1
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Cádiz MI, Tengstedt ANB, Sørensen IH, Pedersen ES, Fox AD, Hansen MM. Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data. Evol Appl 2024; 17:e70008. [PMID: 39257569 PMCID: PMC11386304 DOI: 10.1111/eva.70008] [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: 05/11/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with F ROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.
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Affiliation(s)
- María I Cádiz
- Department of Biology Aarhus University Aarhus Denmark
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2
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Manthey JD, Spellman GM. Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana). Mol Phylogenet Evol 2024; 196:108088. [PMID: 38697377 DOI: 10.1016/j.ympev.2024.108088] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
The nonrandom distribution of chromosomal characteristics and functional elements-genomic architecture-impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure-ordination, clustering, and phylogenetic methods-we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University. Lubbock, TX, USA.
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, 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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Müller IA, Thörn F, Rajan S, Ericson PGP, Dumbacher JP, Maiah G, Blom MPK, Jønsson KA, Irestedt M. Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae). PLoS One 2024; 19:e0293715. [PMID: 38781204 PMCID: PMC11115331 DOI: 10.1371/journal.pone.0293715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/26/2024] [Indexed: 05/25/2024] Open
Abstract
The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.
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Affiliation(s)
- Ingo A. Müller
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Filip Thörn
- Department of Zoology, Division of Systematics and Evolution, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Samyuktha Rajan
- Department of Zoology, Division of Ethology, Stockholm University, Stockholm, Sweden
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John P. Dumbacher
- Department of Ornithology and Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America
| | - Gibson Maiah
- New Guinea Binatang Research Center, Madang, Papua New Guinea
| | - Mozes P. K. Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Knud A. Jønsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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5
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Dalapicolla J, Weir JT, Vilaça ST, Quaresma TF, Schneider MPC, Vasconcelos ATR, Aleixo A. Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary. Ecol Evol 2024; 14:e11250. [PMID: 38660467 PMCID: PMC11040105 DOI: 10.1002/ece3.11250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.
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Affiliation(s)
- Jeronymo Dalapicolla
- Instituto Tecnológico ValeBelémParáBrazil
- Departamento de Sistemática e EcologiaUniversidade Federal da Paraíba, João PessoaParaíbaBrazil
| | - Jason T. Weir
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoOntarioCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural History, Royal Ontario MuseumTorontoOntarioCanada
| | | | | | - Maria P. C. Schneider
- Laboratório de Genômica e BiotecnologiaInstituto de Ciências Biológicas, UFPABelémBrazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de BioinformáticaLaboratório Nacional de Computação Científica, PetrópolisRio de JaneiroBrazil
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6
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Bolívar‐Leguizamón SD, Bocalini F, Silveira LF, Bravo GA. The role of biogeographical barriers on the historical dynamics of passerine birds with a circum-Amazonian distribution. Ecol Evol 2024; 14:e10860. [PMID: 38450322 PMCID: PMC10915597 DOI: 10.1002/ece3.10860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 03/08/2024] Open
Abstract
Common distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the "circum-Amazonian distribution", which surrounds Amazonia across the forested lowlands south and east of the basin, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. The underlying evolutionary and biogeographical mechanisms responsible for this widespread pattern of avian distribution have yet to be elucidated. Here, we test the effects of biogeographical barriers in four species in the passerine family Thamnophilidae by performing comparative demographic analyses of genome-scale data. Specifically, we used flanking regions of ultraconserved regions to estimate population historical parameters and genealogical trees and tested demographic models reflecting contrasting biogeographical scenarios explaining the circum-Amazonian distribution. We found that taxa with circum-Amazonian distribution have at least two main phylogeographical clusters: (1) Andes, often extending into Central America and the Tepuis; and (2) the remaining of their distribution. These clusters are connected through corridors along the Chaco-Cerrado and southeastern Amazonia, allowing gene flow between Andean and eastern South American populations. Demographic histories are consistent with Pleistocene climatic fluctuations having a strong influence on the diversification history of circum-Amazonian taxa, Refugia played a crucial role, enabling both phenotypic and genetic differentiation, yet maintaining substantial interconnectedness to keep considerable levels of gene flow during different dry/cool and warm/humid periods. Additionally, steep environmental gradients appear to play a critical role in maintaining both genetic and phenotypic structure.
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Affiliation(s)
- Sergio D. Bolívar‐Leguizamón
- Seção de AvesMuseu de Zoologia da Universidade de São PauloSão PauloBrazil
- Laboratório de Zoologia de Vertebrados, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz” –ESALQ–Universidade de São PauloPiracicabaBrazil
| | - Fernanda Bocalini
- Seção de AvesMuseu de Zoologia da Universidade de São PauloSão PauloBrazil
| | - Luís F. Silveira
- Seção de AvesMuseu de Zoologia da Universidade de São PauloSão PauloBrazil
| | - Gustavo A. Bravo
- Seção de AvesMuseu de Zoologia da Universidade de São PauloSão PauloBrazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von HumboldtClaustro de San AgustínVilla de Leyva, BoyacáColombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
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7
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Gabrielli M, Leroy T, Salmona J, Nabholz B, Milá B, Thébaud C. Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing. Mol Ecol 2024; 33:e17243. [PMID: 38108507 DOI: 10.1111/mec.17243] [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: 09/06/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long-term population processes.
