1
|
Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun 2024; 15:6609. [PMID: 39098897 DOI: 10.1038/s41467-024-50852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/16/2024] [Indexed: 08/06/2024] Open
Abstract
Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.
Collapse
Affiliation(s)
- Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | | | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Mateo Garcia-Olazabal
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MI, USA
| | - Tristram O Dodge
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Molly Schumer
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA.
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
| |
Collapse
|
2
|
Reyna-Blanco CS, Caduff M, Galimberti M, Leuenberger C, Wegmann D. Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies. Mol Biol Evol 2024; 41:msae137. [PMID: 38958167 PMCID: PMC11255385 DOI: 10.1093/molbev/msae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
Collapse
Affiliation(s)
- Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| |
Collapse
|
3
|
Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
Collapse
Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| |
Collapse
|
4
|
Du K, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge T, Schumer M, Park H, Meyer A, Schartl M. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573732. [PMID: 38260540 PMCID: PMC10802237 DOI: 10.1101/2023.12.30.573732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.
Collapse
|
5
|
Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
Collapse
Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| |
Collapse
|
6
|
Chen X, Wang Z, Zhang C, Hu J, Lu Y, Zhou H, Mei Y, Cong Y, Guo F, Wang Y, He K, Liu Y, Li F. Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature. BMC Biol 2023; 21:265. [PMID: 37981687 PMCID: PMC10658929 DOI: 10.1186/s12915-023-01762-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved. RESULTS Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms. CONCLUSIONS Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.
Collapse
Affiliation(s)
- Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chaowei Zhang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingheng Hu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yueqi Lu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hang Zhou
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fangyuan Guo
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
7
|
Laetsch DR, Bisschop G, Martin SH, Aeschbacher S, Setter D, Lohse K. Demographically explicit scans for barriers to gene flow using gIMble. PLoS Genet 2023; 19:e1010999. [PMID: 37816069 PMCID: PMC10610087 DOI: 10.1371/journal.pgen.1010999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/27/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Progress has been impeded by a conceptual and methodological divide between analyses that infer the demographic history of speciation and genome scans aimed at identifying locally maladaptive alleles i.e. genomic barriers to gene flow. Here we implement genomewide IM blockwise likelihood estimation (gIMble), a composite likelihood approach for the quantification of barriers, that bridges this divide. This analytic framework captures background selection and selection against barriers in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. gIMble includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied pair of sister species of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analyses uncover both large-effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of a polygenic barrier architecture.
Collapse
Affiliation(s)
- Dominik R. Laetsch
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Gertjan Bisschop
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon H. Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Derek Setter
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
8
|
Thawornwattana Y, Huang J, Flouri T, Mallet J, Yang Z. Inferring the Direction of Introgression Using Genomic Sequence Data. Mol Biol Evol 2023; 40:msad178. [PMID: 37552932 PMCID: PMC10439365 DOI: 10.1093/molbev/msad178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here, we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences from Heliconius butterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength.
Collapse
Affiliation(s)
| | - Jun Huang
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, P.R. China
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| |
Collapse
|
9
|
Crawford NG, McGreevy TJ, Mullen SP, Schneider CJ. The genetic basis of conspicuous coloration in the Guadeloupean anole: Evolution by sexual and ecological selection. Ecol Evol 2023; 13:e10266. [PMID: 37435022 PMCID: PMC10330958 DOI: 10.1002/ece3.10266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding how natural selection acts on the genome and contributes to the process of speciation is a primary aim of the study of evolution. Here we used natural variation in two subspecies of the Guadeloupean anole (Anolis marmoratus ssp.), from the island of Guadeloupe in the Lesser Antilles, to explore the genomic basis of adaptation and speciation in Anolis lizards. These subspecies inhabit distinct ecological environments and display marked differences in adult male color and pattern. We sequenced the complete genomes of 20 anoles, 10 from each subspecies, at 1.4× coverage. We used genome-wide scans of population differentiation, allele frequency spectrum, and linkage disequilibrium to characterize the genomic architecture within and between the subspecies. While most of the genome was undifferentiated, we observed five large divergent regions. Within these regions we identified blocks, 5 kb pairs in length, enriched for fixed single nucleotide polymorphisms. These blocks encompass 97 genes, two of which are candidate pigmentation genes. One is melanophilin (mlph), which helps transport melanosomes within melanocytes. The other is a cluster of differentiation 36 (cd36), which regulates carotenoid pigment sequestration. We used high-pressure liquid chromatography to confirm that carotenoid pigments are significantly more abundant in the conspicuous orange-pigmented skin of male A. m. marmoratus suggesting that cd36 may be regulating pigment deposition in this tissue. We identified for the first time a carotenoid gene that is a potential target of divergent sexual selection and may be contributing to the early stages of speciation in Anolis lizards.
Collapse
Affiliation(s)
| | - Thomas J. McGreevy
- Department of BiologyBoston UniversityBostonMassachusettsUSA
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sean P. Mullen
- Department of BiologyBoston UniversityBostonMassachusettsUSA
| | | |
Collapse
|
10
|
Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae). Chromosome Res 2023; 31:9. [PMID: 36745262 PMCID: PMC9902428 DOI: 10.1007/s10577-023-09715-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 02/07/2023]
Abstract
Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
Collapse
|
11
|
Mallet J, Mullen SP. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1175-1182. [PMID: 36063161 DOI: 10.1111/jeb.14052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022]
Abstract
Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.
