In the western United States (U.S.), there are many regionally restricted, rare species resulting from complex demographic and ecological processes through time. In addition to the inherent risks associated with being rare (i.e., having few individuals spread over a limited area that could be disproportionately affected by chance events), anthropogenic disturbances are increasing in magnitude across the region (e.g., energy extraction activities, recreation, livestock, invasive species).
These disturbances can threaten the continued persistence of rare species by diminishing habitat, altering ecosystem properties, and changing the climate. Thus, the need to document the historical and contemporary properties of and project the future impacts on rare species is critical. Examples of Genetics for Western Restoration and Conservation (GWRC) group research that facilitates the conservation of species across the western U.S. are highlighted below.
Genetics for Western Restoration and Conservation (GWRC) research highlights:
Connectivity across the fragmented distribution of Graham’s beardtongue: investigating the factors influencing gene flow
Graham’s beardtongue (Penstemon grahamii) is a narrowly endemic flowering plant distributed across the Green River geologic formation in the Uinta Basin, Utah. The Green River formation is also an important substrate indicating deposits of energy resources, and development for extraction activities is a common land disturbance.
We performed high throughput DNA sequencing to 1) examine population genetic structure across the species’ range and 2) estimate how genetic diversity and rates of gene flow are influenced by various landscape features (e.g., climate, soil, and habitat disturbance).
Knowledge of these biological processes may help managers prioritize the protection of important areas of the species’ range to support its continued persistence.
Assessing patterns of genetic differentiation and interactions among rare, closely related milkvetch species
Milkvetches (i.e., plants in the genus Astragalus) comprise the most diverse genus of flowering plants in the world, and many endemic and rare milkvetch species are distributed across the western U.S. A clade of two of these species—Astragalus sabulosus (composed of varieties sabulosus and vehiculus) and A. iselyi—occupies a narrow distribution in southeastern Utah.
The distributions of these species and varieties do not overlap, yet they share morphological characteristics that suggest close evolutionary relationships. Given their limited distributions, small population sizes, and impending listing decisions under the U.S. Endangered Species Act, we used genomic data to determine: 1) the rate of gene flow among these taxa; 2) how long they have been isolated from one another; 3) how much genetic diversity is present across each taxon’s range; 4) if signatures of inbreeding depression exist; and 4) whether taxa harbor unique, adaptive genetic variation.
Additional GWRC projects:
Navajo sedge (Carex specuicola)
This rare sedge grows where water trickles out of Navajo sandstone and is found in “hanging gardens” on the Navajo Nation in Arizona and Utah. Given this restricted, often disconnected habitat, it is unknown how gene flow affects the genetic identity of plants, and thus how the plant should be managed to protect patterns of genetic diversity.
Arizona willow (Salix arizonica)
Arizona willow has few, widely scattered populations across Arizona, New Mexico, Colorado, and Utah. Not only do these geographic distances make it unlikely that gene flow occurs among populations, but the populations persist across a range of environmental conditions, suggesting the possibility of local adaptation. In addition, gene flow may occur with closely related species, necessitating a genomic perspective to inform appropriate management actions.
Pagosa skyrocket (Ipomopsis polyantha)
Pagosa skyrocket persists in two close but disconnected locations in southwestern Colorado. One location has hundreds of thousands of individuals, while the other only has hundreds. Given that the travel distance of known pollinators is not expected to be far enough to facilitate pollination between the two locations, it is unknown how genetically differentiated the populations are or if the smaller population is genetically healthy (i.e., retains sufficient genetic diversity and has low levels of inbreeding).
Arizona cliffrose (Purshia subintegra)
The endangered Arizona cliffrose is known from four populations across central Arizona. However, previous research suggested that of these four populations, one was a distinct species, Purshia pinkavae, while the remaining three resulted from hybridization events (P. pinkavae x P. stansburiana). While these analyses were informative for the management of P. subintegra, they raised additional questions that need to be addressed before appropriate management actions can be determined. Outstanding questions revolve around the timing of hybridization events that led to the creation of three of the P. subintegra populations, the ongoing nature of gene flow between P. subintegra and P. stansburiana where their ranges overlap, and relationships among P. subintegra, P. stansburiana, and other regional taxa in the genus.
