1
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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2
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Poikela N, Laetsch DR, Hoikkala V, Lohse K, Kankare M. Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana. Genome Biol Evol 2024; 16:evae024. [PMID: 38482698 PMCID: PMC10972691 DOI: 10.1093/gbe/evae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 04/01/2024] Open
Abstract
Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.
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Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ville Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
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3
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Meyer L, Barry P, Riquet F, Foote A, Der Sarkissian C, Cunha RL, Arbiol C, Cerqueira F, Desmarais E, Bordes A, Bierne N, Guinand B, Gagnaire PA. Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Mol Ecol 2024:e17277. [PMID: 38279695 DOI: 10.1111/mec.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
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Affiliation(s)
- Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Barry
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Vairão, Portugal
| | | | - Andrew Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, CNRS, University of Toulouse Paul Sabatier, Toulouse, France
| | - Regina L Cunha
- Centre of Marine Sciences-CCMAR, University of Algarve, Faro, Portugal
| | | | | | - Erick Desmarais
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anaïs Bordes
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Bruno Guinand
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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4
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Wang Z, Luo W, Ping J, Xia Y, Ran J, Zeng X. Large X-effects are absent in torrent frogs with nascent sex chromosomes. Mol Ecol 2023; 32:5338-5349. [PMID: 37602937 DOI: 10.1111/mec.17113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/23/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023]
Abstract
Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered to act as the driver of reproductive isolation. Here, we examined several hybrid zones of torrent frog Amolops mantzorum species complex, using an approach by mapping species-diagnostic loci onto the reference genome to compare sex-linked versus autosomal patterns of introgression. We find little support in sex-linked incompatibilities for large X-effects for these populations in hybrid zones with homomorphic sex chromosomes, due to the absence of the hemizygous effects. As expected, the large X-effects were not found in those with heteromorphic but newly evolved sex chromosomes, owing to the absence of strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest little role for sex-linked genes in speciation. The large X-effects in those with nascent sex chromosomes may not be as ubiquitous as presumed across the animal kingdom.
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Affiliation(s)
- Ziwen Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Luo
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jun Ping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianghong Ran
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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5
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Lundberg M, Mackintosh A, Petri A, Bensch S. Inversions maintain differences between migratory phenotypes of a songbird. Nat Commun 2023; 14:452. [PMID: 36707538 PMCID: PMC9883250 DOI: 10.1038/s41467-023-36167-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.
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Affiliation(s)
- Max Lundberg
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Anna Petri
- Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
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6
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Yusuf LH, Tyukmaeva V, Hoikkala A, Ritchie MG. Divergence and introgression among the virilis group of Drosophila. Evol Lett 2022; 6:537-551. [PMID: 36579165 PMCID: PMC9783487 DOI: 10.1002/evl3.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 12/03/2022] Open
Abstract
Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.
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Affiliation(s)
- Leeban H. Yusuf
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
| | - Venera Tyukmaeva
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom,Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Anneli Hoikkala
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskylä40014Finland
| | - Michael G. Ritchie
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
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7
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David JR, Ferreira EA, Jabaud L, Ogereau D, Bastide H, Yassin A. Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species. Ecol Evol 2022; 12:e8821. [PMID: 35432924 PMCID: PMC9006235 DOI: 10.1002/ece3.8821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Adaptive introgression is ubiquitous in animals, but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during 1 year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after 4 years (~60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically distinct and reproductively isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step toward understanding the genome-wide dynamics of speciation-through-introgression.
