Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies.
Ontology highlight
ABSTRACT:
SUBMITTER: Tahami MS
PROVIDER: S-EPMC8700966 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:For centuries, biologists have used phenotypes to infer evolution. For decades, a handful of gene markers have given us a glimpse of the genotype to combine with phenotypic traits. Today, we can sequence entire genomes from hundreds of species and gain yet closer scrutiny. To illustrate the power of genomics, we have chosen skipper butterflies (Hesperiidae). The genomes of 250 representative species of skippers reveal rampant inconsistencies between their current classification and a genome-based phylogeny. We use a dated genomic tree to define tribes (six new) and subtribes (six new), to overhaul genera (nine new) and subgenera (three new), and to display convergence in wing patterns that fooled researchers for decades. We find that many skippers with similar appearance are distantly related, and several skippers with distinct morphology are close relatives. These conclusions are strongly supported by different genomic regions and are consistent with some morphological traits. Our work is a forerunner to genomic biology shaping biodiversity research.
| S-EPMC6442542 | biostudies-literature
Project description:Human-mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4,279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry-informative markers. We identified a type of introduced mussels, called "dock mussels," associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine-scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration-selection tension zone models, and instead suggest habitat choice and early-stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human-mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome-wide effect of admixture seems repeatable and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and at fine spacial scales.
| S-EPMC7045717 | biostudies-literature
Project description:Giraffe lineages are shaped by major ancient admixture events
| PRJEB66216 | ENA
Project description:Admixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of "admixture mapping" in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.
| S-EPMC2954470 | biostudies-literature
Project description:Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST) were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations.
| S-EPMC3527209 | biostudies-literature
Project description:The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25-55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38-75%) appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.
| S-EPMC4334544 | biostudies-literature
Project description:ObjectiveYunnan is not only a frontier zone that connects China with South and Southeast Asia, but also represents an admixture zone between taurine (Bos taurus) and zebu (Bos indicus) cattle. The purpose of this study is to understand the level of genomic diversity and the extent of admixture in each Yunnan native cattle breed.MethodsAll 120 individuals were genotyped using Illumina BovineHD BeadChip (777,962 single nucleotide polymorphisms [SNPs]). Quality control and genomic diversity indexes were calculated using PLINK software. The principal component analysis (PCA) was assessed using SMARTPCA program implemented in EIGENSOFT software. The ADMIXTURE software was used to reveal admixture patterns among breeds.ResultsA total of 604,630 SNPs was obtained after quality control procedures. Among six breeds, the highest level of mean heterozygosity was found in Zhaotong cattle from Northeastern Yunnan, whereas the lowest level of heterozygosity was detected in Dehong humped cattle from Western Yunnan. The PCA based on a pruned dataset of 233,788 SNPs clearly separated Dehong humped cattle (supposed to be a pure zebu breed) from other five breeds. The admixture analysis further revealed two clusters (K = 2 with the lowest cross validation error), corresponding to taurine and zebu cattle lineages. All six breeds except for Dehong humped cattle showed different degrees of admixture between taurine and zebu cattle. As expected, Dehong humped cattle showed no signature of taurine cattle influence.ConclusionOverall, considerable genomic diversity was found in six Yunnan native cattle breeds except for Dehong humped cattle from Western Yunnan. Dehong humped cattle is a pure zebu breed, while other five breeds had admixed origins with different extents of admixture between taurine and zebu cattle. Such admixture by crossbreeding between zebu and taurine cattle facilitated the spread of zebu cattle from tropical and subtropical regions to other highland regions in Yunnan.
| S-EPMC6599958 | biostudies-literature
Project description:Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.
| S-EPMC6770841 | biostudies-literature
Project description:Mimicry is one of the best-studied examples of adaptation, and recent studies have provided new insights into the role of mimicry in speciation and diversification. Classical Müllerian mimicry theory predicts convergence in warning signal among protected species, yet tropical butterflies are exuberantly diverse in warning colour patterns, even within communities. We tested the hypothesis that microhabitat partitioning in aposematic butterflies and insectivorous birds can lead to selection for different colour patterns in different microhabitats and thus help maintain mimicry diversity. We measured distribution across flight height and topography for 64 species of clearwing butterflies (Ithomiini) and their co-mimics, and 127 species of insectivorous birds, in an Amazon rainforest community. For the majority of bird species, estimated encounter rates were non-random for the two most abundant mimicry rings. Furthermore, most butterfly species in these two mimicry rings displayed the warning colour pattern predicted to be optimal for anti-predator defence in their preferred microhabitats. These conclusions were supported by a field trial using butterfly specimens, which showed significantly different predation rates on colour patterns in two microhabitats. We therefore provide the first direct evidence to support the hypothesis that different mimicry patterns can represent stable, community-level adaptations to differing biotic environments.
| S-EPMC5454276 | biostudies-literature
Project description:Lecanosticta acicola is the causal agent for brown spot needle blight that affects pine trees across the northern hemisphere. Based on marker genes and microsatellite data, two distinct lineages have been identified that were introduced into Europe on two separate occasions. Despite their overall distinct geographic distribution, they have been found to coexist in regions of northern Spain and France. Here, we present the first genome-wide study of Lecanosticta acicola, including assembly of the reference genome and a population genomics analysis of 70 natural isolates from northern Spain. We show that most of the isolates belong to the southern lineage but show signs of introgression with northern lineage isolates, indicating mating between the two lineages. We also identify phenotypic differences between the two lineages based on the activity profiles of 20 enzymes, with introgressed strains being more phenotypically similar to members of the southern lineage. In conclusion, we show undergoing genetic admixture between the two main lineages of L. acicola in a region of recent expansion.ImportanceLecanosticta acicola is a fungal pathogen causing severe defoliation, growth reduction, and even death in more than 70 conifer species. Despite the increasing incidence of this species, little is known about its population dynamics. Two divergent lineages have been described that have now been found together in regions of France and Spain, but it is unknown how these mixed populations evolve. Here we present the first reference genome for this important plant pathogenic fungi and use it to study the population genomics of 70 isolates from an affected forest in the north of Spain. We find signs of introgression between the two main lineages, indicating that active mating is occurring in this region which could propitiate the appearance of novel traits in this species. We also study the phenotypic differences across this population based on enzymatic activities on 20 compounds.
| S-EPMC10949461 | biostudies-literature