Below are other science projects associated with this project.
Informing seed transfer guidelines and native plant materials development: Research supporting restoration across the Colorado Plateau and beyond
Genetics for Western Restoration and Conservation (GWRC)
Data for the research can be accessed by following the links below.
Carex specuicola genomic data for the southern Colorado Plateau Desert
Penstemon grahamii genetic data from a dryland region of the western United States
Astragalus species complex genetic data from southeast Utah (Grand County and San Juan County), USA
Genetic analyses of Astragalus sect. Humillimi data in the southwest USA
Journal articles for genomic research supporting western conservation can be found at the links below.
Evolutionary dynamics inform management interventions of a hanging garden obligate, Carex specuicola
Spatially explicit management of genetic diversity using ancestry probability surfaces
Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue
The demographic and ecological factors shaping diversification among rare Astragalus species
Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species
Genetic analyses of Astragalus sect. Humillimi (Fabaceae) resolve taxonomy and enable effective conservation
POPMAPS: An R package to estimate ancestry probability surfaces
This research is supported by many partners.
- Overview
In the western United States (U.S.), there are many regionally restricted, rare species resulting from complex demographic and ecological processes through time. In addition to the inherent risks associated with being rare (i.e., having few individuals spread over a limited area that could be disproportionately affected by chance events), anthropogenic disturbances are increasing in magnitude across the region (e.g., energy extraction activities, recreation, livestock, invasive species).
These disturbances can threaten the continued persistence of rare species by diminishing habitat, altering ecosystem properties, and changing the climate. Thus, the need to document the historical and contemporary properties of and project the future impacts on rare species is critical. Examples of Genetics for Western Restoration and Conservation (GWRC) group research that facilitates the conservation of species across the western U.S. are highlighted below.
Graham’s beardstongue (Penstemon grahamii) on the Green River Formation in the Uinta Basin, UT. (Credit: Daniel Winkler, USGS Southwest Biological Science Center. Public domain.) Genetics for Western Restoration and Conservation (GWRC) research highlights:
Connectivity across the fragmented distribution of Graham’s beardtongue: investigating the factors influencing gene flow
Graham’s beardtongue (Penstemon grahamii) is a narrowly endemic flowering plant distributed across the Green River geologic formation in the Uinta Basin, Utah. The Green River formation is also an important substrate indicating deposits of energy resources, and development for extraction activities is a common land disturbance.
We performed high throughput DNA sequencing to 1) examine population genetic structure across the species’ range and 2) estimate how genetic diversity and rates of gene flow are influenced by various landscape features (e.g., climate, soil, and habitat disturbance).
Knowledge of these biological processes may help managers prioritize the protection of important areas of the species’ range to support its continued persistence.
Assessing patterns of genetic differentiation and interactions among rare, closely related milkvetch species
Milkvetches (i.e., plants in the genus Astragalus) comprise the most diverse genus of flowering plants in the world, and many endemic and rare milkvetch species are distributed across the western U.S. A clade of two of these species—Astragalus sabulosus (composed of varieties sabulosus and vehiculus) and A. iselyi—occupies a narrow distribution in southeastern Utah.
The distributions of these species and varieties do not overlap, yet they share morphological characteristics that suggest close evolutionary relationships. Given their limited distributions, small population sizes, and impending listing decisions under the U.S. Endangered Species Act, we used genomic data to determine: 1) the rate of gene flow among these taxa; 2) how long they have been isolated from one another; 3) how much genetic diversity is present across each taxon’s range; 4) if signatures of inbreeding depression exist; and 4) whether taxa harbor unique, adaptive genetic variation.