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Affiliation(s)
- Jean R. David
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Laure Jabaud
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - David Ogereau
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Héloïse Bastide
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
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8
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Suvorov A, Kim BY, Wang J, Armstrong EE, Peede D, D'Agostino ERR, Price DK, Waddell P, Lang M, Courtier-Orgogozo V, David JR, Petrov D, Matute DR, Schrider DR, Comeault AA. Widespread introgression across a phylogeny of 155 Drosophila genomes. Curr Biol 2022; 32:111-123.e5. [PMID: 34788634 PMCID: PMC8752469 DOI: 10.1016/j.cub.2021.10.052] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 01/12/2023]
Abstract
Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here, we leverage 155 genome assemblies from 149 species to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the 9 clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the tree of life.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jeremy Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - David Peede
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas, NV 89119, USA
| | - Peter Waddell
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Michael Lang
- CNRS, Institut Jacques Monod, Université de Paris, Paris 75013, France
| | | | - Jean R David
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE) CNRS, IRD, Univ. Paris-sud, Université Paris-Saclay, Gif sur Yvette 91190, France; Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Aaron A Comeault
- Molecular Ecology & Evolution Group, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2DGA, UK.
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9
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How Important Are Structural Variants for Speciation? Genes (Basel) 2021; 12:genes12071084. [PMID: 34356100 PMCID: PMC8305853 DOI: 10.3390/genes12071084] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribution of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation.
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10
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Wiberg RAW, Tyukmaeva V, Hoikkala A, Ritchie MG, Kankare M. Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana. Mol Ecol 2021; 30:3783-3796. [PMID: 34047417 DOI: 10.1111/mec.16003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022]
Abstract
Detecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here, we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and tested for signatures of cold adaptation in population genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the scale of environmental variation experienced by the species, and measured variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements, while controlling for effects of demography and population structure. The top candidate SNPs were enriched on the X and fourth chromosomes, and they also lay near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and fourth chromosomes, which also showed highest interpopulation FST . This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.
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Affiliation(s)
- R A W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - V Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - A Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - M G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - M Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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11
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Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023]
Abstract
A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Current Address: Sean Stankowski, IST Austria, Klosterneuburg, 3400, Austria
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, 0316, Norway.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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12
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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13
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A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly. BMC Evol Biol 2020; 20:141. [PMID: 33138771 PMCID: PMC7607883 DOI: 10.1186/s12862-020-01703-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics. RESULTS Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS). CONCLUSIONS Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.
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14
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Perrier C, Rougemont Q, Charmantier A. Demographic history and genomics of local adaptation in blue tit populations. Evol Appl 2020; 13:1145-1165. [PMID: 32684952 PMCID: PMC7359843 DOI: 10.1111/eva.13035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France.,Centre de Biologie pour la Gestion des Populations UMR CBGP INRAE CIRAD IRD Montpellier SupAgro Univ Montpellier Montpellier France
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France
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15
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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16
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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17
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Delprat A, Guillén Y, Ruiz A. Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage. J Hered 2020; 110:102-117. [PMID: 30407542 DOI: 10.1093/jhered/esy057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/03/2018] [Indexed: 12/27/2022] Open
Abstract
We investigated rates of chromosomal evolution in Drosophila mojavensis using whole-genome sequence information from D. mojavensis, Drosophila buzzatii, and Drosophila virilis. Drosophila mojavensis is a cactophilic species of the repleta group living under extreme ecological conditions in the deserts of the Southwestern United States and Northwestern México. The genome of D. buzzatii, another member of the repleta group, was recently sequenced and the largest scaffolds anchored to all chromosomes using diverse procedures. Chromosome organization between D. mojavensis and D. buzzatii was compared using MUMmer and GRIMM software. Our results corroborate previous cytological analyses that indicated chromosome 2 differed between these 2 species by 10 inversions, chromosomes X and 5 differed by one inversion each, and chromosome 4 was homosequential. In contrast, we found that chromosome 3 differed by 5 inversions instead of the expected 2 that were previously inferred by cytological analyses. Thirteen of these inversions occurred in the D. mojavensis lineage: 12 are fixed and one of them is a polymorphic inversion previously described in populations from Sonora and Baja California, México. We previously investigated the breakpoints of chromosome 2 inversions fixed in D. mojavensis. Here we characterized the breakpoint regions of the 5 inversions found in chromosome 3 in order to infer the molecular mechanism that generated each inversion and its putative functional consequences. Overall, our results reveal a number of gene alterations at the inversion breakpoints with putative adaptive consequences that point to natural selection as the cause for fast chromosomal evolution in D. mojavensis.