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Affiliation(s)
- Maëva Gabrielli
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - Jordi Salmona
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
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8
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Garg KM, Dovih P, Chattopadhyay B. Hybrid de novo genome assembly of the sexually dimorphic Lady Amherst's pheasant. DNA Res 2024; 31:dsae001. [PMID: 38168719 PMCID: PMC10799330 DOI: 10.1093/dnares/dsae001] [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: 09/04/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/05/2024] Open
Abstract
Pheasants are an important group of birds, valued for their economic benefit as poultry birds, game birds, and as ornamental species for their plumage. Lady Amherst's pheasant Chrysolophus amherstiae is an ornamental species, valued for its elaborate and beautiful plumage. In this study, we present a high-quality de novo hybrid genome assembly of C. amherstiae. Previous attempts to sequence the genome of this species resulted in draft-level assemblies, which are not available in the public domain. Using a combination of Illumina short reads and Oxford Nanopore's long-reads, we assembled a high-quality genome of N50 ~3.9 Mb and near complete BUSCO assessment. We observed a correlation between effective population size and past climatic conditions, with an increase in population size during the warm interglacial periods. We further observed significant fluctuations in genes involved with the immune system and visual perception. C. amherstiae is a highly dimorphic species, and significant fluctuations in gene families involved in immune response, visual perception, among others, suggesting a role of mate choice and sexual selection in the evolution and maintenance of exaggerated traits in the males.
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Affiliation(s)
- Kritika M Garg
- Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, Haryana 131029, India
- Department of Biology, Ashoka University, Sonipat, Haryana 131029, India
| | - Pilot Dovih
- School of Chemistry and Biotechnology, Sastra University, Thanjavur, Tamil Nadu 613401, India
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana 131029, India
| | - Balaji Chattopadhyay
- Department of Biology, Ashoka University, Sonipat, Haryana 131029, India
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana 131029, India
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9
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Batalha-Filho H, Barreto SB, Silveira MHB, Miyaki CY, Afonso S, Ferrand N, Carneiro M, Sequeira F. Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil. Heredity (Edinb) 2024; 132:77-88. [PMID: 37985738 PMCID: PMC10844224 DOI: 10.1038/s41437-023-00662-1] [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: 01/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.
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Affiliation(s)
- Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Silvia Britto Barreto
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Mario Henrique Barros Silveira
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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10
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Schultz ED, Thom G, Zuquim G, Hickerson MJ, Tuomisto H, Ribas CC. Habitat specialization predicts demographic response and vulnerability of floodplain birds in Amazonia. Mol Ecol 2024; 33:e17221. [PMID: 38018028 DOI: 10.1111/mec.17221] [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: 04/18/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The annual flooding cycle of Amazonian rivers sustains the largest floodplains on Earth, which harbour a unique bird community. Recent studies suggest that habitat specialization drove different patterns of population structure and gene flow in floodplain birds. However, the lack of a direct estimate of habitat affinity prevents a proper test of its effects on population histories. In this work, we used occurrence data, satellite images and genomic data (ultra-conserved elements) from 24 bird species specialized on a variety of seasonally flooded environments to classify habitat affinities and test its influence on evolutionary histories of Amazonian floodplain birds. We demonstrate that birds with higher specialization in river islands and dynamic environments have gone through more recent demographic expansion and currently have less genetic diversity than floodplain generalist birds. Our results indicate that there is an intrinsic relationship between habitat affinity and environmental dynamics, influencing patterns of population structure, demographic history and genetic diversity. Within the floodplains, historical landscape changes have had more severe impacts on island specialists, making them more vulnerable to current and future anthropogenic changes, as those imposed by hydroelectric dams in the Amazon Basin.
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Affiliation(s)
- Eduardo D Schultz
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Department of Ornithology, American Museum of Natural History, New York, New York, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Gabriela Zuquim
- Department of Biology, University of Turku, Turku, Finland
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | - Camila C Ribas
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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11
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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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12
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Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA. High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 2024; 7:54. [PMID: 38184717 PMCID: PMC10771460 DOI: 10.1038/s42003-023-05748-4] [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: 12/06/2022] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
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Affiliation(s)
- Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
| | - Crystal Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Nathan Backenstose
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Trevor Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
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13
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [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: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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14
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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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15
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Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (BETHESDA, MD.) 2023; 13:jkad239. [PMID: 37847748 PMCID: PMC10700114 DOI: 10.1093/g3journal/jkad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
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Affiliation(s)
- Alba Marino
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Jorge Contreras-Garduño
- Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
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16
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Bocalini F, Bolívar-Leguizamón SD, Silveira LF, Bravo GA. Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests. Mol Ecol 2023; 32:6874-6895. [PMID: 37902123 DOI: 10.1111/mec.17180] [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: 10/31/2022] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
An open and dry vegetation belt separates Amazonia (AM) and the Atlantic Forest (AF). Evidence from palaeoclimatic and phylogenetic studies suggests past connections between these forests during cycles of increased humidity through the formation of forest corridors. The distinctive northern AF avifauna is known to have affinities both with AM and the southern AF. Still, the extent of how these two regions contributed to the assemblage of this avifauna remains poorly understood. Using historical demographic analyses and comparative phylogeography based on sub-genomic genetic sampling, we assessed how past connections between AM and AF led to shared vicariance and colonization events in four avian AF endemic taxa. Our results supported the occurrence of humid forest corridors promoting the contact between AF and AM populations and suggested two vicariant events and two colonization events from AF to AM. Population divergences were mostly non-synchronous and occurred multiple times during the Pleistocene. Historical gene flow was prevalent across study groups, supporting migration flows after the initial separation between AM and AF - a pattern previously unknown in birds between these regions. Idiosyncratic histories and divergent demographic syndromes suggest that organisms' responses to climate-driven habitat shifts broadly depend on their ecological attributes. This study strengthened our knowledge of past connections between AM and AF and provided demographic scenarios amenable for testing in other groups of co-distributed organisms.
