Mark P. Miller

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species’ range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus’ range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum ∼12 000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajimas D and patterns associated with location‐specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

Genetic diversity and divergence among freshwater mussel (Anodonta) populations in the Bonneville Basin of Utah

Populations of the freshwater mussel genus Anodonta appear to be in a state of rapid decline in western North America, following a trend that unfortunately seems to be prevalent among these animals (Mollusca: Unionoida). Here we describe the patterns of molecular divergence and diversity among Anodonta populations in the Bonneville Basin, a large sub‐basin of the Great Basin in western North America. Using amplified fragment length polymorphism (AFLP) analysis, we found a striking lack of nuclear diversity within some of these populations, along with a high degree of structuring among populations (FST = 0.61), suggesting post‐Pleistocene isolation, due either to a long‐term loss of hydrologic connectivity among populations or to more recent fish introductions. We also found evidence of recent hybridization in one of these populations, possibly mediated by fish‐stocking practices. Using mitochondrial sequence data, we compared the Bonneville Basin populations to Anodonta in several other drainages in western North America. We found a general lack of resolution in these phylogenetic reconstructions, although there was a tendency for the Bonneville Basin Anodonta (tentatively A. californiensis) to cluster with A. oregonensis from the adjacent Lahontan Basin in Nevada. We recommend further investigation of anthropogenic factors that may be contributing to the decline of western Anodonta and a broad‐scale analysis and synthesis of genetic and morphological variation among Anodonta in western North America.

Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

Aims:u2002 The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties.

Genetic diversity among Brazilian isolates of Beauveria bassiana: comparisons with non‐Brazilian isolates and other Beauveria species

Aims:u2002 The genetic diversity of Beauveria bassiana was investigated by comparing isolates of this species to each other (49 from different geographical regions of Brazil and 4 from USA) and to other Beauveria spp.

Rangewide molecular structuring in the Utah sucker (Catostomus ardens)

The Utah sucker (Catostomus ardens) is endemic to the Bonneville Basin and the upper Snake River drainage in western North America, and is thought to hybridize with the federally endangered June sucker (Chasmistes liorus mictus) in Utah Lake (Bonneville Basin). Here we describe the discovery of a major subdivision in Utah suckers (4.5% mitochondrial sequence divergence) between the ancient Snake River drainage and the Bonneville Basin. This boundary has not previously been recognized in Utah suckers based on morphologic variation, but has been recently described in two endemic cyprinids in the region. Populations in valleys east of the Wasatch Mountains in Utah clustered with the Snake River populations, suggesting that these valleys may have had an ancient hydrologic connection to the Snake River. We also found evidence of population isolation within the Bonneville Basin, corresponding to two Pleistocene sub‐basins of the ancient Lake Bonneville. In contrast, we found no molecular evidence for deep divergence between Utah suckers and June suckers in Utah Lake or for a history of hybridization between divergent lineages in that population, although we recognize that demographic events may have obscured this signal. These findings suggest that the morphological differences between Utah and June suckers in Utah Lake may be the result of strong, and relatively recent, ecological selection. In summary, morphological and molecular characters seem to vary along different axes in different portions of the range of this taxon, providing an interesting system for studying the contributions of neutral and adaptive variation to species diversity.

Rapid natural selection for resistance to an introduced parasite of rainbow trout.

Introduced species and infectious diseases both independently pose challenges for the preservation of existing biodiversity. However, native species or disease hosts are by no means ‘unarmed’ when faced with novel environmental challenges, provided that adequate adaptive genetic variation exists to mount effective evolutionary responses. In this study, we examined the consequences of the recently introduced parasite and causative agent of whirling disease (Myxobolus cerebralis) in a wild rainbow trout (Oncorhynchus mykiss) population from Harrison Lake, Montana (USA). Consistent with the parasite’s age‐specific effects, juvenile rainbow trout recruitment into Harrison Lake was substantially reduced following parasite detection in 1995. However, experimental data suggest that natural selection has rapidly reduced whirling disease susceptibility within the population over time. The rapid observed temporal change in resistance patterns argues that the standing genetic variation for parasite resistance facilitated this process. Our findings ultimately underscore the importance of preserving genetic diversity to ensure that species of economic importance or of conservation concern have maximal chances for persistence in future changing environments.

Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon slender salamander (Batrachoseps wrighti): Implications for conservation efforts and species management

Endemic to Oregon in the northwestern US, the Oregon slender salamander (Batrachoseps wrighti) is a terrestrial plethodontid found associated with late successional mesic forests. Consequently, forest management practices such as timber harvesting may impact their persistence. Therefore, to infer possible future effects of these practices on population structure and differentiation, we used mitochondrial DNA sequences (cytochrome b) and RAPD markers to analyze 22 populations across their range. Phylogenetic analyses of sequence data (774 bp) revealed two historical lineages corresponding to northern and southern-distributed populations. Relationships among haplotypes and haplotype diversity within lineages suggested that the northern region may have more recently been colonized compared to the southern region. In contrast to the mitochondrial data, analyses of 46 RAPD loci suggested an overall pattern of isolation-by-distance in the set of populations examined and no particularly strong clustering of populations based on genetic distances. We propose two non-exclusive hypotheses to account for discrepancies between mitochondrial and nuclear data sets. First, our data may reflect an overall ancestral pattern of isolation-by-distance that has subsequently been influenced by vicariance. Alternately, our analyses may suggest that male-mediated gene flow and female philopatry are important contributors to the pattern of genetic diversity. We discuss the importance of distinguishing between these two hypotheses for the purposes of identifying conservation units and note that, regardless of the relative contribution of each mechanism towards the observed pattern of diversity, protection of habitat will likely prove critical for the long-term persistence of this species.

SSR_pipeline: A Bioinformatic Infrastructure for Identifying Microsatellites From Paired-End Illumina High-Throughput DNA Sequencing Data

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

Evaluation of Disease Resistance of the Fish Lake–DeSmet, Wounded Man, and Harrison Lake Strains of Rainbow Trout Exposed to Myxobolus cerebralis

Abstract Several tests evaluated the whirling disease resistance of three stocks of rainbow trout Oncorhynchus mykiss: the Fish Lake–DeSmet (FD), Wounded Man (WM), and Harrison Lake (HL) strains. In one series, FD fish were exposed to Myxobolus cerebralis triactinomyxons (TAMs; one exposure of 1,000 TAMs/fish). Histological scores ranged from 4.28 to 4.95 (MacConnnell−Baldwin scale) among FD fish from three different hatcheries. In addition, FD fish were exposed either acutely (1,000 TAMs/fish in one dose) or chronically (100 or 200 TAMs/fish on each of 10 d). There was no significant difference in mean myxospore counts among the three different exposure treatments. Histological scores ranged from 3.76 to 3.86 among the exposure groups and did not differ among exposure treatments. The correlation between histological scores and myxospore counts was significant (r = 0.57). Three different ages of WM rainbow trout were challenged with 1,000 TAMs/fish; histological scores for 62-d-old fish were significantly...

Patterns of Molecular Diversity in Naturally Occurring and Refugial Populations of the Least Chub

Abstract The least chub Iotichthys phlegethontis is a small, rare cyprinid fish endemic to the Bonneville basin, Utah. Although it was once widely distributed within the basin, naturally occurring populations are now known to exist only in four isolated geographical regions. We used nuclear (amplified fragment length polymorphism) and mitochondrial genetic markers to describe the patterns of genetic divergence and diversity within and among populations from these regions and to assess genetic diversity in two refugial populations. We found that a large proportion of the diversity in this species was attributable to population structuring (F ST = 0.52). Given that a high proportion of the genetic variation is accounted for by population differentiation and that three of the existing populations have been discovered in the last 10 years, we suggest that surveys to discover additional populations be a high management priority. We also recommend that existing populations be studied for evidence of adaptive di...