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Affiliation(s)
- Alejandra Delprat
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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18
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Pfeiler E. Genetic Diversity and Demographic History in the Cactophilic Drosophila repleta Species Group (Diptera: Drosophilidae) in North America Inferred from Mitochondrial DNA Barcodes. J Hered 2020; 110:34-45. [PMID: 29868793 DOI: 10.1093/jhered/esy023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 05/17/2018] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity in mitochondrial DNA barcodes, comprising a segment of the cytochrome c oxidase subunit I (COI) gene, was used to infer demographic histories in selected taxa of the cactophilic Drosophila repleta species group in North America. Haplotype and nucleotide diversities were determined in 16 taxa based on both previously published and new sequences. Haplotype diversity (h) differed dramatically in different taxa, varying from h = 0 in Drosophila eremophila, Drosophila hexastigma, and Drosophila bifurca to h = 0.99 in Drosophila hamatofila. Genetic diversity indices and sample sizes were sufficient to infer demographic histories from mismatch distribution analysis and Bayesian skyline plots for 9 taxa: Drosophila mojavensis baja, Drosophila mojavensis sonorensis, Drosophila arizonae, Drosophila aldrichi, D. hamatofila, Drosophila spenceri, Drosophila mainlandi, Drosophila mettleri, and Drosophila nigrospiracula. Evidence was found for both population expansions and relatively stable populations in these species. Demographic history varied dramatically in subspecies of D. mojavensis, showing a relatively stable population size over time in D. m. sonorensis from the mainland Sonoran Desert whereas a large population expansion was evident in D. m. baja from the Baja California Peninsula, providing support for the hypothesis that the split of sister species D. mojavensis and D. arizonae from a common ancestor occurred on the mainland rather than the peninsula as proposed by others. No evidence was found for a causal relationship between a stable or expanding population and host plant shifts from prickly-pear cactus to columnar cacti, which has occurred independently in many taxa of the repleta group.
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Affiliation(s)
- Edward Pfeiler
- Centro de Investigación en Alimentación y Desarrollo, A.C., Unidad Guaymas, Guaymas, Sonora, México
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19
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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20
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Cooper BS, Vanderpool D, Conner WR, Matute DR, Turelli M. Wolbachia Acquisition by Drosophila yakuba-Clade Hosts and Transfer of Incompatibility Loci Between Distantly Related Wolbachia. Genetics 2019; 212:1399-1419. [PMID: 31227544 PMCID: PMC6707468 DOI: 10.1534/genetics.119.302349] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
Maternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts codiversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The three Drosophila yakuba-clade hosts [(D. santomea, D. yakuba) D. teissieri] diverged ∼3 MYA and currently hybridize on the West African islands Bioko and São Tomé. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when uninfected females mate with infected males. D. yakuba-clade Wolbachia are closely related to wMel, globally polymorphic in D. melanogaster We use draft Wolbachia and mitochondrial genomes to demonstrate that D. yakuba-clade phylogenies for Wolbachia and mitochondria tend to follow host nuclear phylogenies. However, roughly half of D. santomea individuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressed D. yakuba mitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate chronogram-based statistical tests. Loci that cause CI in wMel are disrupted in D. yakuba-clade Wolbachia; but a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.