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Affiliation(s)
| | - Sergio D Bolívar-Leguizamón
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Biológicas, Escola Superior de Agricultura 'Luiz de Queiroz' - ESALQ - Universidade de São Paulo, Piracicaba, Brazil
| | - Luís F Silveira
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Gustavo A Bravo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
- Colecciones Ornitológicas, Centro de Colecciones y Gestión de Especies, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Boyacá, Colombia
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17
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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [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: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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18
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Hernández-Alonso G, Ramos-Madrigal J, van Grouw H, Ciucani MM, Cavill EL, Sinding MHS, Gopalakrishnan S, Pacheco G, Gilbert MTP. Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Mol Biol Evol 2023; 40:msad243. [PMID: 37950889 PMCID: PMC10667084 DOI: 10.1093/molbev/msad243] [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: 05/03/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023] Open
Abstract
The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
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Affiliation(s)
- Germán Hernández-Alonso
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, United Kingdom
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily Louisa Cavill
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - George Pacheco
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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19
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Zhang H, Lundberg M, Tarka M, Hasselquist D, Hansson B. Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird. Genome Biol Evol 2023; 15:evad180. [PMID: 37793164 PMCID: PMC10627410 DOI: 10.1093/gbe/evad180] [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: 06/09/2023] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.
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Affiliation(s)
- Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Maja Tarka
- Department of Biology, Lund University, Lund, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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20
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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21
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Lavretsky P, Hernández F, Swale T, Mohl JE. Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos). G3 (BETHESDA, MD.) 2023; 13:jkad171. [PMID: 37523777 PMCID: PMC10542157 DOI: 10.1093/g3journal/jkad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023]
Abstract
The mallard (Anas platyrhynchos) is one of the most common, economically, and socially important birds around the world. Mallards were not only an important food source for early humans but eventually becoming intimately linked with people as they were domesticated over the last 2,000 years. To date, mallard genomes are largely reconstructed from samples of domestic or unknown genetic heritage. Here, we report the first high-quality genome assembly and annotation of a genetically vetted wild mallard from North America (NAwild_v1.0). The genome was assembled using a combination of shotgun libraries, proximity ligation Chicago, and Dovetail Hi-C libraries. The final assembly is ∼1.04 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome-level scaffolds, and with a N50/L50 of 79.1 Mb/4 scaffolds. We used a combination of gene prediction and similarity approaches to annotate a total of 23,584 functional genes, of which 19,242 were associated to GO terms. The genome assembly and the set of annotated genes yielded a 95.4% completeness score when compared with the BUSCO aves_odb10 dataset. Next, we aligned 3 previously published mallard genomes to ours, and demonstrate how runs of homozygosity and nucleotide diversity are substantially higher and lower, respectively, to ours and how these artificially changed genomes resulted in profoundly different and biased demographic histories. Our wild mallard assembly not only provides a valuable resource to shed light onto genome evolution, speciation, and other adaptive processes, but also helping with identifying functional genes that have been significantly altered during the domestication process.
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Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Thomas Swale
- Cantata Bio, 100 Enterprise Way Suite A101, Scotts Valley, CA 95066
| | - Jonathon E Mohl
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
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22
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Afonso RO, Pina-Martins F, Friesen V, Sun Z, Campioni L, Madeiros J, Silva MC. No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow). J Hered 2023; 114:459-469. [PMID: 37162284 DOI: 10.1093/jhered/esad030] [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: 10/28/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.
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Affiliation(s)
- Rita O Afonso
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Letizia Campioni
- MARE-Marine and Environmental Sciences Centre, Ispa-Instituto Universitário, Lisboa, Portugal
| | - Jeremy Madeiros
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton, Bermuda
| | - Mónica C Silva
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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23
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Tan HZ, Jansen JJFJ, Allport GA, Garg KM, Chattopadhyay B, Irestedt M, Pang SEH, Chilton G, Gwee CY, Rheindt FE. Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds. eLife 2023; 12:e85422. [PMID: 37549057 PMCID: PMC10406428 DOI: 10.7554/elife.85422] [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: 12/07/2022] [Accepted: 06/27/2023] [Indexed: 08/09/2023] Open
Abstract
Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.
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Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | | | | | - Kritika M Garg
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Sean EH Pang
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Glen Chilton
- Department of Biology, St. Mary's UniversityCalgaryCanada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
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24
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Winker K, Withrow JJ, Gibson DD, Pruett CL. Beringia as a high-latitude engine of avian speciation. Biol Rev Camb Philos Soc 2023; 98:1081-1099. [PMID: 36879465 DOI: 10.1111/brv.12945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Jack J Withrow
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Daniel D Gibson
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Christin L Pruett
- Department of Biology, Ouachita Baptist University, 410 Ouachita St, Arkadelphia, AR, 71998, USA
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25
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Luo H, Jiang X, Li B, Wu J, Shen J, Xu Z, Zhou X, Hou M, Huang Z, Ou X, Xu L. A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes). Commun Biol 2023; 6:746. [PMID: 37463976 PMCID: PMC10354230 DOI: 10.1038/s42003-023-05137-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.
