36,949 research outputs found
Dynamics of mtDNA introgression during species range expansion. Insights from an experimental longitudinal study
Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern
An HMM-based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
One outcome of interspecific hybridization and subsequent effects of
evolutionary forces is introgression, which is the integration of genetic
material from one species into the genome of an individual in another species.
The evolution of several groups of eukaryotic species has involved
hybridization, and cases of adaptation through introgression have been already
established. In this work, we report on a new comparative genomic framework for
detecting introgression in genomes, called PhyloNet-HMM, which combines
phylogenetic networks, that capture reticulate evolutionary relationships among
genomes, with hidden Markov models (HMMs), that capture dependencies within
genomes. A novel aspect of our work is that it also accounts for incomplete
lineage sorting and dependence across loci.
Application of our model to variation data from chromosome 7 in the mouse
(Mus musculus domesticus) genome detects a recently reported adaptive
introgression event involving the rodent poison resistance gene Vkorc1, in
addition to other newly detected introgression regions. Based on our analysis,
it is estimated that about 12% of all sites withinchromosome 7 are of
introgressive origin (these cover about 18 Mbp of chromosome 7, and over 300
genes). Further, our model detects no introgression in two negative control
data sets. Our work provides a powerful framework for systematic analysis of
introgression while simultaneously accounting for dependence across sites,
point mutations, recombination, and ancestral polymorphism
Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone
Background: Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits.
Results: Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species.
Conclusions: Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow
The Genomic Signature of Crop-Wild Introgression in Maize
The evolutionary significance of hybridization and subsequent introgression
has long been appreciated, but evaluation of the genome-wide effects of these
phenomena has only recently become possible. Crop-wild study systems represent
ideal opportunities to examine evolution through hybridization. For example,
maize and the conspecific wild teosinte Zea mays ssp. mexicana, (hereafter,
mexicana) are known to hybridize in the fields of highland Mexico. Despite
widespread evidence of gene flow, maize and mexicana maintain distinct
morphologies and have done so in sympatry for thousands of years. Neither the
genomic extent nor the evolutionary importance of introgression between these
taxa is understood. In this study we assessed patterns of genome-wide
introgression based on 39,029 single nucleotide polymorphisms genotyped in 189
individuals from nine sympatric maize-mexicana populations and reference
allopatric populations. While portions of the maize and mexicana genomes were
particularly resistant to introgression (notably near known
cross-incompatibility and domestication loci), we detected widespread evidence
for introgression in both directions of gene flow. Through further
characterization of these regions and preliminary growth chamber experiments,
we found evidence suggestive of the incorporation of adaptive mexicana alleles
into maize during its expansion to the highlands of central Mexico. In
contrast, very little evidence was found for adaptive introgression from maize
to mexicana. The methods we have applied here can be replicated widely, and
such analyses have the potential to greatly informing our understanding of
evolution through introgressive hybridization. Crop species, due to their
exceptional genomic resources and frequent histories of spread into sympatry
with relatives, should be particularly influential in these studies
Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone
Background: Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits.
Results: Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species.
Conclusions: Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow
Hominin evolution was caused by introgression from Gorilla
The discovery of Paranthropus deyiremeda in 3.3-3.5 million year old fossil
sites in Afar, together with 30% of the gorilla genome showing lineage sorting
between humans and chimpanzees, and a NUMT ("nuclear mitochondrial DNA
segment") on chromosome 5 that is shared by both gorillas, humans and
chimpanzees, and shown to have diverged at the time of the Pan-Homo split
rather than the Gorilla/Pan-Homo split, provides conclusive evidence that
introgression from the gorilla lineage caused the Pan-Homo split, and the
speciation of both the Australopithecus lineage and the Paranthropus lineage.Comment: arXiv admin note: text overlap with arXiv:1808.0630
Removing exogenous information using pedigree data
Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking partofthe founder population anddifferent numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders? contribution and partial coancestry. The ef?ciency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders? contributions was the most powerful method, removing the largest amount of genetic information in just one generation.However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very dif?cult to recover, pointing out the importance of being careful about introgression events in populatio
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