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Affiliation(s)
- Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - William R Conner
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Daniel R Matute
- Biology Department, University of North Carolina at Chapel Hill, North Carolina 27510
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, California 95616
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21
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Lehnert SJ, Bentzen P, Kess T, Lien S, Horne JB, Clément M, Bradbury IR. Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon. Mol Ecol 2019; 28:2074-2087. [DOI: 10.1111/mec.15065] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Paul Bentzen
- Biology Department Dalhousie University Halifax Nova Scotia Canada
| | - Tony Kess
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - John B. Horne
- Gulf Coast Research Laboratory University of Southern Mississippi Ocean Springs Mississippi USA
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's Newfoundland Canada
- Labrador Institute Memorial University of Newfoundland Happy Valley‐Goose Bay Newfoundland Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
- Biology Department Dalhousie University Halifax Nova Scotia Canada
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22
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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23
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Fuller ZL, Koury SA, Phadnis N, Schaeffer SW. How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis. Mol Ecol 2019; 28:1283-1301. [PMID: 30402909 PMCID: PMC6475473 DOI: 10.1111/mec.14923] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023]
Abstract
The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barriers. This review examines the genetic causes and consequences of inversions as recombination suppressors and the role that recombination suppression plays in establishing inversions in populations as they are involved in adaptation within heterogeneous environments. This often results in the formation of clines of gene arrangement frequencies among populations. Recombination suppression leads to the differentiation of the gene arrangements which may accelerate the accumulation of fixed genetic differences among populations. If these fixed mutations cause incompatibilities, then inversions pose important reproductive barriers between species. This review uses the evolution of inversions in Drosophila pseudoobscura and D. persimilis as a case study for how inversions originate, establish and contribute to the evolution of reproductive isolation.
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Affiliation(s)
- Zachary L. Fuller
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
| | - Spencer A. Koury
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Nitin Phadnis
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Stephen W. Schaeffer
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
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24
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Guillén Y, Casillas S, Ruiz A. Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis. J Hered 2019; 110:92-101. [PMID: 30124907 DOI: 10.1093/jhered/esy041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022] Open
Abstract
Evolutionary rates for protein-coding genes are determined not only by natural selection but also by multiple genomic factors including mutation rates, recombination, gene expression levels, and chromosomal location. To investigate the joint effects of different genomic determinants on protein evolution, we compared the coding sequences of 9017 single-copy orthologs between 2 cactophilic species from the Drosophila subgenus, Drosophila mojavensis and D. buzzatii, whose genomes have been previously sequenced. We assessed the impact of 7 genomic determinants, that is, chromosome type, recombination, chromosomal inversions, expression breadth, expression level, gene length, and the number of exons, on divergence rates of protein-coding genes to understand patterns of evolutionary variation. Integrative analysis of these factors revealed that 1) X-linked and autosomal genes evolve at significantly different rates in agreement with the faster-X hypothesis, 2) genes located on the dot chromosome and pericentromeric regions have higher divergence rates, 3) genes located at chromosomes with more fixed inversions have higher pairwise divergence than those located at nearly collinear chromosomes, and 4) gene expression patterns can be considered the strongest determinant of protein evolution. In addition, the number of exons and protein length had a significant effect on pairwise divergence at synonymous sites. All in all, our results show the relative importance of each genomic factor on the rates of protein evolution and functional constraint in these 2 cactophilic Drosophila species.
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Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sònia Casillas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,The Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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25
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Maxwell CS, Mattox K, Turissini DA, Teixeira MM, Barker BM, Matute DR. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 2019; 73:42-58. [PMID: 30414183 PMCID: PMC6430640 DOI: 10.1111/evo.13643] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.
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Affiliation(s)
- Colin S Maxwell
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Mattox
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Marcus M Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, University of Brasília, Brasília, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
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26
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Presgraves DC. Evaluating genomic signatures of "the large X-effect" during complex speciation. Mol Ecol 2018; 27:3822-3830. [PMID: 29940087 PMCID: PMC6705125 DOI: 10.1111/mec.14777] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 12/16/2022]
Abstract
The ubiquity of the "two rules of speciation"-Haldane's rule and the large X-effect-implies a general, special role for sex chromosomes in the evolution of intrinsic postzygotic reproductive isolation. The recent proliferation of genome-scale analyses has revealed two further general observations: (a) complex speciation involving some form of gene flow is not uncommon, and (b) sex chromosomes in male- and in female-heterogametic taxa tend to show elevated differentiation relative to autosomes. Together, these observations are consistent with speciation histories in which population genetic differentiation at autosomal loci is reduced by gene flow while natural selection against hybrid incompatibilities renders sex chromosomes relatively refractory to gene flow. Here, I summarize multilocus population genetic and population genomic evidence for greater differentiation on the X (or Z) vs. the autosomes and consider the possible causes. I review common population genetic circumstances involving no selection and/or no interspecific gene flow that are nevertheless expected to elevate differentiation on sex chromosomes relative to autosomes. I then review theory for why large X-effects exist for hybrid incompatibilities and, more generally, for loci mediating local adaptation. The observed levels of sex chromosome vs. autosomal differentiation, in many cases, appear consistent with simple explanations requiring neither large X-effects nor gene flow. Discerning signatures of large X-effects during complex speciation will therefore require analyses that go beyond chromosome-scale summaries of population genetic differentiation, explicitly test for differential introgression, and/or integrate experimental genetic data.