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Affiliation(s)
- Haoran Luo
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Xinrui Jiang
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Boping Li
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jiexin Shen
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zaoxu Xu
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Minghao Hou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, 350108, China.
- Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Xiaobin Ou
- Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong University, Qingyang, Gansu Province, 745000, China.
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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26
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Germain RR, Feng S, Chen G, Graves GR, Tobias JA, Rahbek C, Lei F, Fjeldså J, Hosner PA, Gilbert MTP, Zhang G, Nogués-Bravo D. Species-specific traits mediate avian demographic responses under past climate change. Nat Ecol Evol 2023:10.1038/s41559-023-02055-3. [PMID: 37106156 DOI: 10.1038/s41559-023-02055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.
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Affiliation(s)
- Ryan R Germain
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China
| | - Guangji Chen
- BGI Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - 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
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Life Sciences, Imperial College London, Ascot, UK
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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27
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Reboud EL, Nabholz B, Chevalier E, Tilak MK, Bito D, Condamine FL. Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing. Genome Biol Evol 2023; 15:evad040. [PMID: 36896590 PMCID: PMC10101050 DOI: 10.1093/gbe/evad040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
The world's largest butterfly is the microendemic Papua New Guinean Ornithoptera alexandrae. Despite years of conservation efforts to protect its habitat and breed this up-to-28-cm butterfly, this species still figures as endangered in the IUCN Red List and is only known from two allopatric populations occupying a total of only ∼140 km². Here we aim at assembling reference genomes for this species to investigate its genomic diversity, historical demography and determine whether the population is structured, which could provide guidance for conservation programs attempting to (inter)breed the two populations. Using a combination of long and short DNA reads and RNA sequencing, we assembled six reference genomes of the tribe Troidini, with four annotated genomes of O. alexandrae and two genomes of related species Ornithoptera priamus and Troides oblongomaculatus. We estimated the genomic diversity of the three species, and we proposed scenarios for the historical population demography using two polymorphism-based methods taking into account the characteristics of low-polymorphic invertebrates. Indeed, chromosome-scale assemblies reveal very low levels of nuclear heterozygosity across Troidini, which appears to be exceptionally low for O. alexandrae (lower than 0.01%). Demographic analyses demonstrate low and steadily declining Ne throughout O. alexandrae history, with a divergence into two distinct populations about 10,000 years ago. These results suggest that O. alexandrae distribution has been microendemic for a long time. It should also make local conservation programs aware of the genomic divergence of the two populations, which should not be ignored if any attempt is made to cross the two populations.
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Affiliation(s)
- Eliette L Reboud
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Marie-ka Tilak
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Darren Bito
- Pacific Adventist University, Private Mail Bag, BOROKO 111, National Capital District, Port Moresby, Papua New Guinea
| | - Fabien L Condamine
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
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28
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Sun XY, Yuan JJ, Dong ZE. Small population of the largest water strider after the late Pleistocene and the implications for its conservation. Gene 2023; 859:147219. [PMID: 36702394 DOI: 10.1016/j.gene.2023.147219] [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: 07/21/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Climate oscillation and its synergistic impacts on habitat fragmentation have been identified as threatening the survival of some extant species. However, the mechanisms by which semi-aquatic insects impacted by such events remain poorly understood. Herein, we studied the largest water strider in the world, Gigantometra gigas, to explore the effect of these two factors on its evolutionary history. The sequences of mitogenomic and nrDNA cluster were utilized to reconstruct phylogenetic relationship among G. gigas populations and its demographic history. Mitochondrial genes were separately reconstructed topologies of that populations and detected remarkable differences. We found that G. gigas populations conform to the isolation-by-distance model, and decline occurred at about 120 ka, which was probably influenced by the climate change during the late Pleistocene and eventually maintained a small effective population size (Ne) around 85,717. The populations in Guangdong Province of China are worthy of note in that they exhibit low genetic diversity, a small Ne around 18,899 individuals, and occupy an area with little suitable future habitat for G. gigas. This work recommends that conservation efforts are implemented to ensure the long-term survival of small G. gigas populations, and notes that further evaluation of their extinction risk under the impacts of human activities is required.
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Affiliation(s)
- Xiao-Ya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China; Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China.
| | - Juan-Juan Yuan
- College of Life Sciences, Zaozhuang University, Shandong 277160, China
| | - Zhuo-Er Dong
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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29
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Wang Y, Zhan H, Zhang Y, Long Z, Yang X. Mitochondrial genome analysis, phylogeny and divergence time evaluation of Strixaluco (Aves, Strigiformes, Strigidae). Biodivers Data J 2023; 11:e101942. [PMID: 38327340 PMCID: PMC10848841 DOI: 10.3897/bdj.11.e101942] [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: 02/14/2023] [Accepted: 03/11/2023] [Indexed: 02/09/2024] Open
Abstract
Background Prior research has shown that the European peninsulas were the main sources of Strixaluco colonisation of Northern Europe during the late glacial period. However, the phylogenetic relationship and the divergence time between S.aluco from Leigong Mountain Nature Reserve, Guizhou Province, China and the Strigiformes from overseas remains unclear. The mitochondrial genome structure of birds is a covalent double-chain loop structure that is highly conserved and, thus, suitable for phylogenetic analysis. This study examined the phylogenetic relationship and divergence time of Strix using the whole mitochondrial genome of S.aluco. New information In this study, the complete mitochondrial genome of Strixaluco, with a total length of 18,632 bp, is reported for the first time. A total of 37 genes were found, including 22 tRNAs, two rRNAs, 13 protein-coding genes and two non-coding control regions. Certain species of Tytoninae were used as out-group and PhyloSuite software was applied to build the ML-tree and BI-tree of Strigiformes. Finally, the divergence time tree was constructed using BEAST 2.6.7 software and the age of Miosurniadiurna fossil-bearing sediments (6.0-9.5 Ma) was set as internal correction point. The common ancestor of Strix was confirmed to have diverged during the Pleistocene (2.58-0.01 Ma). The combined action of the dramatic uplift of the Qinling Mountains in the Middle Pleistocene and the climate oscillation of the Pleistocene caused Strix divergence between the northern and southern parts of mainland China. The isolation of glacial-interglacial rotation and glacier refuge was the main reason for the divergence of Strixuralensis and S.aluco from their common ancestor during this period. This study provides a reference for the evolutionary history of S.aluco.
