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Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun 2024; 15:6609. [PMID: 39098897 PMCID: PMC11298535 DOI: 10.1038/s41467-024-50852-6] [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: 12/31/2023] [Accepted: 07/16/2024] [Indexed: 08/06/2024] Open
Abstract
Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.
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Affiliation(s)
- Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | | | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Mateo Garcia-Olazabal
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MI, USA
| | - Tristram O Dodge
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Molly Schumer
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA.
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
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2
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Berv JS, Singhal S, Field DJ, Walker-Hale N, McHugh SW, Shipley JR, Miller ET, Kimball RT, Braun EL, Dornburg A, Parins-Fukuchi CT, Prum RO, Winger BM, Friedman M, Smith SA. Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction. SCIENCE ADVANCES 2024; 10:eadp0114. [PMID: 39083615 PMCID: PMC11290531 DOI: 10.1126/sciadv.adp0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024]
Abstract
Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K-Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mitochondrial genomes. Bird clades originating near the K-Pg boundary exhibited numerous shifts in the mode of molecular evolution, suggesting a burst of genomic heterogeneity at this point in Earth's history. These inferred shifts in substitution patterns were closely related to evolutionary shifts in developmental mode, adult body mass, and patterns of metabolic scaling. Our results suggest that the end-Cretaceous mass extinction triggered integrated patterns of evolution across avian genomes, physiology, and life history near the dawn of the modern bird radiation.
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Affiliation(s)
- Jacob S. Berv
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
- Museum of Paleontology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
- Museum of Zoology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Daniel J. Field
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
- Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nathanael Walker-Hale
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Sean W. McHugh
- Department of Evolution, Ecology, and Population Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - J. Ryan Shipley
- Department of Forest Dynamics, Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Zürcherstrasse 111 8903, Birmensdorf, Switzerland
| | - Eliot T. Miller
- Center for Avian Population Studies, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - C. Tomomi Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Richard O. Prum
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Benjamin M. Winger
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
- Museum of Zoology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matt Friedman
- Museum of Paleontology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Earth and Environmental Sciences, University of Michigan, 1100 North University Avenue, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen A. Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Biological Sciences Building, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Dey P, Ray SD, Kochiganti VHS, Pukazhenthi BS, Koepfli KP, Singh RP. Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails. Genes (Basel) 2024; 15:742. [PMID: 38927678 PMCID: PMC11202683 DOI: 10.3390/genes15060742] [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: 04/29/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau's geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
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Affiliation(s)
- Prateek Dey
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
- Bharathiar University, Coimbatore 641046, Tamil Nadu, India
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Swapna Devi Ray
- Sálim Ali Centre for Ornithology and Natural History (South India Centre of Wildlife Institute of India), Anaikatti, Coimbatore 641108, Tamil Nadu, India; (P.D.); (S.D.R.)
| | | | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya 824236, Bihar, India
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4
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Du K, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge T, Schumer M, Park H, Meyer A, Schartl M. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573732. [PMID: 38260540 PMCID: PMC10802237 DOI: 10.1101/2023.12.30.573732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.
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5
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Aardema ML, Schmidt KL, Amato G. Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America. Genetica 2023; 151:281-292. [PMID: 37612519 PMCID: PMC10654179 DOI: 10.1007/s10709-023-00193-x] [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: 05/15/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset of genetic markers derived from their nuclear genomes. Our analyses show clear nuclear divergence between A. m. macao and A. m. cyanoptera in Central America. Collectively however, samples from this region appear genetically more similar to one another than they do to the examined South American (Brazilian) A. m. macao sample. This observation contradicts our previous assessments based on mitochondrial DNA analyses that A. m. macao in Central and South America represent a single phylogeographical group that is evolutionarily distinct from Central American A. m. cyanoptera. Nonetheless, in agreement with our previous findings, ongoing genetic exchange between the two subspecies appears limited. Rather, our analyses indicate that incomplete lineage sorting is the best supported explanation for cytonuclear discordance within these parrots. High-altitude regions in Central America may act as a reproductive barrier, limiting contemporary hybridization between A. m. macao and A. m. cyanoptera. The phylogeographic complexities of scarlet macaw taxa in this region highlight the need for additional evolutionary examinations of these populations.
