1
|
Cutter AD. Beyond Haldane's rule: Sex-biased hybrid dysfunction for all modes of sex determination. eLife 2024; 13:e96652. [PMID: 39158559 PMCID: PMC11333046 DOI: 10.7554/elife.96652] [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: 02/07/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024] Open
Abstract
Haldane's rule occupies a special place in biology as one of the few 'rules' of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane's rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane's rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane's rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane's rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| |
Collapse
|
2
|
Platt RN, Enabulele EE, Adeyemi E, Agbugui MO, Ajakaye OG, Amaechi EC, Ejikeugwu CE, Igbeneghu C, Njom VS, Dlamini P, Arya GA, Diaz R, Rabone M, Allan F, Webster B, Emery A, Rollinson D, Anderson TJC. Genomic data reveal a north-south split and introgression history of blood fluke ( Schistosoma haematobium) populations from across Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606828. [PMID: 39149400 PMCID: PMC11326172 DOI: 10.1101/2024.08.06.606828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the extent of hybridization in nature is unclear. We analyzed 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We found no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. We identified 19 regions that were resistant to introgression; these were enriched on the sex chromosomes. These results (i) demonstrate strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of interspecific hybridization between schistosomes of medical and veterinary importance.
Collapse
Affiliation(s)
- Roy N Platt
- Texas Biomedical Research Institute, San Antonio TX, United States
| | - Egie E Enabulele
- Texas Biomedical Research Institute, San Antonio TX, United States
| | - Ehizogie Adeyemi
- Department of Pathology, University of Benin Teaching Hospital, Edo State, Nigeria
| | - Marian O Agbugui
- Department of Biological Sciences, Edo State University, Uzairue, Nigeria
| | | | - Ebube C Amaechi
- Department of Zoology, University of Ilorin, Kwara State, Nigeria
| | | | - Christopher Igbeneghu
- Department of Medical Laboratory Science, Ladoke Akintola University of Technology, Nigeria
| | - Victor S Njom
- Department of Applied Biology and Biotechnology, Enugu State University of Science and Technology, Nigeria
| | | | - Grace A Arya
- Texas Biomedical Research Institute, San Antonio TX, United States
| | - Robbie Diaz
- Texas Biomedical Research Institute, San Antonio TX, United States
| | - Muriel Rabone
- Science Department, Natural History Museum, London, United Kingdom
| | - Fiona Allan
- Science Department, Natural History Museum, London, United Kingdom
| | - Bonnie Webster
- Science Department, Natural History Museum, London, United Kingdom
| | - Aidan Emery
- Science Department, Natural History Museum, London, United Kingdom
| | - David Rollinson
- Science Department, Natural History Museum, London, United Kingdom
- Global Schistosomiasis Alliance, London, United Kingdom
| | | |
Collapse
|
3
|
Shogren EH, Sardell JM, Muirhead CA, Martí E, Cooper EA, Moyle RG, Presgraves DC, Uy JAC. Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species. PLoS Genet 2024; 20:e1011360. [PMID: 39172766 PMCID: PMC11340901 DOI: 10.1371/journal.pgen.1011360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/28/2024] [Indexed: 08/24/2024] Open
Abstract
Secondary contact between closely related taxa represents a "moment of truth" for speciation-an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family-Myzomela cardinalis and Myzomela tristrami-carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.
Collapse
Affiliation(s)
- Elsie H. Shogren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Jason M. Sardell
- PrecisionLife Ltd, Hanborough Business Park, Long Hanborough, Witney, Oxon, United Kingdom
| | - Christina A. Muirhead
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- The Ronin Institute, Montclair, New Jersey, United States of America
| | - Emiliano Martí
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Elizabeth A. Cooper
- Department of Bioinformatics & Genomics, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Robert G. Moyle
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Daven C. Presgraves
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - J. Albert C. Uy
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| |
Collapse
|
4
|
Fujiwara K, Kubo S, Endo T, Takada T, Shiroishi T, Suzuki H, Osada N. Inference of selective forces on house mouse genomes during secondary contact in East Asia. Genome Res 2024; 34:366-375. [PMID: 38508692 PMCID: PMC11067880 DOI: 10.1101/gr.278828.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
The house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspecies castaneus and musculus, particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to the musculus-type haplogroup, potentially explained by genomic conflict under sex-ratio distortion owing to varying copy numbers of ampliconic genes on sex chromosomes, Slx and Sly Our computer simulations, designed to replicate the observed scenario, show that the preferential fixation of musculus-type Y Chromosomes can be achieved with a slight increase in the male-to-female birth ratio. We also investigated the influence of selection on the posthybridization of the subspecies castaneus and musculus in Japan. Even though the genetic background of most Japanese samples closely resembles the subspecies musculus, certain genomic regions overrepresented the castaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block (∼2 Mbp) containing a vomeronasal/olfactory receptor gene cluster predominantly harbored castaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.
Collapse
Affiliation(s)
- Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Shunpei Kubo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Toshinori Endo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Toyoyuki Takada
- Integrated BioResource Information Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | | | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan;
| |
Collapse
|
5
|
Harris M, Kim BY, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. Genetics 2024; 226:iyae019. [PMID: 38366786 PMCID: PMC10990427 DOI: 10.1093/genetics/iyae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
Collapse
Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
6
|
Harris M, Kim B, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545888. [PMID: 38106201 PMCID: PMC10723260 DOI: 10.1101/2023.06.21.545888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
Collapse
Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles California, United States of America
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Nandita Garud
- Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles California, United States of America
- Department of Human Genetics, University of California, Los Angeles, California, United States of America
| |
Collapse
|
7
|
Johnson JA, Novak B, Athrey G, Sharo AG, Chase T, Toepfer J. Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse. Mol Phylogenet Evol 2023; 189:107927. [PMID: 37714443 DOI: 10.1016/j.ympev.2023.107927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/20/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater's Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater's Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genomic components associated with the Z-chromosome influence the phenotype and thereby impact species limits among prairie grouse taxa despite ongoing contemporary gene flow.
Collapse
Affiliation(s)
- Jeff A Johnson
- The Peregrine Fund, Boise, ID 83709, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
| | - Ben Novak
- Revive & Restore, Sausalito, CA 94965, USA
| | - Giridhar Athrey
- Department of Poultry Science & Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
| | - Andrew G Sharo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tom Chase
- Village and Wilderness, Martha's Vineyard, MA 02557, USA
| | - John Toepfer
- George Miksch Sutton Avian Research Center, Bartlesville, OK 74005, USA
| |
Collapse
|
8
|
Hanly JJ, Francescutti CM, Loh LS, Corning OBWH, Long DJ, Nakatani MA, Porter AH, Martin A. Genetics of yellow-orange color variation in a pair of sympatric sulphur butterflies. Cell Rep 2023; 42:112820. [PMID: 37481719 DOI: 10.1016/j.celrep.2023.112820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
Continuous color polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits. Here we investigated continuous color variation in Colias eurytheme and Colias philodice, two species of sulphur butterflies that hybridize in sympatry. Using quantitative trait locus (QTL) analysis and high-throughput color quantification, we found two interacting large-effect loci affecting orange-to-yellow chromaticity. Knockouts of red Malpighian tubules (red), likely involved in endosomal maturation, result in depigmented wing scales. Additionally, the transcription factor bric-a-brac can act as a modulator of orange pigmentation. We also describe the QTL architecture of other continuously varying traits, together supporting a large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the range of possible genetic architectures that can underpin a continuously varying trait and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.
Collapse
Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC, USA; Smithsonian Tropical Research Institute, Gamboa, Panama.
| | | | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Olaf B W H Corning
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Derek J Long
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Marshall A Nakatani
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
| |
Collapse
|
9
|
vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
Collapse
Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
10
|
Swaegers J, Sánchez-Guillén RA, Chauhan P, Wellenreuther M, Hansson B. Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies. Proc Biol Sci 2022; 289:20220968. [PMID: 35855603 PMCID: PMC9297008 DOI: 10.1098/rspb.2022.0968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and may shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridization. Moreover, they are thought to contribute to Haldane's rule, which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes, and (ii) that males are underrepresented among admixed individuals, as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data add to the few studies on species with X0 sex determination system and contradict the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.
Collapse
Affiliation(s)
- Janne Swaegers
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden,Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, Leuven, Belgium
| | | | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden
| |
Collapse
|
11
|
Bendall EE, Bagley RK, Sousa VC, Linnen CR. Faster-haplodiploid evolution under divergence-with-gene-flow: simulations and empirical data from pine-feeding hymenopterans. Mol Ecol 2022; 31:2348-2366. [PMID: 35231148 DOI: 10.1111/mec.16410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022]
Abstract
Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.