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Affiliation(s)
- Yeying Wang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Haofeng Zhan
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Yu Zhang
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Zhengmin Long
- Guizhou Normal University, Guiyang, ChinaGuizhou Normal UniversityGuiyangChina
| | - Xiaofei Yang
- Guizhou University, Guiyang, ChinaGuizhou UniversityGuiyangChina
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30
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Bergeron LA, Besenbacher S, Zheng J, Li P, Bertelsen MF, Quintard B, Hoffman JI, Li Z, St Leger J, Shao C, Stiller J, Gilbert MTP, Schierup MH, Zhang G. Evolution of the germline mutation rate across vertebrates. Nature 2023; 615:285-291. [PMID: 36859541 PMCID: PMC9995274 DOI: 10.1038/s41586-023-05752-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies2. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis3. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.
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Affiliation(s)
- Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Judy St Leger
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | | | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Evolutionary & Organismal Biology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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31
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Germain RR, Feng S, Buffan L, Carmona CP, Chen G, Graves GR, Tobias JA, Rahbek C, Lei F, Fjeldså J, Hosner PA, Gilbert MTP, Zhang G, Nogués-Bravo D. Changes in the functional diversity of modern bird species over the last million years. Proc Natl Acad Sci U S A 2023; 120:e2201945119. [PMID: 36745783 PMCID: PMC9963860 DOI: 10.1073/pnas.2201945119] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/28/2022] [Indexed: 02/08/2023] Open
Abstract
Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturbances. We combine morphological, ecological, and life-history trait data for >260 extant bird species with genomic-based estimates of changing effective population size (Ne) to quantify demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. We show that functional diversity was relatively stable over this period, but underwent significant changes in some key areas of trait space due to changing species abundances. Our results suggest that patterns of population decline over the Pleistocene have been concentrated in particular regions of trait space associated with extreme reproductive strategies and low dispersal ability, consistent with an overall erosion of functional diversity. Further, species most sensitive to climate warming occupied a relatively narrow region of functional space, indicating that the largest potential population increases and decreases under climate change will occur among species with relatively similar trait sets. Overall, our results identify fluctuations in functional space of extant species over evolutionary timescales and represent the demographic-based vulnerability of different regions of functional space among these taxa. The integration of paleodemographic dynamics with functional trait data enhances our ability to quantify losses of biosphere integrity before anthropogenic disturbances and attribute contemporary biodiversity loss to different drivers over time.
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Affiliation(s)
- Ryan R. Germain
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen2100, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Shenzhen518083, China
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou311121, China
| | - Lucas Buffan
- Département de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon69342 Cedex 07, France
| | - Carlos P. Carmona
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51005, Estonia
| | - Guangii Chen
- BGI-Shenzhen, Shenzhen518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100101, China
| | - Gary R. Graves
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington20560, DC
| | - Joseph A. Tobias
- Department of Life Sciences, Imperial College London, AscotSL5 7PY, UK
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Institute of Ecology, Peking University, Beijing100871, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense5230, Denmark
| | - Fumin Lei
- Institute of Zoology, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Sciences, Beijing100101, China
| | - Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen2100, Denmark
| | - Peter A. Hosner
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen2100, Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen, Copenhagen1353, Denmark
- Department of Natural History, University Museum, Norwegian University of Science and Technology, Trondheim7491, Norway
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen2100, Denmark
- BGI-Shenzhen, Shenzhen518083, China
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou311121, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650223, China
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen2100, Denmark
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32
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Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol 2023; 32:2234-2251. [PMID: 36748940 DOI: 10.1111/mec.16875] [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: 11/04/2022] [Revised: 01/17/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Ting Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Jen Cheng
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Tau Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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33
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Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [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: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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34
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Kimmitt AA, Pegan TM, Jones AW, Wacker KS, Brennan CL, Hudon J, Kirchman JJ, Ruegg K, Benz BW, Herman R, Winger BM. Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum. Proc Biol Sci 2023; 290:20221334. [PMID: 36695033 PMCID: PMC9874272 DOI: 10.1098/rspb.2022.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.
