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Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
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Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
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52
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Mateos M, Domínguez‐Domínguez O, Varela‐Romero A. A multilocus phylogeny of the fish genus Poeciliopsis: Solving taxonomic uncertainties and preliminary evidence of reticulation. Ecol Evol 2019; 9:1845-1857. [PMID: 30847076 PMCID: PMC6392363 DOI: 10.1002/ece3.4874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/06/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, that is, concatenated (also known as super-matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans-Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north-south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north-south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US-Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by "breakdown" of an asexual hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome-wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.
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Affiliation(s)
- Mariana Mateos
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTexas
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática, Facultad de BiologíaUniversidad Michoacana de San Nicolás de HidalgoMoreliaMichoacánMexico
| | - Alejandro Varela‐Romero
- Departamento de Investigaciones Científicas y TecnológicasUniversidad de SonoraHermosilloSonoraMexico
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Meiklejohn CD, Landeen EL, Gordon KE, Rzatkiewicz T, Kingan SB, Geneva AJ, Vedanayagam JP, Muirhead CA, Garrigan D, Stern DL, Presgraves DC. Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. eLife 2018; 7:e35468. [PMID: 30543325 PMCID: PMC6292695 DOI: 10.7554/elife.35468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.
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Affiliation(s)
| | - Emily L Landeen
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Kathleen E Gordon
- School of Biological SciencesUniversity of NebraskaLincolnUnited States
| | | | - Sarah B Kingan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Anthony J Geneva
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | | | | | - Daniel Garrigan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
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55
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Patten MM. The X chromosome favors males under sexually antagonistic selection. Evolution 2018; 73:84-91. [PMID: 30421421 DOI: 10.1111/evo.13646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/25/2022]
Abstract
The X chromosome is found twice as often in females as males. This has led to an intuition that X-linked genes for traits experiencing sexually antagonistic selection should tend to evolve toward the female optimum. However, this intuition has never been formally examined. In this paper, I present a simple mathematical model and ask whether the X chromosome is indeed biased toward effecting female-optimal phenotypes. Counter to the intuition, I find that the exact opposite bias exists; the X chromosome is revealed to be a welcome spot for mutations that benefit males at the expense of females. Not only do male-beneficial alleles have an easier time of invading and spreading through a population, but they also achieve higher equilibrium frequencies than comparable female-beneficial alleles. The X chromosome is therefore expected over evolutionary time to nudge phenotypes closer to the male optimum. Consequently, the X chromosome should find itself engaged in perpetual intragenomic conflicts with the autosomes and the mitochondria over developmental outcomes. The X chromosome's male bias and the intragenomic conflicts that ensue bear on the evolution of gene regulation, speciation, and our concept of organismality.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, Washington, District of Columbia, 20057
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Abstract
Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness. [1-6] Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts. Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the gene-centred views of evolution popularized by George Williams[7] and Richard Dawkins,[8] two papers were published back-to-back in Nature in 1980-by Leslie Orgel and Francis Crick[9] and Ford Doolittle and Carmen Sapienza[10] respectively-introducing the concept of selfish genetic elements (at the time called "selfish DNA") to the wider scientific community. Both papers emphasized that genes can spread in a population regardless of their effect on organismal fitness as long as they have a transmission advantage. Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission.[11] Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.[12].
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Affiliation(s)
- J. Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
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Abstract
Evolutionary conflict occurs when two parties can each affect a joint phenotype, but they gain from pushing it in opposite directions. Conflicts occur across many biological levels and domains but share many features. They are a major source of biological maladaptation. They affect biological diversity, often increasing it, at almost every level. Because opponents create selection that can be strong, persistent, and malevolent, conflict often leads to accelerated evolution and arms races. Conflicts might even drive the majority of adaptation, with pathogens leading the way as selective forces. The evolution of conflicts is complex, with outcomes determined partly by the relative evolvability of each party and partly by the kinds of power that each evolves. Power is a central issue in biology. In addition to physical strength and weapons, it includes strength from numbers and complexity; abilities to bind and block; advantageous timing; and abilities to acquire, use, and distort information.
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Affiliation(s)
- David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;,
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;,
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Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
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Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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Yoshida K, Ishikawa A, Toyoda A, Shigenobu S, Fujiyama A, Kitano J. Functional divergence of a heterochromatin‐binding protein during stickleback speciation. Mol Ecol 2018; 28:1563-1578. [DOI: 10.1111/mec.14841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Kohta Yoshida
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Asano Ishikawa
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities National Institute for Basic Biology Okazaki Aichi Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory National Institute of Genetics Mishima Shizuoka Japan
| | - Jun Kitano
- Division of Ecological Genetics National Institute of Genetics Mishima Shizuoka Japan
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60
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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Brom T, Massot M, Laloi D. The sex chromosome system can influence the evolution of sex-biased dispersal. J Evol Biol 2018; 31:1377-1385. [PMID: 29927019 DOI: 10.1111/jeb.13340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/17/2018] [Accepted: 06/12/2018] [Indexed: 12/01/2022]
Abstract
Sex-biased dispersal is a much-discussed feature in literature on dispersal. Diverse hypotheses have been proposed to explain the evolution of sex-biased dispersal, a difference in dispersal rate or dispersal distance between males and females. An early hypothesis has indicated that it may rely on the difference in sex chromosomes between males and females. However, this proposal was quickly rejected without a real assessment. We propose a new perspective on this hypothesis by investigating the evolution of sex-biased dispersal when dispersal genes are sex-linked, that is when they are located on the sex chromosomes. We show that individuals of the heterogametic sex disperse relatively more than do individuals of the homogametic sex when dispersal genes are sex-linked rather than autosomal. Although such a sex-biased dispersal towards the heterogametic sex is always observed in monogamous species, the mating system and the location of dispersal genes interact to modulate sex-biased dispersal in monandry and polyandry. In the context of the multicausality of dispersal, we suggest that sex-linked dispersal genes can influence the evolution of sex-biased dispersal.
