1
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Péron G. The effect of the demographic history on the evolution of senescence: A potential new test of the mutation accumulation theory. Mech Ageing Dev 2024; 219:111927. [PMID: 38499252 DOI: 10.1016/j.mad.2024.111927] [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: 11/09/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
The different evolutionary theories of senescence predict different directions for the correlation between the population size and the intensity of senescence. Using simulations, I highlighted how the effect of the population size on the intensity of senescence could be reinforced by the time since populations have been large or small. I devised a mutation-selection model in which the effect of the mutations was age-specific. Several small populations diverged from a same large population at different points in time. At the end of the simulation, the correlation between the time since the populations had been small and the rate of senescence was positive under the mutation accumulation theory and negative under the antagonistic pleiotropy theory. The phenomenon was strong enough to reverse the usually negative relationship between the intensity of senescence and the generation time. These mutually-exclusive predictions could help broaden the taxonomic support for the mutation accumulation theory of senescence, currently mostly supported in humans and lab invertebrates. I briefly mention a few potential applications in real-life systems.
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Affiliation(s)
- Guillaume Péron
- CNRS, Université Lyon 1, 43 bd du 11 novembre 1918, VILLEURBANNE cedex 69622, France.
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2
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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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3
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Xu X, Wang C, Xu C, Yuan J, Wang G, Wu Y, Huang C, Jing H, Yang P, Xu L, Peng S, Shan F, Xia X, Jin F, Hou F, Wang J, Mi D, Ren Y, Liu Y, Irwin DM, Li X, Chen W, Li G. Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 2024; 24:e13896. [PMID: 37955396 DOI: 10.1111/1755-0998.13896] [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: 07/05/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
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Affiliation(s)
- Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yajiang Wu
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shiming Peng
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Xiaochao Xia
- Guangdong Wildlife Monitoring, Rescue and Conservation Center, Guangzhou, China
| | - Fuyuan Jin
- Guangdong Maoming Forest Park Administrative Office, Maoming, China
| | - Fanghui Hou
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an, China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Guangzhou Zoo, Guangzhou, China
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4
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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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5
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Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
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Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
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6
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Li XJ, Wang XY, Yang C, Lin LL, Zhao L, Yu XP, Lei FM, Huang Y. The De Novo Genome Sequencing of Silver Pheasant (Lophura nycthemera). Genome Biol Evol 2021; 13:6460815. [PMID: 34904656 PMCID: PMC8691047 DOI: 10.1093/gbe/evab275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 02/03/2023] Open
Abstract
Silver pheasant (Lophura nycthemera) belongs to Phasianidae, Galliformes, which exhibits high subspecific differentiation. In this study, we assembled a novel genome based on 98.42 Gb of Illumina sequencing data and 30.20 Gb of PacBio sequencing data. The size of the final assembled genome was 1.01 Gb, with a contig N50 of 6.96 Mb. Illumina paired-end reads (94.96%) were remapped to the contigs. The assemble genome shows high completeness, with a complete BUSCO score of 92.35% using the avian data set. A total of 16,747 genes were predicted from the generated assembly, and 16,486 (98.44%) of the genes were annotated. The average length of genes, exons, and introns were 19,827.53, 233.69, and 1841.19 bp, respectively. Noncoding RNAs included 208 miRNAs, 40 rRNAs, and 264 tRNAs, and a total of 189 pseudogenes were identified; 116.31 Mb (11.47%) of the genome consisted of repeat sequences, with the greatest proportion of LINEs. This assembled genome provides a valuable reference genome for further studies on the evolutionary history and conversion genetics of L. nycthemera and the phylogenomics of the Galliformes lineage.
