Defense Date

1-6-2020

Graduation Date

Spring 5-8-2020

Availability

One-year Embargo

Submission Type

dissertation

Degree Name

PhD

Department

Biological Sciences

Committee Chair

Jan E. Janecka

Committee Member

Michael I. Seaman

Committee Member

Charles J. Welsh

Committee Member

John R. Wible

Keywords

biology, genomics, bobcat, lynx, ddradseq, genetic, evolution

Abstract

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx (Lynx canadensis). The lynx is another North American felid whose range overlaps with the bobcats at the United States-Canadian border. The lynx, unlike the bobcat, is a habitat and prey specialist highly adapted to the northern boreal forests and the snowshoe hare. In an effort to better understand the unique local adaptations and histories of these and other species, wildlife genomics has become increasingly common with the development of Next Generation Sequencing and additional bioinformatic tools. Low coverage genome-wide pooled sequencing was used to sequence northwestern (MT, ID) and southwestern (CA, NM, AZ, TX) bobcats to identify potential candidate adaptive loci between the two populations living in disparate ecological conditions. Genes dealing with keratin proteins, limb morphology and osteogenesis, sensory perception of temperature, and metabolism were identified with signals of selective sweeps. Three Canada lynx were similarly sequenced to identify species-level divergence and identify potential northern adaptations shared between lynx and northern bobcats. The X chromosome had higher species-specific differentiation in FSTvalues and that overall, the lynx had lower nucleotide diversity than both bobcat populations. Genes relating to hemoglobin, lung function, adipogenesis, body growth and size, and hypothyroidism and BMI changes were found to differentiate between the species. When examining loci that differentiated in the lynx and northern bobcats compared to those in the south, genes related to eosinophil counts and BMI came up as outliers. A third study exploring the potential of reduced representation libraries was performed using double-digest Restriction-site Associated DNA Sequencing (ddRADSeq) to sequence bobcats in New Mexico, Montana, and Vermont as well as Canada lynx to verify its potential for wildlife studies. FSTaverages were similar between datasets revealing the same trends and point distribution patterns. These data also showed a greater east-west differentiation than north-south in the genomic dataset, which was previously shown in microsatellite and mtDNA. Nucleotide diversity, however, deviated between datasets, likely due to low representation and biases based on restriction enzyme cut sites. This work as the first genomic study on bobcat and Canada lynx populations has allowed a better understanding of population differentiation, adaptation between and within species, introgression, and how sequencing methods compare.


Language

English

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