Polar bears at Cape Lisburne (US Fish & Wildlife Service photo)Scientists at the UAF School of Natural Resources and Agricultural Sciences are launching a new study of the genetics of endangered species.
The project, funded by a $400,000 grant from the Alaska Department of Commerce, Community, and Economic Development, will assess the history of polar bears and their relative, the brown/grizzly bear. Project leader and associate professor Matthew Cronin hopes to quantify the extent of DNA divergence within and between the species. He will also assess sea lion and beluga whale population genetic structures over time.
Cronin will study the timing of polar bear evolution from brown bear ancestors and what the sea ice and shoreline conditions were like in the ancient past.
“This will give insights regarding previous warming and cooling periods to which the bears were exposed and how and where they adapted,” Cronin said.
Collaborators on the project include the U.S. Department of Agriculture, the Alaska Department of Fish and Game, Texas Tech University, the University of California Davis, and Purdue University.
Cronin’s work has focused on population genetics and phylogenetics of large mammals, including bears, caribou, deer, and domestic livestock. He has published several genetics papers on bears, including polar bears, in collaboration with US Geological Survey scientists. He has also worked on wildlife, primarily caribou and grizzly bears in the oil fields on the North Slope. He serves on the Alaska Board of Forestry.
SNRAS Dean Carol Lewis said Cronin's work is an important part of the school's animal husbandry program. "It is absolutely critical for us in our mission to consider the responsible use of resources and be assured that science is an underpinning of the laws and policies that govern land use in this state."
In his proposal to the Department of Commerce, Cronin stated (excerpts):
"The best available science should be used in decisions about the Endangered Species Act and other resource management. The science of genetics is increasingly being used in ESA cases, including those in Alaska, to determine population, subspecies, and species status, evolutionary history, and taxonomy, and to assess fitness and hybridization. These are topics relevant to the ESA listings in Alaska. However, the use of scientific data, genetic data in particular, must be done properly with a thorough understanding and differentiation of fact from interpretation...
The ESA listing of polar bears (Ursus maritimus) is based on the premise that global warming is leading to reduction of summer sea ice habitat. However, it can be argued that polar bears survived previous warming periods and will be able to survive a new one. This can be addressed with study of the timing of evolution of polar bears from their ancestral species, brown/grizzly bears (Ursus arctos) and assessment of the climate and sea ice conditions that have occurred since polar bears occurred as a species.
The fossil record of polar bears is very limited, but recent research indicates that polar bears have likely existed as a species for at least 110,000 to 150,000 years. A fossil polar bear jawbone was recently discovered and dated as between 110,000 and 130,000 years old and mtDNA sequence of this fossil allowed a molecular dating estimate of about 150,000 years. This has implications regarding the time and extent of polar bears’ exposure to previous warming periods and their response to future warming. Advances in genomics and biotechnology will allow assessment of many genes that will allow refinement of the molecular dating and the timing of polar bear evolution. Colleagues and I have preliminary DNA sequence data for mtDNA, k-casein and Mc1r genes and several other genes will be assessed.
The entire species of polar bears was listed as threatened under the Endangered Species Act in 2008. Distinct population segments (DPS) were not designated under the ESA, but 19 populations are recognized around the world, although there is limited genetic differentiation among them. Genetic assessments can contribute to monitoring possible changes in population structure and provide information relevant to DPS designations.
A basic tenet of 'conservation biology' is that small populations experience inbreeding with a resulting decrease in fitness and eventual extinction. However, loss of fitness through inbreeding depends on many factors and needs case-by-case assessment. These considerations could become relevant to polar bears in local populations and the entire species if there are significant declines in numbers.
Interspecies hybridization-polar bears and grizzly bears. One of the predictions of loss of summer sea ice is that polar bears will spend more time on shore, with increasing contact and potential interbreeding with grizzly bears. The two species can interbreed and produce viable (and possibly fertile) offspring. A putative hybrid was shot in Canada within the last few years. This has been suggested as another factor that will negatively affect polar bears and contribute to eventual extinction. Genetic studies can contribute to an understanding of the nature and extent of such hybridization. I have published papers on the genetics of grizzly bears in areas of Alaska where hybridization with polar bears is possible that will allow assessment of potential hybridization of the species in Alaska.
Contaminants causing genetic damage (i.e., mutations) are a potential problem from spills of hazardous materials and oil. Hypotheses of such effects are common and the field of 'genotoxicology' has grown dramatically in recent years. This may be an issue with regard to oil and gas development in the Arctic, and its impact on polar bears. Assessing baseline conditions of polar bear genetics will be useful in this regard.
Steller sea lions and beluga whales in Cook Inlet are examples of distinct population segments (DPS) listed under the ESA. There are two DPS of Steller sea lions in Alaska. Eastern and western DPS have been designated in Alaska based on genetics and movements data. Beluga whales in Cook Inlet have similarly been designated a DPS, different from other belugas in Alaska, based on genetic and geographic data. However, the criteria for designating DPS are subjective and not quantitative science. The sea lions and belugas have some evidence of limited gene flow among areas, but there are shared alleles and mtDNA haplotypes among DPS and genetic differentiation is not particularly high. In the case of sea lions, there are data on movements from tagging and branding studies that may provide information on the actual level of inter-population movement and gene flow. Synthesis of the genetic and movements data is needed to properly assess the relationships of Steller sea lions and beluga whale populations with regard to DPS designation and population numbers. Immigration and emigration can be important demographic factors that influence population numbers that can be addressed with our assessment.
