Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 25
Filter
Add more filters










Publication year range
1.
Mol Ecol ; 33(4): e17250, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38179694

ABSTRACT

While haplotype-specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed-haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame-shifting variants as the most deleterious type, followed by mutations in the 5'-UTR, 3'-UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high-impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter-haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype-resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.


Subject(s)
Genetic Variation , Perciformes , Animals , Haplotypes/genetics , Genetic Load , Mutation , Perciformes/genetics , China
2.
Nat Commun ; 12(1): 4165, 2021 07 06.
Article in English | MEDLINE | ID: mdl-34230464

ABSTRACT

Insects use sex pheromones as a reproductive isolating mechanism to attract conspecifics and repel heterospecifics. Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Using whole-genome sequences to infer the kinship among 99 drosophilids, we investigate how phylogenetic and chemical traits have interacted at a wide evolutionary timescale. Through a series of chemical syntheses and electrophysiological recordings, we identify 52 sex-specific compounds, many of which are detected via olfaction. Behavioral analyses reveal that many of the 43 male-specific compounds are transferred to the female during copulation and mediate female receptivity and/or male courtship inhibition. Measurement of phylogenetic signals demonstrates that sex pheromones and their cognate olfactory channels evolve rapidly and independently over evolutionary time to guarantee efficient intra- and inter-specific communication systems. Our results show how sexual isolation barriers between species can be reinforced by species-specific olfactory signals.


Subject(s)
Communication , Drosophila/physiology , Pheromones/metabolism , Sex Attractants/physiology , Animals , Biological Evolution , Copulation/physiology , Courtship , Drosophila melanogaster/physiology , Female , Male , Phylogeny , Sexual Behavior, Animal/physiology , Smell/physiology , Species Specificity
3.
Mol Ecol ; 30(14): 3610-3623, 2021 07.
Article in English | MEDLINE | ID: mdl-33998095

ABSTRACT

Whether freshwater fish colonize remote islands following tectonic or transoceanic dispersal remains an evolutionary puzzle. Integrating dating of known tectonic events with phylogenomics and current species distribution, we find that killifish species distribution is not explained by species dispersal by tectonic drift only. Investigating the colonization of a nonannual killifish (golden panchax, Pachypanchax playfairii) on the Seychelle islands, we found genetic support for transoceanic dispersal and experimentally discovered an adaptation to complete tolerance to seawater. At the macroevolutionary scale, despite their long-lasting isolation, nonannual golden panchax show stronger genome-wide purifying selection than annual killifishes from continental Africa. However, progressive decline in effective population size over a more recent timescale has probably led to the segregation of slightly deleterious mutations across golden panchax populations, which represents a potential threat for species preservation in the long term.


Subject(s)
Fundulidae , Africa , Animals , Biological Evolution , Fundulidae/genetics , Phylogeny , Seychelles
4.
Curr Biol ; 31(5): 923-935.e11, 2021 03 08.
Article in English | MEDLINE | ID: mdl-33513352

ABSTRACT

Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.


Subject(s)
Biological Evolution , Cyprinodontiformes/anatomy & histology , Cyprinodontiformes/genetics , Genetic Variation , Mating Preference, Animal , Animals , Female , Male , Phenotype , Quantitative Trait Loci
5.
Elife ; 92020 09 01.
Article in English | MEDLINE | ID: mdl-32869739

ABSTRACT

The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.