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Affiliation(s)
- Thomas Brom
- CNRS, Univ. Lille, UMR8198-Evo-Eco-Paleo, Lille, France.,CNRS, Sorbonne Université, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES Paris, Paris, France
| | - Manuel Massot
- CNRS, Sorbonne Université, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES Paris, Paris, France
| | - David Laloi
- CNRS, Sorbonne Université, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES Paris, Paris, France
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62
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Verspoor RL, Smith JML, Mannion NLM, Hurst GDD, Price TAR. Strong hybrid male incompatibilities impede the spread of a selfish chromosome between populations of a fly. Evol Lett 2018; 2:169-179. [PMID: 30283674 PMCID: PMC6121854 DOI: 10.1002/evl3.55] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/22/2018] [Indexed: 01/08/2023] Open
Abstract
Meiotically driving sex chromosomes manipulate gametogenesis to increase their transmission at a cost to the rest of the genome. The intragenomic conflicts they produce have major impacts on the ecology and evolution of their host species. However, their ecological dynamics remain poorly understood. Simple population genetic models predict meiotic drivers will rapidly reach fixation in populations and spread across landscapes. In contrast, natural populations commonly show spatial variation in the frequency of drivers, with drive present in clines or mosaics across species ranges. For example, Drosophila subobscura harbors a sex ratio distorting drive chromosome (SRs) at 15-25% frequency in North Africa, present at less than 2% frequency in adjacent southern Spain, and absent in other European populations. Here, we investigate the forces preventing the spread of the driver northward. We show that SRs has remained at a constant frequency in North Africa, and failed to spread in Spain. We find strong evidence that spread is impeded by genetic incompatibility between SRs and Spanish autosomal backgrounds. When we cross SRs from North Africa onto Spanish genetic backgrounds we observe strong incompatibilities specific to hybrids bearing SRs. The incompatibilities increase in severity in F2 male hybrids, leading to almost complete infertility. We find no evidence supporting an alternative hypothesis, that there is resistance to drive in Spanish populations. We conclude that the source of the stepped frequency variation is genetic incompatibility between the SRs chromosome and the genetic backgrounds of the adjacent population, preventing SRs spreading northward. The low frequency of SRs in South Spain is consistent with recurrent gene flow across the Strait of Gibraltar combined with selection against the SRs element through genetic incompatibility. This demonstrates that incompatibilities between drive chromosomes and naïve populations can prevent the spread of drive between populations, at a continental scale.
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Affiliation(s)
- Rudi L. Verspoor
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Jack M. L. Smith
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Natasha L. M. Mannion
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Gregory D. D. Hurst
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Tom A. R. Price
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
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63
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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64
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Liu X, Karrenberg S. Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation. Mol Ecol 2018; 27:3889-3904. [PMID: 29577481 DOI: 10.1111/mec.14562] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/02/2023]
Abstract
The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.
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Affiliation(s)
- Xiaodong Liu
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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65
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Patten MM. Selfish X chromosomes and speciation. Mol Ecol 2018; 27:3772-3782. [PMID: 29281152 DOI: 10.1111/mec.14471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 12/24/2022]
Abstract
In two papers published at about the same time almost thirty years ago, Frank (Evolution, 45, 1991a, 262) and Hurst and Pomiankowski (Genetics, 128, 1991, 841) independently suggested that divergence of meiotic drive systems-comprising genes that cheat meiosis and genes that suppress this cheating-might provide a general explanation for Haldane's rule and the large X-effect in interspecific hybrids. Although at the time, the idea was met with skepticism and a conspicuous absence of empirical support, the tide has since turned. Some of the clearest mechanistic explanations we have for hybrid male sterility involve meiotic drive systems, and several other cases of hybrid sterility are suggestive of a role for meiotic drive. In this article, I review these ideas and their descendants and catalog the current evidence for the meiotic drive model of speciation. In addition, I suggest that meiotic drive is not the only intragenomic conflict to involve the X chromosome and contribute to hybrid incompatibility. Sexually and parentally antagonistic selection pressures can also pit the X chromosome and autosomes against each other. The resulting intragenomic conflicts should lead to co-evolution within populations and divergence between them, thus increasing the likelihood of incompatibilities in hybrids. I provide a sketch of these ideas and interpret some empirical patterns in the light of these additional X-autosome conflicts.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, Washington, DC, USA
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66
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Case AL, Finseth FR, Barr CM, Fishman L. Selfish evolution of cytonuclear hybrid incompatibility in Mimulus. Proc Biol Sci 2017; 283:rspb.2016.1493. [PMID: 27629037 DOI: 10.1098/rspb.2016.1493] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 08/23/2016] [Indexed: 11/12/2022] Open
Abstract
Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility.
