Geology topics

Julia G. Smith

Publications and source records attributed to Julia G. Smith.

7 recordsLinked to original sources

USGS2026

Genetic analysis of Harbison’s Dun Skipper to inform population management and restoration on conserved lands in San Diego County

This report details the development and analysis of single nucleotide polymorphic loci to understand population genetic structure and diversity among local populations of the Harbison’s dun skipper, Euphyes vestris harbisoni , primarily in San Diego County, California, USA. We developed a set of 2984 SNPs. Local populations were clustered into two to three regional genetic clusters throughout the San Diego County study area: a southeast cluster, an admixed northeast cluster, and a cluster comprised of the two local populations sampled west of Interstate 15 in Lake Hodges and Elfin Forest. Increasing genetic isolation with geographic distance was significant among local populations. While effective population size estimates calculated for the 2016 cohorts in the Southeast and Lake Hodges clusters were both high (point estimates above 500), individual heterozygosity appeared to decline in both clusters over time, and notably so in the Lake Hodges cluster after 2016, suggesting that this cluster may have lost genetic diversity over time. The Southeast cluster appears to have the highest observed heterozygosity across all surveyed areas, but sample sizes in the Northeast cluster were low which may affect these estimates. Future collection efforts may benefit from additional sampling in the Northeast cluster to improve representation. The management plan for Harbison’s dun skipper encourages restoration and re-establishment efforts in unoccupied or recently extirpated sites, particularly in the central portion of the range. Re-establishment efforts could target individuals from large and annually stable local populations in the Southeast portion of the range for transplant, as these populations were also the most genetically diverse.

California↗

USGS2025

Phylogenomics of endangered troglobiotic rove beetles (Coleoptera: Staphylinidae: Pselaphinae) from central Texas karst regions

The karst habitats of central Texas, USA, are home to an array of endemic subterranean-obligate (troglobiotic) invertebrates. This includes several species of rove beetles (Coleoptera: Staphylinidae: Pselaphinae). Here we developed a molecular dataset using sequence capture of Ultra-Conserved Elements (UCEs) from the Coleoptera-UCE-1.1 K v1 baits kit. These data were used to assess species relationships and patterns of diversification in this group, specifically among species within the genera Batrisodes Reitter 1882 and Texamaurops Barr and Steeves 1963 ; with a specific focus on the relationships of the federally listed as endangered B. texanus Chandler 1992 and B.cryptotexanus Chandler and Reddell 2001 . Our final datasets consisted of 69 individuals (two genera, Batrisodes [five species] and Texamaurops [one species], from 34 localities), and a molecular dataset of 658,560 aligned base pairs across 672 UCE loci. Concatenated and species-tree phylogenetic analyses resolved all troglobiotic taxa as a monophyletic group. Within the Travis and Williamson County troglobionts, we recovered four well-supported clades that generally follow hypothesized geologic barriers to dispersal formalized as karst fauna regions (KFRs). A northward pattern of diversification was observed among these groups: (A) Texamaurops reddelli Barr and Steeves 1963 (Jollyville Plateau KFR); (B) Batrisodes reyesi Chandler 1997 (West Cedar Park and Post Oak Ridge KFRs); (C) B. reyesi (McNeil-Round Rock KFR); (D) B. cryptotexanus + B. texanus (Georgetown and North Williamson KFRs). The morphologically defined Batrisodes texanus and B. cryptotexanus were not reciprocally monophyletic, nor clustered into two unique groups in clustering analyses of single nucleotide polymorphisms (SNPs). Rather, we found support for five major subclades and five to seven genetic clusters. These results suggest that diversification and subsequent isolation of clades may have occurred with the progressive availability of karst habitats over time in the North Williamson and Georgetown KFRs resulting from the interactions of faulting, geologic structure, and drainage basin evolution. Comparison with recent U.S. Fish and Wildlife Service cave habitat resiliency assessments indicated that four genetic clusters occur within at least partially resilient habitat, whereas three are confined to caves with low or impaired resiliency. Integrating genetic results presented here along with results of other molecular studies of co-occurring troglobiotic invertebrates supports considering additional geological substructure within the North Williamson KFR in conservation efforts for these rare and unique lineages and systems.

