population genetics

Kristen Hasenstab-Lehman, C. Matt Guilliams, Santa Barbara Botanic Gardens

Dithyrea maritima (Davidson), or beach spectaclepod, is a dune specialist endemic to coastal dunes from central California, United States, to northwestern Baja California, Mexico. Individuals of this perennial herb spread by rhizomes, forming a diffuse colony of ramets, each terminating in rosette of 1 to several fleshy leaves, and a two-chambered fruit (silicle). It is listed on the California Native Plant Society Rare and Endangered Plant Inventory on list 1B.1 and was listed as Threatened under the California Endangered Species Act. Studied occurrences of the self-incompatible D. maritima have low seed set, though manual outcrosses boost seed production. Knowledge of the distribution of genotypes on the landscape is be a critical first step toward any number of recovery actions. In this study, we sample from approximately 30 individuals from each of eleven samplinglocations spanning the range of the taxon from Morro Bay, CA, USA to San Quintín, Baja CA, MX. We used double digestion RADseq to prepare libraries for high-throughput sequencing, assemble the dataset in ipyrad producing 5092 SNPs, and analyze population genomics of the species. We place the observed population genomic patterns into the context of regional biogeography, and conclude with recommendations for managing the species.

Date Recorded: 
Wednesday, September 11, 2019

Christy Powell, Brian Dorsey, San Diego Zoo Global, Huntington Botanical Garden

As the most endangered group of plants on the planet, cycads (Cycadales) face a number of threats to their continued existence. Efforts to preserve these iconic plants (in situ reserves and ex situ collections) could benefit greatly from a better understanding of population genetic dynamics and recent demographic history. We have shown that within the genus Dioon most species likely diverged between 30-80 kya. This very recent divergence along with long generation times suggests the possibility of shared polymorphisms across species and potentially incomplete speciation between accepted taxa. Conversely, the distribution of populations and the pollination/dispersal system suggests that migration rates may be quite low. Determining the relative influence of these processes will better inform conservation efforts. Given the nearly 50 Gb genomes of this group, we are using a hybrid of two RADseq methods to produce high coverage/highly multiplexed reduced representation data sets to assess connectivity, historical demography, and genetic diversity. While data for Dioon is still coming in, we have a pilot study using the same technique to assess the genetic diversity among Encephalartos latifrons plants held in botanical gardens in the USA, which we plan to extend to include wild populations with similar goals.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019

Kyle L. Gunther, Sula Vanderplank, Jon P. Rebman, Andres Orduño Cruz, & Lluvia Flores-Rentería, San Diego State University, San Diego Natural History Museum, San Diego Zoo Global, Centro de Investigaciones Biológicas del Noroeste

California and the Baja peninsula are home to high levels of floral abundance, diversity, and endemism. Much of this region is part of a biodiversity hotspot and therefore a conservation priority. The Mission Manzanita (Xylococcus bicolor) is endemic to this area, an ecologically and ethnobotanically important shrub, and the sole member of a monotypic genus within Ericaceae. Xylococcus bicolor is narrowly distributed from the middle of Baja California to the Los Angeles area, and has been predicted to experience up to 88% habitat loss due to climate change and development. However, little is known about its population structure, demographics, and genetic diversity, which may be useful information for conservation purposes. In order to fill this gap in knowledge, we are studying these aspects from a genetic perspective. Using a genome skimming technique to reveal thousands of single nucleotide polymorphisms, we are analyzing the population structure, genetic diversity, gene flow, and effective population sizes across the X. bicolor distribution. Preliminary results suggest the presence of intraspecific divergence and population structure, while niche models show loss of suitable habitat using climate change scenarios. We hope our study will provide useful information for land management and conservation decisions.

Date Recorded: 
Wednesday, September 11, 2019

Cynthia Steiner, Aryn Wilder, Debra Shier and Natalie Calatayud, San Diego Zoo Institute of Conservation Research

Among the main roles of conservation management is to mitigate the negative effect of anthropogenic activities in nature by ensuring the persistence of biodiversity and species in the wild. Conservation geneticists have recently developed a new toolbox of genomic methods to address the management of species in-situ and ex-situ. Among these approaches, the reduce representation or ddRADseq method allows to sample a fraction of the genome-wide genetic variation to estimate population summary statistics and individuals’ relationships for breeding management. The study of the southern mountain yellow-legged frog, an endemic and critically endangered amphibian species from southern California provides importance lessons about the use of ddRADseq in species with large genome size, in terms of quality/quantity of DNA samples required for generating genomic libraries, quality control of restriction enzymes chosen, optimization of parameters in the STACK pipeline for data analysis and selection of criteria for filtering genetic variants.

Date Recorded: 
Tuesday, September 10, 2019

Dr. Jennifer Ramp Neale, Director of Research and Conservation, Denver Botanic Garden 

The primary objective of research at Denver Botanic Gardens is the conservation, preservation, and documentation of native Colorado flora by serving as an active center of biodiversity research for the Southern Rocky Mountain region. In order to fill a gap in botanical expertise in the region, the Gardens launched a conservation genetic program in 2009. Through an integrated approach we have assessed population genetic diversity levels and patterns in several endangered plant species. We are now expanding our skill set through staffing, collaboration, and student mentorship. Staying on top of current methodology while providing results to funding agencies in a timely manner has its challenges that we are working to address in creative ways.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019

Shannon Fehlberg,Desert Botanical Garden

The Acu–a cactus, Echinomastus erectocentrus var. acunensis, is an endangered species with a restricted distribution in the Sonoran Desert in southern Arizona and northern Sonora, Mexico. Population-level genetic analyses for this species are lacking, and taxonomic boundaries between E. erectocentrus var. acunensis and its close relatives E. erectocentrus var. erectocentrus and E. johnsonii are unclear. Detailed morphological data that have been collected for these three taxa indicate the existence of a geographical cline from the Mojave Desert to the Sonoran Desert. The goal of this project is to document genetic diversity within and among populations of E. erectocentrus var. acunensis, as well as between E. erectocentrus var. acunensis and its close relatives. The addition of genetic data to our current knowledge of morphology and distribution may enable us to form stronger species definitions, make more accurate field identifications, and begin to clarify taxonomic confusion in the group. To acquire genetic data, seven known populations of E. erectocentrus var. acunensis, three populations of E. erectocentrus var. erectocentrus and four populations of E. johnsonii were visited, and more than 230 spine or floral tissue samples were taken. DNA was extracted, and data were collected for 11 microsatellite regions specifically developed for these taxa, and two microsatellite regions previously developed for Sclerocactus. Standard population genetic measures were used to determine genetic variation and structure, and observed genetic differentiation was compared to the current morphological understanding of the group. These analyses help improve our knowledge of the genetic structure of E. erectocentrus var. acunensis populations and inform our understanding of species boundaries and evolutionary relationships within the group, thereby allowing us to refine conservation and management plans aimed at protecting and restoring populations of this endangered species.

Contributing Author(s): 
Date Recorded: 
Friday, May 3, 2019