The genomic legacy from the extinct Lepus timidus to the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes

• Published in: Molecular Ecology
• Main Authors: Melo-Ferreira, José, Alves, Paulo, C., Freitas, Helder, Ferrand, Nuno, Boursot, Pierre
• Other Authors: Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2009
• Subjects: sex chromosomes; autosome; hybridization; introgression; Lepus; mtDNA; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; Arctic; Lepus timidus
• Online Access: https://hal.umontpellier.fr/hal-02348046; https://hal.umontpellier.fr/hal-02348046/document; https://hal.umontpellier.fr/hal-02348046/file/Melo-Ferreira-2009-The%20genomic%20legacy%20from%20the.pdf; https://doi.org/10.1111/j.1365-294X.2009.04221.x

International audience Extensive interspecific genetic introgression is often reported, and appraising its genomic impact can serve to determine whether it results from selection on specific loci or from demographic processes affecting the whole genome. The three species of hares present in the Iberian Peninsula harbour high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species now extinct in the region. This could result from the invasive replacement of L. timidus by the temperate species during deglaciation but should then have left traces in the nuclear genome. We typed single nucleotide polymorphisms (SNPs) discovered by sequencing 10 autosomal loci, two X-linked and one Y-linked in species-wide samples of the four taxa. Based on lineage-diagnostic SNPs, we detected no trace of L. timidus sex chromosomes in Iberia. From the frequencies of inferred haplotypes, autosomal introgression into L. granatensis appeared mostly sporadic but always widespread instead of restricted to the north as mtDNA. Autosomal introgression into Iberian L. europaeus, inhabiting the Pyrenean foothills, was hardly detectable, despite quasifixation of L. timidus mtDNA. L. castroviejoi, endemic to the Cantabrian Mountains and fixed for L. timidus mtDNA, showed little traces of autosomal introgression. The absence of sex-chromosome introgression presumably resulted from X-linked hybrid male unfitness. The contrasting patterns between the autosomes and mtDNA could reflect general gender asymmetric processes such as frequency-dependent female assortative mating, lower mtDNA migration and higher male dispersal, but adaptive mtDNA introgression cannot be dismissed. Additionally, we document reciprocal introgression between L. europaeus and both L. granatensis in Iberia and L. timidus outside Iberia.