Zoologische Staatssammlung München, Münchhausenstrasse 21, 81247, Munich, Germany.
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33
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Andersen MJ, McCullough JM, Gyllenhaal EF, Mapel XM, Haryoko T, Jønsson KA, Joseph L. Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds. Mol Ecol 2021; 30:2087-2103. [PMID: 33615597 PMCID: PMC8252742 DOI: 10.1111/mec.15856] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/02/2021] [Accepted: 02/12/2021] [Indexed: 01/03/2023]
Abstract
Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or “captured” by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch‐flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot‐winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations of S. trivirgatus form two paraphyletic clades, one being sister to and presumably introgressed by S. guttula despite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event between S. guttula and Australian S. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies of S. trivirgatus into an island population of S. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction of S. guttula from mainland Australia resulted from range expansion by S. trivirgatus.
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Affiliation(s)
- Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Ethan F Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Xena M Mapel
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.,Animal Genomics, ETH Zürich, Lindau, Switzerland
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Canberra, Australian Capital Territory, Australia
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34
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Douglas J, Zhang R, Bouckaert R. Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model. PLoS Comput Biol 2021; 17:e1008322. [PMID: 33529184 PMCID: PMC7880504 DOI: 10.1371/journal.pcbi.1008322] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/12/2021] [Accepted: 11/30/2020] [Indexed: 11/18/2022] Open
Abstract
Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. Under the (uncorrelated) relaxed clock model, tree branches are associated with molecular substitution rates which are independently and identically distributed. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an operator scheme that is up to 65 times more efficient at exploring continuous relaxed clock parameters compared with previous setups, depending on the dataset. Finally, we explored variants of the standard narrow exchange operator which are specifically designed for the relaxed clock model. In the most extreme case, this new operator traversed tree space 40% more efficiently than narrow exchange. The methodologies introduced are adaptive and highly effective on short as well as long alignments. The results are available via the open source optimised relaxed clock (ORC) package for BEAST 2 under a GNU licence (https://github.com/jordandouglas/ORC).
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Affiliation(s)
- Jordan Douglas
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Rong Zhang
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
- Max Planck Institute for the Science of Human History, Jena, Germany
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35
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Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Syst Biol 2021; 70:49-66. [PMID: 32359157 PMCID: PMC7823230 DOI: 10.1093/sysbio/syaa034] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022] Open
Abstract
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].
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Affiliation(s)
- Paul M Hime
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Elizabeth Prendini
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Justin D Kratovil
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Pedro L V Peloso
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, 66075-750, Brazil
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | | | - Christopher J Raxworthy
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala 680653, India
| | - Nikhil Gaitonde
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - David M Green
- Redpath Museum, McGill University, Montreal, Quebec H3A 0C4, Canada
| | - Jim Labisko
- The Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, The University of Kent, Canterbury, Kent, CT2 7NR, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, PO Box 1348, Anse Royale, Mahé, Seychelles
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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Oswald KN, Lee ATK, Smit B. Seasonal metabolic adjustments in an avian evolutionary relict restricted to mountain habitat. J Therm Biol 2020; 95:102815. [PMID: 33454043 DOI: 10.1016/j.jtherbio.2020.102815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/12/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
For endotherms, maintaining body temperature during cold winters is energetically costly.Greater increase in winter maximum thermogenic capacity (Msum) has typically been correlated with improved cold tolerance. However, seasonal studies have shown equivocal direction change in basal metabolic rate (BMR) in winter, perhaps explained by latitude or phylogeny. We examined seasonal metabolic responses in the Cape rockjumper (Chaetops frenatus; "rockjumper"), a range-restricted mountain bird. We hypothesized that, given their mountain habitat preference, rockjumpers would be physiologically specialized for cooler air temperatures compared to other subtropical passerines. We measured body condition (using the ratio of Mb/tarsus), BMR, and Msum, in wild-living rockjumpers during winter and summer (n = 12 adults in winter -- 4 females, 8 males; n = 12 adults in summer -- 6 females, 6 males). We found birds had lesser BMR and thermal conductance, and greater Msum and body condition, in winter compared to summer. These changes may help rockjumpers conserve energy in winter while still allowing birds to produce more metabolic heat during the coldest air temperatures. When compared with existing data on avian seasonal metabolic adjustments, rockjumper BMR fit general patterns observed in passerines, but their Msum was low compared with other members of the oscine Passeriformes. These patterns may be explained by the narrow temperature range of their habitat not requiring cold-adjustment, or perhaps by their basal placement within passerine phylogeny. Further work on the physiological phenotypic plasticity in habitat specialists across different latitudinal zones and taxa is needed to better understand the relationship between metabolism, habitat, and phylogeny.
