BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session

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Conservation Genomics

Room: Salon 4, Marriott Hotel

09:00 - 10:30

Moderator: Klaus Koepfli, Smithsonian Conservation Biology Institute

7.1  09:10  Source dynamics of the naturally re-established carnivore, Canis lupus. Hendricks S.*, University of Idaho; Schweizer R., University of Montana; Wayne R., University of California, Los Angeles; Hohenlohe P., University of Idaho

Given the increase in anthropogenic influences, decreased genetic connectivity of wildlife populations is particularly important for management planning as it can threaten genetic diversity by reducing effective population size. Increased population genomics resolution with the advances of high throughput sequencing has allowed conservation biologist to assess previously unresolvable questions. For example, wolves in the Pacific Northwest USA (PNW) have recently re-established through colonization either from reintroduced inland US populations or from a unique ecotype found in coastal British Columbia (cBC; Canada). If the PNW wolves are contiguous with the inland populations, less protection may be deemed necessary; however, if genetic connectivity between PNW and cBC populations exists, different protection measures may be recommended. To assess the genetic source of PNW wolf populations, we generated data from a capture array and found that PNW wolves have multiple genetic sources and have varying degrees of admixture across geographic space. Additionally, we used ecological niche modeling to assign each packs probability of presence in inland or coastal habitat. We found that two western PNW packs are more likely to exist in coastal habitat. Continued migration from cBC to PNW will contribute genetic diversity and possibly decrease inbreeding in the re-established PNW population. Our sequence capture array also targeted putative loci under selection, giving us insight into gene flow patterns for functional genetic variation potentially linked to local adaptation in these populations. These findings need to be considered when designing accurate conservation and management plans for wolves naturally re-colonizing the PNW.

7.2  09:30  The Southern Levant wild gazelles genomic profile reveals new conservation priorities. Kahila Bar-Gal G.*, The Hebrew University of Jerusalem; Hadas L., The Hebrew University of Jerusalem

Historically the mountain gazelle (Gazella gazella), Dorcas gazelle (Gazella dorcas) and acacia gazelle (Gazella arabica acaciae) were abundant in the southern Levant. Anthropogenic and environmental changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and their future survival. Genetic profiles of modern wild gazelles from Israel revealed genetic differences not only between species but also within subpopulations of the same species. The genetic assessments of the current populations together with the ongoing habitat degradation and other human effects recognized new conservation priorities of each gazelle species to prevent their extinction in the Southern Levant. The genomic study of modern, museum and ancient specimens from Israel is conducted in order to understand the genetic plasticity, which enabled the gazelle's adaptation of to changing conditions since the Pleistocene. Our ability to predict future gazelle responses to anticipated fundamental changes of its ecosystem through anthropogenic modifications can be integrated in future management programs to conserve the species.

7.3  09:50  Demographic history of the critically endangered greater bamboo lemur (Prolemur simus), evidence of population bottlenecks. . Hawkins MTR*, Omaha Zoo & Aquarium; Culligan RC, Omaha Zoo & Aquarium; Dikow RB, OCIO Smithsonian Institution; Frasier CL, Omaha Zoo & Aquarium; Lei R, Omaha Zoo & Aquarium; Louis EEL, Omaha Zoo & Aquarium

The greater bamboo lemur (Prolemur simus) is a member of the family Lemuridae that, along with its sister genus Hapalemur, is unique in its consumption of bamboo as a majority of its diet. This species is Critically Endangered and presently lives in small patches of forest in eastern Madagascar, occupying a fraction of its original range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species across its distribution. After quality filtering we identified over 153,000 high quality single nucleotide variants (SNVs hereafter), and evaluated geographic structuring across nearly 19k SNVs. We characterize a north-south divide, which recovered a stronger signal than high versus low elevations. We also evaluated the demographic history of this species, and inferred a dramatic, prolonged population crash. This species had the largest effective population size (at least four million individuals) between approximately 250,000-700,000 years ago, a time in which global climate change affected terrestrial mammals worldwide. This study has shown for the first time that this species underwent a drastic decline which long predates the human colonization of Madagascar. Following this probable climate-related decline, the species underwent a secondary bottleneck subsequent to human colonization, which has reduced the entire species to an estimated 1,000 individuals. While the historical distribution was likely a vast portion of Madagascar, which we estimated a minimum area of occupation spanning 44,259 km2, the contemporary distribution is estimated at only ~1,700 km2. The estimated decline in effective population size from the peak was approximately 99.97%, corresponding to an approximate decrease in distribution of ~97-99%. Conservation management of this species is crucial in order to sustain the remaining genetic diversity, and allow for recovery where suitable habitat is available.

7.4  10:10  Harnessing the power of RADseq for biodiversity conservation. Andrews KR*, University of Idaho; Good JM, University of Montana; Miller MR, University of California Davis; Waits L, University of Idaho; Luikart G, University of Montana; Hohenlohe PA, University of Idaho

The development of restriction site-associated DNA sequencing (RADseq) has been deemed among the most important scientific breakthroughs in the past decade. RADseq has fueled conservation genomic studies of hundreds of non-model organisms by harnessing the massive throughput of next-generation sequencing. This technique allows both discovery and genotyping of hundreds to thousands of polymorphic markers in coding and non-coding regions using a time- and cost-efficient approach, and requires no prior genomic information. These advantages have led to an explosion of studies of non-model organisms investigating population structure and delineating conservation units, and estimating gene flow and dispersal, demographic history, genomic diversity, inbreeding, relatedness, and phylogenetics. RADseq also enables investigation into questions that were virtually intractable for non-model species prior to the advent of next-generation sequencing technologies, including questions regarding the genomic basis of fitness, adaptation, and phenotypic variation. However, as with any new method, researchers should exercise caution when using RADseq data. Several sources of bias and error exist for RADseq data, and researchers should consider these carefully when designing and implementing a RADseq experiment. In addition, numerous variant RADseq methods have emerged in recent years (e.g. GBS, ddRAD, 2b-RAD, ezRAD), and it can be difficult for researchers to choose an approach. We provide an overview of the types of research questions RADseq can be used to answer, highlighting examples from the literature for non-model organisms and biodiversity conservation. We also discuss the types of error and bias to which RADseq is susceptible, and new targeted RAD-capture approaches allowing flexibility in the number of RADseq loci that can be targeted. We provide a brief overview of the technical differences among the RADseq methods, recent controversial criticisms of RADseq, and key considerations for choosing among the growing number of methods when designing a study.

10:30 - 10:50 Break

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