Spencer Bruce

Spencer Bruce
University at Albany, The State University of New York | UAlbany · Information Technology Services

Doctor of Philosophy: Ecology and Evolutionary Biology

About

20
Publications
3,253
Reads
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50
Citations
Introduction
My research focuses on big data as a means to answer complex questions regarding both wildlife and disease. I employ genetic and genomic approaches to elucidate the ways in which landscape heterogeneity and habitat shape population structure. My current research ranges from aquatic population genetics to bacterial genomics, with an emphasis on applicability in the context of wildlife conservation and the "one health" approach.
Additional affiliations
June 2018 - February 2019
University at Albany, The State University of New York
Position
  • PostDoc Position

Publications

Publications (20)
Article
Full-text available
As biodiversity is transformed on a global scale, identifying and protecting populations unaffected by habitat disturbances is essential to ensuring natural genetic diversity is not irretrievably lost. Furthermore, knowledge of the interactions between endemic populations and human-introduced conspecifics is imperative to the creation of management...
Article
Full-text available
Context: Preservation of genetic diversity is a commonly cited, yet under-evaluated aspect of species conservation plans. Understanding the influence of human-mediated translocations and habitat constraints on landscape patterns of genetic structure in threatened fish species is essential to maintaining biodiversity and adaptive potential. Object...
Article
Full-text available
Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compa...
Article
Full-text available
Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time...
Article
Full-text available
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses an important threat in human and animal health. In this study, we ask whether resistance and virulence genes in S. aureus are homogeneously distributed or constrained by different animal hosts. We carried out whole genome sequencing of 114 S. aureus isolates from ten species...
Article
Full-text available
Staphylococcus pseudintermedius is a major bacterial colonizer and opportunistic pathogen in dogs. Methicillin-resistant S. pseudintermedius (MRSP) continues to emerge as a significant challenge to maintaining canine health. We sought to determine the phylogenetic relationships of S. pseudintermedius across five states in the New England region of...
Article
Full-text available
Species of extant nautiluses (in Nautilus and Allonautilus) have been anecdotally described as opportunistic scavengers. Here, we examine foraging and scavenging behaviors of Nautilus in field and laboratory settings. Given that nautiluses are nektobenthic, solitary animals living in resource-limited habitats, we predict that odor is the predominan...
Article
Full-text available
Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. I...
Article
Full-text available
Disease outbreaks are a consequence of interactions among the three components of a host–parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmi...
Article
Full-text available
The genetic constitution of populations is affected by myriad factors including both natural and anthropogenic habitat transformations. Previous work on Brook Trout (Salvelinus fontinalis) population structure has suggested that supplemental stocking for fishery enhancement has transformed natural genetic diversity. In this study, we utilize micros...
Preprint
Full-text available
Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compa...
Article
Full-text available
As anthropogenic impacts accelerate changes to landscapes across the globe, understanding how genetic population structure is influenced by habitat features and dispersal is key to preserving evolutionary potential at the species level. Furthermore, knowledge of these interactions is essential to identifying potential constraints on local adaptatio...
Article
Full-text available
In fisheries management, understanding anthropogenic impacts on fish population genetic structure is essential because genetic diversity is a fundamental attribute contributing to a species’ evolutionary capacity. An extended history of supplemental stocking has led to the introgression of genes from non-local, hatchery-reared brook trout (Salvalin...

Questions

Questions (6)
Question
I am looking for a way to extract the coordinates of SNPs unique to pre-defined clusters or clades based on a large WGS data-set mapped to a reference (which I have in .vcf file format). I am able to do this manually using my .vcf file, my .fasta reference file, and my newick tree in Gingr, but it is starting to give me a headache... Any known software out there that might be able to quickly do this for me?
Question
Any geologists, geographers, or geophysicists out there familiar with a way to convert current GPS coordinates to coordinates that are consistent with continental structure during Pangaea? Your input is appreciated!
Question
I have microsat data for multiple fish populations, and I'd like to get the best estimates of effective population size as I possibly can, but my problem is I have no age or size class data. Therefore my dataset contains overlapping generations, and I have no way of discerning what individuals are of what age class. Is there an accepted way to calculate Ne despite this overlap? Most every method I see requires you have age class information or discrete generations. Any help is appreciated.
Thanks!
Question
I'm looking to prepare a grant for some high-throughput work, but the Core Facility at my University does not offer the service. Any suggestions would help, as I know Cornell's GBS program is currently on hiatus (this is what my classmates have used in the past). Thanks in advance!
-Spencer
Question
I'm hoping to compare field sampling data with the results of fish species determined to be present using  eDNA metabarcoding. Will likely send out for the high-throughput portion, but everything else will be done in-house.
Question
Does anyone know of any papers that discuss problems associated with a lack of source populations when attempting to correctly quantify introgression with programs such as STRUCTURE, BAPS or Flock? I'm working on a simulation study that suggests that without both source populations admixture levels are falsely low (if run only with one parental) or falsely high (if run with one parental and a different source pop as a "surrogate"). Trying to wrap my head around this, and wondering if anyone else has experienced this problem. Also wondering if anyone has shown STRUCTURE's inability to correctly quantify ancestry in this scenario in the past. Thanks!

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Projects

Projects (3)
Project
I am currently studying Bacillus anthracis on a global scale using modern techniques for whole genome sequence analysis and bioinformatics. I am directing lab work associated with whole genome library preparation, sequencing, genome assembly, and annotation in Dr. Wendy Turner's lab of Ecology and Evolution of Infectious Disease at the State University of New York at Albany (http://wendyturner.org/).
Archived project
The primary research objective of this project was to characterize the Boreas Pond Watershed and Little Charley Pond brook trout populations relative to other brook trout populations present in New York State.