Evolution and the climatic niche: Using genomics and niche modeling to explore how climate impacts evolutionary processes

Abstract

Climate shapes the distributions of and interactions among species and thus influences many evolutionary processes related to the generation and maintenance of biodiversity. Oscillations in climatic regimes have played an important role in shaping the patterns of diversity by driving speciation events when previously connected populations become allopatrically isolated in different environments. Changing climates also are associated with extinction events when populations are unable to track their climatic niche or adapt to novel conditions. The rapid climate change caused by human activity emphasizes the need to understand the role climate plays in mediating species interactions and distributions. This work combines the use of climatic and genomic data across a variety of vertebrate systems to explore how climate has shaped the processes of speciation and evolution, and how climate may threaten the continued persistence of both recognized and unrecognized diversity. The evolution of a species’ climatic niche, or the climatic conditions under which a species occurs, plays a central role in generating diversity and adaptation to new environmental conditions. Faster rates of climatic niche evolution are associated with increased diversification rates, suggesting that the exploration of novel climate space can facilitate isolation and subsequent diversification. The evolution of traits that may increase or decrease rates of climate niche evolution, then, may play an important role in the colonization of novel environments and the formation of species. In my first chapter, I show that the evolution of a short aquatic larval stage in Desmognathus salamanders led to an increase in the rate of climatic niche evolution, which may have played a central role in the adaptive radiation of this group. Changes in climate have the potential to bring long-isolated species into contact with one another. Oftentimes, these species can produce viable offspring with one another and form hybrid zones. These hybrid zones often form along ecological gradients, with hybrids occurring in habitats intermediate to the climatic conditions occupied by the pure parental populations. In the Southern Appalachian Mountains, Plethodon shermani and Plethodon teyahalee hybridize extensively along an elevational gradient. P. shermani occurs on different mountaintop isolates, and P. teyahalee is distributed in between them at lower elevations. In my second chapter, I explore the genomic evidence for hybridization between these two species and whether climatic variation associated with elevation maintains species boundaries in this system. All surveyed parental P. shermani populations have experienced some degree of introgression from P. teyahalee, and multiple lines of evidence suggest that selection for P. teyahalee alleles drives asummetric introgression from P. teyahalee into P. shermani. We identify no intrinsic genetic barriers to gene flow, suggesting that these hybrid zones are regulated by ecological, rather than intrinsic factors. These findings suggest that all P. shermani populations are in danger of swamping by P. teyahalee as conditions in the Appalachians become warmer and drier. Genomics and niche modeling are powerful tools for identifying cryptic lineages of conservation concern within widespread species. In addition to identifying lineages, these approaches can inform managing agencies about threats to population persistence such as climate change-induced habitat loss and inbreeding. In my final chapter, I assess patterns of genomic and environmental differentiation among populations of Kinosternon hirtipes. Within this group, we identified multiple evolutionarily distinct lineages, many of which correspond to described subspecies. Genetic and ecological differentiation among these lineages appears to be due to vicariance associated with the Trans-Mexican Volcanic Belt. Northern populations exhibit low genetic diversity, high levels of inbreeding, and may lose over 85% of climatically suitable habitat to climate change, raising concern over their long-term viability.