Collapse
Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
12
|
Robbins RK, Cong Q, Zhang J, Shen J, Busby RC, Faynel C, Duarte M, Martins ARP, Prieto C, Lamas G, Grishin NV. Genomics-based higher classification of the species-rich Hairstreaks (Lepidoptera: Lycaenidae: Eumaeini). SYSTEMATIC ENTOMOLOGY 2022; 47:445-469. [PMID: 35782754 PMCID: PMC9246340 DOI: 10.1111/syen.12541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We propose a higher classification of the lycaenid hairstreak tribe Eumaeini - one of the youngest and most species-rich butterfly tribes - based on autosome, Lepidopteran Z sex chromosome, and mitochondrial protein-coding genes. The subtribe Neolycaenina Korb is a synonym of Callophryidina Tutt, and subtribe Tmolusina Bálint is a synonym of Strephonotina K. Johnson, Austin, Le Crom, & Salazar. Proposed names are Rhammina Prieto & Busby, new subtribe; Timaetina Busby & Prieto, new subtribe; Atlidina Martins & Duarte, new subtribe; Evenina Faynel & Grishin, new subtribe; Jantheclina Robbins & Faynel, new subtribe; Paiwarriina Lamas & Robbins, new subtribe; Cupatheclina Lamas & Grishin, new subtribe; Parrhasiina Busby & Robbins, new subtribe; Ipideclina Martins & Grishin, new subtribe; and Trichonidina Duarte & Faynel, new subtribe. Phylogenetic results from the autosome and Z sex chromosome analyses are similar. Future analyses of datasets with hundreds of terminal taxa may be more practical time-wise by focussing on the smaller number of sex chromosome sequences (2.6% of nuclear protein-coding sequences). The phylogenetic classification and biological summaries for each subtribe suggest that a variety of factors affected Eumaeini diversification. About a dozen kinds of male secondary sexual organs with frequent evolutionary gains and losses occur in Atlidina, Evenina, and Jantheclina (141 species combined). Females have been shown to use these organs to discriminate between conspecific and non-conspecific males, facilitating sympatry among close relatives. Eumaeina, Rhammina, and Timaetina (140 species combined) are overwhelmingly montane with some evidence for a higher incidence of sympatric diversification. Seven Neotropical lineages in five subtribes invaded the temperate parts of the Nearctic Region with a diversification increase in the Callophryidina (262 species). North American Satyrium and Callophrys then invaded the Palearctic at least once each, with a major species-richness increase in Satyrium. The evolution of litter feeding detritivores within Calycopidina (172 species) resulted in an increase in diversification rate compared with its flower-feeding sister lineage. Atlidina, Strephonotina, Parrhasiina, and Strymonina (562 species combined) each contain a mixture of genera that specialize on one or two caterpillar food plant families and genera that are polyphagous. These would be appropriate subtribes to assess how the breadth of caterpillar food plants and the frequency of host shifts affected diversification.
Collapse
Affiliation(s)
- Robert K Robbins
- Department of Entomology, National Museum of Natural History, PO Box 37012, NHB Stop 105, Smithsonian Institution, Washington, D.C., USA
| | - Qian Cong
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Jing Zhang
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | - Jinhui Shen
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
| | | | | | - Marcelo Duarte
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, Ipiranga, 04263-000, São Paulo, SP, Brazil
| | - Ananda R P Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Canada, H3A0C4
| | - Carlos Prieto
- Departamento de Biología, Universidad del Atlántico, Barranquilla, Colombia and Corporación Universitaria Autónoma del Cauca, Popayán, Colombia
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Apartado 14-0434, Lima-14, Peru
| | - Nick V Grishin
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9050, USA
| |
Collapse
|
13
|
Xiong T, Li X, Yago M, Mallet J. Admixture of evolutionary rates across a butterfly hybrid zone. eLife 2022; 11:e78135. [PMID: 35703474 PMCID: PMC9246367 DOI: 10.7554/elife.78135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 12/26/2022] Open
Abstract
Hybridization is a major evolutionary force that can erode genetic differentiation between species, whereas reproductive isolation maintains such differentiation. In studying a hybrid zone between the swallowtail butterflies Papilio syfanius and Papilio maackii (Lepidoptera: Papilionidae), we made the unexpected discovery that genomic substitution rates are unequal between the parental species. This phenomenon creates a novel process in hybridization, where genomic regions most affected by gene flow evolve at similar rates between species, while genomic regions with strong reproductive isolation evolve at species-specific rates. Thus, hybridization mixes evolutionary rates in a way similar to its effect on genetic ancestry. Using coalescent theory, we show that the rate-mixing process provides distinct information about levels of gene flow across different parts of genomes, and the degree of rate-mixing can be predicted quantitatively from relative sequence divergence ([Formula: see text]) between the hybridizing species at equilibrium. Overall, we demonstrate that reproductive isolation maintains not only genomic differentiation, but also the rate at which differentiation accumulates. Thus, asymmetric rates of evolution provide an additional signature of loci involved in reproductive isolation.
Collapse
Affiliation(s)
- Tianzhu Xiong
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Xueyan Li
- Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Masaya Yago
- The University Museum, The University of TokyoTokyoJapan
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| |
Collapse
|
14
|
The Build-Up of Population Genetic Divergence along the Speciation Continuum during a Recent Adaptive Radiation of Rhagoletis Flies. Genes (Basel) 2022; 13:genes13020275. [PMID: 35205320 PMCID: PMC8872456 DOI: 10.3390/genes13020275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
New species form through the evolution of genetic barriers to gene flow between previously interbreeding populations. The understanding of how speciation proceeds is hampered by our inability to follow cases of incipient speciation through time. Comparative approaches examining different diverging taxa may offer limited inferences, unless they fulfill criteria that make the comparisons relevant. Here, we test for those criteria in a recent adaptive radiation of the Rhagoletis pomonella species group (RPSG) hypothesized to have diverged in sympatry via adaptation to different host fruits. We use a large-scale population genetic survey of 1568 flies across 33 populations to: (1) detect on-going hybridization, (2) determine whether the RPSG is derived from the same proximate ancestor, and (3) examine patterns of clustering and differentiation among sympatric populations. We find that divergence of each in-group RPSG taxon is occurring under current gene flow, that the derived members are nested within the large pool of genetic variation present in hawthorn-infesting populations of R. pomonella, and that sympatric population pairs differ markedly in their degree of genotypic clustering and differentiation across loci. We conclude that the RPSG provides a particularly robust opportunity to make direct comparisons to test hypotheses about how ecological speciation proceeds despite on-going gene flow.