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Affiliation(s)
- Xue-Juan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao-Yang Wang
- School of Biological and Environmental Engineering, Xi'an University, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Li-Liang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Le Zhao
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Xiao-Ping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Fu-Min Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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7
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Manthey JD, Klicka J, Spellman GM. The Genomic Signature of Allopatric Speciation in a Songbird Is Shaped by Genome Architecture (Aves: Certhia americana). Genome Biol Evol 2021; 13:evab120. [PMID: 34042960 PMCID: PMC8364988 DOI: 10.1093/gbe/evab120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture-the nonrandom distribution of functional elements and chromosomal characteristics-through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and microchromosomes shapes the genomic signatures of speciation: chromosome size has: 1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and 2) a negative relationship with genetic diversity and recombination rate.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Klicka
- Burke Museum of Natural History, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
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8
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Cowles SA, Weeks BC, Perrin L, Chen N, Uy JAC. Comparison of adult census size and effective population size support the need for continued protection of two Solomon Island endemics. THE EMU 2021; 121:45-54. [PMID: 35264816 PMCID: PMC8903160 DOI: 10.1080/01584197.2021.1915163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/05/2021] [Indexed: 06/14/2023]
Abstract
Because a population's ability to respond to rapid change is dictated by standing genetic variation, we can better predict a population's long-term viability by estimating and then comparing adult census size (N) and effective population size (N e ). However, most studies only measure N or N e , which can be misleading. Using a combination of field and genomic sequence data, we here estimate and compare N and N e in two range-restricted endemics of the Solomon Islands. Two Zosterops White-eye species inhabit the small island of Kolombangara, with a high elevation species endemic to the island (Z. murphyi) and a low elevation species endemic to the Solomon Islands (Z. kulambangrae). Field observations reveal large values of N for both species with Z. kulambangrae numbering at 114,781 ± 32,233 adults, and Z. murphyi numbering at 64,412 ± 15,324 adults. In contrast, genomic analyses reveal that N e was much lower than N, with Z. kulambangrae estimated at 694.5 and Z. murphyi at 796.1 individuals. Further, positive Tajima's D values for both species suggest that they have experienced a demographic contraction, providing a mechanism for low values of N e . Comparison of N and N e suggests that Z. kulambangrae and Z. murphyi are not at immediate threat of extinction but may be at genetic risk. Our results provide important baseline data for long-term monitoring of these island endemics, and argue for measuring both population size estimates to better gauge long-term population viability.
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Affiliation(s)
- Sarah A. Cowles
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Brian C. Weeks
- School for Environment & Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Lindsey Perrin
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - J. Albert C. Uy
- Department of Biology, University of Miami, Coral Gables, FL, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
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9
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Sendell-Price AT, Ruegg KC, Robertson BC, Clegg SM. An island-hopping bird reveals how founder events shape genome-wide divergence. Mol Ecol 2021; 30:2495-2510. [PMID: 33826187 DOI: 10.1111/mec.15898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.
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Affiliation(s)
- Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Kristen C Ruegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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10
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Pouchon C, Lavergne S, Fernández Á, Alberti A, Aubert S, Mavárez J. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. AMERICAN JOURNAL OF BOTANY 2021; 108:113-128. [PMID: 33426651 DOI: 10.1002/ajb2.1591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Events of accelerated species diversification represent one of Earth's most celebrated evolutionary outcomes. Northern Andean high-elevation ecosystems, or páramos, host some plant lineages that have experienced the fastest diversification rates, likely triggered by ecological opportunities created by mountain uplifts, local climate shifts, and key trait innovations. However, the mechanisms behind rapid speciation into the new adaptive zone provided by these opportunities have long remained unclear. METHODS We address this issue by studying the Venezuelan clade of Espeletia, a species-rich group of páramo-endemics showing a dazzling ecological and morphological diversity. We performed several comparative analyses to study both lineage and trait diversification, using an updated molecular phylogeny of this plant group. RESULTS We showed that sets of either vegetative or reproductive traits have conjointly diversified in Espeletia along different vegetation belts, leading to adaptive syndromes. Diversification in vegetative traits occurred earlier than in reproductive ones. The rate of species and morphological diversification showed a tendency to slow down over time, probably due to diversity dependence. We also found that closely related species exhibit significantly more overlap in their geographic distributions than distantly related taxa, suggesting that most events of ecological divergence occurred at close geographic proximity within páramos. CONCLUSIONS These results provide compelling support for a scenario of small-scale ecological divergence along multiple ecological niche dimensions, possibly driven by competitive interactions between species, and acting sequentially over time in a leapfrog pattern.
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Affiliation(s)
- Charles Pouchon
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Ángel Fernández
- Herbario IVIC. Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas, 1020-A, Venezuela
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Serge Aubert
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
- Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc, SAJF, Station Alpine Joseph Fourier, 38000, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
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11
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Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KSH, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity. eLife 2020; 9:e62765. [PMID: 33350381 PMCID: PMC7775107 DOI: 10.7554/elife.62765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
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Affiliation(s)
- Chyi Yin Gwee
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Kritika M Garg
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Balaji Chattopadhyay
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Keren R Sadanandan
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Tri Haryoko
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Malcolm CK Soh
- University of Western Australia, School of Biological SciencesPerthAustralia
| | - Kelvin S-H Peh
- University of Southampton, School of Biological Sciences, UniversitySouthamptonUnited Kingdom
| | - Karen MC Rowe
- Sciences Department, Museums VictoriaMelbourneAustralia
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah KualaDarussalamIndonesia
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal UniversityXuzhouChina
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
- Center for Tropical Veterinary Studies – One Health Collaboration Center, Universitas Syiah KualaDarussalamIndonesia
| | - Guinevere OU Wogan
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeleyUnited States
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Frank E Rheindt
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
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12
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Tobias JA, Ottenburghs J, Pigot AL. Avian Diversity: Speciation, Macroevolution, and Ecological Function. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-025023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.