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Affiliation(s)
- Andrea L Case
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Findley R Finseth
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Camille M Barr
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Kerwin RE, Sweigart AL. Mechanisms of Transmission Ratio Distortion at Hybrid Sterility Loci Within and Between Mimulus Species. G3 (BETHESDA, MD.) 2017; 7:3719-3730. [PMID: 28935753 PMCID: PMC5677164 DOI: 10.1534/g3.117.300148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/09/2017] [Indexed: 12/28/2022]
Abstract
Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2) in the closely related yellow monkeyflower species Mimulus guttatus and M. nasutus By performing reciprocal backcrosses with introgression lines (ILs), we find evidence for gametic expression of the hms1-hms2 incompatibility. Surprisingly, however, hybrid transmission ratios at hms1 do not reflect this incompatibility, suggesting that additional mechanisms counteract the effects of gametic sterility. Indeed, our backcross experiment shows hybrid transmission bias toward M. guttatus through both pollen and ovules, an effect that is particularly strong when hms2 is homozygous for M. nasutus alleles. In contrast, we find little evidence for hms1 transmission bias in crosses within M. guttatus, providing no indication of selfish evolution at this locus. Although we do not yet have sufficient genetic resolution to determine if hybrid sterility and transmission ratio distortion (TRD) map to the same loci, our preliminary fine-mapping uncovers a genetically independent hybrid lethality system involving at least two loci linked to hms1 This fine-scale dissection of TRD at hms1 and hms2 provides insight into genomic differentiation between closely related Mimulus species and reveals multiple mechanisms of hybrid dysfunction.
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Affiliation(s)
- Rachel E Kerwin
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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68
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Decato BE, Lopez-Tello J, Sferruzzi-Perri AN, Smith AD, Dean MD. DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta. Mol Biol Evol 2017; 34:1702-1712. [PMID: 28379409 DOI: 10.1093/molbev/msx112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high-resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. We conducted a study of placental DNA methylation at high resolution in multiple strains and closely related species of house mice (Mus musculus musculus, Mus m. domesticus, and M. spretus), across developmental timepoints (embryonic days 15-18), and between two distinct layers (labyrinthine transport and junctional endocrine). We observed substantial genome-wide methylation heterogeneity in mouse placenta compared with other differentiated tissues. Species-specific methylation profiles were concentrated in retrotransposon subfamilies, specifically RLTR10 and RLTR20 subfamilies. Regulatory regions such as gene promoters and CpG islands displayed cross-species conservation, but showed strong differences between layers and developmental timepoints. Partially methylated domains exist in the mouse placenta and widen during development. Taken together, our results characterize the mouse placental methylome as a highly heterogeneous and deregulated landscape globally, intermixed with actively regulated promoter and retrotransposon sequences.
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Affiliation(s)
- Benjamin E Decato
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Jorge Lopez-Tello
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Amanda N Sferruzzi-Perri
- Department of Physiology, Development, and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Matthew D Dean
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
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Barnard‐Kubow KB, Galloway LF. Variation in reproductive isolation across a species range. Ecol Evol 2017; 7:9347-9357. [PMID: 29187973 PMCID: PMC5696433 DOI: 10.1002/ece3.3400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022] Open
Abstract
Reproductive isolation is often variable within species, a phenomenon that while largely ignored by speciation studies, can be leveraged to gain insight into the potential mechanisms driving the evolution of genetic incompatibilities. We used experimental greenhouse crosses to characterize patterns of reproductive isolation among three divergent genetic lineages of Campanulastrum americanum that occur in close geographic proximity in the Appalachian Mountains. Substantial, asymmetrical reproductive isolation for survival due to cytonuclear incompatibility was found among the lineages (up to 94% reduction). Moderate reductions in pollen viability, as well as cytoplasmic male sterility, were also found between some Mountain populations. We then compared these results to previously established patterns of reproductive isolation between these Mountain lineages and a fourth, widespread Western lineage to fully characterize reproductive isolation across the complete geographic and genetic range of C. americanum. Reproductive isolation for survival and pollen viability was consistent across studies, indicating the evolution of the underlying genetic incompatibilities is primarily determined by intrinsic factors. In contrast, reproductive isolation for germination was only found when crossing Mountain populations with the Western lineage, suggesting the underlying genetic incompatibility is likely influenced by environmental or demographic differences between the two lineages. Cytoplasmic male sterility was also limited in occurrence, being restricted to a handful of Mountain populations in a narrow geographic range. These findings illustrate the complexity of speciation by demonstrating multiple, independent genetic incompatibilities that lead to a mosaic of genetic divergence and reproductive isolation across a species range.
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70
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Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:164-176. [PMID: 28602845 PMCID: PMC5487533 DOI: 10.1016/j.gpb.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2017] [Accepted: 01/12/2017] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established “transposition-selection” population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.