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Affiliation(s)
- Daven C. Presgraves
- Department of Biology, University of Rochester, Rochester, New York, 14627, USA
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27
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Schaeffer SW. Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics. Genetics 2018; 210:3-13. [PMID: 30166445 PMCID: PMC6116959 DOI: 10.1534/genetics.118.301084] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 12/22/2022] Open
Abstract
The concept of synteny, or conservation of genes on the same chromosome, traces its origins to the early days of Drosophila genetics. This discovery emerged from comparisons of linkage maps from different species of Drosophila with the goal of understanding the process of speciation. H. J. Muller published a landmark article entitled Bearings of the "Drosophila" work on systematics, where he synthesized genetic and physical map data and proposed a model of speciation and chromosomal gene content conservation. These models have withstood the test of time with the advent of molecular genetic analysis from protein to genome level variation. Muller's ideas provide a framework to begin to answer questions about the evolutionary forces that shape the structure of the genome.
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Affiliation(s)
- Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania 16802-5301
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28
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Cooper BS, Sedghifar A, Nash WT, Comeault AA, Matute DR. A Maladaptive Combination of Traits Contributes to the Maintenance of a Drosophila Hybrid Zone. Curr Biol 2018; 28:2940-2947.e6. [PMID: 30174184 DOI: 10.1016/j.cub.2018.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022]
Abstract
Drosophila teissieri and D. yakuba diverged approximately 3 mya and are thought to share a large, ancestral, African range [1-3]. These species now co-occur in parts of continental Africa and in west Africa on the island of Bioko [1, 4]. While D. yakuba is a human commensal, D. teissieri seems to be associated with Parinari fruits, restricting its range to forests [4-6]. Genome data indicate introgression, despite no evidence of contemporary hybridization. Here we report the discovery of D. yakuba-D. teissieri hybrids at the interface of secondary forests and disturbed, open habitats on Bioko. We demonstrate that hybrids are the F1 progeny of D. yakuba females and D. teissieri males. At high temperatures like those found on Bioko, D. teissieri females are generally less receptive to mating, and in combination with temperature effects on egg lay and egg-to-adult viability, this decreases the potential for gene flow between female D. teissieri and male D. yakuba relative to the reciprocal cross. Field and laboratory experiments demonstrate that F1 hybrids have a maladaptive combination of D. yakuba behavior and D. teissieri physiology, generating additional barriers to gene flow. Nevertheless, analysis of introgressed and non-introgressed regions of the genome indicate that, while rare, gene flow is relatively recent. Our observations identify precise intrinsic and extrinsic factors that, along with hybrid male sterility, limit gene flow and maintain these species. These data contribute to a growing body of literature that suggests the Gulf of Guinea may be a hotspot for hybridization.
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Affiliation(s)
- Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Alisa Sedghifar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - W Thurston Nash
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Aaron A Comeault
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA.
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29
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Fuller ZL, Leonard CJ, Young RE, Schaeffer SW, Phadnis N. Ancestral polymorphisms explain the role of chromosomal inversions in speciation. PLoS Genet 2018; 14:e1007526. [PMID: 30059505 PMCID: PMC6085072 DOI: 10.1371/journal.pgen.1007526] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/09/2018] [Accepted: 06/29/2018] [Indexed: 01/28/2023] Open
Abstract
Understanding the role of chromosomal inversions in speciation is a fundamental problem in evolutionary genetics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in Drosophila persimilis and D. pseudoobscura. We provide a solution to the puzzling origins of the selfish Sex-Ratio arrangement in D. persimilis and uncover surprising patterns of phylogenetic discordance on this chromosome. These patterns show that, contrary to widely held views, all fixed chromosomal inversions between D. persimilis and D. pseudoobscura were already present in their ancestral population long before the species split. Our results suggest that patterns of higher genomic divergence and an association of reproductive isolation genes with chromosomal inversions may be a direct consequence of incomplete lineage sorting of ancestral polymorphisms. These findings force a reconsideration of the role of chromosomal inversions in speciation, not as protectors of existing hybrid incompatibilities, but as fertile grounds for their formation.
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Affiliation(s)
- Zachary L. Fuller
- Department of Biology, Erwin W. Mueller Laboratories, The Pennsylvania State University, University Park, PA, United States of America
| | | | - Randee E. Young
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Stephen W. Schaeffer
- Department of Biology, Erwin W. Mueller Laboratories, The Pennsylvania State University, University Park, PA, United States of America
| | - Nitin Phadnis
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
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30
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Gompert Z, Mandeville EG, Buerkle CA. Analysis of Population Genomic Data from Hybrid Zones. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022652] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322
| | - Elizabeth G. Mandeville
- Department of Botany and Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, Laramie, Wyoming 82071
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
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31
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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32
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Guerrero RF, Hahn MW. Speciation as a sieve for ancestral polymorphism. Mol Ecol 2017; 26:5362-5368. [DOI: 10.1111/mec.14290] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/27/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology Indiana University Bloomington IN USA
- Department of Computer Science Indiana University Bloomington IN USA
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33
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Davey JW, Barker SL, Rastas PM, Pinharanda A, Martin SH, Durbin R, McMillan WO, Merrill RM, Jiggins CD. No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions. Evol Lett 2017; 1:138-154. [PMID: 30283645 PMCID: PMC6122123 DOI: 10.1002/evl3.12] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/21/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Mechanisms that suppress recombination are known to help maintain species barriers by preventing the breakup of coadapted gene combinations. The sympatric butterfly species Heliconius melpomene and Heliconius cydno are separated by many strong barriers, but the species still hybridize infrequently in the wild, and around 40% of the genome is influenced by introgression. We tested the hypothesis that genetic barriers between the species are maintained by inversions or other mechanisms that reduce between-species recombination rate. We constructed fine-scale recombination maps for Panamanian populations of both species and their hybrids to directly measure recombination rate within and between species, and generated long sequence reads to detect inversions. We find no evidence for a systematic reduction in recombination rates in F1 hybrids, and also no evidence for inversions longer than 50 kb that might be involved in generating or maintaining species barriers. This suggests that mechanisms leading to global or local reduction in recombination do not play a significant role in the maintenance of species barriers between H. melpomene and H. cydno.
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Affiliation(s)
- John W. Davey
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Sarah L. Barker
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
| | - Pasi M. Rastas
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
| | - Ana Pinharanda
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Simon H. Martin
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger InstituteCambridgeCB10 1SAUnited Kingdom
| | | | - Richard M. Merrill
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Chris D. Jiggins
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
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34
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Yang M, He Z, Shi S, Wu CI. Can genomic data alone tell us whether speciation happened with gene flow? Mol Ecol 2017; 26:2845-2849. [PMID: 28345182 DOI: 10.1111/mec.14117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/08/2017] [Accepted: 03/20/2017] [Indexed: 01/02/2023]
Abstract
The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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35
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Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nat Ecol Evol 2017; 1:119. [PMID: 28812690 PMCID: PMC5607633 DOI: 10.1038/s41559-017-0119] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/16/2017] [Indexed: 12/23/2022]
Abstract
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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Affiliation(s)
- Cheng-Ruei Lee
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan ROC
| | - Baosheng Wang
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Department of Plant Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Julius P Mojica
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Terezie Mandáková
- Plant Cytogenomics Group, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | | | - Jose Luis Goicoechea
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Nadeesha Perera
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Uffe Hellsten
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Stephen Fairclough
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yeisoo Yu
- Phyzen Genomics Institute, Phyzen Inc., Seoul 151-836, South Korea
| | - Dave Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianwei Zhang
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Wolfgang Golser
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Kathryn Ghattas
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Rod Wing
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Martin A Lysak
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Thomas Mitchell-Olds
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
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36
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Costa RJ, Wilkinson-Herbots H. Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model. Genetics 2017; 205:1597-1618. [PMID: 28193727 PMCID: PMC5378116 DOI: 10.1534/genetics.116.188060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 01/25/2017] [Indexed: 12/03/2022] Open
Abstract
The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, it has been reported that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions-including the assumption of constant gene flow until the present. This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used, by means of likelihood-ratio tests, to distinguish between alternative models representing the following divergence scenarios: (a) divergence with potentially asymmetric gene flow until the present, (b) divergence with potentially asymmetric gene flow until some point in the past and in isolation since then, and (c) divergence in complete isolation. We illustrate the procedure on pairs of Drosophila sequences from ∼30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this article.