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Affiliation(s)
- Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - Jente Ottenburghs
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Alex L. Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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13
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The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes ( Zosterops lateralis). G3-GENES GENOMES GENETICS 2020; 10:3147-3163. [PMID: 32660974 PMCID: PMC7466963 DOI: 10.1534/g3.120.401352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.
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14
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Manthey JD, Oliveros CH, Andersen MJ, Filardi CE, Moyle RG. Gene flow and rapid differentiation characterize a rapid insular radiation in the southwest Pacific (Aves:
Zosterops
). Evolution 2020; 74:1788-1803. [DOI: 10.1111/evo.14043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/08/2020] [Accepted: 05/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Joseph D. Manthey
- Department of Biological Sciences Texas Tech University Lubbock Texas 79409
| | - Carl H. Oliveros
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico 87106
| | | | - Robert G. Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute University of Kansas Lawrence Kansas 66045
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15
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Sendell-Price AT, Ruegg KC, Clegg SM. Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection. Heredity (Edinb) 2020; 124:535-549. [PMID: 32080374 PMCID: PMC7080774 DOI: 10.1038/s41437-020-0298-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/25/2023] Open
Abstract
Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.
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Affiliation(s)
- Ashley T Sendell-Price
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Kristen C Ruegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sonya M Clegg
- Department of Zoology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, OX1 3PS, UK
- Environmental Futures Research Institute, Griffith University, Queensland, 4111, Australia
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16
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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17
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Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K, Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model explains the diversity of island birds worldwide. Nature 2020; 579:92-96. [PMID: 32076267 DOI: 10.1038/s41586-020-2022-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored9, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography7,8 with the temporal information contained in molecular phylogenies10 proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.
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Affiliation(s)
- Luis Valente
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany. .,Naturalis Biodiversity Center, Leiden, The Netherlands. .,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands. .,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | | | - Martim Melo
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal.,Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Sonya M Clegg
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Katja Havenstein
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Mieres, Spain
| | - Christophe Thébaud
- Unité Mixte de Recherche 5174, CNRS-IRD-Paul Sabatier University, Toulouse, France
| | - Tina Aschenbach
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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18
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Nevado B, Wong ELY, Osborne OG, Filatov DA. Adaptive Evolution Is Common in Rapid Evolutionary Radiations. Curr Biol 2019; 29:3081-3086.e5. [PMID: 31495580 DOI: 10.1016/j.cub.2019.07.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/08/2019] [Accepted: 07/19/2019] [Indexed: 10/26/2022]
Abstract
One of the most long-standing and important mysteries in evolutionary biology is why biological diversity is so unevenly distributed across space and taxonomic lineages. Nowhere is this disparity more evident than in the multitude of rapid evolutionary radiations found on oceanic islands and mountain ranges across the globe [1-5]. The evolutionary processes driving these rapid diversification events remain unclear [6-8]. Recent genome-wide studies suggest that natural selection may be frequent during rapid evolutionary radiations, as inferred from work in cichlid fish [9], white-eye birds [10], new world lupins [11], and wild tomatoes [12]. However, whether frequent adaptive evolution is a general feature of rapid evolutionary radiations remains untested. Here we show that adaptive evolution is significantly more frequent in rapid evolutionary radiations compared to background levels in more slowly diversifying lineages. This result is consistent across a wide range of angiosperm lineages analyzed: 12 evolutionary radiations, which together comprise 1,377 described species, originating from some of the most biologically diverse systems on Earth. In addition, we find a significant negative correlation between population size and frequency of adaptive evolution in rapid evolutionary radiations. A possible explanation for this pattern is that more frequent adaptive evolution is at least partly driven by positive selection for advantageous mutations that compensate for the fixation of slightly deleterious mutations in smaller populations.