Collapse
|
15
|
Hench K, Helmkampf M, McMillan WO, Puebla O. Rapid radiation in a highly diverse marine environment. Proc Natl Acad Sci U S A 2022; 119:e2020457119. [PMID: 35042790 PMCID: PMC8794831 DOI: 10.1073/pnas.2020457119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
Collapse
Affiliation(s)
- Kosmas Hench
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
| | - Martin Helmkampf
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
| | - Oscar Puebla
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
- Institute for Chemistry and Biology of the Marine Environment, 26111 Oldenburg, Germany
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| |
Collapse
|
16
|
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: 83] [Impact Index Per Article: 41.5] [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.
Collapse
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.
| |
Collapse
|
17
|
Thawornwattana Y, Seixas FA, Yang Z, Mallet J. OUP accepted manuscript. Syst Biol 2022; 71:1159-1177. [PMID: 35169847 PMCID: PMC9366460 DOI: 10.1093/sysbio/syac009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
Collapse
Affiliation(s)
- Yuttapong Thawornwattana
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ziheng Yang
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - James Mallet
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| |
Collapse
|
18
|
Hibbins MS, Hahn MW. Phylogenomic approaches to detecting and characterizing introgression. Genetics 2021; 220:6425633. [PMID: 34788444 PMCID: PMC9208645 DOI: 10.1093/genetics/iyab173] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/02/2021] [Indexed: 12/26/2022] Open
Abstract
Phylogenomics has revealed the remarkable frequency with which introgression occurs across the tree of life. These discoveries have been enabled by the rapid growth of methods designed to detect and characterize introgression from whole-genome sequencing data. A large class of phylogenomic methods makes use of data across species to infer and characterize introgression based on expectations from the multispecies coalescent. These methods range from simple tests, such as the D-statistic, to model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview of the various signals that different modes of introgression are expected leave in the genome, and how current methods are designed to detect them. We discuss the strengths and pitfalls of these approaches and identify areas for future development, highlighting the different signals of introgression, and the power of each method to detect them. We conclude with a discussion of current challenges in inferring introgression and how they could potentially be addressed.
Collapse
Affiliation(s)
- Mark S Hibbins
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
19
|
Rueda-M N, Salgado-Roa FC, Gantiva-Q CH, Pardo-Díaz C, Salazar C. Environmental Drivers of Diversification and Hybridization in Neotropical Butterflies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.750703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Studying how the environment shapes current biodiversity patterns in species rich regions is a fundamental issue in biogeography, ecology, and conservation. However, in the Neotropics, the study of the forces driving species distribution and richness, is mostly based on vertebrates and plants. In this study, we used 54,392 georeferenced records for 46 species and 1,012 georeferenced records for 38 interspecific hybrids of the Neotropical Heliconius butterflies to investigate the role of the environment in shaping their distribution and richness, as well as their geographic patterns of phylogenetic diversity and phylogenetic endemism. We also evaluated whether niche similarity promotes hybridization in Heliconius. We found that these insects display five general distribution patterns mostly explained by precipitation and isothermality, and to a lesser extent, by altitude. Interestingly, altitude plays a major role as a predictor of species richness and phylogenetic diversity, while precipitation explains patterns of phylogenetic endemism. We did not find evidence supporting the role of the environment in facilitating hybridization because hybridizing species do not necessarily share the same climatic niche despite some of them having largely overlapping geographic distributions. Overall, we confirmed that, as in other organisms, high annual temperature, a constant supply of water, and spatio-topographic complexity are the main predictors of diversity in Heliconius. However, future studies at large scale need to investigate the effect of microclimate variables and ecological interactions.
Collapse
|
20
|
Nelson ED, Cong Q, Grishin NV. Influence of the large-Z effect during contact between butterfly sister species. Ecol Evol 2021; 11:11615-11626. [PMID: 34522328 PMCID: PMC8427592 DOI: 10.1002/ece3.7785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/14/2022] Open
Abstract
Recently diverged butterfly populations in North America have been found to exhibit high levels of divergence on the Z chromosome relative to autosomes, as measured by fixation index, F st . The pattern of divergence appears to result from accumulation of incompatible alleles, obstructing introgression on the Z chromosome in hybrids (i.e., the large-Z effect); however, it is unknown whether this mechanism is sufficient to explain the data. Here, we simulate the effects of hybrid incompatibility on interbreeding butterfly populations using a model in which populations accumulate cross-incompatible alleles in allopatry prior to contact. We compute statistics for introgression and population divergence during contact between model populations and compare our results to those for 15 pairs of butterfly species interbreeding along a suture zone in central Texas. Time scales for allopatry and contact in the model are scaled to glacial and interglacial periods during which real populations evolved in isolation and contact. We find that the data for butterflies are explained well by an otherwise neutral model under slow fusion conditions. In particular, levels of divergence on the Z chromosome increase when interacting clusters of genes are closely linked, consistent with clusters of functionally related genes in butterfly genomes.
