Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

<p>Abstract</p> <p>Background</p> <p>Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the attention focused on the non-coding displacement ("D") loop. We used massively parallel multiplexed sequencing to sequence complete mitochondrial genomes from 40 fishers, a threatened carnivore that possesses low mitogenomic diversity. This allowed us to test a key assumption of conservation genetics, specifically, that the D-loop accurately reflects genealogical relationships and variation of the larger mitochondrial genome.</p> <p>Results</p> <p>Overall mitogenomic divergence in fishers is exceedingly low, with 66 segregating sites and an average pairwise distance between genomes of 0.00088 across their aligned length (16,290 bp). Estimates of variation and genealogical relationships from the displacement (<it>D</it>) loop region (299 bp) are contradicted by the complete mitochondrial genome, as well as the protein coding fraction of the mitochondrial genome. The sources of this contradiction trace primarily to the near-absence of mutations marking the D-loop region of one of the most divergent lineages, and secondarily to independent (recurrent) mutations at two nucleotide position in the D-loop amplicon.</p> <p>Conclusions</p> <p>Our study has two important implications. First, inferred genealogical reconstructions based on the fisher D-loop region contradict inferences based on the entire mitogenome to the point that the populations of greatest conservation concern cannot be accurately resolved. Whole-genome analysis identifies Californian haplotypes from the northern-most populations as highly distinctive, with a significant excess of amino acid changes that may be indicative of molecular adaptation; D-loop sequences fail to identify this unique mitochondrial lineage. Second, the impact of recurrent mutation appears most acute in closely related haplotypes, due to the low level of evolutionary signal (unique mutations that mark lineages) relative to evolutionary noise (recurrent, shared mutation in unrelated haplotypes). For wildlife managers, this means that the populations of greatest conservation concern may be at the highest risk of being misidentified by D-loop haplotyping. This message is timely because it highlights the new opportunities for basing conservation decisions on more accurate genetic information.</p

The Decline And Isolation Of Fisher Populations Prior To European Settlement: Insights From Dna Analysis

Historical and contemporary genetic information can provide insights into the nature of population expansions or contractions and temporal changes in abundance and connectivity. Fisher (Martes pennanti) populations in California are thought to have declined precipitously over the last 150 yrs and currently only two populations remain in the state that are both geographically and genetically isolated from each other. In this study we looked at whether the isolation of these two populations is a result habitat alteration and trapping that accompanied European settlement in the mid-1800s or if it is the result of a more ancient demographic event. We collected both historical and contemporary genetic samples from each of the two extant fisher populations. We successfully obtained microsatellite genotypes at 10 loci for 21 museum specimens (dated 1882-1920) and 275 contemporary individuals (2006-2009). We found significant temporal shifts in allele frequencies between historical and contemporary samples between regions indicating large amounts of genetic drift likely due to isolation and small population size. We found a strong genetic signal for a 90 percent contraction in effective population size of fisher and estimated that this decline occurred over a thousand years ago. As a decline in abundance of this magnitude likely resulted in contraction of the geographic range, our analyses suggest that fisher populations in California became isolated from one another far prior to the European settlement of the state

Genetic Sampling of Palmer\u27s Chipmunks in the Spring Mountains, Nevada

Palmer\u27s chipmunk (Neotamias palmeri) is a medium-sized chipmunk whose range is limited to the higherelevation areas of the Spring Mountain Range, Nevada. A second chipmunk species, the Panamint chipmunk (Neotamias panamintinus), is more broadly distributed and lives in lower-elevation, primarily pinyon-juniper (Pinus monophylla-Juniperus osteosperma) habitat types. Panamint chipmunks are not closely related to Palmer\u27s, but field identification of the 2 species is unreliable. Palmer\u27s chipmunk is a species of concern in the state of Nevada and is listed by the International Union for Conservation of Nature (IUCN) as endangered. As such, conservation of Palmer\u27s chipmunks is a priority in the Spring Mountains National Recreation Area. We sampled putative Palmer\u27s chipmunks from 13 sites distributed across the Spring Mountains during 2010–2011. We removed Panamint chipmunks by using DNA-based identifications and then analyzed the genetic population structure of Palmer\u27s chipmunks by using a panel of 9 microsatellites. Of the 228 samples that were genotyped, 186 were Palmer\u27s; there was no evidence of hybridization between species. Four sites had exclusively Panamint chipmunks, 5 had exclusively Palmer\u27s chipmunks, and 3 had a mixture of the 2 species. In this study, Palmer\u27s chipmunks were exclusively captured at sites above 2400 m elevation, and Panamint chipmunks were exclusively captured at sites below 2200 m. Panamint chipmunks were trapped in areas typed as pinyon-juniper, but they were also trapped at sites typed as ponderosa pine (Pinus ponderosa) and mixed conifer. Both species were trapped at 3 sites; at all 3 sites, the lowerelevation traps contained Panamint chipmunks and the higher ones Palmer\u27s chipmunks. Population structure within Palmer\u27s chipmunks was minimal: heterozygosity was relatively high, and the populations displayed no signs of recent bottlenecks. Indications are that the distribution of Palmer\u27s chipmunk is limited to higher-elevation areas in the Spring Mountains, but within this area, Palmer\u27s chipmunk occurs as a single, large, well-connected, and stable population

