Conservation Genetics of Kangaroo Mice, Genus Microdipodops

Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America

PREMISE

Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata. This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction.

METHODS

The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua, a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events.

RESULTS

The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua, while large-scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19-4.2 Gbp), heterozygosity (2.24-2.25%), and sequence (98.73-99.15% similarity) across scaffolds, and in k-mer analyses, similar patterns of diploid heterozygous k-mers (AB = 41%, 47%, and 47%), triploid heterozygous k-mers (AAB = 18-21%), and tetraploid k-mers (AABB = 13-17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades.

CONCLUSIONS

Our findings suggest population-level TE differentiation after a shared polyploidization-to-diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.

Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis)

The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.

Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert

The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem. The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of the dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mouse, and to evaluate gene flow, demographic trends, and genetic integrity. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem (photo credit J. C. Hafner).