Navajo sedge (Carex specuicola) growing in a hanging garden (to left growing out of sandstone rock face) near the Inscription House site on the Navajo Nation, AZ. (Credit: Rob Massatti, USGS Southwest Biological Science Center. Public domain.) Additional GWRC projects:
Navajo sedge (Carex specuicola)
This rare sedge grows where water trickles out of Navajo sandstone and is found in “hanging gardens” on the Navajo Nation in Arizona and Utah. Given this restricted, often disconnected habitat, it is unknown how gene flow affects the genetic identity of plants, and thus how the plant should be managed to protect patterns of genetic diversity.
Arizona willow (Salix arizonica)
Arizona willow has few, widely scattered populations across Arizona, New Mexico, Colorado, and Utah. Not only do these geographic distances make it unlikely that gene flow occurs among populations, but the populations persist across a range of environmental conditions, suggesting the possibility of local adaptation. In addition, gene flow may occur with closely related species, necessitating a genomic perspective to inform appropriate management actions.
Pagosa skyrocket (Ipomopsis polyantha)
Pagosa skyrocket persists in two close but disconnected locations in southwestern Colorado. One location has hundreds of thousands of individuals, while the other only has hundreds. Given that the travel distance of known pollinators is not expected to be far enough to facilitate pollination between the two locations, it is unknown how genetically differentiated the populations are or if the smaller population is genetically healthy (i.e., retains sufficient genetic diversity and has low levels of inbreeding).
Arizona cliffrose (Purshia subintegra)
The endangered Arizona cliffrose is known from four populations across central Arizona. However, previous research suggested that of these four populations, one was a distinct species, Purshia pinkavae, while the remaining three resulted from hybridization events (P. pinkavae x P. stansburiana). While these analyses were informative for the management of P. subintegra, they raised additional questions that need to be addressed before appropriate management actions can be determined. Outstanding questions revolve around the timing of hybridization events that led to the creation of three of the P. subintegra populations, the ongoing nature of gene flow between P. subintegra and P. stansburiana where their ranges overlap, and relationships among P. subintegra, P. stansburiana, and other regional taxa in the genus.
- Science
Below are other science projects associated with this project.
Informing seed transfer guidelines and native plant materials development: Research supporting restoration across the Colorado Plateau and beyond
As restoration needs for natural landscapes grow due to higher frequency and/or intensity disturbances, pressure from invasive species, and impacts resulting from changing climates, considerable time and resources are being invested to guide the development and deployment of native plant materials (NPMs). Across lower elevations of the Colorado Plateau, a region composed primarily of public land...Genetics for Western Restoration and Conservation (GWRC)
Research using genetic principles, methods, and data provides critical information for restoration and conservation science. Genetic research may rely only upon genomic sequencing techniques, which generate abundant, genome-wide DNA sequences that can provide a glimpse into a species’ evolutionary history and adaptations. Genetic research may also look at an organism’s physical traits to... - Data
Data for the research can be accessed by following the links below.
Carex specuicola genomic data for the southern Colorado Plateau Desert
These data were compiled to investigate the demographic and phylogeographic of Carex specuicola. Objectives of our study were to understand the demographic and dispersal history of Carex specuicola across hanging gardens, the hybridization history between Carex specuicola and Carex utahensis, and the population structure of Carex specuicola across its distribution. The data release consists of thrPenstemon grahamii genetic data from a dryland region of the western United States
These data were compiled to investigate the evolutionary history of Graham's beardtongue (Penstemon grahamii). Objective(s) of our study were to determine the evolutionary history of P. grahamii, including ancestral population sizes, the history of population divergences, and historical connectivity. In addition, we characterized population structure, genetic diversity summary statistics, and landAstragalus species complex genetic data from southeast Utah (Grand County and San Juan County), USA
These data were compiled to investigate the evolutionary history of Astragalus iselyi, A. sabulosus var. sabulosus, and A. sabulosus var. vehiculus. The data release consists of six text files. One file is a bash script (astragalus_MLE_msms.sh) for generating simulated genetic data. Four files contain individual-level (astragalus.fasta, astragalus.nothin.recode.vcf, astragalus.recode.vcf) or populGenetic analyses of Astragalus sect. Humillimi data in the southwest USA
These data were compiled to support effective conservation for species within Astragalus sect. Humillimi. Two species, A. cremnophylax var. cremnophylax and A. humillimus are federally listed as endangered taxa. The data provided herein were used to resolve the relationaships among taxa, the population structure within taxa, and genetic diversity within taxa. The data are provided in a STRUCTURE-f - Publications
Journal articles for genomic research supporting western conservation can be found at the links below.
