Geology topics

T.D. Mullins

Publications and source records attributed to T.D. Mullins.

5 recordsLinked to original sources

USGS2011

Multiplexed microsatellite recovery using massively parallel sequencing

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Molecular Ecology Resources↗

USGS2010

Subspecies status and population genetic structure in Piping Plover ( Charadrius melodus )

Piping Plover (Charadrius melodus) is a migratory shorebird that is listed as endangered in Canada and the U.S. Great Lakes and as threatened throughout the rest of its breeding and winter range. We undertook a comprehensive molecular-genetic investigation to (1) address subspecific taxonomy, (2) characterize population genetic structure, and (3) infer past bottlenecks and demographic processes in this species. Analyses included individuals from 23 U.S. states and Canadian provinces and were based on mitochondrial DNA sequences (580 base pairs, n = 245) and 8 nuclear microsatellite loci (n = 229). Our findings provide support for separate Atlantic and Interior subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies and should be referred to as C. m. circumcinctus. Population genetic analyses illustrated stronger genetic structure among Atlantic than among Interior birds, which may reflect reduced natal- and breeding-site fidelity of Interior individuals. Furthermore, analyses suggested that Interior birds previously experienced genetic bottlenecks, whereas there was no evidence of such patterns in the Atlantic subspecies. We interpret these results in light of 25 years of range-wide census data. Overall, differences between Interior and Atlantic Piping Plovers may reflect differences in spatiotemporal stability of nesting habitat between regions. ?? 2010 The American Ornithologists' Union.

The Auk↗

USGS2008

Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction. ?? 2008 Elsevier Inc.

Molecular Phylogenetics and Evolution↗

USGS2007

Conservation genetics of snowy plovers (Charadrius alexandrinus) in the Western Hemisphere: Population genetic structure and delineation of subspecies

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern. ?? 2007 Springer Science+Business Media, Inc.

Conservation Genetics↗

USGS2005

Taxonomic relationships among Phenacomys voles as inferred by cytochrome b

Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.

Journal of Mammalogy↗