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Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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19
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Ottenburghs J. Digest: White‐eye birds provide possible answer to the paradox of the great speciator*. Evolution 2019; 73:1681-1682. [DOI: 10.1111/evo.13814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 07/29/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jente Ottenburghs
- Department of Ecology and GeneticsUppsala University Norbyvägen 18D 75236 Uppsala Sweden
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20
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Cowles SA, Uy JAC. Rapid, complete reproductive isolation in two closely related
Zosterops
White‐eye bird species despite broadly overlapping ranges*. Evolution 2019; 73:1647-1662. [DOI: 10.1111/evo.13797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah A. Cowles
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
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21
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Rawlence NJ, Scofield RP, McGlone MS, Knapp M. History Repeats: Large Scale Synchronous Biological Turnover in Avifauna From the Plio-Pleistocene and Late Holocene of New Zealand. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00158] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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O’Connell DP, Kelly DJ, Lawless N, O’Brien K, Marcaigh FÓ, Karya A, Analuddin K, Marples NM. A sympatric pair of undescribed white-eye species (Aves: Zosteropidae: Zosterops) with different origins. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Darren P O’Connell
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- School of Biology & Environment Science, University College Dublin, Dublin, Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Naomi Lawless
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Katie O’Brien
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Fionn Ó Marcaigh
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo, Kendari, South-east Sulawesi, Indonesia
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo, Kendari, South-east Sulawesi, Indonesia
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
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23
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Wang Q, Lu W, Yang J, Jiang L, Zhang Q, Kan X, Yang X. Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:27-36. [DOI: 10.1016/j.cbd.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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24
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Phylogenomics, biogeography, and adaptive radiation of grapes. Mol Phylogenet Evol 2018; 129:258-267. [DOI: 10.1016/j.ympev.2018.08.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/27/2022]
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25
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Sohn JI, Nam K, Hong H, Kim JM, Lim D, Lee KT, Do YJ, Cho CY, Kim N, Chai HH, Nam JW. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 2018; 7:5052204. [PMID: 30010758 PMCID: PMC6065499 DOI: 10.1093/gigascience/giy086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/19/2018] [Accepted: 07/04/2018] [Indexed: 12/30/2022] Open
Abstract
Background Yeonsan Ogye (YO), an indigenous Korean chicken breed (Gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short reads (376.6X) and low-depth Pacific Biosciences (PacBio) long reads (9.7X). Findings The contig and scaffold NG50s of the hybrid de novo assembly were 362.3 Kbp and 16.8 Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single-copy orthologous genes using Benchmarking Universal Single-Copy Orthologs and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long reads (50X) and scaffolded with short reads) and superior to other avian genomes (92%-93%; assembled with short read-only or hybrid methods). Compared to galGal4 and galGal5, the draft genome included 551 structural variations including the fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing and reduced representation bisulfite sequencing data were analyzed from 20 tissues, including 4 black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long noncoding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. Conclusions We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.
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Affiliation(s)
- Jang-il Sohn
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Kyoungwoo Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Hyosun Hong
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Dajeong Lim
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Yoon Jung Do
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Chang Yeon Cho
- Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon, 55717, Republic of Korea
| | - Namshin Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Han-Ha Chai
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
- College of Pharmacy, Chonnam National University, Kwangju, 61186, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
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26
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Phuong MA, Mahardika GN. Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution. Mol Biol Evol 2018; 35:1210-1224. [PMID: 29514313 PMCID: PMC5913681 DOI: 10.1093/molbev/msy034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and nontoxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100× coverage) and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are composed of one to six exons and are typically short in length (mean = ∼85 bp). Second, we expanded our understanding of the following genetic features of conotoxin evolution: 1) positive selection, where exons coding the mature toxin region were often three times more divergent than their adjacent noncoding regions, 2) expression regulation, with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome (24-63%), and 3) extensive gene turnover, where Conidae species varied from 120 to 859 conotoxin gene copies. Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. Overall, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.