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Affiliation(s)
- Rui J Costa
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom
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37
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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38
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Etges WJ, de Oliveira CC, Rajpurohit S, Gibbs AG. Effects of temperature on transcriptome and cuticular hydrocarbon expression in ecologically differentiated populations of desert Drosophila. Ecol Evol 2017; 7:619-637. [PMID: 28116058 PMCID: PMC5243788 DOI: 10.1002/ece3.2653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 12/20/2022] Open
Abstract
We assessed the effects of temperature differences on gene expression using whole-transcriptome microarrays and cuticular hydrocarbon variation in populations of cactophilic Drosophila mojavensis. Four populations from Baja California and mainland Mexico and Arizona were each reared on two different host cacti, reared to sexual maturity on laboratory media, and adults were exposed for 12 hr to 15, 25, or 35°C. Temperature differences influenced the expression of 3,294 genes, while population differences and host plants affected >2,400 each in adult flies. Enriched, functionally related groups of genes whose expression changed at high temperatures included heat response genes, as well as genes affecting chromatin structure. Gene expression differences between mainland and peninsular populations included genes involved in metabolism of secondary compounds, mitochondrial activity, and tRNA synthases. Flies reared on the ancestral host plant, pitaya agria cactus, showed upregulation of genes involved in metabolism, while flies reared on organ pipe cactus had higher expression of DNA repair and chromatin remodeling genes. Population × environment (G × E) interactions had widespread effects on the transcriptome where population × temperature interactions affected the expression of >5,000 orthologs, and there were >4,000 orthologs that showed temperature × host plant interactions. Adults exposed to 35°C had lower amounts of most cuticular hydrocarbons than those exposed to 15 or 25°C, including abundant unsaturated alkadienes. For insects adapted to different host plants and climatic regimes, our results suggest that temperature shifts associated with climate change have large and significant effects on transcriptomes of genetically differentiated natural populations.
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Affiliation(s)
- William J. Etges
- Program in Ecology and Evolutionary BiologyDepartment of Biological SciencesUniversity of ArkansasFayettevilleAR 72701USA
| | - Cássia C. de Oliveira
- Program in Ecology and Evolutionary BiologyDepartment of Biological SciencesUniversity of ArkansasFayettevilleAR 72701USA
- Present address: Math and Science DivisionLyon CollegeBatesvilleAR72501USA
| | - Subhash Rajpurohit
- School of Life SciencesUniversity of NevadaLas VegasNV 89919USA
- Present address: Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Allen G. Gibbs
- School of Life SciencesUniversity of NevadaLas VegasNV 89919USA
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Potter S, Moritz C, Eldridge MDB. Gene flow despite complex Robertsonian fusions among rock-wallaby (Petrogale) species. Biol Lett 2016; 11:rsbl.2015.0731. [PMID: 26445985 DOI: 10.1098/rsbl.2015.0731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Complex Robertsonian rearrangements, with shared arms in different fusions, are expected to prevent gene flow between hybrids through missegregation during meiosis. Here, we estimate gene flow between recently diverged and chromosomally diverse rock-wallabies (Petrogale) to test for this form of chromosomal speciation. Contrary to expectations, we observe relatively high admixture among species with complex fusions. Our results reinforce the need to consider alternative roles of chromosome change, together with genic divergence, in driving speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, Australian Capital Territory 2601, Australia Australian Museum Research Institute, Sydney, New South Wales 2010, Australia
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Sydney, New South Wales 2010, Australia
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Abstract
We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.