Subject(s)
Evolution, Molecular , Longevity/genetics , Mutation Accumulation , Population Density , Aging/genetics , Animals , Biological Evolution , Ecosystem , Fundulidae , Genome/genetics , Models, Animal
8.
Cell ; 178(2): 385-399.e20, 2019 07 11.
Article in English | MEDLINE | ID: mdl-31257025

ABSTRACT

To uncover the selective forces shaping life-history trait evolution across species, we investigate the genomic basis underlying adaptations to seasonal habitat desiccation in African killifishes, identifying the genetic variants associated with positive and relaxed purifying selection in 45 killifish species and 231 wild individuals distributed throughout sub-Saharan Africa. In annual species, genetic drift led to the expansion of nuclear and mitochondrial genomes and caused the accumulation of deleterious genetic variants in key life-history modulating genes such as mtor, insr, ampk, foxo3, and polg. Relaxation of purifying selection is also significantly associated with mitochondrial function and aging in human populations. We find that relaxation of purifying selection prominently shapes genomes and is a prime candidate force molding the evolution of lifespan and the distribution of genetic variants associated with late-onset diseases in different species. VIDEO ABSTRACT.


Subject(s)
Longevity , Selection, Genetic , Aging , Animals , DNA Replication , Evolution, Molecular , Gene Frequency , Genome, Mitochondrial , Killifishes/classification , Killifishes/genetics , Mitochondria/genetics , Mitochondria/metabolism , Mutation , Phylogeny , Phylogeography
9.
PLoS One ; 14(3): e0213446, 2019.
Article in English | MEDLINE | ID: mdl-30870444

ABSTRACT

Salvia splendens is a perennial, ornamental herbaceous flower that is widely cultivated as a bedding plant in gardens. The development of novel S. splendens cultivars and investigating the relevant molecular mechanisms are of great significance. In this study, RNA-sequencing and real-time PCR methods were used to analyze the possible molecular mechanism of S. splendens mutant, SX919M. From the wild-type S. splendens 919CK, we firstly selected a natural mutant, SX919M, which displayed multiple branches, clustered spheroids, and radial symmetrical inflorescence with higher numbers of calyces, ovules, stamens, and perianth tubes. Further, the RNA-seq was used to identify the differentially expressed genes (DEGs) in the mutant which included a total of 3568 upregulated and 3290 downregulated unigenes. We further observed that the indole alkaloid biosynthesis pathway showed the highest DEG enrichment, which was supported by a significant increase in the IAA content in mutant SX919M. In addition, we validated three DEGs, namely, CL2200.Contig2_All encoding methyl IAA esterase, CL12462.Contig1_All and CL12462.Contig2_All, which encoded strictosidine synthase, upregulated in mutant SX919M. We selected a novel S. splendens germplasm SX919M with a high ornamental value and determined that the upregulation of IAA biogenesis may be associated with its development.


Subject(s)
Salvia/growth & development , Salvia/genetics , Gene Expression Profiling , Gene Expression Regulation, Plant , Genes, Plant , Indoleacetic Acids/metabolism , Molecular Sequence Annotation , Mutation , Phenotype , Plant Breeding , RNA, Plant/genetics , Salvia/metabolism , Sequence Analysis, RNA , Transcriptome
10.
Gigascience ; 7(7)2018 07 01.
Article in English | MEDLINE | ID: mdl-29931210

ABSTRACT

Background: Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. Findings: We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. Conclusions: We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.


Subject(s)
DNA, Plant/genetics , Genome, Plant , Salvia/genetics , Base Sequence , Genomics , Heterozygote , Molecular Sequence Annotation , Phenotype , Phylogeny , Repetitive Sequences, Nucleic Acid , Whole Genome Sequencing
11.
Proc Natl Acad Sci U S A ; 114(41): 10936-10941, 2017 10 10.
Article in English | MEDLINE | ID: mdl-28973863

ABSTRACT

The emergence of new species is driven by the establishment of mechanisms that limit gene flow between populations. A major challenge is reconciling the theoretical and empirical importance of assortative mating in speciation with the ease with which it can fail. Swordtail fish have an evolutionary history of hybridization and fragile prezygotic isolating mechanisms. Hybridization between two swordtail species likely arose via pollution-mediated breakdown of assortative mating in the 1990s. Here we track unusual genetic patterns in one hybrid population over the past decade using whole-genome sequencing. Hybrids in this population formed separate genetic clusters by 2003, and maintained near-perfect isolation over 25 generations through strong ancestry-assortative mating. However, we also find that assortative mating was plastic, varying in strength over time and disappearing under manipulated conditions. In addition, a nearby population did not show evidence of assortative mating. Thus, our findings suggest that assortative mating may constitute an intermittent and unpredictable barrier to gene flow, but that variation in its strength can have a major effect on how hybrid populations evolve. Understanding how reproductive isolation varies across populations and through time is critical to understanding speciation and hybridization, as well as their dependence on disturbance.


