SEARCH · Geology Reports

Results for “Conservation Genetics”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources

USGS2016

Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

In the southwestern United States (US), the Rio Grande chub ( Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (H O ) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (A R = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (A R = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders ( N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora , consideration must be given as to which populations are selected for translocation.

Arizona, California, Colorado, Nevada, New Mexico,↗

USGS2023

Genetic structure across isolated Virginia populations of the endangered candy darter (Etheostoma osburni)

Candy darter Etheostoma osburni , a federally endangered non-game fish, has been extirpated from most of its historic range in Virginia and now occurs in four isolated populations in the New River drainage. Understanding of population genetic structure will provide insights into the recent natural history of the species and can inform conservation management. Our objectives were to: characterize population genetic structure, estimate and compare effective population sizes ( N e ), and use this information to infer recent population history. Variation at mitochondrial cytochrome b sequences among 150 individuals showed 10 haplotypes separated by 1–14 mutational steps, some shared and some unique to particular populations. Variation at 12 microsatellite loci among 171 individuals showed lower variation in Dismal Creek than in other populations. All populations showed evidence of having experienced a genetic bottleneck and were highly differentiated from one another based on both types of DNA markers. Population genetic structure was related to stream position in regard to the New River, suggesting that populations were once connected. N e estimates for all populations were less than the 500 recommended to maintain evolutionary potential, but most estimates were greater than the 100 needed for use as source populations. Our findings indicate that habitat management to allow expansion of populations, and translocations to exchange genetic material among populations, may be effective tactics to promote conservation of candy darter in Virginia.

North Carolina, Virginia, West Virginia↗

USGS2015

Comparative analysis of riverscape genetic structure in rare, threatened and common freshwater mussels

Freshwater mussels (Bivalvia: Unionoida) are highly imperiled with many species on the verge of local extirpation or global extinction. This study investigates patterns of genetic structure and diversity in six species of freshwater mussels in the central Great Lakes region of Ontario, Canada. These species vary in their conservation status (endangered to not considered at risk), life history strategy, and dispersal capabilities. Evidence of historical genetic connectivity within rivers was ubiquitous across species and may reflect dispersal abilities of host fish. There was little to no signature of recent disturbance events or bottlenecks, even in endangered species, likely as a function of mussel longevity and historical population sizes (i.e., insufficient time for genetic drift to be detectable). Genetic structure was largely at the watershed scale suggesting that population augmentation via translocation within rivers may be a useful conservation tool if needed, while minimizing genetic risks to recipient sites. Recent interest in population augmentation via translocation and propagation may rely on these results to inform management of unionids in the Great Lakes region.

Ontario↗

USGS2024

Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals.

Ecology and Evolution↗

USGS2025

Genetic variation and metapopulation structure inform recovery goals in a threatened species

Background: Monitoring genetic parameters is important for setting effective conservation and management strategies, particularly for small, fragmented, and isolated populations. Small, isolated populations face increased rates of genetic drift and inbreeding, which increase extinction risk especially when gene flow is limited. Methods: Here, we applied a Genotyping-in-Thousands by sequencing (GT-seq) panel to inform recovery action for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ). We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals. Results: We delineated three types of conservation units: (1) three evolutionarily significant units that represent long-term population structure and variation, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective population sizes per management unit were small overall (mean 38.16, range 2.3–220.9), indicating that recovery goals of 10 subpopulations with N e > 500 have not been reached. Conclusions: Our results support the maintenance of connectivity within evolutionarily significant units through the restoration of dispersal corridors. Next steps could include further sampling of some subpopulations with low sample sizes, unsampled subpopulations, and subpopulations that are geographically isolated. Genotyping future samples with the same GT-seq panel would help to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change.