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71
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Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M. Chironomus riparius
(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol 2017; 26:3256-3275. [DOI: 10.1111/mec.14111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Hanno Schmidt
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Marcel Rose
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
| | - Sören Lukas Hellmann
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Florian Dolze
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Fabian Ripp
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Bettina Weich
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy; University of Chicago; 920 E. 58th Street, 1061C Chicago IL 60637 USA
| | - Erwin Schmidt
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Robert Kofler
- Institut für Populationsgenetik; Vetmeduni Vienna 1210 Vienna Austria
| | - Thomas Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Markus Pfenninger
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
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Levin DA, Scarpino SV. On the young age of intraspecific herbaceous taxa. THE NEW PHYTOLOGIST 2017; 213:1513-1520. [PMID: 27726173 DOI: 10.1111/nph.14224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX 78713, USA
| | - Samuel V Scarpino
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT 05401, USA
- Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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74
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Patten MM, Cowley M, Oakey RJ, Feil R. Regulatory links between imprinted genes: evolutionary predictions and consequences. Proc Biol Sci 2017; 283:rspb.2015.2760. [PMID: 26842569 PMCID: PMC4760173 DOI: 10.1098/rspb.2015.2760] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC 20057, USA
| | - Michael Cowley
- Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Robert Feil
- Centre National de Recherche Scientifique (CNRS), Institute of Molecular Genetics (IGMM), 1919 route de Mende, Montpellier 34293, France University of Montpellier, 163 rue Auguste Broussonnet, Montpellier 34090, France Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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75
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Brekke TD, Henry LA, Good JM. Genomic imprinting, disrupted placental expression, and speciation. Evolution 2016; 70:2690-2703. [PMID: 27714796 PMCID: PMC5123974 DOI: 10.1111/evo.13085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/22/2022]
Abstract
The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent-of-origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent-specific epigenetic gene silencing) during early development. Here, we test the long-standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors. We analyzed placental gene expression in reciprocal dwarf hamster hybrids that show extreme parent-of-origin growth effects relative to their parental species. In massively enlarged hybrid placentas, we observed both extensive transgressive expression of growth-related genes and biallelic expression of many genes that were paternally silenced in normal sized hybrids. However, the apparent widespread disruption of paternal silencing was coupled with reduced gene expression levels overall. These patterns are contrary to the predictions of the LOI model and indicate that hybrid misexpression of dosage-sensitive genes is caused by other regulatory mechanisms in this system. Collectively, our results support a central role for disrupted gene expression and imprinting in the evolution of mammalian hybrid inviability, but call into question the generality of the widely invoked LOI model.
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Affiliation(s)
- Thomas D. Brekke
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Lindy A. Henry
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
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76
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Pogson GH. Studying the genetic basis of speciation in high gene flow marine invertebrates. Curr Zool 2016; 62:643-653. [PMID: 29491951 PMCID: PMC5804258 DOI: 10.1093/cz/zow093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
A growing number of genes responsible for reproductive incompatibilities between species (barrier loci) exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms (SNPs) in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying FST-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and non-coding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available.
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Affiliation(s)
- Grant H. Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
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77
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Florez-Rueda AM, Paris M, Schmidt A, Widmer A, Grossniklaus U, Städler T. Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds. Mol Biol Evol 2016; 33:2935-2946. [PMID: 27601611 PMCID: PMC5062328 DOI: 10.1093/molbev/msw175] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviable seeds due to endosperm failure and arrested embryo development. Based on differences of seed size in reciprocal hybrid crosses and developmental evidence implicating endosperm failure, we hypothesized that perturbed genomic imprinting is involved in this strong postzygotic barrier. Consequently, we surveyed the transcriptomes of developing endosperms from intra- and inter-specific crosses using tissues isolated by laser-assisted microdissection. We implemented a novel approach to estimate parent-of-origin–specific expression using both homozygous and heterozygous nucleotide differences between parental individuals and identified candidate imprinted genes. Importantly, we uncovered systematic shifts of “normal” (intraspecific) maternal:paternal transcript proportions in hybrid endosperms; the average maternal proportion of gene expression increased in both crossing directions but was stronger with S. peruvianum in the maternal role. These genome-wide shifts almost entirely eliminated paternally expressed imprinted genes in S. peruvianum hybrid endosperm but also affected maternally expressed imprinted genes and all other assessed genes. These profound, systematic changes in parental expression proportions suggest that core processes of transcriptional regulation are functionally compromised in hybrid endosperm and contribute to hybrid seed failure.