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Affiliation(s)
- Krista N Oswald
- Department of Zoology and Entomology, Rhodes University, Makhanda, 6139, South Africa; Department of Zoology, Nelson Mandela University, Port Elizabeth, 6031, South Africa.
| | - Alan T K Lee
- Fitzpatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Cape Town, 7701, South Africa; Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Ben Smit
- Department of Zoology and Entomology, Rhodes University, Makhanda, 6139, South Africa; Department of Zoology, Nelson Mandela University, Port Elizabeth, 6031, South Africa
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37
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Kaplan G. Play behaviour, not tool using, relates to brain mass in a sample of birds. Sci Rep 2020; 10:20437. [PMID: 33235248 PMCID: PMC7687885 DOI: 10.1038/s41598-020-76572-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022] Open
Abstract
Play behaviour and tool using in birds, two well-delineated and amply researched behaviours, have generally been associated with cognitive abilities. In this study, these behaviours were related to relative brain mass in a sample of Australian native birds. Despite suggestive research results so far between cognition and tool using, this study found no significant difference in relative brain mass or in lifespan between tool-using birds and non-tool users. By contrast, in play behaviour, subdivided into social players and non-social players, the results showed statistically very clear differences in relative brain mass between social, non-social and non-players. Social play was associated with both the largest brain mass to body mass ratios and with the longest lifespans. The results show that play behaviour is a crucial variable associated with brain enlargement, not tool using. Since many of the tool using species tested so far also play, this study suggests that false conclusions can be drawn about the connection between tool using and cognitive ability when the silent variable (play behaviour) is not taken into account.
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Affiliation(s)
- Gisela Kaplan
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
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38
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Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness. Mol Phylogenet Evol 2020; 155:107013. [PMID: 33217578 DOI: 10.1016/j.ympev.2020.107013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/07/2020] [Accepted: 11/11/2020] [Indexed: 01/11/2023]
Abstract
Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia clade was an exception to the generally high support we observed; the topology of this clade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.
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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon. DIVERSITY 2020. [DOI: 10.3390/d12110428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
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40
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Päckert M, Favre A, Schnitzler J, Martens J, Sun Y, Tietze DT, Hailer F, Michalak I, Strutzenberger P. "Into and Out of" the Qinghai-Tibet Plateau and the Himalayas: Centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds. Ecol Evol 2020; 10:9283-9300. [PMID: 32953061 PMCID: PMC7487248 DOI: 10.1002/ece3.6615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/12/2020] [Accepted: 06/29/2020] [Indexed: 01/06/2023] Open
Abstract
Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai-Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one-way street ("out of" the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12-7 Ma). The inferred centers of origin and diversification for some of our target clades matched the "out of Tibet hypothesis' or the "out of Himalayas hypothesis" for others they matched the "into Tibet hypothesis." Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
| | - Adrien Favre
- Entomology IIISenckenberg Research Institute and Natural History Museum FrankfurtFrankfurt am MainGermany
| | - Jan Schnitzler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg‐UniversitätMainzGermany
| | - Yue‐Hua Sun
- Key Laboratory of Animal Ecology and ConservationInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Dieter Thomas Tietze
- Natural History Museum BaselBaselSwitzerland
- Centrum für NaturkundeUniversität HamburgHamburgGermany
| | - Frank Hailer
- School of BiosciencesCardiff UniversityCardiffUK
- Senckenberg Biodiversity and Climate Research CentreFrankfurt am MainGermany
| | - Ingo Michalak
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ)Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Patrick Strutzenberger
- Senckenberg Natural History Collections, Museum of ZoologyDresdenGermany
- Department of Botany and Biodiversity ResearchUniversität WienWienAustria
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41
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Van Dam MH, Henderson JB, Esposito L, Trautwein M. Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction. Syst Biol 2020; 70:307-321. [PMID: 32750133 PMCID: PMC7875437 DOI: 10.1093/sysbio/syaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]
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Affiliation(s)
- Matthew H Van Dam
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - James B Henderson
- Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - Lauren Esposito
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA.,Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA
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42
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Trethowan LA, Eiserhardt WL, Girmansyah D, Kintamani E, Utteridge TM, Brearley FQ. Floristics of forests across low nutrient soils in Sulawesi, Indonesia. Biotropica 2020. [DOI: 10.1111/btp.12838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Liam A. Trethowan
- Manchester Metropolitan University Manchester UK
- Royal Botanic Gardens Kew London UK
| | | | - Deden Girmansyah
- Herbarium Bogoriense Indonesian Institute of Sciences Cibinong Indonesia
| | - Endang Kintamani
- Herbarium Bogoriense Indonesian Institute of Sciences Cibinong Indonesia
