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

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

Hybridization in parasites: consequences for adaptive evolution, pathogenesis and public health in a changing world

[No abstract available

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

Cisgenesis, a new tool for traditional plant breeding, should be exempted from the regulation on genetically modified organisms in a step by step approach

Modern potato breeding requires over 100,000 seedlings per new variety. Main reasons are (1) the increasing number of traits that have to be combined in this tetraploid vegetatively propagated crop, and (2) an increasing number of traits (e.g., resistance to biotic stress) originates from wild species. Pre-breeding by introgression or induced translocation is an expensive way of transferring single traits (such as R-genes, coding for resistance to biotic stress) to the cultivated plant. The most important obstacle is simultaneous transfer of undesired neighbouring alien alleles as linkage drag. Stacking several genes from different wild sources is increasing this linkage drag problem tremendously. Biotechnology has enabled transformation of alien genes into the plant. Initially, transgenes were originating mainly from microorganisms, viruses or non-crossable plant species, or they were chimeric. Moreover, selection markers coding for antibiotic resistance or herbicide resistance were needed. Transgenes are a new gene source for plant breeding and, therefore, additional regulations like the EU Directive 2001/18/EC were developed. Because of a strong opposition against genetic modification of plants in Europe, the application of this Directive is strict, very expensive, hampering the introduction of genetically modified (GM) crops and the use of this technology by small and medium-sized enterprises (SMEs). Currently, GM crops are almost the exclusive domain of multinationals. Meanwhile, not only transgenes but also natural genes from the plant species itself or from crossable plant species, called cisgenes, are available and the alien selection genes can be avoided in the end product. This opens the way for cisgenic crops without alien genes. The existing EU directive for GM organisms is not designed for this new development. The cisgenes belong to the existing breeders¿ gene pool. The use of this classical gene pool has been regulated already in agreements regarding breeders¿ rights. We are proposing a step by step approach starting with a crop and gene specific derogation and monitoring towards a general exemption of cisgenic plants from the Directive. Two examples, i.e. development of cisgenic potato for resistance to Phytophthora infestans and cisgenic apple for resistance to Venturia inaequalis are discussed shortly for illustration of the importance of cisgenesis as a new tool for traditional plant breeding. Cisgenesis is simplifying introgression and induced translocation breeding tremendously and is highly recommended for SMEs and developing countrie

Gene Flow Between Great Lakes Region Populations of the Canadian Tiger Swallowtail Butterfly, \u3ci\u3ePapilio Canadensis\u3c/i\u3e, Near the Hybrid Zone With \u3ci\u3eP. Glaucus\u3c/i\u3e (Lepidoptera: Papilionidae)

Papilio canadensis were sampled from three locations on either side of Lake Michigan to study gene flow near and through a butterfly hybrid zone. Allele frequencies at four polymorphic enzyme loci, as indicated by allozyme electrophoresis, were similar in all samples. Values for FST were close to zero, indicating that gene flow is high among these populations, even when separated by Lake Michigan. We developed a mitochondrial DNA marker with diagnostic differences between P. canadensis and its parapatric sister species Papilio glaucus, based on PCR-RFLP. P. glaucus haplotypes of this mtDNA marker and P. glaucus alleles of a diagnostic allozyme locus (PGD) were found in P. canadensis populations sampled in Michigan’s Lower Peninsula but not in the Upper Peninsula or Northern Minnesota. The presence of P. glaucus alleles in P. canadensis populations could be due to introgression through hybridization, or could be remnants of a P. glaucus population that was inundated by an influx of P. canadensis alleles

A new species in the major malaria vector complex sheds light on reticulated species evolution

Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studied Anopheles fontenillei sp.n., a new species in the Anopheles gambiae complex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, with Anopheles gambiae and Anopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall, An. fontenillei sp.n. analysis improved our understanding of the relationship between species within the An. gambiae complex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa