Widespread introgression of MHC genes in Iberian <i>Podarcis</i> lizards

Gaczorek, Tomasz S.; Chechetkin, Mateusz; Dudek, Katarzyna; Caeiro‐Dias, Guilherme; Crochet, Pierre‐André; Pinho, Catarina; Babik, Wiesław

doi:10.1111/mec.16974

Cited by 5 publications

(8 citation statements)

References 136 publications

(160 reference statements)

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“…Adaptive introgression at the MHC has indeed been suggested in a number of species including humans (Abi-Rached et al, 2011), newts (Gaczorek et al, 2023) and lizards (Gaczorek et al, 2023). The generally high genetic diversity at the MHC loci in domestic livestock was suggested to originate from intentional or accidental backcrosses with their wild ancestors (Vilà et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Münger,

Robin,

Dalén

et al. 2023

Preprint

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Introgression is expected to be adaptive at loci under balancing selection, for instance at loci relevant for the immune response, but these loci generally also contain ancient polymorphisms. Ancient genomics is a promising tool to detect recent introgression and disentangle it from ancient polymorphisms. Alpine ibex (Capra ibex), a wild goat species native to the European Alps, faced near-extinction two centuries ago, but has recovered thanks to successful restoration programs. Previously, signals of introgression from the domestic goat (Capra aegagrus hircus) into the Alpine ibex genome were found at the major histocompatibility complex. This introgression was suggested to potentially be adaptive since it introduced new diversity at a gene locus important for immunity. But no genome-wide analyses of introgression have been performed to confirm the potential relevance of immune loci.Here we take advantage of two ancient whole genomes of Alpine ibex combined with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate genome-wide patterns of introgression. Our complementary analysis of putatively introgressed haplotypes and demographic modelling suggests 2.3% recent domestic goat ancestry among wild Alpine ibex. The introgression was estimated to have happened during the last 300 years coinciding with the time when the species had very small population size. Further analysis suggested an enrichment of immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage.

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Section: Discussionmentioning

confidence: 99%

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Münger,

Robin,

Dalén

et al. 2023

Preprint

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“…Our results show no evidence that the gene flow was considerably replenishing the genetic diversity of PM population, as neither the estimates of recent migration rates nor the analyses of ancestral genomic components point to existence of immigrants or PM individuals of mixed ancestry. Nevertheless, Podarcis species are known for their propensity to hybridize in both their old and the more recent evolutionary history, and P. siculus is no exception (Capula, 2002; Gaczorek et al., 2023; Yang et al., 2021). Thus, due to our limited genomic insights, we cannot completely rule out the possibility of hybridization between the newly translocated P. siculus and native P. melisellensis populations in the short time of their coexistence on Pod Mrčaru island, but we consider this event to be unlikely.…”

Section: Discussionmentioning

confidence: 99%

Plastic and genomic change of a newly established lizard population following a founder event

Sabolić,

Mira,

Brandt

et al. 2023

Molecular Ecology

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Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque‐Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome‐wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between‐population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage.

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“…The copyright holder for this preprint this version posted June 14, 2024. ; https://doi.org/10.1101/2024.06.12.598278 doi: bioRxiv preprint species, in view of the large number of MHC alleles shared between sympatric individuals of the two species compared to allopatric individuals (Caeiro-Dias et al, 2023;Gaczorek et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Performance evaluation of adaptive introgression classification methods

Romieu,

Camarata,

Crochet

et al. 2024

Preprint

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Introgression, the incorporation of foreign variants through hybridization and repeated backcross, is increasingly being studied for its potential evolutionary consequences, one of which is adaptive introgression (AI). In recent years, several statistical methods have been proposed for the detection of loci that have undergone adaptive introgression. Most of these methods have been tested and developed to infer the presence of Neanderthal or Denisovan AI in humans. Currently, the behaviour of these methods when faced with genomic datasets from evolutionary scenarios other than the human lineage remains unknown. This study therefore focuses on testing the performance of the methods using test data sets simulated under an evolutionary scenario inspired by a complex of hybridising lizard species in the Iberian Peninsula:Podarcis hispanicus. Our tests focus on analysing the impact of variations in the strength of selection on the performance of three methods (VolcanoFinder,GenomatnnandMaLAdapt) and a standalone summary statistic (Q95). Furthermore, the hitchhiking effect of the adaptively introgressed mutation can have a strong impact on the flanking regions, and therefore on the best differentiation between the genomic windows classes (i.e. AI/non-AI). For this reason, three different types of non-AI windows are therefore taken into account in our analyses: independently simulated neutral introgression windows, windows adjacent to the window under AI and windows coming from a second neutral chromosome unlinked to the chromosome under AI. Our results highlight the importance of taking into account adjacent windows in the training data in order to correctly identify the window with the mutation under AI. Finally, our tests show that methods based on Q95 seem to be the most efficient for an exploratory study of AI (i.e. without any a priori on the presence of AI).

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Widespread introgression of MHC genes in Iberian Podarcis lizards

Cited by 5 publications

References 136 publications

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Plastic and genomic change of a newly established lizard population following a founder event

Performance evaluation of adaptive introgression classification methods

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