1. Phylogenomics of the Tamias quadrivittatus group
Department of Biological Sciences & Institute for
Bioinformatics and Evolutionary Studies
University of Idaho
Funding
NSF EPS
NIH NCRR 1P20RR
NSF DEB & DEB
NSF BEACON

2. Collaborators John Demboski - DMNS Jeff Good - Montana
Kayce Bell - UNM
Brice Sarver

3. Extensive mtDNA Introgression.
(16)
40% of species
are involved in
introgression,
sometimes with
multiple partners.

4. mtDNA Introgression Throughout the Phylogeny
Reid et al. (2012)
Demboski et al. (in prep)
Fixation
Good et al. (2003;2008)
Reid et al. (2010)
Fixation
quadrivittatus group
Free-love zone
for mtDNA
Sullivan et al. (2014)
Good & Sullivan (2001)
Hird and Sullivan (2009)

5. T. quadrivittatus Species Group

6. T. quadrivittatus group mtDNA gene tree
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
cinereicollis
& dorsalis
Clade A – T. canipes
Clade WTF?-2
New Mexico
umbrinus & dorsalis

7. Estimates of Interspecific Nm from mtDNA
(Migrate)
Tamias dorsalis appears to be a universal recipient of mtDNA intogression.
Other taxa also show substantial interspecific migration of mtDNA

8. T. quadrivittatus Group Genomics
Brice Sarver
Exon Capture (Bi et al. 2012)
5 T. rufus T. dorsalis
5 T. canipes T. quadrivittatus
10 T. umbrinus T. cinereicollis
Included individuals with introgressed and non-introgressed mtDNA.
> 4 million aligned positions at 10X coverage

9. T. quadrivittatus group mtDNA genome tree
(Sarver et al. 2016)
1.0
Clade WTF-2 (New Mexico)
T. cinereicollis & T. dorsalis
T. umbrinus & T. dorsalis
T. dorsalis – Sky Islands
Clade D – T. quadrivittatus
plus one T. dorsalis
Clade C, a.k.a WTF-1 (Front Range)
Clade A – T. canipes
Clade B – T. rufus
Neutral models (PhyML) account for ~96 % of Posterior Probability

10. Exploration of Nuclear Introgression using Admixture
111,441 SNPs
T. dorsalis exhibits heterogeneity, but no co-ancestry with other taxa.
T. canipes
T. cinereicollis
T. dorsalis
T. quadrivittatus
T. rufus
T. umbrinus

11. T. quadrivittatus group phylogenomics
Species-tree Estimation Approaches are Congruent.
T. dorsalis
T. canipes
T. rufus
T. cinereicollis
T. umbrinus
T. quadrivittatus
T. dorsalis
T. striatus
T. canipes
T. cinereicollis
T. quadrivittatus
T. rufus
T. umbrinus
SVDquartets

12. Quartets Analysis of Introgression
Chiffman & Kubatko (2014)
Tst
Tum
Td-i
Td-ni
Species tree
mtDNA tree
No evidence of nuclear introgression in spite of nearly identical mito genomes.

13. 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.

14. Conclusions
There’s 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.

15. Thanks
Thanks.