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Affiliation(s)
- Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Anja Schmidt
- Plant Developmental Genetics, Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Ueli Grossniklaus
- Plant Developmental Genetics, Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich-Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
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Hardy NB, Peterson DA, Normark BB. Nonadaptive radiation: Pervasive diet specialization by drift in scale insects? Evolution 2016; 70:2421-2428. [DOI: 10.1111/evo.13036] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/29/2016] [Accepted: 07/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Nate B. Hardy
- Department of Entomology and Plant Pathology, 301 Funchess Hall Auburn University Auburn Alabama 36849
| | - Daniel A. Peterson
- Graduate Program in Organismic & Evolutionary Biology, Department of Biology University of Massachusetts Amherst Massachusetts 01003
| | - Benjamin B. Normark
- Graduate Program in Organismic & Evolutionary Biology, Department of Biology University of Massachusetts Amherst Massachusetts 01003
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79
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Cutter AD, Gray JC. Ephemeral ecological speciation and the latitudinal biodiversity gradient. Evolution 2016; 70:2171-2185. [PMID: 27502055 DOI: 10.1111/evo.13030] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/29/2016] [Indexed: 01/17/2023]
Abstract
The richness of biodiversity in the tropics compared to high-latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High-latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of "environmental harshness" and "hard selection" as eco-evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Jeremy C Gray
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
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80
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Simon M, Durand S, Pluta N, Gobron N, Botran L, Ricou A, Camilleri C, Budar F. Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana. Genetics 2016; 203:1353-67. [PMID: 27182945 PMCID: PMC4937478 DOI: 10.1534/genetics.115.183707] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/28/2016] [Indexed: 11/18/2022] Open
Abstract
Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations.
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Affiliation(s)
- Matthieu Simon
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Stéphanie Durand
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Natacha Pluta
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Nicolas Gobron
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Lucy Botran
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Anthony Ricou
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, 78026 Versailles Cedex, France
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Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, Manser A, Montchamp-Moreau C, Petrosyan VG, Pomiankowski A, Presgraves DC, Safronova LD, Sutter A, Unckless RL, Verspoor RL, Wedell N, Wilkinson GS, Price TA. The Ecology and Evolutionary Dynamics of Meiotic Drive. Trends Ecol Evol 2016; 31:315-326. [DOI: 10.1016/j.tree.2016.02.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022]
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82
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Hu XS, Filatov DA. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome. Mol Ecol 2016; 25:2609-19. [PMID: 26479725 DOI: 10.1111/mec.13427] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 12/25/2022]
Abstract
The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7) years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.
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Affiliation(s)
- Xin-Sheng Hu
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
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83
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Kaufmann J, Eizaguirre C, Milinski M, Lenz TL. The contribution of post-copulatory mechanisms to incipient ecological speciation in sticklebacks. Biol Lett 2015; 11:20140933. [PMID: 25589488 DOI: 10.1098/rsbl.2014.0933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecology can play a major role in species diversification. As individuals are adapting to contrasting habitats, reproductive barriers may evolve at multiple levels. While pre-mating barriers have been extensively studied, the evolution of post-mating reproductive isolation during early stages of ecological speciation remains poorly understood. In diverging three-spined stickleback ecotypes from two lakes and two rivers, we observed differences in sperm traits between lake and river males. Interestingly, these differences did not translate into ecotype-specific gamete precedence for sympatric males in competitive in vitro fertilization experiments, potentially owing to antagonistic compensatory effects. However, we observed indirect evidence for impeded development of inter-ecotype zygotes, possibly suggesting an early stage of genetic incompatibility between ecotypes. Our results show that pre-zygotic post-copulatory mechanisms play a minor role during this first stage of ecotype divergence, but suggest that genetic incompatibilities may arise at early stages of ecological speciation.
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Affiliation(s)
- Joshka Kaufmann
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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84
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Furness AI, Morrison KR, Orr TJ, Arendt JD, Reznick DN. Reproductive mode and the shifting arenas of evolutionary conflict. Ann N Y Acad Sci 2015; 1360:75-100. [PMID: 26284738 DOI: 10.1111/nyas.12835] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 12/11/2022]
Abstract
In sexually reproducing organisms, the genetic interests of individuals are not perfectly aligned. Conflicts among family members are prevalent since interactions involve the transfer of limited resources between interdependent players. Intrafamilial conflict has traditionally been considered along three major axes: between the sexes, between parents and offspring, and between siblings. In these interactions, conflict is expected over traits in which the resulting phenotypic value is determined by multiple family members who have only partially overlapping fitness optima. We focus on four major categories of animal reproductive mode (broadcast spawning, egg laying, live bearing, and live bearing with matrotrophy) and identify the shared phenotypes or traits over which conflict is expected, and then review the empirical literature for evidence of their occurrence. Major transitions among reproductive mode, such as a shift from external to internal fertilization, an increase in egg-retention time, modifications of embryos and mothers for nutrient transfer, the evolution of postnatal parental care, and increased interaction with the kin network, mark key shifts that both change and expand the arenas in which conflict is played out.
