Genetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath Mountains

Sean Reilly,W Jennings,Mitchell Mulks,Jason Reilly,David Wake

doi:10.3390/d5030657

Sean Reilly, W Jennings + Show 3 more

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https://doi.org/10.3390/d5030657

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Abstract

Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds. Clustering analyses of our thirteen nuclear loci show the Sacramento watershed population to be genetically distinctive. Populations in the Klamath, Smith, and Rogue watersheds are also distinctive but not as differentiated and their boundaries do not correspond to watersheds. Our historical demographic analyses suggest that the Sacramento population has been isolated from the Klamath populations since the mid-Pleistocene, with negligible subsequent gene flow (2 Nm ≤ 0.1). The Smith and Rogue River watershed populations show genetic signals of recent population expansion. These results suggest that the Sacramento River and Klamath River watersheds served as Pleistocene refugia, and that the Rogue and Smith River watersheds were colonized more recently by northward range expansion from the Klamath.

Highlights

Genetic data are widely used for studying microevolutionary processes such as how geographical features shape current patterns of diversity and population structure [1]
Since the long-term persistence of a species partly depends on the preservation of genetic diversity, and these populations each harbor distinct gene pools, we suggest that the populations recovered from our linked-model clustering analysis be treated as distinct management units for conservation purposes
Our genetic analysis of Black Salamanders from the Klamath Mountains has revealed two major mitochondrial clades that are separated by the Trinity Mountains ridge that marks the boundary between the Sacramento River watershed and the Klamath River watershed. These two lineages were estimated to have been physically separated since the mid-Pleistocene, and have had very limited connectivity since

Summary

Introduction

Genetic data are widely used for studying microevolutionary processes such as how geographical features shape current patterns of diversity and population structure [1] This field of study, known as landscape genetics, focuses on evolutionary processes at a finer scale than is the case for typical phylogeography studies, and allows one to assess the impact of landscape features such as mountain ranges or rivers on gene flow and isolation between populations. While population genetics compares discrete populations that have already been identified using ecological, morphological, or phylogenetic data, landscape genetics does not require that discrete populations be designated a priori These types of studies are well suited to landscapes with high heterogeneity in topography, climate, and habitat, each of which are physical aspects of the environment that can restrict gene flow and create spatial genetic structure within species or populations. We focus on the Klamath Mountains of western North America, a region that contains considerable topographic, climatic, and habitat heterogeneity [3]

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