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Affiliation(s)
- Abigail A. Kimmitt
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Teresa M. Pegan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew W. Jones
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Kristen S. Wacker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Courtney L. Brennan
- Department of Ornithology, Cleveland Museum of Natural History, Cleveland, OH 44106, USA
| | - Jocelyn Hudon
- Royal Alberta Museum, Edmonton, Alberta Canada, T5J 0G2
| | | | - Kristen Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
| | - Brett W. Benz
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachael Herman
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin M. Winger
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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35
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Hansen CCR, Láruson ÁJ, Rasmussen JA, Ballesteros JAC, Sinding MHS, Hallgrimsson GT, von Schmalensee M, Stefansson RA, Skarphédinsson KH, Labansen AL, Leivits M, Sonne C, Dietz R, Skelmose K, Boertmann D, Eulaers I, Martin MD, Helgason AS, Gilbert MTP, Pálsson S. Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla). Mol Ecol 2023; 32:1925-1942. [PMID: 36680370 DOI: 10.1111/mec.16858] [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: 10/12/2021] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110-115,000 years ago, (2) population divergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.
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Affiliation(s)
| | - Áki Jarl Láruson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Jacob Agerbo Rasmussen
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Adrian Chimal Ballesteros
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar T Hallgrimsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Madis Leivits
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Christian Sonne
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Kim Skelmose
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Boertmann
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Igor Eulaers
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Agnar S Helgason
- Department of Anthropology, University of Iceland, Reykjavik, Iceland.,deCODE Genetics, Reykjavik, Iceland
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Snaebjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
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36
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Wang Y, Xu J, Hu B, Dong C, Sun J, Li Z, Ye K, Deng F, Wang L, Aslam M, Lv W, Qin Y, Cheng Y. Assembly, annotation, and comparative analysis of Ipomoea chloroplast genomes provide insights into the parasitic characteristics of Cuscuta species. FRONTIERS IN PLANT SCIENCE 2023; 13:1074697. [PMID: 36733590 PMCID: PMC9887335 DOI: 10.3389/fpls.2022.1074697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
In the Convolvulaceae family, around 1650 species belonging to 60 genera are widely distributed globally, mainly in the tropical and subtropical regions of America and Asia. Although a series of chloroplast genomes in Convolvulaceae were reported and investigated, the evolutionary and genetic relationships among the chloroplast genomes of the Convolvulaceae family have not been extensively elucidated till now. In this study, we first reported the complete chloroplast genome sequence of Ipomoea pes-caprae, a widely distributed coastal plant with medical values. The chloroplast genome of I. pes-caprae is 161667 bp in length, and the GC content is 37.56%. The chloroplastic DNA molecule of I. pes-caprae is a circular structure composed of LSC (large-single-copy), SSC (small-single-copy), and IR (inverted repeat) regions, with the size of the three regions being 88210 bp, 12117 bp, and 30670 bp, respectively. The chloroplast genome of I. pes-caprae contains 141 genes, and 35 SSRs are identified in the chloroplast genome. Our research results provide important genomic information for the molecular phylogeny of I. pes-caprae. The Phylogenetic analysis of 28 Convolvulaceae chloroplast genomes showed that the relationship of I. pes-caprae with I. involucrata or I. obscura was much closer than that with other Convolvulaccae species. Further comparative analyses between the Ipomoea species and Cuscuta species revealed the mechanism underlying the formation of parasitic characteristics of Cuscuta species from the perspective of the chloroplast genome.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Xu
- Clinical College of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Bin Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chunxing Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixian Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kangzhuo Ye
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fang Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lulu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Mohammad Aslam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Wenliang Lv
- Clinical College of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
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37
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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38
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Moreira LR, Klicka J, Smith BT. Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age. Mol Ecol 2023; 32:1739-1759. [PMID: 36617622 DOI: 10.1111/mec.16841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpecker, species codistributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (i) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (ii) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.
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Affiliation(s)
- Lucas R Moreira
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, USA.,Department of Ornithology, American Museum of Natural History, New York City, New York, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology, University of Washington, Seattle, Washington, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York City, New York, USA
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Patil AB, Vajja SS, Raghavendra S, Satish BN, Kushalappa CG, Vijay N. Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus. FRONTIERS IN PLANT SCIENCE 2022; 13:1029540. [PMID: 36578332 PMCID: PMC9791056 DOI: 10.3389/fpls.2022.1029540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Sai Samhitha Vajja
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - S. Raghavendra
- College of Agriculture Hassan, University of Agricultural Sciences (UAS), Bangalore, Karnataka, India
| | - B. N. Satish
- College of Forestry, Ponnampet, Karnataka, India
| | | | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
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Negro JJ, Rodríguez-Rodríguez EJ, Rodríguez A, Bildstein K. Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate. PeerJ 2022; 10:e14505. [PMID: 36523450 PMCID: PMC9745957 DOI: 10.7717/peerj.14505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022] Open
Abstract
Europe holds a rich community of diurnal birds of prey, and the highest proportion of transcontinental migratory raptorial species of any landmass. This study will test the hypotheses that the high diversification of the raptor assemblage in Europe is a recent event, that closely related species sharing the same trophic niches can only coexist in sympatry during the breeding period, when food availability is higher, and finally that migration is a function of size, with the smaller species in every trophic group moving further. A consensus molecular phylogeny for the 38 regular breeding species of raptors in Europe was obtained from BirdTree (www.birdtree.org). For the same species, a trophic niche cluster dendrogram was constructed. Size and migratory strategy were introduced in the resulting phylogeny, where trophic groups were also identified. Multispecific trophic groups tended to be composed of reciprocal sister species of different sizes, while monospecific groups (n = 3) were composed of highly specialized species. Many speciation events took place recently, during the glacial cycles of the Quaternary, and size divergence among competing species may be due to character displacement. Nowadays, the smaller species in every trophic group migrate to sub-Saharan Africa. This investigation illustrates how the rich assemblage of diurnal birds of prey in Europe, more diverse and more migratory than, for instance, the North American assemblage at equivalent latitudes, has emerged recently due to the multiplication of look-alike species with similar trophic ecologies, possibly in climate refugia during cold periods.
