Geology topics

Elizabeth R. Milano

Publications and source records attributed to Elizabeth R. Milano.

7 recordsLinked to original sources

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↗

USGS2024

Bay Miwok evening primrose: A new subspecies of Oenothera deltoides (Onagraceae) endemic to California

California contains exceptional biodiversity in geography and plant life, including numerous endemic species, some of which are cryptic. The Oenothera deltoides Torr. & Frém. species complex represents a prime example of cryptic diversity. Here, we recognize a new subspecies of Oenothera deltoides , O. deltoides subsp. julpunensis S.F.Jones, subsp. nov., that is a local endemic of windblown sand deposits on the eastern Antioch Dunes sand sheet in the San Francisco Bay-Delta region of California, USA. With the goal of providing clarity to managers of listed species and better understanding of California's diverse flora, we addressed the puzzle of O. deltoides in the region by combining range-wide field surveys with modern genomic tools. We describe the proposed subspecies, its ecology and distribution, and discuss its conservation. As a somewhat cryptic local endemic with small population size and disappearing habitat, the proposed subspecies would benefit from conservation and management to persist as a member of the California flora.

California↗

USGS2023

Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California

Whitebark pine ( Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.

California, Nevada↗

USGS2023

The energy–water limitation threshold explains divergent drought responses in tree growth, needle length, and stable isotope ratios

Predicted increases in extreme droughts will likely cause major shifts in carbon sequestration and forest composition. Although growth declines during drought are widely documented, an increasing number of studies have reported both positive and negative responses to the same drought. These divergent growth patterns may reflect thresholds (i.e., nonlinear responses) promoted by changes in the dominant climatic constraints on tree growth. Here we tested whether stemwood growth exhibited linear or nonlinear responses to temperature and precipitation and whether stemwood growth thresholds co-occurred with multiple thresholds in source and sink processes that limit tree growth. We extracted 772 tree cores, 1398 needle length records, and 1075 stable isotope samples from 27 sites across whitebark pine's ( Pinus albicaulis Engelm.) climatic niche in the Sierra Nevada. Our results indicated that a temperature threshold in stemwood growth occurred at 8.4°C (7.12–9.51°C; estimated using fall-spring maximum temperature). This threshold was significantly correlated with thresholds in foliar growth, as well as carbon (δ 13 C) and nitrogen (δ 15 N) stable isotope ratios, that emerged during drought. These co-occurring thresholds reflected the transition between energy- and water-limited tree growth (i.e., the E–W limitation threshold). This transition likely mediated carbon and nutrient cycling, as well as important differences in growth-defense trade-offs and drought adaptations. Furthermore, whitebark pine growing in energy-limited regions may continue to experience elevated growth in response to climate change. The positive effect of warming, however, may be offset by growth declines in water-limited regions, threatening the long-term sustainability of the recently listed whitebark pine species in the Sierra Nevada.

Global Change Biology↗

USGS2022

Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation

Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica , is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. Lack of congruence among morphological subspecies hypotheses and lack of measurable genetic structure found in a few genetic markers led to questions about the validity of subspecies within P. californica and the listing status of the coastal California gnatcatcher, P. c. californica . As a U.S. federally threatened subspecies, P. c. californica is recognized as a flagship for coastal sage scrub conservation throughout southern California. We used restriction site-associated DNA sequencing to develop a genomic dataset for the California gnatcatcher. We sampled throughout the species' range, examined genetic structure, gene–environment associations, and demographic history, and tested for concordance between genetic structure and morphological subspecies groups. Our data support two distinct genetic groups with evidence of restricted movement and gene flow near the U.S.- Mexico international border. We found that climate-associated outlier loci were more strongly differentiated than climate neutral loci, suggesting that local climate adaptation may have helped to drive differentiation after Holocene range expansions. Patterns of habitat loss and fragmentation are also concordant with genetic substructure throughout the southern California portion of the range. Finally, our genetic data supported the morphologically defined P. c. californica as a distinct group, but there was little evidence of genetic differentiation among other previously hypothesized subspecies in Baja California. Our data suggest that retaining and restoring connectivity, and protecting populations, particularly at the northern range edge, could help preserve existing adaptive potential to allow for future range expansion and long-term persistence of the California gnatcatcher.

California↗

USGS2020

High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California

Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and habitat loss with concomitant losses of genetic diversity and connectivity. Remaining salt marshes are threatened by rising sea levels, and so these habitats will likely require active restoration and re-establishment efforts. This study aims to provide a reference point for the current status of genetic diversity and range-wide population structure of a federally and state listed endangered plant, Salt Marsh Bird’s Beak (Chloropyron maritimum subsp. maritimum) that can inform future preservation and restoration efforts. We used historical data and current monitoring information to locate and sample all known occurrences throughout the species range in Southern California, and three additional occurrences from Baja California, Mexico. We used flow cytometry and single nucleotide polymorphic markers (SNPs), generated by double-digest restriction-site associated DNA sequencing (ddRAD), to assess relative ploidy, and estimate genetic diversity and population structure across the region. Overall, we found four to five distinct genetic clusters that coincide with geographic regions. Genetic diversity was greatest in the southern part of the range including Baja California and San Diego. These findings can bolster management and restoration efforts by identifying potentially isolated occurrences and areas that are rich sources of allelic diversity, and by providing insight into the amount of genetic differentiation across the species range.

California↗

USGS2018

Population genomic surveys for six rare plant species in San Diego County, California

San Diego County is a hotspot of biodiversity, situated at the intersection of the Baja peninsula, the California floristic province, and the desert southwest. This hotspot is characterized by a high number of rare and endemic species, which persist alongside a major urban epicenter. San Diego County has implemented a strategic management plan that identifies species, based on low numbers of occurrences or high level of threat, for which management practices are recommended. In creating a management plan for rare species, it is important to strike a balance between preserving locally adapted traits and maintaining genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat fragmentation. This project, in partnership with the San Diego Natural History Museum, aims to provide a reference point for the current status of genetic diversity of rare plant species that will inform future preservation and restoration efforts. We focused on six threatened or endangered plant species: Acanthomintha ilicifolia , Baccharis vanessae , Chloropyron maritimum ssp. maritimum , Deinandra conjugens , Dicranostegia orcuttiana , and Monardella viminea . For each species, botanists from the San Diego Natural History Museum visited all known occurrences in San Diego County and collected leaf tissue for genetic and cytological analysis. We then developed a panel of genetic markers to estimate genetic diversity and population structure. This population genetic survey provided insight into the amount of genetic differentiation across each species’ range, identified isolated occurrences potentially subject to inbreeding or genetic bottlenecks, and identified areas that are rich sources of allelic diversity. Finally, we convened a panel of experts to review results and compatible management options for each species. A summary of the management workshop is included in this report. Overall, we found low genetic differentiation among occurrences across the San Diego region for all species, with the exception of A. ilicifolia . Relative inbreeding was low and consistent across sites, and genetic diversity across sites was variable, with noted exceptions. These findings allow for a wide array of management options that are compatible with panmictic population structure in five of the six surveyed species.

California↗