Collapse
Affiliation(s)
- Emily E Bendall
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robin K Bagley
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University at Lima, Lima, OH, 45804, USA
| | - Vitor C Sousa
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande 1749-016, Lisboa, Portugal
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA
| |
Collapse
|
12
|
Ficarrotta V, Hanly JJ, Loh LS, Francescutti CM, Ren A, Tunström K, Wheat CW, Porter AH, Counterman BA, Martin A. A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies. Proc Natl Acad Sci U S A 2022; 119:e2109255118. [PMID: 35012980 PMCID: PMC8784150 DOI: 10.1073/pnas.2109255118] [Citation(s) in RCA: 10] [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] [Received: 05/21/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern United States with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X (or large-Z) effect. Within this chromosome-wide reproductive barrier, linkage mapping indicates that cis-regulatory variation of bric a brac (bab) underlies the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knockout, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results highlight how a genetic switch can regulate a premating signal and integrate with other reproductive barriers during intermediate phases of speciation.
Collapse
Affiliation(s)
- Vincent Ficarrotta
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | | | - Anna Ren
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm S-10691, Sweden
| | | | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
| | | | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052;
| |
Collapse
|
13
|
Banker SE, Bonhomme F, Nachman MW. Bidirectional introgression between Mus musculus domesticus and Mus spretus. Genome Biol Evol 2022; 14:6509516. [PMID: 35038727 PMCID: PMC8784167 DOI: 10.1093/gbe/evab288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles—including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
Collapse
Affiliation(s)
- Sarah E Banker
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - François Bonhomme
- Institut des Sciences de l'Evolution, Université de Montpellier, Montpellier, France
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| |
Collapse
|
14
|
Pazhenkova EA, Lukhtanov VA. Genomic introgression from a distant congener in the Levant fritillary butterfly, Melitaea acentria. Mol Ecol 2021; 30:4819-4832. [PMID: 34288183 DOI: 10.1111/mec.16085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
Introgressive hybridization is more common in nature than previously thought, and its role and creative power in evolution is hotly discussed but not completely understood. Introgression occurs more frequently in sympatry between recently diverged taxa, or when the speciation process has not yet been completed. However, there are relatively few documented cases of hybridization that erodes reproductive barriers between distantly related species. Here, we use whole genome and mitochondrial data to examine how introgression from a distant congener affects pattern of genetic differentiation in the Levant fritillary butterfly Melitaea acentria. We show that this local taxon has evolved as a peripatric geographic isolate of the widespread Melitaea persea, and that there has been significant unidirectional gene flow from the sympatric, nonclosely related Melitaea didyma to M. acentria. We found direct evidence of ongoing sporadic hybridization between M. didyma and M. acentria, which are separated by at least 5 million years of independent evolution. Elevated differentiation and lower level of introgression on the sex Z chromosome compared to autosomes suggest that the Z chromosome has accumulated loci acting as intrinsic postzygotic barriers. Our results show that introgression from M. didyma has been an additional source of nucleotide diversity in the M. acentria population, providing material for drift and selection.
Collapse
Affiliation(s)
- Elena A Pazhenkova
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia.,Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
15
|
Presgraves DC, Meiklejohn CD. Hybrid Sterility, Genetic Conflict and Complex Speciation: Lessons From the Drosophila simulans Clade Species. Front Genet 2021; 12:669045. [PMID: 34249091 PMCID: PMC8261240 DOI: 10.3389/fgene.2021.669045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 12/31/2022] Open
Abstract
The three fruitfly species of the Drosophila simulans clade- D. simulans, D. mauritiana, and D. sechellia- have served as important models in speciation genetics for over 40 years. These species are reproductively isolated by geography, ecology, sexual signals, postmating-prezygotic interactions, and postzygotic genetic incompatibilities. All pairwise crosses between these species conform to Haldane's rule, producing fertile F1 hybrid females and sterile F1 hybrid males. The close phylogenetic proximity of the D. simulans clade species to the model organism, D. melanogaster, has empowered genetic analyses of their species differences, including reproductive incompatibilities. But perhaps no phenotype has been subject to more continuous and intensive genetic scrutiny than hybrid male sterility. Here we review the history, progress, and current state of our understanding of hybrid male sterility among the D. simulans clade species. Our aim is to integrate the available information from experimental and population genetics analyses bearing on the causes and consequences of hybrid male sterility. We highlight numerous conclusions that have emerged as well as issues that remain unresolved. We focus on the special role of sex chromosomes, the fine-scale genetic architecture of hybrid male sterility, and the history of gene flow between species. The biggest surprises to emerge from this work are that (i) genetic conflicts may be an important general force in the evolution of hybrid incompatibility, (ii) hybrid male sterility is polygenic with contributions of complex epistasis, and (iii) speciation, even among these geographically allopatric taxa, has involved the interplay of gene flow, negative selection, and positive selection. These three conclusions are marked departures from the classical views of speciation that emerged from the modern evolutionary synthesis.
Collapse
Affiliation(s)
- Daven C. Presgraves
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Colin D. Meiklejohn
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| |
Collapse
|