Subject(s)
Biological Evolution , Cyprinodontiformes/genetics , Gene Flow , Genetic Speciation , Mating Preference, Animal , Reproductive Isolation , Animals , Cyprinodontiformes/classification , Genome , Whole Genome Sequencing
12.
Proc Biol Sci ; 284(1854)2017 May 17.
Article in English | MEDLINE | ID: mdl-28515207

ABSTRACT

Mate choice can play a pivotal role in the nature and extent of reproductive isolation between species. Mating preferences are often dependent on an individual's social experience with adult phenotypes throughout development. We show that olfactory preference in a swordtail fish (Xiphophorus malinche) is affected by previous experience with adult olfactory signals. We compare transcriptome-wide gene expression levels of pooled sensory and brain tissues between three treatment groups that differ by social experience: females with no adult exposure, females exposed to conspecifics and females exposed to heterospecifics. We identify potential functionally relevant genes and biological pathways differentially expressed not only between control and exposure groups, but also between groups exposed to conspecifics and heterospecifics. Based on our results, we speculate that vomeronasal receptor type 2 paralogs may detect species-specific pheromone components and thus play an important role in reproductive isolation between species.


Subject(s)
Cyprinodontiformes/genetics , Mating Preference, Animal , Reproductive Isolation , Smell , Social Learning , Animals , Cyprinodontiformes/physiology , Female , Gene Expression , Sexual Behavior, Animal
13.
Mol Ecol ; 25(11): 2661-79, 2016 Jun.
Article in English | MEDLINE | ID: mdl-26937625

ABSTRACT

A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human-Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.


Subject(s)
Biological Evolution , Cyprinodontiformes/genetics , Hybridization, Genetic , Animals , Cyprinodontiformes/classification , Genome , Genomics , Phylogeny , Sequence Analysis, DNA
14.
Bioinformatics ; 32(7): 1103-5, 2016 04 01.
Article in English | MEDLINE | ID: mdl-26615212

ABSTRACT

UNLABELLED: We introduce a new forward-time simulator, Admix'em, that allows for rapid and realistic simulations of admixed populations with selection. Complex selection can be achieved through user-defined fitness and mating-preference probability functions. Users can specify realistic genomic landscapes and model neutral SNPs in addition to sites under selection. Admix'em is designed to simulate selection in admixed populations but can also be used as a general population simulator. Usage and examples are in the supplement. AVAILABILITY AND IMPLEMENTATION: C ++ and OpenMP, supports 64-bit Linux/Unix-like platforms. https://github.com/melop/admixem CONTACT: rcui@age.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Genomics/methods , Polymorphism, Single Nucleotide , Epistasis, Genetic , Genetics, Population , Genome , Selection, Genetic , Software
15.
Mol Ecol Resour ; 16(1): 183-92, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26032857

ABSTRACT

Hybridization between closely related species, whether naturally occurring or laboratory generated, is a useful tool for mapping the genetic basis of the phenotypic traits that distinguish species. The development of next-generation sequencing techniques has greatly improved our ability to assign ancestry to hybrid genomes. One such next-generation sequencing technique, multiplexed shotgun genotyping (or MSG), can be a powerful tool for genotyping hybrids. However, it is difficult a priori to predict the accuracy of MSG in natural hybrids because accuracy depends on ancestry tract length and number of ancestry informative markers. Here, we present a simulator, 'simMSG', that will allow researchers to design MSG experiments and show that in many cases MSG can accurately assign ancestry to hundreds of thousands of sites in the genomes of natural hybrids. The simMSG tool can be used to design experiments for diverse applications including QTL mapping, genotyping introgressed lines or admixture mapping.