Evolutionary dynamics inform management interventions of a hanging garden obligate, Carex specuicola
Uncovering the historical and contemporary processes shaping rare species with complex distributions is of growing importance due to threats such as habitat destruction and climate change. Species restricted to specialized, patchy habitat may persist by virtue of life history characteristics facilitating ongoing gene flow and dispersal, but they could also reflect the remnants of formerly widespreAuthorsKenneth James Chapin, Matthew R Jones, Daniel E. Winkler, Glenn Rink, Robert MassattiSpatially explicit management of genetic diversity using ancestry probability surfaces
1. Ecological restoration and conservation efforts are increasing worldwide and the management of intraspecific genetic variation in plants and animals, an important component of biodiversity, is increasingly valued. As a result, tailorable, spatially explicit approaches to map genetic variation are needed to support decision-making and management frameworks related to the recovery of threatened aAuthorsRobert Massatti, Daniel E. WinklerHybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridizatioAuthorsRichard G.J. Hodel, Robert Massatti, L Lacey KnowlesDemographic modeling informs functional connectivity and management interventions in Graham’s beardtongue
Functional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with paAuthorsMatthew Richard Jones, Daniel E. Winkler, Robert MassattiThe demographic and ecological factors shaping diversification among rare Astragalus species
AimEvolutionary radiations are central to the origin and maintenance of biodiversity, yet we rarely understand how they are jointly shaped by demography and ecological opportunity. Astragalus is the largest plant genus in the world and is disproportionately comprised of rare species restricted to narrow geographic and ecological regions. Here, we explored the demographic and ecological mechanismsAuthorsMatthew Richard Jones, Daniel E. Winkler, Robert MassattiTesting which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species
Co‐distributed species may exhibit similar phylogeographic patterns due to shared environmental factors or discordant patterns attributed to the influence of species‐specific traits. Although either concordant or discordant patterns could occur due to chance, stark differences in key traits (e.g., dispersal ability) may readily explain differences between species. Multiple species’ attributes mayAuthorsRichard G.J. Hodel, Robert Massatti, Sasha G.D. Bishop, L. Lacey KnowlesGenetic analyses of Astragalus sect. Humillimi (Fabaceae) resolve taxonomy and enable effective conservation
Premise of the StudyAstragalus sect. Humillimi is distributed across the southwestern United States and contains two endangered taxa, A. cremnophylax var. cremnophylax and A. humillimus. The former was originally described from the South Rim of the Grand Canyon. Analysis of individuals discovered on the North Rim of the Grand Canyon yielded some evidence that the population represented a distinctAuthorsRobert Massatti, Matthew Belus, Shahed Dowlatshahi, Gerard J. Allan - Software
POPMAPS: An R package to estimate ancestry probability surfaces
This software code was developed to estimate the probability that individuals found at a geographic location will belong to the same genetic cluster as individuals at the nearest empirical sampling location for which ancestry is known. POPMAPS includes 5 main functions to calculate and visualize these results (see Table 1 for functions and arguments). Population assignment coefficients and a raste - News
- Partners
This research is supported by many partners.