genetic diversity

Joe Davitt, Institute for Conservation Research, San Diego Zoo Global

Maintaining a plant species’ genetic diversity can contribute to adaptive potential, prevent inbreeding effects, and potentially preserve traits such as drought tolerance and disease resistance, all of which are critical in a changing climate. Seed collections are often the best method of conserving the genetic diversity of rare plant populations ex-situ, however most seed collections are made with no available genetic data from the target species. Ideally, this genetic data would give us a clear picture of which populations are the most critical to conserve and how genetically structured a species’ populations are in relationship to one another, but this can be a time consuming and costly process. Seed collection protocols, such as those published by the Center for Plant Conservation, can inform our general best practices, but as seed collectors we must also infer best practice on a species by species basis. The life history and reproductive biology of the target species, as well as our sampling methods can greatly impact the effectiveness of seed collections to capture the entire target populations’ genetic diversity. Taking all available information about a species into consideration, we can infer the best seed collection methods to ensure genetic conservation.

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

Manuel Luján, Jian Liu, Nathalie Nagalingum, California Academy of Sciences, Kunming Institute of Botany, Chinese Academy of Sciences

Rare plant species exhibit narrow geographic distribution and are often considered to have smaller populations and lower levels of genetic diversity compared to their more common relatives. The genus Cycas includes about 117 species, 32 of which are native to Australia and 20 occur only in the subtropical and tropical regions of Queensland. Most of the Queensland species of Cycas are known from only a handful of localities and their population characteristics remain to be investigated. Our main objective was to assess genetic diversity and population size of the rare species of Cycas and compare it them the more widely distributed species. We used RADseq to generate genomic data to estimate percentage of polymorphic loci (P), heterozygosity (Ho and He) and nucleotide diversity (π), and footage from unmanned aerial vehicles to estimate populations size. Our preliminary results suggest that rare species (C. terryana) have levels of genetic diversity that are comparable to more common species (C. ophiolitica and C. media). Population size of rare species (e. g. C. tuckeri) tend to be smaller than more common species (C. cairnsiana). Given that Cycas are long-lived plants, rare and small populations constituted by old plants, may be maintaining ancestral allelic variants from previously more widespread and common populations. Further study considering the populations demographic structure are needed to better understand this pattern and inform conservation efforts.

Date Recorded: 
Wednesday, September 11, 2019

Alexander G. Linan, Porter P. Lowry II, Allison Miller, George E. Schatz, Jean-Claude Sevathian, Christine E. Edwards, Saint Louis University, Missouri Botanical Garden, Institut de Systématique, Évolution et Biodiversité (ISYEB), Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle/École, Pratique des Hautes Études, Université Pierre et Marie Curie, Sorbonne Universités, Donald Danforth Plant Science Center

The ebony and persimmon genus (Diospyros) is a diverse group of largely tropical trees and shrubs, comprising >800 species, many of which are poorly known, and/or are of dire conservation concern. Some of the most endangered members of the genus are endemic to islands of the Western Indian Ocean. The Mascarene Islands, comprising the islands Reunion, Rodrigues, and Mauritius is located east of Madagascar, and harbor 14 endemic species of Diospyros. Most of the species diversity is endemic to Mauritius are of dire conservation concern with the majority of species listed as either Critically Endangered or Endangered by IUCN Red List assessments. Despite their conservation status, nothing is known about patterns of genetic diversity or whether these sympatrically distributed and closely related species represent distinct genetic units. In this study we conducted population level sampling on all extant species of endemic Mascarene Diospyros and genotyped samples using 2bRAD seq in order to: 1) clarify species limits within the group, 2) determine and compare levels of genetic diversity across species and, 3) assess patterns of genetic structure within species and prioritize populations for conservation efforts. We found the morphologically described species correspond to unique genetic units despite the presence of hybrids and provide recommendations for future/ongoing conservation efforts.

Date Recorded: 
Wednesday, September 11, 2019

Fred Gouker, Abigail Moore, Kevin Conrad, Margaret Pooler, USDA-ARS U.S. National Arboretum, Floral and Nursery Plants Research Unit, Enviromental and Plant Biology Department, Ohio University

Sassafras albidum is a well-known, ecologically important tree that is dispersed throughout the Eastern United States. Its root and bark oil were commonly used as a flavoring agent for many products including tea and root beer. This tree can be used to restore depleted soils and rehabilitate disturbed sites. Sassafras also serves as a host plant for the Spicebush Swallowtail butterfly, providing a strong wildlife value. S. albidum is a member of the Lauraceae family that is presently threatened by laurel wilt disease originating from the fungus Raffaelea lauricola. Laurel wilt and is transferred by the insect vector, redbay ambrosia beetle (Xyleborus glabratus) through burrowing. While fungicides may help treat individual trees, the drastic spread of this disease has led us to believe broad-scale, preventative, efforts must be made to conserve the genetic diversity of this species. In this study we strive to isolate microsatellite loci from a diverse collection of sassafras found across the eastern and midwest regions of the United States to help protect and potentially recover this tree species through germplasm conservation before laurel wilt advances through the extensive native range of Sassafras and becomes a broad-scale epidemic.