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Affiliation(s)
- Andrew I Furness
- Department of Biology, University of California, Riverside, California.,Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Keenan R Morrison
- Department of Biology, University of California, Riverside, California
| | - Teri J Orr
- Department of Biology, University of California, Riverside, California.,Department of Biology, University of Massachusetts, Amherst, Massachusetts
| | - Jeff D Arendt
- Department of Biology, University of California, Riverside, California
| | - David N Reznick
- Department of Biology, University of California, Riverside, California
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85
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Gómez J, Ariza-Mateos A, Cacho I. Virus is a Signal for the Host Cell. BIOSEMIOTICS 2015; 8:483-491. [PMID: 26640606 PMCID: PMC4661187 DOI: 10.1007/s12304-015-9245-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/25/2015] [Indexed: 06/05/2023]
Abstract
Currently, the concept of the cell as a society or an ecosystem of molecular elements is gaining increasing acceptance. The basic idea arose in the 19th century, from the surmise that there is not just a single unit underlying an individual's appearance, but a plurality of entities with both collaborative and conflicting relationships. The following hypothesis is based around this model. The incompatible activities taking place between different original elements, which were subsumed into the first cell and could not be eliminated, had to be controlled very closely. Similarly, a strong level of control had to be developed over many cellular elements after the cell changed its genome to DNA. We assume that at least some of those original RNA agents and other biomolecules which carry incompatibilities and risks, are retained within current cells, although they are now under strict control. A virus functions as a signal informing these repressed cellular RNAs and other elements of ancient origin how to restore suppressed degrees of molecular freedom, favoring pre-existing molecular affinities and activities, re-establishing ancient molecular webs of interactions, and giving fragments of ancient coded information (mostly in the form of RNA structural motifs) the opportunity to be re-expressed. Collectively, these newly activated mechanisms lead to different possibilities for pathological cell states. All these processes are opposed by cell-control mechanisms. Thus, in this new scenario, the battle is considered intracellular rather than between the virus and the cell. And so the virus is treated as the signal that precipitates the cell's change from a latent to an active pathological state.
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Affiliation(s)
- Jordi Gómez
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
| | - Ascensión Ariza-Mateos
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
| | - Isabel Cacho
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', Consejo Superior de Ivestigaciones Científicas, Armilla 18100 Granada, Spain
- Centro de Investigación Biomedicina En Red de enfermedades hepáticas y digestivas, Barcelona, Spain
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86
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Abstract
Recent research has filled many gaps about Caenorhabditis natural history, simultaneously exposing how much remains to be discovered. This awareness now provides means of connecting ecological and evolutionary theory with diverse biological patterns within and among species in terms of adaptation, sexual selection, breeding systems, speciation, and other phenomena. Moreover, the heralded laboratory tractability of C. elegans, and Caenorhabditis species generally, provides a powerful case study for experimental hypothesis testing about evolutionary and ecological processes to levels of detail unparalleled by most study systems. Here, I synthesize pertinent theory with what we know and suspect about Caenorhabditis natural history for salient features of biodiversity, phenotypes, population dynamics, and interactions within and between species. I identify topics of pressing concern to advance Caenorhabditis biology and to study general evolutionary processes, including the key opportunities to tackle problems in dispersal dynamics, competition, and the dimensionality of niche space.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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87
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Chou JY, Leu JY. The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease. Front Genet 2015; 6:187. [PMID: 26042149 PMCID: PMC4437034 DOI: 10.3389/fgene.2015.00187] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/05/2015] [Indexed: 01/08/2023] Open
Abstract
Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education , Changhua, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica , Taipei, Taiwan
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88
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Bolton PE, Rollins LA, Griffith SC. The danger within: the role of genetic, behavioural and ecological factors in population persistence of colour polymorphic species. Mol Ecol 2015; 24:2907-15. [PMID: 25870951 DOI: 10.1111/mec.13201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/01/2023]
Abstract
Polymorphic species have been the focus of important work in evolutionary biology. It has been suggested that colour polymorphic species have specific evolutionary and population dynamics that enable them to persist through environmental changes better than less variable species. We suggest that recent empirical and theoretical work indicates that polymorphic species may be more vulnerable to extinction than previously thought. This vulnerability arises because these species often have a number of correlated sexual, behavioural, life history and ecological traits, which can have a simple genetic underpinning. When exacerbated by environmental change, these alternate strategies can lead to conflict between morphs at the genomic and population levels, which can directly or indirectly affect population and evolutionary dynamics. In this perspective, we identify a number of ways in which the nature of the correlated traits, their underpinning genetic architecture, and the inevitable interactions between colour morphs can result in a reduction in population fitness. The principles illustrated here apply to all kinds of discrete polymorphism (e.g. behavioural syndromes), but we focus primarily on colour polymorphism because they are well studied. We urge further empirical investigation of the genetic architecture and interactions in polymorphic species to elucidate the impact on population fitness.
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Affiliation(s)
- Peri E Bolton
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Lee A Rollins
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., 3217, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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89
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Abstract
Eukaryotes were born of a chimeric union between two prokaryotes--the progenitors of the mitochondrial and nuclear genomes. Early in eukaryote evolution, most mitochondrial genes were lost or transferred to the nucleus, but a core set of genes that code exclusively for products associated with the electron transport system remained in the mitochondrion. The products of these mitochondrial genes work in intimate association with the products of nuclear genes to enable oxidative phosphorylation and core energy production. The need for coadaptation, the challenge of cotransmission, and the possibility of genomic conflict between mitochondrial and nuclear genes have profound consequences for the ecology and evolution of eukaryotic life. An emerging interdisciplinary field that I call "mitonuclear ecology" is reassessing core concepts in evolutionary ecology including sexual reproduction, two sexes, sexual selection, adaptation, and speciation in light of the interactions of mitochondrial and nuclear genomes.
