Deterministic processes may uniquely affect codistributed species' phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet-adapted species. However, in the dry-adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species-specific responses to climate change.

Understanding the drivers of divergence in historically dynamic systems, such as sky islands, therefore rests on addressing key questions about the genetic consequences of different types of movement. Here we leverage recent conceptual and computational advances to capture variation in movement that can occur among individuals, over time, and across landscapes, under different hypotheses about the processes structuring genetic variation. Specifically, we use an integrative model-based approach (Fig. 1) that employs spatially explicit models of distributions in the present and past in a montane grasshopper from the Rocky Mountains, Melanoplus oregonensis (Orthoptera: Acrididae) to test hypotheses about the processes driving genetic divergence. Because this region was heavily impacted by Pleistocene glaciations (Fig. 2), and given that the grasshoppers are flightless montane specialists, we focus on two hypotheses: 1) restricted movement associated with the geographic isolation of contemporary sky islands, versus 2) movement related to colonization during shifting species distributions, may drive patterns of genetic divergence. Given the limited dispersal capability and habitat specificity of the species, we also consider alternative determinants of population connectivity (i.e. dispersal determined either by geographic distance or by differences in habitat suitability across the Rocky Mountain

Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate-sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site-associated DNA sequencing (RADSeq) data set containing 4156 single nucleotide polymorphisms with ecological niche models (ENMs) of present and past habitat suitability to characterize population composition and evaluate the effects of historical range shifts, contemporary climates and landscape factors on gene flow in Collared Pikas, which are found in Alaska and adjacent regions of northwestern Canada and are the lesser-studied of North America's two pika species. The results suggest that contemporary environmental factors contribute little to current population connectivity. Instead, genetic diversity is strongly shaped by the presence of three ancestral lineages isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and genetic data, populations originating from a northern refugium experienced longer-term stability, whereas both southern lineages underwent population expansion - contradicting the southern stability and northern expansion patterns seen in many other taxa. Current populations are comparable with respect to generally low diversity within populations and little-to-no recent admixture. The predominance of divergent histories structuring populations implies that if we are to understand and manage pika populations, we must specifically assess and accurately account for the forces underlying genetic similarity.

By selecting codistributed, closely related montane sedges from the Rocky Mountains that are similar in virtually all respects but one-their microhabitat affinities-we test predictions about how patterns of genetic variation are expected to differ betweenCarex nova, an inhabitant of wetlands, and Carex chalciolepis, an inhabitant of drier meadows, slopes, and ridges. Although contemporary populations of the taxa are similarly isolated, the distribution of glacial moraines suggests that their past population connectedness would have differed. Sampling of codistributed population pairs from different mountain ranges combined with the resolution provided by over 24,000 single nucleotide polymorphism loci supports microhabitat-mediated differences in the sedges' patterns of genetic variation that are consistent with their predicted differences in the degree of isolation of ancestral source populations. Our results highlight how microhabitat preferences may interact with glaciations to produce fundamental differences in the past distributions of presently codistributed species. We discuss the implications of these findings for generalizing the impacts of climate-induced distributional shifts for communities, as well as for the prospects of gaining insights about speciesspecific deterministic processes, not just deterministic community-level responses, from comparative phylogeographic study.

Objective: Our purpose was to characterize vegetation compositional patterns, tree regeneration, and plant diversity, and their relationships to landscape context, topography, and light availability across the margins of four stand‐replacing subalpine burns. Location: Four 1977 to 1978 burns east of the Continental Divide in Colorado: the Ouzel burn, a burn near Kenosha Pass, the Badger Mountain burn, and the Maes Creek burn. Methods: Vegetation and environmental factors were sampled in 200 0.01‐ha plots on transects crossing burn edges, and stratified by elevation. We utilized dissimilarity indices, mixed‐effects models, and randomization tests to assess relationships between vegetation and environment. Results: Three decades after wildfire, plant communities exhibited pronounced compositional shifts across burn edges. Tree regeneration decreased with increasing elevation and distance into burn interiors; concomitant increases in forbs and graminoids were linked to greater light availability. Richness was roughly doubled in high‐severity burn interiors due to the persistence of a suite of native species occurring primarily in this habitat. Richness rose with distance into burns, but declined with increasing elevation. Only three of 188 plant species were non‐native; these were widespread, naturalized species that comprised <1% total cover. Conclusions: These subalpine wildfires generated considerable, persistent increases in plant species richness at local and landscape scales, and a diversity of plant communities. The findings suggest that fire suppression in such systems must lead to reduced diversity. Concerns about post‐fire invasion by exotic plants appear unwarranted in high‐elevation wilderness settings.

Aim Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species‐specific or shared manner. Location Alaska and adjacent north‐western Canada. Methods For each taxon we generated 3500–7500 single‐nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between principal components analysis maps of genetic variation and geographical maps of sample locations. We generate stability maps using projected distributions from ecological niche models of the Last Glacial Maximum and the present. Results Significant similarity between genes and geography exists across taxa. However, the extent to which geography is predictive of patterns of genetic variation not only differs among taxa, but the correspondence between genes and geography varies over space. Geographical areas where genetic structure aligns poorly with the geographical coordinates are of particular interest because they indicate regions where processes other than isolation by distance (IBD) have influenced genetic variation. The clustering of individuals according to their sample location does not support suppositions of admixture, despite the presumed high vagility of some species (e.g. arctic ground squirrels). Main conclusions Genomic data indicate a more nuanced biogeographical history for the taxa than suggested by previous studies based on mtDNA alone. These include departures from IBD that are shared among taxa, which suggest some shared processes structuring genetic variation, including new potential ancestral source populations. In addition, some regions fit expectations of IBD where incremental migration and gene flow play a strong role in population structure, despite any ecological difference among taxa. Differences in dispersal capabilities do not result in different species‐specific local patterns of population structure, at least at the sampling scale examined here. We highlight how the general fit to, as well as departures from, expectations for patterns of genetic variation based on the Procrustes analyses can be used to generate hypotheses about the underlying processes.

Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.

A species’ population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next‐generation sequencing data to investigate the processes that shaped P. spicata's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.