Subject(s)
Chimera/genetics , Genotyping Techniques/methods , Computer Simulation , Genotype , Genotyping Techniques/instrumentation , High-Throughput Nucleotide Sequencing , Hybridization, Genetic
16.
Cell ; 163(6): 1539-54, 2015 Dec 03.
Article in English | MEDLINE | ID: mdl-26638078

ABSTRACT

Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.


Subject(s)
Biological Evolution , Killifishes/genetics , Aging , Animals , DNA Helicases/genetics , Genome , Humans , Longevity , Molecular Sequence Annotation , Molecular Sequence Data , Selection, Genetic
17.
PLoS Genet ; 11(3): e1005041, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25768654

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.


Subject(s)
Genetic Speciation , Hybridization, Genetic , Reproductive Isolation , Selection, Genetic , Gene Flow , Genetic Drift , Genetic Variation , Genetics, Population , Models, Genetic , Models, Theoretical
18.
Plant Cell ; 27(3): 620-32, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25783029

ABSTRACT

Although seed size is one of the most important agronomic traits in plants, the genetic and molecular mechanisms that set the final size of seeds are largely unknown. We previously identified the ubiquitin receptor DA1 as a negative regulator of seed size, and the Arabidopsis thaliana da1-1 mutant produces larger seeds than the wild type. Here, we describe a B3 domain transcriptional repressor NGATHA-like protein (NGAL2), encoded by the suppressor of da1-1 (SOD7), which acts maternally to regulate seed size by restricting cell proliferation in the integuments of ovules and developing seeds. Overexpression of SOD7 significantly decreases seed size of wild-type plants, while the simultaneous disruption of SOD7 and its closest homolog DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4/NGAL3) increases seed size. Genetic analyses indicate that SOD7 and DPA4 act in a common pathway with the seed size regulator KLU to regulate seed growth, but do so independently of DA1. Further results show that SOD7 directly binds to the promoter of KLUH (KLU) in vitro and in vivo and represses the expression of KLU. Therefore, our findings reveal the genetic and molecular mechanisms of SOD7, DPA4, and KLU in seed size regulation and suggest that they are promising targets for seed size improvement in crops.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/anatomy & histology , Cytochrome P-450 Enzyme System/metabolism , Repressor Proteins/metabolism , Seeds/anatomy & histology , Transcription Factors/metabolism , Arabidopsis/cytology , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Base Sequence , Cell Proliferation , Cloning, Molecular , Cytochrome P-450 Enzyme System/genetics , Endosperm/embryology , Endosperm/genetics , Epistasis, Genetic , Gene Expression Regulation, Developmental , Gene Expression Regulation, Plant , Genes, Plant , Genes, Suppressor , Molecular Sequence Data , Mutation , Organ Size , Phenotype , Plants, Genetically Modified , Promoter Regions, Genetic , Protein Binding , Protein Transport , Seeds/cytology , Subcellular Fractions/metabolism , Suppression, Genetic , Transcription Factors/genetics
19.
Elife ; 32014 Jun 04.
Article in English | MEDLINE | ID: mdl-24898754

ABSTRACT

Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species.


Subject(s)
Chromosome Mapping/methods , Epistasis, Genetic , Fishes/genetics , Hybridization, Genetic , Animals , Computer Simulation , Female , Gene Flow , Gene Library , Genome , Genotype , Linkage Disequilibrium , Male , Models, Genetic , X Chromosome
20.
Evolution ; 67(8): 2166-79, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23888843

ABSTRACT

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high-confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long-standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.


Subject(s)
Biological Evolution , Cyprinodontiformes/genetics , Phylogeny , Animals , Cyprinodontiformes/anatomy & histology , Cyprinodontiformes/classification , Female , Genomics , Male , Sex Characteristics
SELECTION OF CITATIONS
SEARCH DETAIL
...