Collapse
Affiliation(s)
- Erik D. Nelson
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Qian Cong
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| |
Collapse
|
21
|
Liu X, Ogilvie HA, Nakhleh L. Variational inference using approximate likelihood under the coalescent with recombination. Genome Res 2021; 31:2107-2119. [PMID: 34426513 PMCID: PMC8559707 DOI: 10.1101/gr.273631.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 08/17/2021] [Indexed: 11/30/2022]
Abstract
Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large genomic alignments, which are increasingly common, is coalescent hidden Markov model (coalHMM) methods, but these methods have lacked general usability and flexibility. We introduce a novel method for automatically learning a coalHMM and inferring the posterior distributions of evolutionary parameters using black-box variational inference, with the transition rates between local genealogies derived empirically by simulation. This derivation enables our method to work directly with three or four taxa and through a divide-and-conquer approach with more taxa. Using a simulated data set resembling a human–chimp–gorilla scenario, we show that our method has comparable or better accuracy to previous coalHMM methods. Both species divergence times and population sizes were accurately inferred. The method also infers local genealogies, and we report on their accuracy. Furthermore, we discuss a potential direction for scaling the method to larger data sets through a divide-and-conquer approach. This accuracy means our method is useful now, and by deriving transition rates by simulation, it is flexible enough to enable future implementations of various population models.
Collapse
Affiliation(s)
- Xinhao Liu
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
22
|
Kozak KM, Joron M, McMillan WO, Jiggins CD. Rampant Genome-Wide Admixture across the Heliconius Radiation. Genome Biol Evol 2021; 13:evab099. [PMID: 33944917 PMCID: PMC8283734 DOI: 10.1093/gbe/evab099] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.
Collapse
Affiliation(s)
- Krzysztof M Kozak
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| | - Mathieu Joron
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, France
| | | | - Chris D Jiggins
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| |
Collapse
|
23
|
Van Belleghem SM, Cole JM, Montejo-Kovacevich G, Bacquet CN, McMillan WO, Papa R, Counterman BA. Selection and isolation define a heterogeneous divergence landscape between hybridizing Heliconius butterflies. Evolution 2021; 75:2251-2268. [PMID: 34019308 DOI: 10.1111/evo.14272] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 04/26/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Hybridizing species provide a powerful system to identify the processes that shape genomic variation and maintain species boundaries. However, complex histories of isolation, gene flow, and selection often generate heterogeneous genomic landscapes of divergence that complicate reconstruction of the speciation history. Here, we explore patterns of divergence to reconstruct recent speciation in the erato clade of Heliconius butterflies. We focus on the genomic landscape of divergence across three contact zones of the species H. erato and H. himera. We show that these hybridizing species have an intermediate level of divergence in the erato clade, which fits with their incomplete levels of reproductive isolation. Using demographic modeling and the relationship between admixture and divergence with recombination rate variation, we reconstruct histories of gene flow, selection, and demographic change that explain the observed patterns of genomic divergence. We find that periods of isolation and selection within populations, followed by secondary contact with asymmetrical gene flow are key factors in shaping the heterogeneous genomic landscapes. Collectively, these results highlight the effectiveness of demographic modeling and recombination rate estimates to disentangling the distinct contributions of gene flow and selection to patterns of genomic divergence.
Collapse
Affiliation(s)
| | - Jared M Cole
- Department of Biological Sciences, Mississippi State University, Mississippi State, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | | | | | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico.,Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Mississippi State, USA.,Department of Biological Sciences, Auburn University, Alabama, USA
| |
Collapse
|
24
|
Matute DR, Cooper BS. Comparative studies on speciation: 30 years since Coyne and Orr. Evolution 2021; 75:764-778. [PMID: 33491225 PMCID: PMC8247902 DOI: 10.1111/evo.14181] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/28/2022]
Abstract
Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.
Collapse
Affiliation(s)
- Daniel R. Matute
- Biology DepartmentUniversity of North CarolinaChapel HillNorth Carolina27510
| | - Brandon S. Cooper
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
| |
Collapse
|
25
|
Massardo D, VanKuren NW, Nallu S, Ramos RR, Ribeiro PG, Silva-Brandão KL, Brandão MM, Lion MB, Freitas AVL, Cardoso MZ, Kronforst MR. The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena. BMC Biol 2020; 18:84. [PMID: 32620168 PMCID: PMC7334841 DOI: 10.1186/s12915-020-00797-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed in widespread species with contiguous distributions, many Heliconius species inhabit patchy or rare habitats that may strongly influence the origin and spread of species and color patterns. Here, we assess the effects of historical population fragmentation and unique biology on the origins, genetic health, and color pattern evolution of two rare and sparsely distributed Brazilian butterflies, Heliconius hermathena and Heliconius nattereri. RESULTS We assembled genomes and re-sequenced whole genomes of eight H. nattereri and 71 H. hermathena individuals. These species harbor little genetic diversity, skewed site frequency spectra, and high deleterious mutation loads consistent with recent population bottlenecks. Heliconius hermathena consists of discrete, strongly isolated populations that likely arose from a single population that dispersed after the last glacial maximum. Despite having a unique color pattern combination that suggested a hybrid origin, we found no genome-wide evidence that H. hermathena is a hybrid species. However, H. hermathena mimicry evolved via introgression, from co-mimetic Heliconius erato, of a small genomic region upstream of the color patterning gene cortex. CONCLUSIONS Heliconius hermathena and H. nattereri population fragmentation, potentially driven by historical climate change and recent deforestation, has significantly reduced the genetic health of these rare species. Our results contribute to a growing body of evidence that introgression of color patterning alleles between co-mimetic species appears to be a general feature of Heliconius evolution.