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90
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Jones EP, Searle JB. Differing Y chromosome versus mitochondrial DNA ancestry, phylogeography, and introgression in the house mouse. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12522] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Eleanor P. Jones
- Population Biology and Conservation Biology; Evolutionary Biology Centre; University of Uppsala; Uppsala Sweden
- Food and Environment Research Agency; Sand Hutton York YO41 1LZ UK
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
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91
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Kropáčková L, Piálek J, Gergelits V, Forejt J, Reifová R. Maternal-foetal genomic conflict and speciation: no evidence for hybrid placental dysplasia in crosses between two house mouse subspecies. J Evol Biol 2015; 28:688-98. [PMID: 25682889 DOI: 10.1111/jeb.12602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 02/05/2015] [Indexed: 11/29/2022]
Abstract
Interspecific hybridization between closely related mammalian species, including various species of the genus Mus, is commonly associated with abnormal growth of the placenta and hybrid foetuses, a phenomenon known as hybrid placental dysplasia (HPD). The role of HPD in speciation is anticipated but still poorly understood. Here, we studied placental and foetal growth in F1 crosses between four inbred mouse strains derived from two house mouse subspecies, Mus musculus musculus and Mus musculus domesticus. These subspecies are in the early stage of speciation and still hybridize in nature. In accordance with the maternal-foetal genomic conflict hypothesis, we found different parental influences on placental and foetal development, with placental weight most affected by the father's body weight and foetal weight by the mother's body weight. After removing the effects of parents' body weight, we did not find any significant differences in foetal or placental weights between intra-subspecific and inter-subspecific F1 crosses. Nevertheless, we found that the variability in placental weight in inter-subspecific crosses is linked to the X chromosome, similarly as for HPD in interspecific mouse crosses. Our results suggest that maternal-foetal genomic conflict occurs in the house mouse system, but has not yet diverged sufficiently to cause abnormalities in placental and foetal growth in inter-subspecific crosses. HPD is thus unlikely to contribute to speciation in the house mouse system. However, we cannot rule out that it might have contributed to other speciation events in the genus Mus, where differences in the levels of polyandry exist between the species.
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Affiliation(s)
- L Kropáčková
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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92
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Schumer M, Cui R, Rosenthal GG, Andolfatto P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet 2015; 11:e1005041. [PMID: 25768654 PMCID: PMC4359097 DOI: 10.1371/journal.pgen.1005041] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/29/2015] [Indexed: 12/25/2022] Open
Abstract
Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
- Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Gil G. Rosenthal
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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93
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Case LK, Wall EH, Osmanski EE, Dragon JA, Saligrama N, Zachary JF, Lemos B, Blankenhorn EP, Teuscher C. Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. Genome Biol 2015; 16:28. [PMID: 25886764 PMCID: PMC4396973 DOI: 10.1186/s13059-015-0591-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/20/2015] [Indexed: 12/11/2022] Open
Abstract
Background The prevalence of some autoimmune diseases is greater in females compared with males, although disease severity is often greater in males. The reason for this sexual dimorphism is unknown, but it may reflect negative selection of Y chromosome-bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the sexual dimorphism in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in Y chromosome multicopy genes. Here, we test the hypothesis that CNV in Y chromosome multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice. Results We show that C57BL/6 J consomic strains of mice possessing an identical X chromosome and CNV in Y chromosome multicopy genes exhibit sperm head abnormalities and female-biased sex ratio. This is consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous X:Y chromosome multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of microRNAs within the sperm nucleus. Furthermore, in humans, families of probands with multiple sclerosis similarly exhibit a female-biased sex ratio, whereas families of probands affected with non-sexually dimorphic autoimmune diseases exhibit unbiased sex ratios. Conclusions These findings provide evidence for a mechanism at the level of the male gamete that contributes to the sexual dimorphism in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the sexual dimorphism in multiple sclerosis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0591-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Emma H Wall
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Erin E Osmanski
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Julie A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
| | - Naresha Saligrama
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Current address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - James F Zachary
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Department of Pathology, University of Vermont, Burlington, VT, 05405, USA.
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94
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Bromham L, Hua X, Lanfear R, Cowman PF. Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants. Am Nat 2015; 185:507-24. [PMID: 25811085 DOI: 10.1086/680052] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population-level processes and to patterns of lineage divergence.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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95
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Abstract
The extraordinary species richness of freshwater fishes has attracted much research on mechanisms and modes of speciation. We here review research on speciation in freshwater fishes in light of speciation theory, and place this in a context of broad-scale diversity patterns in freshwater fishes. We discuss several major repeated themes in freshwater fish speciation and the speciation mechanisms they are frequently associated with. These include transitions between marine and freshwater habitats, transitions between discrete freshwater habitats, and ecological transitions within habitats, as well as speciation without distinct niche shifts. Major research directions in the years to come include understanding the transition from extrinsic environment-dependent to intrinsic reproductive isolation and its influences on species persistence and understanding the extrinsic and intrinsic constraints to speciation and how these relate to broad-scale diversification patterns through time.
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Affiliation(s)
- Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
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96
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Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, Martín-Pizarro C, Laitinen RAE, Rowan BA, Tenenboim H, Lechner S, Demar M, Habring-Müller A, Lanz C, Rätsch G, Weigel D. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 2014; 159:1341-51. [PMID: 25467443 DOI: 10.1016/j.cell.2014.10.049] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/22/2014] [Accepted: 10/07/2014] [Indexed: 01/07/2023]
Abstract
Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.