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43
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Zhu Z, Gao X, Hu Y. The complete mitochondrial genome of Norfolk Robin ( Petroica multicolor: Petroicidae), an endemic endangered species in Norfolk Island. Mitochondrial DNA B Resour 2020; 5:2366-2367. [PMID: 33457793 PMCID: PMC7782817 DOI: 10.1080/23802359.2020.1773953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Norfolk Robin (Petroica multicolor) is mainly distributed in the islands of the southwest Pacific Ocean. It is an endangered species with a declining population and needs urgent protection. Here, we report the first complete mitochondrial genome of Norfolk Robin in the Petroicidae family. The mitochondrial genome is a typically circular genome with a total length of 16,861 bp, and it contains 13 protein-coding genes, 22 tRNA, and 2 rRNA genes. The GC content is 46.3%, and the percent of A, C, G, and T is 29.9%, 31.8%, 14.5%, and 23.7%, respectively. Phylogenetic analysis based on mitochondrial genomes fully supported that the white-eared catbird is closely related to P. goodenovii. The complete mitochondrial genome obtained from the current study can provide more genomic resources and guidance for the conservation biology, taxonomy and population genetics of Norfolk Robin.
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Affiliation(s)
- Zirui Zhu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Xiang Gao
- College of Chemistry & Materials Science, Northwest University, Xi’an, Shaanxi, China
| | - Yiheng Hu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
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44
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Manthey JD, Oliveros CH, Andersen MJ, Filardi CE, Moyle RG. Gene flow and rapid differentiation characterize a rapid insular radiation in the southwest Pacific (Aves:
Zosterops
). Evolution 2020; 74:1788-1803. [DOI: 10.1111/evo.14043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/08/2020] [Accepted: 05/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Joseph D. Manthey
- Department of Biological Sciences Texas Tech University Lubbock Texas 79409
| | - Carl H. Oliveros
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico 87106
| | | | - Robert G. Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute University of Kansas Lawrence Kansas 66045
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45
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Chen D, Liu Y, Davison G, Yong DL, Gao S, Hu J, Li SH, Zhang Z. Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences. Mol Phylogenet Evol 2020; 151:106895. [PMID: 32562823 DOI: 10.1016/j.ympev.2020.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/06/2020] [Accepted: 06/12/2020] [Indexed: 11/18/2022]
Abstract
The advent of the phylogenomic era has significantly improved our understanding of the evolutionary history and biogeography of Southeast Asia's diverse avian fauna. However, the taxonomy and phylogenetic relationships of many Southeast Asian birds remain poorly resolved, especially for those with large geographic ranges, which might have experienced both ancient and recent geological and environmental changes. In this study, we examined the evolutionary history and biogeography of the hill partridges (Galliformes: Phasianidae: Arborophila spp.), currently the second most speciose galliform genus, and thought to have colonized Southeast Asia from Africa. We present a well-resolved phylogeny of 14 Arborophila species inferred from ultra-conserved elements, exons, and mitochondrial genomes from both fresh and museum samples, which representing almost complete coverage of the genus. Our fossil-calibrated divergence time estimates and biogeographic modeling showed the ancestor of Arborophila arrived in Indochina during the early Miocene, but the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification within Arborophila were driven by several tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling and extensive dispersal and speciation of Sundaic Arborophila during the Pleistocene sea-level fluctuations. Taken together, these results suggest that the evolutionary history and biogeography of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Geoffrey Davison
- National Biodiversity Centre, National Parks Board, 1 Cluny Road, 259569, Singapore
| | - Ding Li Yong
- BirdLife International (Asia), 354 Tanglin Road, #01-16/17, Tanglin International Centre, Singapore 247672, Singapore; Fenner School of Environment and Society, The Australian National University, Linnaeus Way, Canberra, ACT 2601, Australia
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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46
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Biologia Futura: rapid diversification and behavioural adaptation of birds in response to Oligocene-Miocene climatic conditions. Biol Futur 2020; 71:109-121. [PMID: 34554530 DOI: 10.1007/s42977-020-00013-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
Abstract
Our knowledge about the origin of landbirds (Telluraves) is increasing rapidly but new questions are arising because of the contradictory findings from previous studies. All of the major lineages in the highly diverse clade of Neoaves have a Gondwanan origin, although studies often disagree about the origin of different sub-lineages. Nevertheless, understanding the biogeographical histories of these groups (e.g. Accipitriformes, Passeriformes) is important when studying the evolution of variation in life history and behavioural traits. Therefore, we would like to find answers to questions such as which biogeographic changes affected the radiation of birds? When did the most influential climatic events affect the diversification of birds? What behavioural adaptations occurred in response to those large-scale changes? The major orogenetic events in Asia and South America formed specific corridors that enabled the radiation of birds. The climatic changes and habitat differentiation they caused during the Oligocene-Miocene era made the divergence of birds possible through their adaptation to newly available niches. Consequently, variation in life history and behavioural traits emerged as adaptive outcomes of changes in foraging, nestling and migratory behaviours.