Collapse
Affiliation(s)
- Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Nicholas W VanKuren
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Renato R Ramos
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Pedro G Ribeiro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Karina L Silva-Brandão
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Marcelo M Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marília B Lion
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - André V L Freitas
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Márcio Z Cardoso
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
26
|
Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
Collapse
|
27
|
Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, Elias M. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Mol Ecol 2020; 29:1328-1343. [PMID: 32145112 DOI: 10.1111/mec.15403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022]
Abstract
Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
Collapse
Affiliation(s)
- Jérémy Gauthier
- Inria, CNRS, IRISA, University Rennes, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| | - Donna Lisa de Silva
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Céline Houssin
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France.,Fakultat für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| |
Collapse
|
28
|
Moest M, Van Belleghem SM, James JE, Salazar C, Martin SH, Barker SL, Moreira GRP, Mérot C, Joron M, Nadeau NJ, Steiner FM, Jiggins CD. Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation. PLoS Biol 2020; 18:e3000597. [PMID: 32027643 PMCID: PMC7029882 DOI: 10.1371/journal.pbio.3000597] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/19/2020] [Accepted: 01/15/2020] [Indexed: 11/21/2022] Open
Abstract
Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.
Collapse
Affiliation(s)
- Markus Moest
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Steven M. Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Jennifer E. James
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota D.C., Colombia
| | - Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L. Barker
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gilson R. P. Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Claire Mérot
- IBIS, Department of Biology, Université Laval, Québec, Canada
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS—Université de Montpellier—Université Paul Valéry Montpellier—EPHE, Montpellier, France
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
29
|
Semenov GA, Safran RJ, Smith CC, Turbek SP, Mullen SP, Flaxman SM. Unifying Theoretical and Empirical Perspectives on Genomic Differentiation. Trends Ecol Evol 2019; 34:987-995. [DOI: 10.1016/j.tree.2019.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/17/2023]
|
30
|
Stankowski S, Chase MA, Fuiten AM, Rodrigues MF, Ralph PL, Streisfeld MA. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers. PLoS Biol 2019; 17:e3000391. [PMID: 31339877 PMCID: PMC6660095 DOI: 10.1371/journal.pbio.3000391] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
Collapse
Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Madeline A. Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Allison M. Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Peter L. Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew A. Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| |
Collapse
|
31
|
Pfeifer B, Kapan DD. Estimates of introgression as a function of pairwise distances. BMC Bioinformatics 2019; 20:207. [PMID: 31014244 PMCID: PMC6480520 DOI: 10.1186/s12859-019-2747-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.
Collapse
Affiliation(s)
- Bastian Pfeifer
- Institute for Medical Informatics, Statistics and Documentation, Medical University, Graz, Austria
| | - Durrell D. Kapan
- Department of Entomology and Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, USA
| |
Collapse
|
32
|
Pfeifer B, Kapan DD. Estimates of introgression as a function of pairwise distances. BMC Bioinformatics 2019; 20:207. [PMID: 31014244 DOI: 10.1101/154377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 03/18/2019] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.
Collapse
Affiliation(s)
- Bastian Pfeifer
- Institute for Medical Informatics, Statistics and Documentation, Medical University, Graz, Austria
| | - Durrell D Kapan
- Department of Entomology and Center for Comparative Genomics, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, USA.
| |
Collapse
|
33
|
Martin SH, Davey JW, Salazar C, Jiggins CD. Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol 2019; 17:e2006288. [PMID: 30730876 PMCID: PMC6366726 DOI: 10.1371/journal.pbio.2006288] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across the genome and between populations. Introgression can also erode species differences over time, but selection against introgression at certain loci acts to maintain postmating species barriers. Theory predicts that species barriers made up of many loci throughout the genome should lead to a broad correlation between introgression and recombination rate, which determines the extent to which selection on deleterious foreign alleles will affect neutral alleles at physically linked loci. Here, we describe the variation in genealogical relationships across the genome among three species of Heliconius butterflies: H. melpomene (mel), H. cydno (cyd), and H. timareta (tim), using whole genomes of 92 individuals, and ask whether this variation can be explained by heterogeneous barriers to introgression. We find that species relationships vary predictably at the chromosomal scale. By quantifying recombination rate and admixture proportions, we then show that rates of introgression are predicted by variation in recombination rate. This implies that species barriers are highly polygenic, with selection acting against introgressed alleles across most of the genome. In addition, long chromosomes, which have lower recombination rates, produce stronger barriers on average than short chromosomes. Finally, we find a consistent difference between two species pairs on either side of the Andes, which suggests differences in the architecture of the species barriers. Our findings illustrate how the combined effects of hybridisation, recombination, and natural selection, acting at multitudes of loci over long periods, can dramatically sculpt the phylogenetic relationships among species.
Collapse
Affiliation(s)
- Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - John W. Davey
- Department of Biology, University of York, York, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota, Colombia
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
34
|
Doellman MM, Feder JL. Genomic transitions during host race and species formation. CURRENT OPINION IN INSECT SCIENCE 2019; 31:84-92. [PMID: 31109679 DOI: 10.1016/j.cois.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Darwin recognized species as discontinuous, yet considered them to be formed by an incremental process of natural selection. Recent theoretical work on 'genome-wide congealing' is bridging this gap between the gradualism of divergent selection and rapid genome-wide divergence, particularly during ecological speciation-with-gene-flow. Host races and species of phytophagous insects, displaying a spectrum of divergence and gene flow among member taxa, provide model systems for testing predicted non-linear transitions from 'genic' divergence at a few uncoupled loci to 'genomic' divergence with genome-wide coupling of selected loci and strong reproductive isolation. Integrating across natural history, genomics, and evolutionary theory, emerging research suggests a tipping point from 'genic' to 'genomic' divergence between host races and species, during both sympatric speciation and secondary contact.
