DOI: 10.5061/dryad.21f62
title: Data from: The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation

description: Hybridization drives the evolutionary trajectory of many species or local
 populations, and assessing the geographic extent and genetic impact of
 interspecific gene flow may provide invaluable clues to understand
 population divergence or the adaptive relevance of admixture. In North
 America, hares (Lepus spp.) are key species for ecosystem dynamics and
 their evolutionary history may have been affected by hybridization. Here
 we reconstructed the speciation history of the three most widespread hares
 in North America - the snowshoe hare (Lepus americanus), the white-tailed
 jackrabbit (L. townsendii) and the black-tailed jackrabbit (L.
 californicus) - by analyzing sequence variation at eight nuclear markers
 and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A
 multilocus-multispecies coalescent-based phylogeny suggests that L.
 americanus diverged ~2.7 Mya and that L. californicus and L. townsendii
 split more recently (~1.2 Mya). Within L. americanus a deep history of
 cryptic divergence (~2.0 Mya) was inferred, which coincides with major
 speciation events in other North American species. While the
 isolation-with-migration model suggested that nuclear gene flow was
 generally rare or absent among species or major genetic groups, coalescent
 simulations of mtDNA divergence revealed historical mtDNA introgression
 from L. californicus into the Pacific Northwest populations of L.
 americanus. This finding marks a history of past reticulation between
 these species, which may have affected other parts of the genome and
 influence the adaptive potential of hares during climate change.
description: SPTBN1_pre-phaseSPTBN1 alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).1_SPTBN1_raw.fasPRKCI_pre-phasePRKCI alignment before phasing (see GenBank accession numbers in Sup. Table 1).2_PRKCI_raw.fasDARC_pre-phaseDARC alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).3_DARC_raw_final_final.fasKITLG_pre-phaseKITLG alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).4_KITLG_raw.fasTF_pre-phaseTF alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).5_TF_raw.fasPOLA1_pre-phasePOLA1 alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).6_POLA1_raw_final.fasGRIA3_pre-phaseGRIA3 alignment before phase detemrination (see GenBank accession numbers in Sup. Table 1).7_GRIA3_raw.fasSRYSRY alignment (see GenBank accession numbers in Sup. Table 1).8_SRY_raw.fasCYTBCYTB alignment (see GenBank accession numbers in Sup. Table 1).9_CYTB_raw.fasSPTBN1_phasedSPTBN1 phased alignment (see GenBank accession numbers in Sup. Table 1).1_SPTBN1_phased.fasPRKCI_phasedPRKCI phased alignment (see GenBank accession numbers in Sup. Table 1).2_PRKCI_phased.fasDARC_phasedDARC phased alignment (see GenBank accession numbers in Sup. Table 1).3_DARC_phased_final.fasKITLG_phasedKITLG phased alignment (see GenBank accession numbers in Sup. Table 1).4_KITLG_phased.fasTF_phasedTF phased alignment (see GenBank accession numbers in Sup. Table 1).5_TF_phased.fasPOLA1_phasedPOLA1 phased alignment (see GenBank accession numbers in Sup. Table 1).6_POLA1_phased_final.fasGRIA3_phasedGRIA3 phased alignment (see GenBank accession numbers in Sup. Table 1).7_GRIA3_phased_final.fasSPTBN1_lnrbSPTBN1 phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).1_SPTBN1_lnrb.fasPRKCI_lnrbPRKCI phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).2_PRKCI_lnrb.fasDARC_lnrbDARC phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).3_DARC_lnrb_final.fasKITLG_lnrbKITLG phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).4_KITLG_lnrb.fasTF_lnrbTF phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).5_TF_lnrb.fasPOLA1_lnrbPOLA1 phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).6_POLA1_lnrb.fasGRIA3_lnrbGRIA3 phased alignment of longest non-recombining blocks (see GenBank accession numbers in Sup. Table 1).7_GRIA3_lnrb_final.fasSPTBN1_with_outgroupSPTBN1 phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).1SPTBN1_with_outgroup.fasPRKCI_with_outgroupPRKCI phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).2_PRKCI_with_outgroup.fasDARC_with_outgroupDARC phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).3_DARC_with_outgroup_final.fasKITLG_with_outgroupKITLG phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).4_KITLG_with_outgroup.fasTF_with_outgroupTF phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).5_TF_with_outgroup.fastaPOLA1_with_outgroupPOLA1 phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).6_POLA1_with_outgroup.fasGRIA3_with_outgroupGRIA3 phased alignment of longest non-recombining blocks with outgroup (see GenBank accession numbers in Sup. Table 1).7_GRIA3_with_outgroup_final.fasSRY_with_outgroupSRY alignment with outgroup (see GenBank accession numbers in Sup. Table 1).8_SRY_with_outgroup.fasCYTB_with_outgroupsCYTB alignment with outgroups (see GenBank accession numbers in Sup. Table 1).9_CYTB_with_outgroups.fasCYTB_Lepus_sppCYTB alignment of haplotypes obtained in this work and other Lepus species available in GenBank (see Sup. Figure 4).