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47
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Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, Suyama Y, Tagane S, Wieringa JJ, Yahara T, Hinsinger DD. Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea. PLoS One 2020; 15:e0232936. [PMID: 32442164 PMCID: PMC7244142 DOI: 10.1371/journal.pone.0232936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
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Affiliation(s)
- Joeri S. Strijk
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | | | | | - Joan T. Pereira
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - J. W. Ferry Slik
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S. Sukri
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Yoshihisa Suyama
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, Kagoshima, Japan
| | | | - Tetsukazu Yahara
- Center for Asian Conservation Ecology, Kyushu University, Fukuoka, Japan
| | - Damien D. Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l′Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
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48
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Oliver PM, Heiniger H, Hugall AF, Joseph L, Mitchell KJ. Oligocene divergence of frogmouth birds (Podargidae) across Wallace's Line. Biol Lett 2020; 16:20200040. [PMID: 32396783 PMCID: PMC7280043 DOI: 10.1098/rsbl.2020.0040] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Wallace's Line demarcates the transition between the differentiated regional faunas of Asia and Australia. However, while patterns of biotic differentiation across these two continental landmasses and the intervening island groups (Wallacea) have been extensively studied, patterns of long-term dispersal and diversification across this region are less well understood. Frogmouths (Aves: Podargidae) are a relictual family of large nocturnal birds represented by three extant genera occurring, respectively, in Asia, 'Sahul' (Australia and New Guinea) and the Solomon Islands, thus spanning Wallace's Line. We used new mitochondrial genomes from each of the extant frogmouth genera to estimate the timeline of frogmouth evolution and dispersal across Wallace's Line. Our results suggest that the three genera diverged and dispersed during the mid-Cenozoic between approximately 30 and 40 Mya. These divergences are among the oldest inferred for any trans-Wallacean vertebrate lineage. In addition, our results reveal that the monotypic Solomons frogmouth (Rigidipenna inexpectata) is one of the most phylogenetically divergent endemic bird lineages in the southwest Pacific. We suggest that the contemporary distribution of exceptionally deep divergences among extant frogmouth lineages may be explained by colonization of, and subsequent long-term persistence on, island arcs in the southwest Pacific during the Oligocene. These island arcs may have provided a pathway for biotic dispersal out of both Asia and Australia that preceded the formation of extensive emergent landmasses in Wallacea by at least 10 million years.
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Affiliation(s)
- Paul M. Oliver
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Holly Heiniger
- Centre for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide 5005, Australia
| | - Andrew F. Hugall
- Department of Sciences, Museums Victoria, Melbourne Victoria 3001, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700 Canberra ACT 2601
| | - Kieren J. Mitchell
- Centre for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, North Terrace Campus, Adelaide 5005, Australia
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49
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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.
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50
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Lim HC, Shakya SB, Harvey MG, Moyle RG, Fleischer RC, Braun MJ, Sheldon FH. Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA. Ecol Evol 2020; 10:3222-3247. [PMID: 32273983 PMCID: PMC7141000 DOI: 10.1002/ece3.5964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome-wide set of 753-4,501 variable loci and 3,919-18,472 single nucleotide polymorphisms. The formation of major within-species lineages occurred within a similar span of time (0.5-1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east-west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high-throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.
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Affiliation(s)
- Haw Chuan Lim
- Department of BiologyGeorge Mason UniversityFairfaxVirginia
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Subir B. Shakya
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - Michael G. Harvey
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
| | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDistrict of Columbia
| | - Michael J. Braun
- Department of Vertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Frederick H. Sheldon
- Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
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