Collapse
Affiliation(s)
- Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
35
|
Southcott L, Kronforst MR. Female mate choice is a reproductive isolating barrier in Heliconius butterflies. Ethology 2018; 124:862-869. [PMID: 31024190 PMCID: PMC6475913 DOI: 10.1111/eth.12818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022]
Abstract
In sexually reproducing organisms, speciation involves the evolution of reproductive isolating mechanisms that decrease gene flow. Premating reproductive isolation, often the result of mate choice, is a major obstacle to gene flow between species because it acts earlier in the life cycle than other isolating barriers. While female choice is often considered the default mode in animal species, research in the butterfly genus Heliconius, a frequent subject of speciation studies, has focused on male mate choice. We studied mate choice by H. cydno females by pairing them with either conspecific males or males of the closely related species H. pachinus. Significantly more intraspecific trials than interspecific trials resulted in mating. Because male courtship rates did not differ between the species when we excluded males that never courted, we attribute this difference to female choice. Females also performed more acceptance behaviours towards conspecific males. Premating isolation between these two species thus entails both male and female mate choice, and female choice may be an important factor in the origin of Heliconius species.
Collapse
Affiliation(s)
- Laura Southcott
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Marcus R Kronforst
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| |
Collapse
|
36
|
Westerman EL, VanKuren NW, Massardo D, Tenger-Trolander A, Zhang W, Hill RI, Perry M, Bayala E, Barr K, Chamberlain N, Douglas TE, Buerkle N, Palmer SE, Kronforst MR. Aristaless Controls Butterfly Wing Color Variation Used in Mimicry and Mate Choice. Curr Biol 2018; 28:3469-3474.e4. [PMID: 30415702 PMCID: PMC6234856 DOI: 10.1016/j.cub.2018.08.051] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/24/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Neotropical Heliconius butterflies display a diversity of warningly colored wing patterns, which serve roles in both Müllerian mimicry and mate choice behavior. Wing pattern diversity in Heliconius is controlled by a small number of unlinked, Mendelian "switch" loci [1]. One of these, termed the K locus, switches between yellow and white color patterns, important mimicry signals as well as mating cues [2-4]. Furthermore, mate preference behavior is tightly linked to this locus [4]. K controls the distribution of white versus yellow scales on the wing, with a dominant white allele and a recessive yellow allele. Here, we combine fine-scale genetic mapping, genome-wide association studies, gene expression analyses, population and comparative genomics, and genome editing with CRISPR/Cas9 to characterize the molecular basis of the K locus in Heliconius and to infer its evolutionary history. We show that white versus yellow color variation in Heliconius cydno is due to alternate haplotypes at a putative cis-regulatory element (CRE) downstream of a tandem duplication of the homeodomain transcription factor aristaless. Aristaless1 (al1) and aristaless2 (al2) are differentially regulated between white and yellow wings throughout development with elevated expression of al1 in developing white wings, suggesting a role in repressing pigmentation. Consistent with this, knockout of al1 causes white wings to become yellow. The evolution of wing color in this group has been marked by retention of the ancestral yellow color in many lineages, a single origin of white coloration in H. cydno, and subsequent introgression of white color from H. cydno into H. melpomene.
Collapse
Affiliation(s)
- Erica L Westerman
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA; Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nicholas W VanKuren
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Darli Massardo
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA
| | | | - Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ryan I Hill
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Michael Perry
- Department of Biology, New York University, New York, NY 10003, USA
| | - Erick Bayala
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Kenneth Barr
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Nicola Chamberlain
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Tracy E Douglas
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Nathan Buerkle
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Stephanie E Palmer
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
37
|
Fincke OM, Xu M, Khazan ES, Wilson M, Ware JL. Tests of hypotheses for morphological and genetic divergence in Megaloprepus damselflies across Neotropical forests. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ola M Fincke
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Mingzi Xu
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Emily S Khazan
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Megan Wilson
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Jessica L Ware
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| |
Collapse
|
38
|
Walsh J, Kovach AI, Olsen BJ, Shriver WG, Lovette IJ. Bidirectional adaptive introgression between two ecologically divergent sparrow species. Evolution 2018; 72:2076-2089. [PMID: 30101975 DOI: 10.1111/evo.13581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 12/24/2022]
Abstract
Natural hybrid zones can be used to dissect the mechanisms driving key evolutionary processes by allowing us to identify genomic regions important for establishing reproductive isolation and that allow for transfer of adaptive variation. We leverage whole-genome data in a system where two bird species, the saltmarsh (Ammospiza caudacuta) and Nelson's (A. nelsoni) sparrow, hybridize despite their relatively high background genetic differentiation and past ecological divergence. Adaptive introgression is plausible in this system because Nelson's sparrows are recent colonists of saltwater marshes, compared to the specialized saltmarsh sparrow that has a longer history of saltmarsh adaptation. Comparisons among whole-genome sequences of 34 individuals from allopatric and sympatric populations show that ongoing gene flow is shaping the genomic landscape, with allopatric populations exhibiting genome-wide FST estimates close to double of that observed in sympatry. We characterized patterns of introgression across the genome and identify regions that exhibit biased introgression into hybrids from one parental species. These regions offer compelling candidates for genes related to tidal marsh adaptations suggesting that adaptive introgression may be an important consequence of hybridization. These findings highlight the value of considering the landscapes of both genome-wide introgression and divergence when characterizing the evolutionary forces that drive speciation.
Collapse
Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire 03824
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware 19716
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Ithaca, New York 14850.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853
| |
Collapse
|
39
|
Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
Collapse
Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | | |
Collapse
|
40
|
Schilling MP, Mullen SP, Kronforst M, Safran RJ, Nosil P, Feder JL, Gompert Z, Flaxman SM. Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow. Genes (Basel) 2018; 9:E274. [PMID: 29795050 PMCID: PMC6027428 DOI: 10.3390/genes9060274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022] Open
Abstract
During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under several evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics. We used these simulations to investigate, in a preliminary way, if and how selected and neutral sites differ in the conditions they require for transitions during speciation. For the parameter combinations we explored, as the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence-and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence-farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of effective gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that fixation index ( F S T ) outliers and allele-frequency outliers exhibited stronger patterns of within-deme LD than the genomic background, as expected. The statistical characteristics of within-deme LD-likely indicative of the strength of coupling of barrier loci-varied between chromosomes and taxonomic comparisons. Qualitatively, the patterns we observed in the empirical data and in our simulations suggest that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.
Collapse
Affiliation(s)
- Martin P Schilling
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, MA 02215, USA.
| | - Marcus Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA.
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Patrik Nosil
- Department of Biology & Ecology Center, Utah State University, Logan, UT 84322, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, South Bend, IN 46556, USA.
| | - Zachariah Gompert
- Department of Biology & Ecology Center, Utah State University, Logan, UT 84322, USA.
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| |
Collapse
|
41
|
Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, Martin SH. Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography. Mol Ecol 2018; 27:3852-3872. [PMID: 29569384 PMCID: PMC6151167 DOI: 10.1111/mec.14560] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/14/2018] [Accepted: 02/20/2018] [Indexed: 12/31/2022]
Abstract
Sex chromosomes are disproportionately involved in reproductive isolation and adaptation. In support of such a “large‐X” effect, genome scans between recently diverged populations and species pairs often identify distinct patterns of divergence on the sex chromosome compared to autosomes. When measures of divergence between populations are higher on the sex chromosome compared to autosomes, such patterns could be interpreted as evidence for faster divergence on the sex chromosome, that is “faster‐X”, barriers to gene flow on the sex chromosome. However, demographic changes can strongly skew divergence estimates and are not always taken into consideration. We used 224 whole‐genome sequences representing 36 populations from two Heliconius butterfly clades (H. erato and H. melpomene) to explore patterns of Z chromosome divergence. We show that increased divergence compared to equilibrium expectations can in many cases be explained by demographic change. Among Heliconius erato populations, for instance, population size increase in the ancestral population can explain increased absolute divergence measures on the Z chromosome compared to the autosomes, as a result of increased ancestral Z chromosome genetic diversity. Nonetheless, we do identify increased divergence on the Z chromosome relative to the autosomes in parapatric or sympatric species comparisons that imply postzygotic reproductive barriers. Using simulations, we show that this is consistent with reduced gene flow on the Z chromosome, perhaps due to greater accumulation of incompatibilities. Our work demonstrates the importance of taking demography into account to interpret patterns of divergence on the Z chromosome, but nonetheless provides evidence to support the Z chromosome as a strong barrier to gene flow in incipient Heliconius butterfly species.
Collapse
Affiliation(s)
- Steven M Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA.,Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico.,Smithsonian Tropical Research Institute, Apartado, Panamá, Panama
| | - Margarita Baquero
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Riccardo Papa
- Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera, Bogota, Colombia
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado, Panamá, Panama
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| |
Collapse
|
42
|
Nazaripanah N, Adelirad F, Delbari A, Sahaf R, Abbasi-Asl T, Ohadi M. Genome-scale portrait and evolutionary significance of human-specific core promoter tri- and tetranucleotide short tandem repeats. Hum Genomics 2018; 12:17. [PMID: 29622039 PMCID: PMC5887250 DOI: 10.1186/s40246-018-0149-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/20/2018] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution. RESULTS Following a comparative genomics study of all human protein-coding genes annotated in the GeneCards database, here we provide a genome-scale portrait of human-specific short- and medium-size (≥ 3-repeats) tri- and tetranucleotide STRs and STR motifs in the critical core promoter region between - 120 and + 1 to the TSS and evidence of skewing of this compartment in reference to the STRs that are not human-specific (Levene's test p < 0.001). Twenty-five percent and 26% enrichment of human-specific transcripts was detected in the tri and tetra human-specific compartments (mid-p < 0.00002 and mid-p < 0.002, respectively). CONCLUSION Our findings provide the first evidence of genome-scale skewing of STRs at a specific region of the human genome and a link between a number of these STRs and TSS selection/transcript specificity. The STRs and genes listed here may have a role in the evolution and development of characteristics and phenotypes that are unique to the human species.
Collapse
Affiliation(s)
- N Nazaripanah
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - F Adelirad
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - R Sahaf
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - T Abbasi-Asl
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| |
Collapse
|
43
|
Meier JI, Marques DA, Wagner CE, Excoffier L, Seehausen O. Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids. Mol Biol Evol 2018; 35:1489-1506. [DOI: 10.1093/molbev/msy051] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Joana Isabel Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - David Alexander Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Catherine Elise Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| |
Collapse
|
44
|
Abstract
Helicoverpa armigera is a major agricultural and horticultural pest that recently spread from its historical distribution throughout much of the Old World to the Americas, where it is already causing hundreds of millions of dollars in damage every year. The species is notoriously quick to generate and disseminate pesticide resistance throughout its range and has a wider host range than the native Helicoverpa zea. Hybridization between the two species increases the opportunity for novel, agriculturally problematic ecotypes to emerge and spread through the Americas. Within the mega-pest lineage of heliothine moths are a number of polyphagous, highly mobile species for which the exchange of adaptive traits through hybridization would affect their properties as pests. The recent invasion of South America by one of the most significant agricultural pests, Helicoverpa armigera, raises concerns for the formation of novel combinations of adaptive genes following hybridization with the closely related Helicoverpa zea. To investigate the propensity for hybridization within the genus Helicoverpa, we carried out whole-genome resequencing of samples from six species, focusing in particular upon H. armigera population structure and its relationship with H. zea. We show that both H. armigera subspecies have greater genetic diversity and effective population sizes than do the other species. We find no signals for gene flow among the six species, other than between H. armigera and H. zea, with nine Brazilian individuals proving to be hybrids of those two species. Eight had largely H. armigera genomes with some introgressed DNA from H. zea scattered throughout. The ninth resembled an F1 hybrid but with stretches of homozygosity for each parental species that reflect previous hybridization. Regions homozygous for H. armigera-derived DNA in this individual included one containing a gustatory receptor and esterase genes previously associated with host range, while another encoded a cytochrome P450 that confers insecticide resistance. Our data point toward the emergence of novel hybrid ecotypes and highlight the importance of monitoring H. armigera genotypes as they spread through the Americas.