The polar bear project will focus on the phylogenetics, time of evolution, and age of polar bears as a species. It will involve generation of new DNA sequence data with which to quantify the genetic differences of polar bears and brown/grizzly bears, and provide molecular dating to estimate the time of divergence of these species (and thus the age of polar bears as a species).
Lab work: Obtain DNA Sequences for 30-50 bears from each of the following:
- Polar bears (Alaska) 6
- Polar bears (Canada and Eurasia)
- Brown bears from Admiralty, Baranof, Chichigoff Islands in southeast Alaska
- Brown and grizzly bears from other Alaska locations
- Grizzly bears from the U.S. Rocky Mountain region
- Grizzly bears from Canada
- Black bears from Alaska, Canada, and the lower 48 US States
- Wolf, coyote, dogs, from North America (to be used as an out group in phylogenetic analyses)
Several approaches to quantifying genetic relationships of polar bears, brown/grizzly bears, and black bears will be used. Because polar bears and brown bears share recent common ancestry, (as indicated by paraphyletic mtDNA relationships) nuclear DNA divergence between the species may be small and of limited phylogenetically utility, particularly for neutral DNA regions or genes under selective constraints. For example, preliminary data for the k-casein gene shows polyphyletic relationships of polar, brown, and black bears suggesting relatively slow molecular evolution (i.e., low mutation rate and/or selective constraints). Conversely, the rapid adaptive evolution of polar bears suggests that some genes under selection may have diverged more quickly. Consideration of the appropriate model of molecular evolution (neutral or selective) will be important in our phylogenetic analysis.
The first approach will be to obtain DNA sequences from mitochondrial DNA (mtDNA) and nuclear DNA to assess phylogenies of several genes. This will include genes for which PCR primers are available (mtDNA cytochrome b and flanking control region, Y chromosome DNA, k-casein, mc1r, and other nuclear genes previously used in mammalian and carnivore phylogenetics. PCR primers for other nuclear genes can be developed from the whole genome sequencing described below. Both coding and non-coding DNA sequences will be included to allow assessment of neutral DNA sequences and genes potentially under selection. Initial analyses will target 30-50 individuals of each group identified above to assess both intra- and inter-species variation.
The DNA sequences we generate will be submitted to GenBank, and related sequences obtained with BLAST searches. Sequences will be aligned and subjected to phylogenetic analysis as single gene trees and combined datasets with maximum parsimony, maximum likelihood, Bayesian, and distance methods, using canids as an outgroup. Individual gene sequences will be tested for selection, and phylogenetic inferences adapted accordingly. Recent literature will be reviewed to derive the best estimates of rates of molecular evolution for different genes’ coding and non-coding regions. The level of DNA sequence divergence and rates of evolution will be used to estimate the time of separation of gene lineages (i.e. haplotypes or alleles). The dates from different genes will be used to estimate a range of dates of divergence of gene lineages between polar bears and brown/grizzly bears.
A second approach will be to sequence the genome of one individual of each group (polar bear, southeast Alaska brown bear, mainland grizzly bear, and black bear) with high-7 throughput sequencing. PCR primers for candidate gene sequencing and identification of single nucleotide polymorphisms (SNP) can be identified from these extensive sequences. This approach has been applied to livestock with considerable success. The presence/absence and allele frequencies of SNPs will be used to quantify the genetic divergence of the bear species. This work is planned to be done at the University of California Davis.
A third approach will be to employ amplified fragment polymorphisms in which restriction fragments are amplified with PCR, generating large numbers of variable fragments that may show intra- and inter-species variation. This work is under development at Texas Tech University.
Paleoenvironments in the Arctic and sub-Arctic will be assessed from the literature and through collaborations with the US Geological Survey. Seasonal and multi-year sea ice, sea level and shoreline locations, and other physical factors such as water and air temperatures, will be estimated for time intervals from the present to several million years ago. The extent of this analysis will depend on the availability of data with which to characterize paleoenvironments. This work will be done with the US Geological Survey in Reston, Va.
Paleoenvironmental characteristics will be considered in light of polar bear habitat characteristics to determine likely times and places where polar bears evolved and established populations. The phylogenetic patterns from genetic data will be assessed with regard to age of the gene lineages and the paleoenvironments in which polar bear habitats are indicated. The combination of molecular dating of gene lineages in different groups of bears with identification of paleoenvironments will give insights into where and when, and under what warming or cooling conditions, polar bears existed in past time intervals.
An additional aspect, unique to our project is the assessment of polar bears’ adaptive phenotypic traits (e.g., white fur, aquatic and cold adaptations). Collaboration with livestock geneticists with the US Department of Agriculture Agricultural Research Service (USDA) will provide expertise in understanding the relationships between phenotype and molecular genetic variation and fitness. The science of genetics is advanced in agriculture, including livestock. Livestock geneticists are experts in quantitative genetics and assessing fitness (i.e., performance) related traits, and assessing genetic variation and breed (i.e. population and subspecies) characteristics.
Steller sea lion and beluga whales in Cook Inlet. The designations of distinct population segments (DPS) of Steller sea lions and beluga whales in Cook Inlet are based on both genetic and geographic information. The genetic data need to be reviewed and synthesized and compared with other DPS designations for consistency. The genetic data also need to be combined with data on animal movements to assess the extent of gene flow and movements among the DPS. We will obtain genetic data from papers, reports, and agency files for each species and quantify the level of genetic differentiation and estimate effective population size and gene flow among them."
No comments:
Post a Comment