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Affiliation(s)
- Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Darya Karelina
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Stephan Ossowski
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Carmen Martín-Pizarro
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Roosa A E Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Hezi Tenenboim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sarah Lechner
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Monika Demar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anette Habring-Müller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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97
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Abstract
At the end of the last century, sexual conflict was identified as a powerful engine of speciation, potentially even more important than ecological selection. Earlier work that followed--experimental, comparative, and mathematical--provided strong initial support for this assertion. However, as the field matures, both the power of sexual conflict and constraints on the evolution of reproductive isolation as driven by sexual conflict are becoming better understood. From theoretical studies, we now know that speciation is only one of several possible evolutionary outcomes of sexual conflict. In line with these predictions, both experimental evolution studies and comparative analyses of fertilization proteins and of species richness show that sexual conflict leads to, or is associated with, reproductive isolation and speciation in some cases but not in others. Increased genetic variation (especially in females) without reproductive isolation is an underappreciated consequence of sexually antagonistic selection.
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Affiliation(s)
- Sergey Gavrilets
- Department of Ecology and Evolutionary Biology, Department of Mathematics, National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996
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98
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Brekke TD, Good JM. Parent-of-origin growth effects and the evolution of hybrid inviability in dwarf hamsters. Evolution 2014; 68:3134-48. [PMID: 25130206 PMCID: PMC4437546 DOI: 10.1111/evo.12500] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/11/2014] [Indexed: 12/24/2022]
Abstract
Mammalian hybrids often show abnormal growth, indicating that developmental inviability may play an important role in mammalian speciation. Yet, it is unclear if this recurrent phenotype reflects a common genetic basis. Here, we describe extreme parent-of-origin-dependent growth in hybrids from crosses between two species of dwarf hamsters, Phodopus campbelli and Phodopus sungorus. One cross type resulted in massive placental and embryonic overgrowth, severe developmental defects, and maternal death. Embryos from the reciprocal cross were viable and normal sized, but adult hybrid males were relatively small. These effects are strikingly similar to patterns from several other mammalian hybrids. Using comparative sequence data from dwarf hamsters and several other hybridizing mammals, we argue that extreme hybrid growth can contribute to reproductive isolation during the early stages of species divergence. Next, we tested if abnormal growth in hybrid hamsters was associated with disrupted genomic imprinting. We found no association between imprinting status at several candidate genes and hybrid growth, though two interacting genes involved in embryonic growth did show reduced expression in overgrown hybrids. Collectively, our study indicates that growth-related hybrid inviability may play an important role in mammalian speciation but that the genetic underpinnings of these phenotypes remain unresolved.
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Affiliation(s)
- Thomas D. Brekke
- Division of Biological Sciences, The University of Montana, Missoula Montana, 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, The University of Montana, Missoula Montana, 59812
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99
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Feder JL, Nosil P, Flaxman SM. Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations. Front Genet 2014; 5:295. [PMID: 25206365 PMCID: PMC4144205 DOI: 10.3389/fgene.2014.00295] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 08/08/2014] [Indexed: 12/03/2022] Open
Abstract
Many hypotheses have been put forth to explain the origin and spread of inversions, and their significance for speciation. Several recent genic models have proposed that inversions promote speciation with gene flow due to the adaptive significance of the genes contained within them and because of the effects inversions have on suppressing recombination. However, the consequences of inversions for the dynamics of genome wide divergence across the speciation continuum remain unclear, an issue we examine here. We review a framework for the genomics of speciation involving the congealing of the genome into alternate adaptive states representing species (“genome wide congealing”). We then place inversions in this context as examples of how genetic hitchhiking can potentially hasten genome wide congealing. Specifically, we use simulation models to (i) examine the conditions under which inversions may speed genome congealing and (ii) quantify predicted magnitudes of these effects. Effects of inversions on promoting speciation were most common and pronounced when inversions were initially fixed between populations before secondary contact and adaptation involved many genes with small fitness effects. Further work is required on the role of underdominance and epistasis between a few loci of major effect within inversions. The results highlight five important aspects of the roles of inversions in speciation: (i) the geographic context of the origins and spread of inversions, (ii) the conditions under which inversions can facilitate divergence, (iii) the magnitude of that facilitation, (iv) the extent to which the buildup of divergence is likely to be biased within vs. outside of inversions, and (v) the dynamics of the appearance and disappearance of exceptional divergence within inversions. We conclude by discussing the empirical challenges in showing that inversions play a central role in facilitating speciation with gene flow.
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Affiliation(s)
- Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
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100
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Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014; 15:176-92. [PMID: 24535286 DOI: 10.1038/nrg3644] [Citation(s) in RCA: 597] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Affiliation(s)
- Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden
| | - Irene Keller
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Janette W Boughman
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA
| | - Catherine L Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Glenn-Peter Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Claudia Bank
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ake Brännström
- Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA
| | - Martin C Fischer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martine E Maan
- Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands
| | - David A Marques
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Markus Möst
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA
| | - Etsuko Nonaka
- Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Diana J Rennison
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Eric T Watson
- Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA
| | - Anja M Westram
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
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