Idaho↗

USGS2020

Phylogeographic analysis of Mudpuppies (Necturus maculosus)

The geology of the Pleistocene, and particularly the Last Glacial Maximum approximately 26.5 ka, is a critical driver of species’ present-day distributions and levels of genetic diversity in northern regions. Using mitochondrial DNA sequence data, we tested several predictions relating to the postglacial recolonization of the northern United States and southern Canada by Mudpuppies (Necturus maculosus). Our analyses revealed a significant split between western and eastern lineages, with the divide corresponding to the location of the Mississippi River. Our data support the presence of one or more Mississippian glacial refugia, with subsequent expansion and diversification of a western cluster into the upper Midwest, and an eastern cluster into the eastern Great Lakes and New England. As predicted in cases of postglacial colonization, each of these clusters contains a single widespread and common haplotype, along with numerous low-frequency, closely related haplotypes. Given recent conservation concerns about amphibians in general, and Mudpuppies specifically, we discuss our results in light of species conservation. Knowledge of a species’ genetic diversity allows for informed management and facilitates decisions that preserve local adaptation and evolutionary potential.

Journal of Herpetology↗

USGS2015

Developing a conservation strategy to maximize persistence of an endangered freshwater mussel species while considering management effectiveness and cost

We used a structured decision-making process to develop conservation strategies to increase persistence of Dwarf Wedgemussel ( Alasmidonta heterodon ) in North Carolina, USA, while accounting for uncertainty in management effectiveness and considering costs. Alternative conservation strategies were portfolios of management actions that differed by location of management actions on the landscape. Objectives of the conservation strategy were to maximize species persistence, maintain genetic diversity, maximize public support, and minimize management costs. We compared 4 conservation strategies: 1) the ‘status quo’ strategy represented current management, 2) the ‘protect the best’ strategy focused on protecting the best populations in the Tar River basin, 3) the ‘expand the distribution’ strategy focused on management of extant populations and establishment of new populations in the Neuse River basin, and 4) the ‘hybrid’ strategy combined elements of each strategy to balance conservation in the Tar and Neuse River basins. A population model informed requirements for population management, and experts projected performance of alternative strategies over a 20-y period. The optimal strategy depended on the relative value placed on competing objectives, which can vary among stakeholders. The protect the best and hybrid strategies were optimal across a wide range of relative values with 2 exceptions: 1) if minimizing management cost was of overriding concern, then status quo was optimal, or 2) if maximizing population persistence in the Neuse River basin was emphasized, then expand the distribution strategy was optimal. The optimal strategy was robust to uncertainty in management effectiveness. Overall, the structured decision process can help identify the most promising strategies for endangered species conservation that maximize conservation benefit given the constraint of limited funding.

North Carolina↗

USGS2016

Exploring climate niches of ponderosa pine (Pinus ponderosa Douglas ex Lawson) haplotypes in the western United States: Implications for evolutionary history and conservation

Ponderosa pine ( Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific ( P . p . var. ponderosa ) and Rocky Mountain ( P . p . var. scopulorum ) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P . p . vars. ponderosa and scopulorum , respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with discrete temporary glacial refugia. Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate.

PLoS ONE↗

USGS2022

Population genetics of three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana

Many tiger beetles (Family Cicindelidae ) are critically imperiled due to their dependence on small patches of suitable habitat that are frequently threatened by natural and anthropogenic disturbances. In the eastern United States, conservation of three tiger beetles - Habroscelimorpha dorsalis dorsalis , H. dorsalis media , and Ellipsoptera puritana - has been inhibited by the absence of population genetic information that is needed for effective recovery planning and potential reintroductions. Using microsatellite panels, we performed population genetic analyses and compared patterns in diversity and differentiation within and between taxa. Nearly all collections of the three taxa had less observed heterozygosity than expected under Hardy-Weinberg Equilibrium, and there was a strong latitudinal gradient in genetic diversity in H. d. dorsalis distributed along the eastern and western shores of the Chesapeake Bay. We also found clear spatial patterns of genetic differentiation which reflected strong isolation-by-distance within all three taxa and between collections of H. d. dorsalis and H. d. media. However, there was evidence of admixture in current (mouth of the Chesapeake Bay) and former (coastal New Jersey) contact zones of H. d. dorsalis and H. d. media . Taken together, our study suggests that relatively few adult tiger beetles may maintain many populations, and that gene flow among nearby habitat patches is common in all three taxa – a characteristic that may help tiger beetles persist in dynamic coastal environments. Results of our analyses can be used to support conservation and management by identifying the spatial scale of metapopulation connectivity and locating populations at the greatest risk of extirpation.

Maryland, Virginia↗

USGS2018

A portfolio framework for prioritizing conservation efforts for Yellowstone Cutthroat Trout populations

Managing and conserving native taxa are becoming increasingly challenging because of mounting threats and limited resources, predicating the need for frameworks to prioritize conservation actions. We integrated attributes of population persistence, genetic status, threats from nonnative species, and threats from climatic shifts to prioritize conservation actions for Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri . We used the individual attributes to rank populations and provide a framework for identifying the benefits of individual conservation actions. The majority of extant populations (57%) had a high probability (>0.75) of persistence, but nearly 70% of populations were either slightly hybridized or sympatric with nonnative species, and 44% of extant populations occupied habitat with low climatic resilience. Overall, we found that 36% of populations ranked as high (>0.75) conservation priority, and these populations primarily occupied large, relatively high‐elevation habitats. The prioritization framework provides a platform for identifying and ranking actions with the greatest conservation effectiveness.

Idaho, Montana, Nevada, Utah, Wyoming↗

USGS2023

Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods

Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.

California↗

USGS2022

Average kinship within bighorn sheep populations is associated with connectivity, augmentation, and bottlenecks

Understanding the influence of population attributes on genetic diversity is important to advancement of biological conservation. Because bighorn sheep ( Ovis canadensis ) populations vary in size and management history, the species provides a unique opportunity to observe the response of average pairwise kinship, inversely related to genetic diversity, to a spectrum of natural and management influences. We estimated average pairwise kinship of bighorn sheep herds and compared estimates with population origin (native/indigenous/extant or reintroduced), historical minimum count, connectivity, and augmentation history, to determine which predictors were the most important. We evaluated 488 bighorn sheep from 19 wild populations with past minimum counts of 16–562 animals, including native and reintroduced populations that received 0–165 animals in augmentations. Using the Illumina High Density Ovine array, we generated a dataset of 7728 single nucleotide polymorphisms and calculated average pairwise kinship for each population. Multiple linear regression analysis determined that connectivity between populations via dispersal, greater number of animals received in augmentations, and greater minimum count were correlated with lower average pairwise kinship at the population level, and whether the population was extant or reintroduced was less important. Thus, our results indicated that genetic isolation of populations can result in increased levels of inbreeding. By determining that natural and human-assisted gene flow were likely the most important influences of average pairwise kinship at the population level, this study can serve as a benchmark for future management of bighorn sheep populations and aid in identifying populations of genetic concern to define priorities for conservation of wild populations.

Montana, Wyoming↗

USGS2004

Winter philopatry of harlequin ducks in Prince William Sound, Alaska

We used capture-mark-recapture data to assess winter philopatry by Harlequin Ducks ( Histrionicus histrionicus ) in Prince William Sound, Alaska, during winters 1995–1997 and 2000–2001. Philopatry was quantified using homing rates, which were estimated as the proportion of birds recaptured at their original site out of all recaptured birds. Between-year homing rates of 0.95 (95% CI: 0.87–1.00) and 1.00 (0.92–1.00) were estimated for females and males, respectively, at three locations on Montague Island. Similar homing rates were measured in western Prince William Sound, where estimates were 0.92 (0.80–0.98) for females and 0.96 (0.79–1.00) for males, with a scale of detected movements for all recapture birds ranging from 3–52 km. Our results indicate that wintering aggregations may be demographically independent at a much finer spatial scale than genetic data indicate, and that conservation efforts should recognize this degree of demographic separation among population segments.

Alaska↗

USGS2006

Environmental Effects of Agricultural Practices - Summary of Workshop Held on June 14-16, 2005

A meeting between the U.S. Geological Survey (USGS) and its partners was held June 14-16, 2005, in Denver, CO, to discuss science issues and needs related to agricultural practices. The goals of the meeting were to learn about the (1) effects of agricultural practices on the environment and (2) tools for identifying and quantifying those effects. Achieving these goals required defining the environmental concerns, developing scientific actions to address assessment of environmental effects, and creating collaborations to identify future research requirements and technical gaps. Five areas of concern were discussed-emerging compounds; water availability; genetically modified organisms; effects of conservation practices on ecosystems; and data, methods, and tools for assessing effects of agricultural practices.

Scientific Investigations Report↗

USGS2016

Conservation status of the American horseshoe crab, (Limulus polyphemus): A regional assessment

Horseshoe crabs have persisted for more than 200 million years, and fossil forms date to 450 million years ago. The American horseshoe crab ( Limulus polyphemus ), one of four extant horseshoe crab species, is found along the Atlantic coastline of North America ranging from Alabama to Maine, USA with another distinct population on the coasts of Campeche, Yucatán and Quintana Roo in the Yucatán Peninsula, México. Although the American horseshoe crab tolerates broad environmental conditions, exploitation and habitat loss threaten the species. We assessed the conservation status of the American horseshoe crab by comprehensively reviewing available scientific information on its range, life history, genetic structure, population trends and analyses, major threats, and conservation. We structured the status assessment by six genetically-informed regions and accounted for sub-regional differences in environmental conditions, threats, and management. The transnational regions are Gulf of Maine (USA), Mid-Atlantic (USA), Southeast (USA), Florida Atlantic (USA), Northeast Gulf of México (USA), and Yucatán Peninsula (México). Our conclusion is that the American horseshoe crab species is vulnerable to local extirpation and that the degree and extent of risk vary among and within the regions. The risk is elevated in the Gulf of Maine region due to limited and fragmented habitat. The populations of horseshoe crabs in the Mid-Atlantic region are stable in the Delaware Bay area, and regulatory controls are in place, but the risk is elevated in the New England area as evidenced by continuing declines understood to be caused by over-harvest. The populations of horseshoe crabs in the Southeast region are stable or increasing. The populations of horseshoe crabs in the Florida Atlantic region show mixed trends among areas, and continuing population reductions at the embayment level have poorly understood causes. Within the Northeast Gulf of Mexico, causes of population trends are poorly understood and currently there is no active management of horseshoe crabs. Horseshoe crabs within México have conservation protection based on limited and fragmented habitat and geographic isolation from other regions, but elevated risk applies to the horseshoe crabs in the Yucatán Peninsula region until sufficient data can confirm population stability. Future species status throughout its range will depend on the effectiveness of conservation to mitigate habitat loss and manage for sustainable harvest among and within regions.

Reviews in Fish Biology and Fisheries↗

USGS2018

Genetic integrity, population status, and long-term viability of isolated populations of shoal bass in the upper Chattahoochee River basin, Georgia