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Giménez MD, Förster DW, Jones EP, Jóhannesdóttir F, Gabriel SI, Panithanarak T, Scascitelli M, Merico V, Garagna S, Searle JB, Hauffe HC. A Half-Century of Studies on a Chromosomal Hybrid Zone of the House Mouse. J Hered 2016; 108:25-35. [PMID: 27729448 DOI: 10.1093/jhered/esw061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
The first natural chromosomal variation in the house mouse was described nearly 50 years ago in Val Poschiavo on the Swiss side of the Swiss-Italian border in the Central Eastern Alps. Studies have extended into neighboring Valtellina, and the house mice of the Poschiavo-Valtellina area have been subject to detailed analysis, reviewed here. The maximum extent of this area is 70 km, yet it has 4 metacentric races and the standard 40-chromosome telocentric race distributed in a patchwork fashion. The metacentric races are characterized by highly reduced diploid numbers (2n = 22-26) resulting from Robertsonian fusions, perhaps modified by whole-arm reciprocal translocations. The races hybridize and the whole Poschiavo-Valtellina area can be considered a "hybrid zone." The studies of this area have provided insights into origin of races within hybrid zones, gene flow within hybrid zones and the possibility of speciation in hybrid zones. This provides a case study of how chromosomal rearrangements may impact the genetic structure of populations and their diversification.
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Affiliation(s)
- Mabel D Giménez
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Daniel W Förster
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Eleanor P Jones
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Fríða Jóhannesdóttir
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Sofia I Gabriel
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Thadsin Panithanarak
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Moira Scascitelli
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Valeria Merico
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Silvia Garagna
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Jeremy B Searle
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Heidi C Hauffe
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
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Dennenmoser S, Vamosi SM, Nolte AW, Rogers SM. Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq. Mol Ecol 2016; 26:25-42. [DOI: 10.1111/mec.13805] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Dennenmoser
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Steven M. Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Arne W. Nolte
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Institute for Biology; Carl von Ossietzky University Oldenburg; Carl von Ossietzky Str. 9-11 26111 Oldenburg Germany
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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Gloss AD, Groen SC, Whiteman NK. A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016; 47:165-187. [PMID: 28736510 DOI: 10.1146/annurev-ecolsys-121415-032220] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.
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Affiliation(s)
- Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Simon C Groen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
| | - Noah K Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California
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47
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Korunes KL, Noor MAF. Gene conversion and linkage: effects on genome evolution and speciation. Mol Ecol 2016; 26:351-364. [DOI: 10.1111/mec.13736] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/07/2016] [Accepted: 06/22/2016] [Indexed: 12/12/2022]
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Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
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Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Kenney AM, Sweigart AL. Reproductive isolation and introgression between sympatric
Mimulus
species. Mol Ecol 2016; 25:2499-517. [DOI: 10.1111/mec.13630] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Amanda M. Kenney
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Biological Sciences St. Edward's University Austin TX 78704 USA
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He Q, Knowles LL. Identifying targets of selection in mosaic genomes with machine learning: applications inAnopheles gambiaefor detecting sites within locally adapted chromosomal inversions. Mol Ecol 2016; 25:2226-43. [DOI: 10.1111/mec.13619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 03/01/2016] [Accepted: 03/08/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Qixin He
- Department of Ecology & Evolutionary Biology, Museum of Zoology; University of Michigan; 1109 Geddes Ave. Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology & Evolutionary Biology, Museum of Zoology; University of Michigan; 1109 Geddes Ave. Ann Arbor MI 48109-1079 USA
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