Texas↗

USGS2025

Genetic structure and diversity in wild populations of the Light-footed Ridgway’s Rail reflect 20 years of augmentation through captive breeding and release

Captive breeding and release programs aimed at recovery of rare species can be informed by genetic data to help select high-diversity source populations, make pairing decisions to minimize inbreeding, and manage release strategies. We developed a set of 54 microsatellite loci to assess genetic structure and diversity across the United States range of the Light-footed Ridgway’s Rail ( Rallus obsoletus levipes ), a federally endangered marsh bird for which populations have been augmented by a captive breeding program annually since 2001. We identified three regional genetic clusters, with the highest genetic diversity reported in the central cluster, which included all sampled wetlands in north San Diego County. Recent (2019–24) captive-breeding adults all clustered within the northernmost cluster (Orange and Ventura Counties), which was expected given that this cluster included the source wetland for the captive breeding program. Gene flow rates, which approximate the proportions of individuals in a population originating from other populations, were relatively high among clusters (4–24 percent) and may have been enhanced through the release of captive-bred rails. Based on the genetic data analyzed in a genetic rescue decision framework, sourcing new breeding birds from the north San Diego County cluster could provide the greatest genetic diversity benefits. The northernmost cluster, which included Mugu Lagoon and all sampled Orange County wetlands, was considered the most in need of genetic rescue. Recent breeding pairs in the captive breeding program have comparatively low diversity and high interrelatedness. Sourcing birds from wetlands with high genetic diversity and population sizes, assessing genetic relatedness before pairing, and focusing releases in areas that have low estimates of genetic diversity could improve the distribution of genetic diversity across wild populations in the future.

California↗

USGS2024

High inter-population connectivity and occasional gene flow between subspecies improves recovery potential for the endangered Least Bell’s Vireo

Increasingly, genomic data are being used to supplement field-based ecological studies to help evaluate recovery status and trends in endangered species. We collected genomic data to address two related questions regarding the Least Bell’s Vireo ( Vireo bellii ), an endangered migratory songbird restricted to southern California riparian habitat for breeding. First, we sought to delineate the range limits and potential overlap between Least Bell’s Vireo and its sister subspecies, the Arizona Bell’s Vireo, by analyzing samples from the deserts of eastern California, southwestern Nevada, Utah and Arizona. Second, we evaluated genetic structure among Least Bell’s Vireo populations in coastal California and estimated effective population size. Clustering analyses based on 10,571 single nucleotide polymorphisms (SNPs) from 317 samples supported two major groups that aligned closely to the previously defined subspecies ranges. The first cluster included birds in the Central Valley, all coastal drainages, and westernmost deserts of California, with no further sub-structuring among coastal drainages. Almost all birds from the Amargosa River in eastern California and eastward assigned to the second cluster; however, low levels of gene flow were detected across the subspecies groups, with greater rates of gene flow from Arizona Bell’s Vireo to Least Bell’s Vireo than the reverse. Admixed individuals occurred in the California deserts; and although smaller than coastal populations, desert populations may be important for maintaining and replenishing genetic diversity and facilitating the movement of potentially adaptive genes between subspecies. Within Least Bell’s Vireo, local populations in coastal drainages comprised a single genetic population, with some evidence of close relatives distributed across drainages, suggesting these could function as a well-connected metapopulation. These results are consistent with previous Least Bell’s Vireo banding studies that reported high rates of dispersal among drainages. Effective population size for both subspecies was high, suggesting that adaptive potential has been maintained despite previous declines.

Ornithological Applications↗

USGS2022

Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California

Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren ( Campylorhynchus brunneicapillus ) in San Diego County in 2011–2012 and again in 2017–2019, using 22 microsatellite loci. We found a significant decline in heterozygosity in one population (San Pasqual) and a decline in allelic richness and effective population size in another (Sweetwater). Genetic diversity in the remaining two populations was not significantly different over time. Local diversity declined despite evidence of dispersal among some populations. Approximately 12% of genetically determined family groups (parents, offspring, siblings) included one or more members sampled in different territories with distances ranging from 0.2 to 10 km. All but one inferred dispersal events occurred within the same genetic population. Population structure remained relatively stable, although genetic differentiation tended to increase in the later sampling period. Simulations suggest that at currently estimated effective sizes, populations of Cactus Wrens will continue to lose genetic diversity for many generations, even if gene flow among them is enhanced. However, the rate of loss of heterozygosity could be reduced with increased gene flow. Habitat restoration may help bolster local population sizes and allelic richness over the long term, whereas translocation efforts from source populations outside of San Diego may be needed to restore genetic diversity in the short term.

California↗

USGS2019

DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)

Throughout the western United States, efforts are underway to better understand and preserve migration and movement corridors for mule deer and other big game and to minimize the impacts of development and other land-use change on populations. San Diego County is home to a unique non-migratory subspecies of mule deer, the Southern mule deer ( Odocoileus hemionus fuliginatus ; herein referred to as “mule deer”). Because it is the only large herbivorous mammal in San Diego, connectivity among mule deer groups is an important indicator of functional connectivity throughout San Diego County urban preserves and has therefore been monitored within central and eastern San Diego County using DNA fingerprinting since 2005. To continue this effort and to assess genetic connectivity in north San Diego County (herein “North County”), we genotyped scat samples from preserves in the area and tissue samples from Marine Corps Base Camp Pendleton (MCBCP). We used non-invasive capture/recapture analyses and pedigree analyses for assessing short-term movement and population clustering analyses to assess gene flow in North County. Additionally, we performed similar analyses on the combined San Diego County dataset, which was composed of the North County dataset collected for this study and a previously collected dataset from central and eastern San Diego County. Using recapture data, we found multiple instances of mule deer crossing roads in urban North County preserves, with several of these events occurring in areas where there are underpasses and culverts known to be used by mule deer. Corroborating previous studies in the region and statewide, pedigree and population structure analyses support the presence of two genetic clusters for mule deer in San Diego County—the “Coastal” and “Inland/Mountain” clusters. Low estimates of effective population size, especially in the Coastal cluster, suggest that to further understand potential vulnerabilities of mule deer in this region, it is important to continue to monitor connectivity, in particular, at the boundary between these two clusters.

California↗

USGS2019

Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard ( Uma inornata )

The Coachella Valley fringe-toed lizard ( Uma inornata ) is a federally threatened, aeolian sand dune obligate, endemic to the Coachella Valley, California. Historically, U. inornata is thought to have formed a large interconnected metapopulation across the valley, with local dune habitat and population size fluctuations linked to stochastic droughts and flooding. Since the 1950s, aeolian habitat in Coachella Valley has declined by 91–95 percent. What remains is highly fragmented by highways and development in the urban communities of the Coachella Valley, raising concerns that fringe-toed lizard movement and gene flow among remaining habitat fragments is limited or nonexistent. We examined population genetic structure across three sample periods (1996, 2008, and 2017). Over that time, this species has shifted from a panmictic condition (1996) with little or no genetic structure between sites to the current (2017) condition where there are now genetically distinct populations. Two severe droughts (2000–04 and 2012–16) may have accelerated this shift through drought-related population declines and subsequent genetic bottlenecks. Using a combination of microsatellite loci and single nucleotide polymorphisms, we found patterns of decreasing genetic connectivity and diversity over time. These patterns are consistent with reduced fringe-toed lizard movement and gene flow among isolated sand dune systems. Low effective population sizes were recovered in some sites, suggesting genetic drift in smaller and fluctuating populations is likely responsible for loss of genetic diversity. A U.S. Fish and Wildlife Service recovery objective for this species is to maintain genetic diversity; however, evidence of fragmentation suggests that genetic cohesiveness has been altered and that the diversity maintained in individual fragments is lower than in the total metapopulation. Management actions that increase genetic diversity could be implemented, including translocation. We modeled increasing gene flow between 1–10 percent, which showed that allelic richness could increase rapidly if translocated individuals can survive and reproduce. Establishing translocation protocols could help to avoid the high mortality that has occurred with other reptile translocations. Successful translocations could be a useful strategy to replenish lost genetic diversity after bottlenecks and could mitigate the loss of natural gene flow among populations.

California↗