This report characterizes the status of multiple isolated Shoal Bass ( Micropterus cataractae ) populations in the upper Chattahoochee River basin (UCRB), Georgia. The Shoal Bass, a sport fish endemic to the Apalachicola-Chattahoochee-Flint River (ACF) basin, is a fluvial-specialist species considered vulnerable to local extirpations and extinction due to habitat fragmentation and introgression with non-native congeners. Perhaps one of the most isolated populations of Shoal Bass exists in a 2-km reach of Big Creek, a tributary of the Chattahoochee River located near Roswell, Georgia. Big Creek is partially contained within the Chattahoochee River National Recreation Area, although the Big Creek watershed is riddled with urban land cover. Roswell Mill Dam limits the upstream extent of the Shoal Bass population at Big Creek, and the downstream extent is presumably limited to the confluence of Big Creek and the Chattahoochee River. This reach of the Chattahoochee River is thermally depressed because of coldwater releases from Lake Lanier, and is considered unsuitable for Shoal Bass. Herein, we examine the genetic integrity, population status, and long-term viability of the Shoal Bass population in Big Creek. We also examine two additional Shoal Bass populations that occur in the UCRB, specifically the Chestatee River and the upper Chattahoochee River, both of which are impounded at Lake Lanier. Together, the Shoal Bass inhabiting these three stream systems comprise a distinct genetic stock of Shoal Bass (Taylor 2017), underscoring the importance of conserving these populations towards maintaining the overall diversity and adaptive potential of the species. We assessed genetic diversity and estimated effective population sizes within these three rivers by genotyping fish with 16 microsatellite DNA markers. Results demonstrated that the Shoal Bass population in Big Creek has experienced high rates of introgression with non-native Smallmouth Bass (M. dolomieu), purportedly introduced into the Chattahoochee River in the past 10-15 years. Alarmingly, only 24% (15 of 62) of putative Shoal Bass collected from Big Creek were genetically pure Shoal Bass, whereas the majority of fish were first-filial (F1) generation hybrids and unidirectional backcrosses towards Shoal Bass. Fleeting opportunity may remain to conserve the native genome of the Shoal Bass population in Big Creek. High hybridization rates prevented genetic diversity analysis for the Big Creek population. Shoal Bass populations in the Chestatee and Chattahoochee rivers displayed levels of genetic diversity similar to populations that persist in other rivers in the ACF basin, namely the Flint and Chipola rivers. Effective population sizes of 93.8– 197.4 for the Chestatee and Chattahoochee rivers (combined) suggest that the conservation status of these populations is stable for the short-term, but may be at risk of losing genetic diversity and adaptive potential in the long-term. To estimate age and mortality of the three populations, we used fish scales and capture-markrecapture (CMR) as complementary, non-lethal methods for age estimation. Estimated ages of phenotypic Shoal Bass ranged from 1-12 years in all three populations, demonstrating increased longevity compared to populations elsewhere within the native range. Catch-curve estimates of annual mortality ranged from 18.4-23.7%, which are markedly lower than those observed in other Shoal Bass populations in the ACF basin. These differences in life-history characteristics underscore the need for the development of population-specific management and conservation strategies for Shoal Bass in the UCRB. The lowest recruitment variability (i.e., the variation in year-class strength) was observed in the Chestatee River, a forested watershed, whereas the highest variability was observed in Big Creek, an urbanized watershed. Recruitment strength in Big Creek was negatively influenced by discharge variability in the summer months, suggesting that flashy, sediment-laden flows hinder survival of recently hatched young. Other statistically significant models from Big Creek and the Chattahoochee River indicated that over-winter survival could be an important pinch-point for recruitment in UCRB populations. A multi-agency sampling effort was conducted from May 2013-May 2016 to estimate the population size of Shoal Bass occupying the 1-km of wadeable shoal habitats in Big Creek. Using CMR models, we estimated that approximately 219-348 Shoal Bass (≥ 70 mm total length) occupied the area throughout the duration of our study. These estimates largely reflect abundance of individuals aged 0-2 years, as only 9% (36 of 408) tagged fish were aged ≥ 7 years. Local abundance appeared similar to that reported for a population that inhabited Little Uchee Creek, a similar-sized tributary of the Chattahoochee River, prior to its recent functional extirpation. The low abundance of large, adult Shoal Bass further suggests the long-term viability of the Big Creek population may be in jeopardy. Perhaps most importantly, CMR estimates reflect abundance of phenotypic Shoal Bass – genetic analyses suggest the abundance of pure Shoal Bass could be an order of magnitude smaller. To evaluate the potential for adult Shoal Bass to emigrate from Big Creek into the mainstem Chattahoochee River, we tagged eight adults with acoustic telemetry tags and assessed their seasonal residency at two stationary receiver locations located in increasing proximity to the confluence with the Chattahoochee River. Fish took up residency near the confluence during the fall and winter months, during which time water temperatures in Big Creek were periodically colder than the Chattahoochee River. Although we were unable to document emigration, we conclude that the potential for emigration is highest during the winter months when the Chattahoochee River may be warmer than Big Creek. Two of the tagged fish were caught by anglers near the confluence, suggesting that angling pressure at Big Creek may be higher than previously suspected. Overall, this study observed unique life-history characteristics and characterized the population status of multiple Shoal Bass populations in the UCRB. Populations in the Chestatee and Chattahoochee rivers appear stable at present and likely represent the last remaining strongholds for pure Shoal Bass in the UCRB. Efforts to preserve forested watershed conditions, natural hydrology, and shoal habitats would contribute to the long-term persistence of Shoal Bass populations in these two rivers. Additionally, the detection of non-native Alabama Bass and their associated hybrids in both rivers is cause for concern. Diligent monitoring of hybridization dynamics between Alabama Bass and Shoal Bass is warranted, along with an assessment of Alabama Bass invasion extent upstream of Lake Lanier. The Shoal Bass population in Big Creek is threatened by elevated levels of introgression with nonnative Smallmouth Bass, recruitment variability, low abundance of adults, and isolation from other populations. Conservation intervention is urgently needed to restore and preserve this genetically distinct population, which would contribute to preservation of range wide genetic diversity and adaptability of the species. Additionally, an urban sport fishery for Shoal Bass at Big Creek has the potential to serve as a tool for increasing public awareness, engagement, and support of Shoal Bass conservation efforts in the UCRB. We suggest strategies for conservation of the remnant shoal habitats and Shoal Bass population in Big Creek, including potential development of a supplemental stocking program, selective removal of non-native congeners, and delivery of environmental education programs that could bolster awareness and appreciation.