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Affiliation(s)
- Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Kari L Schmidt
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - George Amato
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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6
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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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7
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Benham PM, Cicero C, Escalona M, Beraut E, Marimuthu MPA, Nguyen O, Nachman MW, Bowie RCK. A highly contiguous genome assembly for the California quail (Callipepla californica). J Hered 2023; 114:418-427. [PMID: 36763048 PMCID: PMC10287149 DOI: 10.1093/jhered/esad008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/09/2023] [Indexed: 02/11/2023] Open
Abstract
The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
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8
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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9
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Kuo PC, Benson RBJ, Field DJ. The influence of fossils in macroevolutionary analyses of 3D geometric morphometric data: A case study of galloanseran quadrates. J Morphol 2023; 284:e21594. [PMID: 37183494 DOI: 10.1002/jmor.21594] [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: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/16/2023]
Abstract
In birds and other reptiles, the quadrate acts as a hinge between the lower jaw and the skull and plays an important role in avian cranial kinesis. Though previous studies have qualitatively described substantial variation in quadrate morphology among birds, none have attempted to quantify evolutionary changes in quadrate shape. Here, we investigate geometric evolution of the quadrate in Galloanserae, a major clade of extant birds uniting chicken-like (Galliformes) and duck-like (Anseriformes) fowl. We quantified morphological variation in the quadrate across 50 extant galloanseran species covering all major extant subclades using three-dimensional geometric morphometrics, and performed ancestral shape reconstructions in the context of an up-to-date neornithine phylogeny. We find that our results based only on extant quadrates may overlook plesiomorphic features captured by fossil taxa, resulting in an ancestral state reconstruction for Galloanserae that is seemingly an approximation of the average shape of the extant data set. By contrast, analyses incorporating early fossil galloanseran quadrates (from taxa such as Asteriornis, Presbyornis, and Conflicto) result in ancestral geometric reconstructions more similar to the morphology of extant galliforms, indicating that the quadrate of the last common ancestor of galloanserans may have been more morphologically and functionally similar to those of extant galliforms than to extant anseriforms. These results generally corroborate previous inferences of galloanseran quadrate plesiomorphies and identify several additional plesiomorphic features of the galloanseran quadrate for the first time. Our results illustrate the importance of incorporating fossil taxa into ancestral shape reconstructions and help elucidate important aspects of the morphology and function of the avian feeding apparatus early in crown bird evolutionary history.
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Affiliation(s)
- Pei-Chen Kuo
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Roger B J Benson
- Department of Earth Sciences, University of Oxford, Oxford, UK
- American Museum of Natural History, New York, New York, USA
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
- Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London, UK
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10
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Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
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Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Ambu J, Martínez-Solano Í, Suchan T, Hernandez A, Wielstra B, Crochet PA, Dufresnes C. Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes). Mol Phylogenet Evol 2023; 183:107783. [PMID: 37044190 DOI: 10.1016/j.ympev.2023.107783] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 03/28/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The advent of genomic methods allows us to revisit the evolutionary history of organismal groups for which robust phylogenies are still lacking, particularly in species complexes that frequently hybridize. In this study, we conduct RAD-sequencing (RAD-seq) analyses of midwife toads (genus Alytes), an iconic group of western Mediterranean amphibians famous for their parental care behavior, but equally infamous for the difficulties to reconstruct their evolutionary history. Through admixture and phylogenetic analyses of thousands of loci, we provide the most comprehensive phylogeographic framework for the A. obstetricans complex to date, as well as the first fully resolved phylogeny for the entire genus. As part of this effort, we carefully explore the influence of different sampling schemes and data filtering thresholds on tree reconstruction, showing that several, slightly different, yet robust topologies may be retrieved with small datasets obtained by stringent SNP calling parameters, especially when admixed individuals are included. In contrast, analyses of incomplete but larger datasets converged on the same phylogeny, irrespective of the reconstruction method used or the proportion of missing data. The Alytes tree features three Miocene-diverged clades corresponding to the proposed subgenera Ammoryctis (A. cisternasii), Baleaphryne (A. maurus, A. dickhilleni and A. muletensis), and Alytes (A. obstetricans complex). The latter consists of six evolutionary lineages, grouped into three clades of Pliocene origin, and currently delimited as two species: (1) A. almogavarii almogavarii and A. a. inigoi; (2) A. obstetricans obstetricans and A. o. pertinax; (3) A. o. boscai and an undescribed taxon (A. o. cf. boscai). These results contradict the mitochondrial tree, due to past mitochondrial captures in A. a. almogavarii (central Pyrenees) and A. o. boscai (central Iberia) by A. obstetricans ancestors during the Pleistocene. Patterns of admixture between subspecies appear far more extensive than previously assumed from microsatellites, causing nomenclatural uncertainties, and even underlying the reticulate evolution of one taxon (A. o. pertinax). All Ammoryctis and Baleaphryne species form shallow clades, so their taxonomy should remain stable. Amid the prevalence of cyto-nuclear discordance among terrestrial vertebrates and the usual lack of resolution of conventional nuclear markers, our study advocates for phylogeography based on next-generation sequencing, but also encourages properly exploring parameter space and sampling schemes when building and analyzing genomic datasets.
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Affiliation(s)
- Johanna Ambu
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Íñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Tomasz Suchan
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Axel Hernandez
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | | | - Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
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Vázquez-Miranda H, Zink RM, Pinto BJ. Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence. Mol Phylogenet Evol 2022; 171:107466. [DOI: 10.1016/j.ympev.2022.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
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13
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Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference. Ecol Evol 2021; 11:16354-16364. [PMID: 34824832 PMCID: PMC8601899 DOI: 10.1002/ece3.8199] [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: 06/30/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections Museum of Zoology Dresden Germany
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14
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Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds. DIVERSITY 2021. [DOI: 10.3390/d13110555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
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