Contributing Author(s): 
Date Recorded: 
Wednesday, September 11, 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

Dr. Aryn Wilder, Institute for Conservation Research, San Diego Zoo Global

Human activity has left species worldwide on the brink of extinction, where they are susceptible to the loss of genetic diversity and the accumulation of deleterious mutations that reduce adaptive potential and increase extinction risk. The application of modern genomic tools allows us to more accurately assess the conservation status of populations and examine the genetic factors that contribute to extinction. I will present case studies from animal populations where we are applying genomics as a conservation tool. First, we compared genomic characteristics of two closely related white rhino subspecies, the northern white rhino (NWR) which has been driven effectively to extinction, and the southern white rhino which has mounted a remarkable recovery, to provide insight into the potential for restoration of NWR. Second, we are currently generating low-coverage, whole genome sequence data from hundreds of wild and captive Pacific pocket mice. Combined with imputation, low coverage sequencing provides a cost-effective way to infer genotypes across the genome for a large number of individuals, providing statistical power needed to measure the genetic basis of fitness-related traits. The advancement and increasing cost-effectiveness of genomic technologies will continue to provide valuable insights applicable to conservation across taxa.

Date Recorded: 
Tuesday, September 10, 2019

Trees Will Adapt, Migrate or Die

Barbara Crane, US Forest Service, National Forest System (SePPCon 2016)

Barbara Crane, USFS, describes special considerations for trees.  Because the are long-lived, they cannot respond quickly to multiple threats from pathogens, fire, drought and climate change. Rates of historic migration of 300 to 1200 ft/yr cannot keep up with the rate of changing climate. Understanding genetic variation related to environment and response to change is necessary to conserve forest diversity. For the USFS Southern Region, which is home to 140 tree species, we developed a Genetic Risk Assessment System and identified the top 10 species at risk from climate change. Barbara gives examples of actions with several species and emphasizes that collecting from southern edge of a species range may capture valuable unique genes.

This work was presented at the Southeast Partners in Plant Conservation (SePPCon) 2016 Meeting. Learn more about SePPCon here.

Date Recorded: 
Tuesday, November 1, 2016

Use of dry tissue for comparing ploidy among rare plant populations?

Given the reproductive difficulties that differences in plant ploidy may cause in the movement or mixture of plant populations, our group is considering incoporating analysis of plant ploidy into a grant evaluating

Seana Walsh, Dustin Wolkis, and Ken Wood, National Tropical Botanical Garden

Phyllostegia electra (Lamiaceae) is endemic to the mesic and wet forests of Kaua'i. It is listed as Critically Endangered on the IUCN Red List of Threatened Species and is a focal species for achieving conservation objectives outlined in the Hawai'i Strategy for Plant Conservation. With less than 50 known wild individuals among 15 subpopulations, P. electra is also a focal species of the University of Hawai'i's Plant Extinction Prevention Program. It is not, however, protected by the Endangered Species Act.

A grant from the Mohamed bin Zayed Species Conservation Fund is supporting NTBG staff to: 1) make conservation collections from wild populations, 2) conduct a genetic diversity study in collaboration with Chicago Botanic Garden (CBG), 3) outplant into protected and managed habitat, and 4) investigate optimal seed storage methods.

Eighteen remote field work trips have been undertaken since March 2017 to secure conservation collections and obtain leaf material for the genetic diversity study. Genetic marker (microsatellites) development was recently completed and silica-dried leaf material sent to CBG for DNA extraction. Since June 2017, 215 individuals have been outplanted into Kalalau Exclosure and NTBG Gardens and Preserves. Preliminary results of our investigation into optimal seed storage indicate that seeds do not tolerate exposure to liquid nitrogen without prior desiccation. We also found that germination was significantly higher in the 42% eRH frozen treatment compared to the 30% eRH frozen treatment. This work is directly contributing to the conservation of this rare taxon and we are using this multi-faceted project model in our approach to conserving other rare plant taxa as well.

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

Valerie Pence and Megan Philpott, Cincinnati Zoo & Botanical Garden

Crotalaria avonensis is a Florida endemic found in three populations and characterized by low seed production. In the late 1990s, CREW developed protocols for tissue culture propagation from field collected shoot cuttings as well as cryopreservation methods. In order to develop a genetically representative collection for conservation, in vitro lines were established from shoots collected at all three populations from 2008-2012. Plants were produced and sent to Bok Tower Garden for further growth and for use in an outplanting by Archbold Biological Station. The resulting collection of genotypes in culture at CREW provides an example of the challenges of a genetically diverse collection of an exceptional species. C. avonensis cultures require maintenance subculturing every 2-3 months. Only a low number of replicates could be maintained for each genotype, resulting in some loss of genotypes over time. Cryopreservation offered a solution to this challenge and over the course of 16 years, a number of lines were cryopreserved. In a study of lines stored for 5.5 Ð 16 years in liquid nitrogen, there was no change in average viability of the collection in storage, although specific survival differed by genotype. A cost estimation indicated that cryopreservation could decrease the cost of maintaining the collection over 20 years by at least 1/3. Genetic analysis of the collection and the wild populations is also underway in order to determine the genetic representation of the collection.

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