Georgia↗

USGS2013

Population genetic structure of rare and endangered plants using molecular markers

This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different k ī puka and 96% when individuals were pooled from all k ī puka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different k ī puka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings, approaches that can assist conservation efforts of these species are proposed.

Hawai`i↗

USGS2013

Interspecific hybridization contributes to high genetic diversity and apparent effective population size in an endemic population of mottled ducks (Anas fulvigula maculosa)

Under drift-mutation equilibrium, genetic diversity is expected to be correlated with effective population size (N e ). Changes in population size and gene flow are two important processes that can cause populations to deviate from this expected relationship. In this study, we used DNA sequences from six independent loci to examine the influence of these processes on standing genetic diversity in endemic mottled ducks ( Anas fulvigula ) and geographically widespread mallards ( A. platyrhynchos ), two species known to hybridize. Mottled ducks have an estimated census size that is about two orders-of-magnitude smaller than that of mallards, yet these two species have similar levels of genetic diversity, especially at nuclear DNA. Coalescent analyses suggest that a population expansion in the mallard at least partly explains this discrepancy, but the mottled duck harbors higher genetic diversity and apparent N e than expected for its census size even after accounting for a population decline. Incorporating gene flow into the model, however, reduced the estimated N e of mottled ducks to 33 % of the equilibrium N e and yielded an estimated N e consistent with census size. We also examined the utility of these loci to distinguish among mallards, mottled ducks, and their hybrids. Most putatively pure individuals were correctly assigned to species, but the power for detecting hybrids was low. Although hybridization with mallards potentially poses a conservation threat to mottled ducks by creating a risk of extinction by hybridization, introgression of mallard alleles has helped maintain high genetic diversity in mottled ducks and might be important for the adaptability and survival of this species.

Conservation Genetics↗