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Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Denpasar, Bali, Indonesia
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27
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Wickramasinghe N, Robin VV, Ramakrishnan U, Reddy S, Seneviratne SS. Non-sister Sri Lankan white-eyes (genus Zosterops) are a result of independent colonizations. PLoS One 2017; 12:e0181441. [PMID: 28792950 PMCID: PMC5549887 DOI: 10.1371/journal.pone.0181441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/02/2017] [Indexed: 11/18/2022] Open
Abstract
Co-occurrence of closely related taxa on islands could be attributed to sympatric speciation or multiple colonization. Sympatric speciation is considered to be rare in small islands, however multiple colonizations are known to be common in both oceanic and continental islands. In this study we investigated the phylogenetic relatedness and means of origin of the two sympatrically co-occurring Zosterops white-eyes, the endemic Zosterops ceylonensis and its widespread regional congener Z. palpebrosus, in the island of Sri Lanka. Sri Lanka is a continental island in the Indian continental shelf of the Northern Indian Ocean. Our multivariate morphometric analyses confirmed the phenotypic distinctness of the two species. Maximum Likelihood and Bayesian phylogenetic analyses with ~2000bp from two mitochondrial (ND2 and ND3) and one nuclear (TGF) gene indicated that they are phylogenetically distinct, and not sister to each other. The two subspecies of the peninsula India; Z. p. egregius of Sri Lanka and India and Z. p. nilgiriensis of Western Ghats (India) clustered within the Z. palpebrosus clade having a common ancestor. In contrast, the divergence of the endemic Z. ceylonensis appears to be much deeper and is basal to the other Zosterops white-eyes. Therefore we conclude that the two Zosterops species originated in the island through independent colonizations from different ancestral lineages, and not through island speciation or multiple colonization from the same continental ancestral population. Despite high endemism, Sri Lankan biodiversity is long considered to be a subset of southern India. This study on a speciose group with high dispersal ability and rapid diversification rate provide evidence for the contribution of multiple colonizations in shaping Sri Lanka’s biodiversity. It also highlights the complex biogeographic patterns of the South Asian region, reflected even in highly vagile groups such as birds.
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Affiliation(s)
- Nelum Wickramasinghe
- Avian Evolution Node, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - V. V. Robin
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Uma Ramakrishnan
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Sampath S. Seneviratne
- Avian Evolution Node, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
- * E-mail:
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28
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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29
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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30
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Husemann M, Sturm S, Curto M, Meimberg H, Habel JC. Four new mitochondrial genomes of the genus zosterops (aves: passeriformes: zosteropidae) from East Africa with a phylogenetic evaluation of the group. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:544-548. [PMID: 33473551 PMCID: PMC7799947 DOI: 10.1080/23802359.2016.1198937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The white-eye birds of the genus Zosterops have been recognized for their high speciation rates in the past, but the relationships of the East African populations are not yet fully resolved. We sequenced and annotated mitogenomes of four populations currently assigned to three East African white-eye species, Zosterops senegalensis, Z. abyssinicus and Z. poliogaster. For Z. senegalensis specimens from two distant populations were sequenced; for the other taxa we used samples collected at one site. The mitogenomes ranged between 17,827 and 17,974 bp, in size similar to previously published mitogenomes analyzed for this genus from other geographic regions. The mitogenomes contain the classical set of 13 coding genes, two structural rRNA genes and 22 tRNA genes. We constructed a phylogeny using all complete mitogenomes currently available for the genus. The phylogeny supports an Asian or Oceanic origin of the genus Zosterops. The East African species represent a monophyletic clade, but the two specimens of Zosterops senegalensis from different regions do not group together, supporting previous hypotheses of cryptic species within the genus. The new genetic resources provided here may help to further explore the relationships and evolution of the genus.
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Affiliation(s)
- Martin Husemann
- Department of General Zoology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Saale, Germany.,Department of Ecology and Ecosystem Management, Terrestrial Ecology Research Group, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany.,Centrum Für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Sarah Sturm
- Department of Ecology and Ecosystem Management, Terrestrial Ecology Research Group, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Manuel Curto
- Research Center in Biodiversity and Genetic Resources (CIBIO)/InBio Associated Laboratory, University of Porto, Vairão, Portugal.,Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BoKu), Vienna, Austria
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BoKu), Vienna, Austria
| | - Jan Christian Habel
- Department of Ecology and Ecosystem Management, Terrestrial Ecology Research Group, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
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31
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Nevado B, Atchison GW, Hughes CE, Filatov DA. Widespread adaptive evolution during repeated evolutionary radiations in New World lupins. Nat Commun 2016; 7:12384. [PMID: 27498896 PMCID: PMC4979066 DOI: 10.1038/ncomms12384] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/28/2016] [Indexed: 01/13/2023] Open
Abstract
The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification. Species radiations can be driven by both adaptive and non-adaptive processes, but the relative importance of these drivers is unknown. Here, Nevado et al. show that multiple radiations in the New World lupins were associated with genome-wide accelerations in both coding and regulatory evolution, suggesting a strong influence of adaptive processes.
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Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Guy W Atchison
- Institute of Systematic Botany, University of Zurich, Zurich 8008, Switzerland
| | - Colin E Hughes
- Institute of Systematic Botany, University of Zurich, Zurich 8008, Switzerland
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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32
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Venton D. Highlight: Unpicking the Secrets of the “Great Speciator”. Genome Biol Evol 2015; 7:2779-80. [PMID: 26419753 PMCID: PMC4607537 DOI: 10.1093/gbe/evv181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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