Historical and Contemporary DNA Indicate Fisher Decline and Isolation Occurred Prior to the European Settlement of California

Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatelliteloci from 275 contemporary and 21 historical fisher samples (1880-1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19th and early 20th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement

Something’s Fishy: A Genetic Investigations Of Sculpin Species In Western Montana

Sculpin (Cottus spp.) are small, cryptic, bottom-dwelling fish native to cool and coldwater systems throughout North America. Although three species of primarily streamdwelling sculpin are thought to occur in Montana (one of which is a species of concern), their taxonomy, distribution, and origin are not well understood. In western Montana, the present distribution of sculpin species may have been shaped by both historical events, e.g., the Columbian Ice Sheet, and contemporary landscape changes (passage barriers, climate change, pollution, etc.). To evaluate sculpin presence, and species diversity, we analyzed sculpins from river drainages throughout western Montana—the Clark Fork, Blackfoot, Flathead, Bitterroot, Kootenai, Gallatin, Madison, and Missouri—east and west of the Continental Divide. We analyzed 135 samples at the mitochondrial DNA COXI gene and at 11 microsatellite DNA loci. Preliminary results of genetic analysis suggest the presence of four distinct species with hybridization among three of the species in some locations. Hybridization led to uncertainty in species designations based on morphology, but even genetically pure fish were occasionally misidentified. One species may represent an undescribed taxon that is limited in its distribution to the St. Regis drainage, although its relation to sculpin in Idaho is unknown. A second species, previously thought to be Cottus bairdii, is distinct from that taxon and is distributed on both sides of the Continental Divide

Assessing temporal genetic variation in a cougar population: influence of harvest and neighboring populations

The geography of the Black Hills region of South Dakota and Wyoming may limit connectivity for many species. For species with large energetic demands and large home ranges or species at low densities this can create viability concerns. Carnivores in this region, such as cougars (Puma concolor), have the additive effect of natural and human-induced mortality; this may act to decrease long-term viability. In this study we set out to explore genetic diversity among cougar populations in the Black Hills and surrounding areas. Specifically, our objectives were to first compare genetic variation and effective number of breeders of cougars in the Black Hills during three harvest regimes: pre (2003–2006), moderate (2007–2010), and heavy (2011–2013), to determine if harvest impacted genetic variation. Second, we compared genetic structure of the Black Hills cougar population with cougar populations in neighboring eastern Wyoming and North Dakota. Using 20 microsatellite loci, we conducted genetic analysis on DNA samples from cougars in the Black Hills (n = 675), North Dakota (n = 113), and eastern Wyoming (n = 62) collected from 2001–2013. Here we report that the Black Hills cougar population maintained genetic variation over the three time periods. Our substructure analysis suggests that the maintenance of genetic variation was due to immigration from eastern Wyoming and possibly North Dakota

When Reintroductions are Augmentations: The Genetic Legacy of Fishers (Martes Pennanti) in Montana

Fishers (Martes pennanti) were purportedly extirpated from Montana by 1930 and extant populations are assumed to be descended from translocated fishers. To determine the lineage of fisher populations, we sequenced 2 regions of the mitochondrial DNA genome from 207 tissue samples from British Columbia, Minnesota, Wisconsin, and Montana. In northwestern Montana, fishers share haplotypes with samples from the upper Midwest and British Columbia; in west-central Montana, we detected haplotypes found in British Columbia samples, but also detected a control region and cytochrome-b haplotype not found in source populations. Based on the unique haplotypes found in west-central Montana, we propose that individuals with these haplotypes are descended from a relic population. Fishers in northwestern Montana are likely descended from fishers from the Midwest and British Columbia

SCAT-DETECTION DOGS SURVEY LOW DENSITY MOOSE IN NEW YORK

The difficulty of collecting occurrence and population dynamics data in mammalian populations of low density poses challenges for making informed management decisions. We assessed the use of scat-detection dogs to search for fecal pellets in a low density moose (Alces alces) population in the Adirondack Park in New York State, and the success rate of DNA extraction from moose fecal pellets collected during the surveys. In May 2008, two scat-detection dog teams surveyed 20, 4-km transects and located 138 moose scats. In 2011 we successfully amplified DNA from 39 scats (28%) and were able to uniquely identify 25 individuals. Improved storage protocols and earlier lab analysis would increase the amplification success rate. Scat-detection dogs proved to be a reasonable, non-invasive method to collect useful data from the low density moose population in the Adirondack Park