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Affiliation(s)
- Juan J. Negro
- Estación Biológica de Doñana-CSIC, Department of Evolutionary Ecology, Sevilla, Spain
| | | | - Airam Rodríguez
- Grupo de Ornitología e Historia Natural de las islas Canarias (GOHNIC), C/La Malecita s/n, Buenavista del Norte, Canary Islands, Spain,Terrestrial Ecology Group (TEG-UAM), Department of Ecology, Universidad Autónoma de Madrid, Madrid, Spain,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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von Seth J, van der Valk T, Lord E, Sigeman H, Olsen RA, Knapp M, Kardailsky O, Robertson F, Hale M, Houston D, Kennedy E, Dalén L, Norén K, Massaro M, Robertson BC, Dussex N. Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics 2022; 23:747. [PMID: 36357860 PMCID: PMC9647977 DOI: 10.1186/s12864-022-08963-1] [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: 06/17/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation. RESULTS We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations. CONCLUSION Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
- Ecology and Genetics Research Unit, University of Oulu, 90014, Oulu, Finland
| | - Remi-André Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17121, Solna, Sweden
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
- Coastal People Southern Skies Centre of Research Excellence, University of Otago, PO Box 56, Dunedin, 9054, Aotearoa, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Marie Hale
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Dave Houston
- Department of Conservation, Biodiversity Group, Auckland, New Zealand
| | - Euan Kennedy
- Department of Conservation, Science and Capability, Christchurch, New Zealand
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Melanie Massaro
- School of Agricultural, Environmental and Veterinary Sciences and Gulbali Institute, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
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Eliason CM, Hains T, McCullough J, Andersen MJ, Hackett SJ. Genomic novelty within a "great speciator" revealed by a high-quality reference genome of the collared kingfisher (Todiramphus chloris collaris). G3 (BETHESDA, MD.) 2022; 12:jkac260. [PMID: 36156134 PMCID: PMC9635628 DOI: 10.1093/g3journal/jkac260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin's finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr's "great speciators," the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.
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Affiliation(s)
- Chad M Eliason
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL 60605, USA
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Taylor Hains
- Department of Ecology and Evolution, Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jenna McCullough
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael J Andersen
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
- Department of Ecology and Evolution, Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
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Srinivas Y, Yumnam B, Dutta S, Jhala Y. Assessing genetic diversity and population structure for prioritizing conservation of the critically endangered Great Indian Bustard (Aredotis nigriceps). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
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Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands. Heredity (Edinb) 2022; 129:281-294. [PMID: 36175501 PMCID: PMC9613907 DOI: 10.1038/s41437-022-00562-w] [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: 02/22/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/14/2022] Open
Abstract
Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.
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Dong F, Zhang Q, Chen YL, Lei FM, Li SH, Wu F, Yang XJ. Potential millennial-scale avian declines by humans in southern China. GLOBAL CHANGE BIOLOGY 2022; 28:5505-5513. [PMID: 35665575 DOI: 10.1111/gcb.16289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Mounting observational records demonstrate human-caused faunal decline in recent decades, while accumulating archaeological evidence suggests an early biodiversity impact of human activities during the Holocene. A fundamental question arises concerning whether modern wildlife population declines began during early human disturbance. Here, we performed a population genomic analysis of six common forest birds in East Asia to address this question. For five of them, demographic history inference based on 25-33 genomes of each species revealed dramatic population declines by 4- to 48-fold over millennia (e.g. 2000-5000 thousand years ago). Nevertheless, summary statistics detected nonsignificant correlations between these population size trajectories and Holocene temperature variations, and ecological niche models explicitly predicted extensive range persistence during the Holocene, implying limited demographic consequence of Holocene climate change. Further analyses suggest high negative correlations between the reconstructed population declines and human disturbance intensities and indicate a potential driver of human activities. These findings provide a deep-time and large-scale insight into the recently recognized avifaunal decline and support an early origin hypothesis of human effects on biodiversity. Overall, our study sheds light on the current biodiversity crisis in the context of long-term human-environment interactions and offers a multi-evidential framework for quantitatively assessing the ecological consequences of human disturbance.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yi-Lin Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Fei Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Sawakuchi AO, Schultz ED, Pupim FN, Bertassoli DJ, Souza DF, Cunha DF, Mazoca CE, Ferreira MP, Grohmann CH, Wahnfried ID, Chiessi CM, Cruz FW, Almeida RP, Ribas CC. Rainfall and sea level drove the expansion of seasonally flooded habitats and associated bird populations across Amazonia. Nat Commun 2022; 13:4945. [PMID: 35999209 PMCID: PMC9399099 DOI: 10.1038/s41467-022-32561-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/05/2022] [Indexed: 01/27/2023] Open
Abstract
Spatial arrangement of distinct Amazonian environments through time and its effect on specialized biota remain poorly known, fueling long-lasting debates about drivers of biotic diversification. We address the late Quaternary sediment deposition that assembled the world's largest seasonally flooded ecosystems. Genome sequencing was used to reconstruct the demographic history of bird species specialized in either early successional vegetation or mature floodplain forests. Sediment deposition that built seasonally flooded habitats accelerated throughout the Holocene (last 11,700 years) under sea level highstand and intensification of the South American Monsoon, at the same time as global increases in atmospheric methane concentration. Bird populations adapted to seasonally flooded habitats expanded due to enlargement of Amazonian river floodplains and archipelagos. Our findings suggest that the diversification of the biota specialized in seasonally flooded habitats is coupled to sedimentary budget changes of large rivers, which rely on combined effects of sea level and rainfall variations. This study found that millennial periods of higher rainfall combined with rising sea level enhanced sediment accumulation in Amazonian rivers valleys. This fuelled synchronous expansion of vegetation adapted to seasonally flooded substrates and its specialized bird populations, showing how global climate changes can affect specific Amazonian species.
