Phylogenomics of the Tamias quadrivittatus group Department of

Phylogenomics of the Tamias quadrivittatus group Department of Biological Sciences & Institute for Bioinformatics and Evolutionary Studies University of Idaho Funding NSF EPS-9720634 NIH NCRR 1P20RR016454-01 NSF DEB-0717426 & DEB-0716200 NSF BEACON Collaborators John Demboski - DMNS Jeff Good - Montana Kayce Bell - UNM Brice Sarver Extensive mtDNA Introgression. 40% of species are involved in introgression, sometimes with multiple partners. Taxon N

#Int. (%) Source T. ruficaudus. ruficaudus T. ruficaudussimulans T. amoenuscanicaudus T. amoenusluteiventris Other T. amoenus T. dorsalis 131 175 46 148 122 54 0 (0) 63 (36) 46 (100) 43 (29) 0 (0) 35 (65) NA T. r.ruficaudus T.r.simulans T.r.ruficaudus NA cinereicollis,

umbrinus, quadrivittatus not assignablea not assignablea not assignablea NA NA not assignablea NA NA NA NA NA NA NA T. minimus NA T. minimus NA NA NA NA NA T. cinereicollis 25 7 (28) T. umbrinus 64 9 (19) T. canipes 8 0 (0)

T. rufus 14 0 (0) T. quadrivittatus 38 14 (37) T. townsendii 6 0 (0) T. ochrogenys 0 NA T. sonomae 4 0 (0) T. siskiyou 5 0 (0) T. senex 155 0 (0) T. quadrimaculatus 221 0 (0) T. minimus 305 0 (0) T. panamintinus 15 15 (100) T. alpinus 34 0 (0)

T. speciosus 56 56 (100) T. merriami 155 0 (0) T. obscurus 87 0 (0) T. bulleri 1 ? T. durangae 1 ? T. palmeri 1 ? Totals 1871 298 (16) *Only introgressed mtDNA has been identified. Div. Time (MYA) -0.35 2.75 2.75 -1.33 1.78 1.33 -------------2.75

-2.75 ------ Max. mtDNA % Div -4.7% 3.2%* 10.0% -4.6% 4.7% 4.7% 4.7% 4.7% 4.7% --4.7% -------10.0%* -10.0%* ------ Ref. 1,2 1,2 2,3 2,3 4 5 5 5 5 5 5 5

5 5 6 NA 6 6 5,6 5,6 5 6,7 6,7 6,7 7 7 6 6 5 mtDNA Introgression Throughout the Phylogeny quadrivittatusFixation group Free-love zone Fixation for mtDNA Fixation Good Sullivan (2001) Reid Goodet& etal.

al.(2012) (2003;2008) Sullivan et al. (2014) Hird Demboski et al. (in(2009) prep) Reidand et al.Sullivan (2010) T. quadrivittatus Species Group T. umbrinus T. rufus T. dorsalis T. cinereicollis T. canipes T. quadrivittatus 231 individual Cyt b sequences T. quadrivittatus group mtDNA gene tree Clade D quadrivittatus plus one dorsalis

Clade C umbrinus & quadrivittatus Front Range plus dorsalis E. Flaming Gorge a.k.a WTF?-1 T. dorsalis Sky Islands Clade B T. rufus cinereicollis & dorsalis Clade A T. canipes Clade WTF?-2 New Mexico umbrinus & dorsalis cinereicollis & dorsalis Estimates of Interspecific Nm from mtDNA (Migrate) Source Species cinereicollis dorsalis quadrivittatus umbrinus cinereicollis ------------------0.326 0.326 1.304

Receiving Species dorsalis quadrivittatus 1.768 2.3 x 10-9 ------------------0.796 1.010 ------------------2.020 1.393 umbrinus 1.148 0.383 2.55 x 10-16 ------------------- Tamias dorsalis appears to be a universal recipient of mtDNA intogression. Other taxa also show substantial interspecific migration of mtDNA T. quadrivittatus Group Genomics Brice Sarver Exon Capture (Bi et al. 2012) 5 T. rufus 5 T. canipes 10 T. umbrinus 11 T. dorsalis 11 T. quadrivittatus 10 T. cinereicollis Included individuals with introgressed and non-introgressed mtDNA.

> 4 million aligned positions at 10X coverage T. quadrivittatus group mtDNA genome tree (Sarver et al. 2016) 1.0 Clade WTF-2 (New Mexico) 1.0 1.0 T. cinereicollis & T. dorsalis 1.0 1.0 T. umbrinus & T. dorsalis 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

T. dorsalis Sky Islands Clade D T. quadrivittatus plus one T. dorsalis Clade C, a.k.a WTF-1 (Front Range) 1.0 Clade B T. rufus 1.0 Clade A T. canipes Neutral models (PhyML) account for ~96 % of Posterior Probability Exploration of Nuclear Introgression using Admixture 111,441 SNPs T. canipes T. cinereicollis T. dorsalis T. quadrivittatus T. rufus T. umbrinus T. dorsalis exhibits heterogeneity, but no co-ancestry with other taxa. T. quadrivittatus group phylogenomics Species-tree Estimation Approaches are Congruent.

T. quadrivittatus SVDquartets T. cinereicollis T. rufus T. striatus T. dorsalis T. canipes T. canipes T. cinereicollis T. dorsalis T. umbrinus T. umbrinus T. quadrivittatus T. rufus Quartets Analysis of Introgression Chiffman & Kubatko (2014) mtDNA tree Quartet 1 Tst Td-i

3 Td-ni Tum Tum Tst 2 Td-ni Td-i Tst Td-i 1 Tum Td-ni 0 0 0 0 0 0

0 Species tree No evidence of nuclear introgression in spite of nearly identical mito genomes. Quartets Analysis of Introgression HyDe (Kubatko & Chiffman 2016) Automates assessment of introgression across all quartets. No evidence of introgression in the nuclear genomes for any quartet. Conclusions Theres been extensive introgression of the mito-genome across species boundaries in the Tamias quadrivittatus group. We detect no signatures of selection on the mito-genome. We can detect no signatures of introgression in the nuclear genome, even between individuals that share a virtually identical mitochondrial genome. Thanks Thanks.