Odocoileus virginianus (white-tailed deer) and O. hemionus (mule deer) are sympatric across much of North America. Molecular evidence suggests that up to 24% of individuals in some populations are a product of hybrid ancestry. Several studies have alluded to ancient and recent introgression between Odocoileus spp.; however, no divergence dates were proposed. Herein, phylogenetic analyses of DNA sequences obtained from the mitochondrial Cytochrome b gene in 690 individuals identified three clades corresponding to black-tailed deer, white-tailed deer, or a unique combination of both white-tailed deer and mule deer. White-tailed deer and mule deer diverged from a common ancestor of approximately 3.13 mya followed by an ancient hybridization event of approximately 1.32 mya, in which the white-tailed deer mitochondrial genome was “captured” by mule deer. This hybridization event produced a novel haplogroup for white-tailed deer and mule deer located west of the Appalachian Mountains and east of the Cascade Range, south to Veracruz, Mexico, and north to the Yukon Territory, Canada. The ancestral mule deer-like mitochondrial genome appears to be restricted to black-tailed deer distributed along the western portion of the Cascade and Sierra Nevada Ranges of the United States and Canada, whereas the ancestral white-tailed deer-like mitochondrial genome is restricted to the eastern United States and portions of Latin America and Caribbean regions. The “captured mitochondrial genome” has continued on an independent evolutionary trajectory and represents a unique and broadly distributed haplogroup that is 7.25% and 2.84% different from the ancestral mule deer and ancestral white-tailed deer haplogroups, respectively.

Background Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediates species-specific adhesion to the egg’s zona pellucida, is a speciation gene in placental mammals. Results Genomic ontogeny reveals that Zan arose by repurposing of a stem vertebrate gene that was lost in multiple lineages but retained in Eutheria on acquiring a function in egg recognition. A 112-species Zan sequence phylogeny, representing 17 of 19 placental Orders, resolves all species into monophyletic groups corresponding to recognized Orders and Suborders, with <5% unsupported nodes. Three other rapidly evolving germ cell genes (Adam2, Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a mitochondrial gene commonly used for phylogenetic analyses (Cytb) all yield trees with poorer resolution than the Zan tree and inferior topologies relative to a widely accepted mammalian supertree. Zan divergence by intense positive selection produces dramatic species differences in the protein’s properties, with ordinal divergence rates generally reflecting species richness of placental Orders consistent with expectations for a speciation gene that acts across a wide range of taxa. Furthermore, Zan’s combined phylogenetic utility and divergence exceeds those of all other genes known to have evolved in Eutheria by positive selection, including the only other mammalian speciation gene, Prdm9. Conclusions Species-specific egg recognition conferred by Zan’s functional divergence served as a mode of prezygotic reproductive isolation that promoted the extraordinary adaptive radiation and success of Eutheria.

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Axis deer ( Axis axis ) occur both in captivity and free-ranging populations in portions of North America, but to-date, no data exist pertaining to the species’ susceptibility to CWD. We sequenced the prion protein gene ( PRNP ) from axis deer. We then compared axis deer PrP C sequences and amino acid polymorphisms to those of CWD susceptible species. A single PRNP allele with no evidence of intraspecies variation was identified in axis deer that indicates axis deer PRNP is most similar to North American elk ( Cervus canadensis ) PRNP . Therefore, axis deer may be susceptible to CWD. We recommend proactively increasing CWD surveillance for axis deer, particularly where CWD has been detected and axis deer are sympatric with native North American CWD susceptible species.

Human-mediated introductions and subsequent establishment and spread of nonnative species have the potential to create a founder effect in such populations, which typically results in low genetic diversity and potential for inbreeding. However, several exotic invasive species exhibit a “genetic paradox” in which they thrive and adapt to novel environments while also avoiding complications from low genetic diversity. Axis deer (Axis axis) were introduced into Texas, Hawaii, South America, Australia, and Croatia during the 19th and 20th centuries and successfully established large populations from a few founding individuals. Mitochondrial (Cytochrome-b, Cytb; displacement loop, D-loop) and nuclear (10 microsatellites) markers were used to assess genetic diversity within and between axis deer populations in Texas and Hawaii and then compared to other introduced (Australia and Croatia) and native (India) populations. Overall, mtDNA divergence was 0.54% (Cytb) and 1.55% (D-loop) indicating high mitochondrial similarity within the species. Further, each invasive population was composed of only one or two mtDNA haplotypes. Microsatellite allele diversity also was low within and between populations in Texas and Hawaii resulting in monomorphic loci and Hardy–Weinberg equilibrium violations in both populations. The low genetic diversity in native Indian axis deer and within and between invasive populations suggests that the introduced populations experienced founder effects following introduction, and yet overcame this potential handicap by undergoing successful establishment and expansion. Axis deer appear to be another successful invasive species characterized by the genetic paradox where they exhibit genetic profiles that suggest inbreeding effects should be imminent, yet display no signs of inbreeding and are highly successful adapting to novel environments.