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Affiliation(s)
- A O Sawakuchi
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil.
| | - E D Schultz
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil.,Department of Ornithology, American Museum of Natural History, 200 Central Park West, New York, NY, USA
| | - F N Pupim
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo (UNIFESP), Rua São Nicolau 210, Diadema, SP, Brazil
| | - D J Bertassoli
- School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio 1000, São Paulo, SP, Brazil
| | - D F Souza
- Gerência de Hidrologia e Gestão Territorial, Serviço Geológico do Brasil (CPRM-SGB), Rua Costa 55, São Paulo, SP, Brazil
| | - D F Cunha
- Programa de Pós-Graduação em Geoquímica e Geotectônica, Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C E Mazoca
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - M P Ferreira
- Programa de Pós-Graduação em Geoquímica e Geotectônica, Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C H Grohmann
- Institute of Energy and Environment, University of São Paulo, Av. Prof. Luciano Gualberto 1289, São Paulo, SP, Brazil
| | - I D Wahnfried
- Departamento de Geociências, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos 6200, Manaus, AM, Brazil
| | - C M Chiessi
- School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio 1000, São Paulo, SP, Brazil
| | - F W Cruz
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - R P Almeida
- Institute of Geosciences, University of São Paulo, Rua do Lago 562, São Paulo, SP, Brazil
| | - C C Ribas
- Programa de Pós-Graduação em Biologia (Ecologia), Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil.,Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Manaus, AM, Brazil
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Ericson PGP, Irestedt M, Zuccon D, Larsson P, Tison JL, Emslie SD, Götherström A, Hume JP, Werdelin L, Qu Y. A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture. Commun Biol 2022; 5:857. [PMID: 35999361 PMCID: PMC9399080 DOI: 10.1038/s42003-022-03811-0] [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: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution. 14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Dario Zuccon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Jean-Luc Tison
- Department of Laboratory Medicine, Örebro University Hospital; Södra Grev Rosengatan, SE-70185, Örebro, Sweden
| | - Steven D Emslie
- Department of Biology and Marine Biology, University of North Carolina; Wilmington, 601S. College Road, Wilmington, NC, 28403, USA
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, SE-10691, Stockholm, Sweden
| | - Julian P Hume
- Bird Group, Department of Life Sciences, Natural History Museum, Akeman St, Tring, Herts, UK
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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Ericson PGP, Irestedt M, Qu Y. Demographic history, local adaptation and vulnerability to climate change in a tropical mountain bird in New Guinea. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
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Hu T, Chen G, Xu Z, Luo S, Wang H, Li C, Shan L, Zhang B. De Novo Whole-Genome Sequencing and Assembly of the Yellow-Throated Bunting (Emberiza elegans) Provides Insights into Its Evolutionary Adaptation. Animals (Basel) 2022; 12:ani12152004. [PMID: 35953992 PMCID: PMC9367368 DOI: 10.3390/ani12152004] [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: 04/22/2022] [Revised: 07/06/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary We report the genomic sequence of Emberiza elegans for understanding the evolutionary mechanisms of environmental adaptation and for studying a more effective genetic monitoring of this species. The E. elegans assembly was approximately 1.14 Gb, with a scaffold N50 of 28.94 Mb. About 15,868 protein-coding genes were predicted, and 16.62% of the genome was identified as having repetitive elements. Our genomic evolution analyses found considerable numbers of adaptive genes that may help the yellow-throated bunting cope with migratory behavior and environmental stressors of diseases. These results provide us with new insights into genomic evolution and adaptation, thus providing a valuable resource for further studies of population genetic diversity and genome evolution in this species. Abstract Yellow-throated bunting is a small migratory songbird unique to the Palearctic region. However, the genetic studies of this species remain limited, with no nuclear genomic sequence reported to date. In this study, the genomic DNA from the bird was sequenced in long reads using Nanopore sequencing technology. Combining short-read sequencing, the genome was well-assembled and annotated. The final length of the assembly is approximately 1.14 Gb, with a scaffold N50 of 28.94 Mb. About 15,868 protein-coding genes were predicted, and 16.62% of the genome was identified as having repetitive elements. Comparative genomic analysis showed numerous expanded gene families and positively selected genes significantly enriched in those KEGG pathways that are associated with migratory behavior adaptation and immune response. Here, this newly generated de novo genome of the yellow-throated bunting using long reads provide the research community with a valuable resource for further studies of population genetic diversity and genome evolution in this species.
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Affiliation(s)
- Tingli Hu
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Guotao Chen
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Zhen Xu
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Site Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Wang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China
| | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Lei Shan
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (L.S.); (B.Z.)
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei 230601, China
- Correspondence: (L.S.); (B.Z.)
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