Collapse
|
45
|
Warren KA, Ritzman TB, Humphreys RA, Percival CJ, Hallgrímsson B, Ackermann RR. Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization. J Hum Evol 2018; 116:57-74. [PMID: 29477182 PMCID: PMC6699179 DOI: 10.1016/j.jhevol.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022]
Abstract
Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.
Collapse
Affiliation(s)
- Kerryn A Warren
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Terrence B Ritzman
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa; Department of Neuroscience, Washington University School of Medicine, USA; School of Human Evolution and Social Change, Arizona State University, USA
| | - Robyn A Humphreys
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Christopher J Percival
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada; Department of Anthropology, Stony Brook, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, Alberta Children's Hospital Research Institute, University of Calgary, Canada; The Alberta Children's Hospital Research Institute, University of Calgary, Canada; The McCaig Institute for Bone and Joint Health, University of Calgary, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa.
| |
Collapse
|
46
|
Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
Collapse
Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
| |
Collapse
|
47
|
RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics 2018; 208:1585-1599. [PMID: 29437826 PMCID: PMC5887150 DOI: 10.1534/genetics.117.300567] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races.
Collapse
|
48
|
Garzón‐Orduña IJ, Brower AVZ. Quantified reproductive isolation in Heliconius butterflies: Implications for introgression and hybrid speciation. Ecol Evol 2018; 8:1186-1195. [PMID: 29375789 PMCID: PMC5773317 DOI: 10.1002/ece3.3729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/15/2017] [Accepted: 11/20/2017] [Indexed: 12/02/2022] Open
Abstract
Heliconius butterflies have become a model for the study of speciation with gene flow. For adaptive introgression to take place, there must be incomplete barriers to gene exchange that allow interspecific hybridization and multiple generations of backcrossing. The recent publication of estimates of individual components of reproductive isolation between several species of butterflies in the Heliconius melpomene-H. cydno clade allowed us to calculate total reproductive isolation estimates for these species. According to these estimates, the butterflies are not as promiscuous as has been implied. Differences between species are maintained by intrinsic mechanisms, while reproductive isolation of geographical races within species is mainly due to allopatry. We discuss the implications of this strong isolation for basic aspects of the hybrid speciation with introgression hypothesis.
Collapse
Affiliation(s)
- Ivonne J. Garzón‐Orduña
- Evolution and Ecology Group, Department of BiologyMiddle Tennessee State UniversityMurfreesboroTNUSA
| | - Andrew V. Z. Brower
- Evolution and Ecology Group, Department of BiologyMiddle Tennessee State UniversityMurfreesboroTNUSA
| |
Collapse
|
49
|
Wang Y, Kim KS, Guo W, Li Q, Zhang Y, Wang Z, Coates BS. Introgression between divergent corn borer species in a region of sympatry: Implications on the evolution and adaptation of pest arthropods. Mol Ecol 2017; 26:6892-6907. [PMID: 29105878 DOI: 10.1111/mec.14387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/09/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
The Asian corn borer, Ostrinia furnacalis, and European corn borer, O. nubilalis (Lepidoptera: Crambidae), cause damage to cultivated maize in spatially distinct geographies and have evolved divergent hydrocarbons as the basis of sexual communication. The Yili area of Xinjiang Uyghur Autonomous Region in China represents the only known region where O. furnacalis has invaded a native O. nubilalis range, and these two corn borer species have made secondary contact. Genetic differentiation was estimated between Ostrinia larvae collected from maize plants at 11 locations in Xinjiang and genotyped using high-throughput SNP and microsatellite markers. Maternal lineages were assessed by direct sequencing of mitochondrial cytochrome c oxidase subunit I and II haplotypes, and a high degree of genotypic diversity was demonstrated between lineages based on SNP genotypes. Furthermore, historical introgression was predicted among SNP genotypes only at sympatric locations in the Yili area, whereas in Xinjiang populations only O. furnacalis haplotypes were detected and no analogous introgressed genotypes were predicted. Our detection of putative hybrids and historical evidence of introgression defines Yili area as a hybrid zone between the species in normal ecological interactions and furthermore, might indicate that adaptive traits could spread even between seemingly divergent species through horizontal transmission. Results of this study indicate there may be a continuum in the degree of reproductive isolation between Ostrinia species and that the elegance of distinct and complete speciation based on modifications to the pheromone communication might need to be reconsidered.
Collapse
Affiliation(s)
- Yangzhou Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kyung Seok Kim
- Iowa State University, Department of Natural Resource Ecology and Management, Ames, IA, USA
| | - Wenchao Guo
- Research Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiyun Li
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yunyue Zhang
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA
| |
Collapse
|
50
|
Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
Collapse
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| |
Collapse
|