Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.

Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Plant regeneration from an endangered valuable cork oak tree by somatic embryogenesis.

Among the several applications of in vitro tissue culture techniques, the conservation of plant germplasm is one of the most widely used. The cork oak is one of the principal tree species in the Western Mediterranean región. Within this área, the Balearic Islands are considered to be a glacial refuge, and therefore a reservoir of genetic resources. A singular tree has been found in the small Minorca Island population. The haplotype of this tree is of Tyrrhenian origin, showing a past link between Minorca and Sardinia. Moreover, this tree do not bear a deletion within an ITS from ribosimic nuclear DNA, which is fairly common in many populations of this species, and indicates that ir may be the descendant of a very ancient population. This tree is currently in a precarious condition, and it has not produced acorns in the last years. Hence there is a clear need of vegetative propagation to conserve this genotype. We have previously developed methods to clone adult cork oak tres by somatic embryogenesis, and therefore the aim of the present work was to clone this singular tree. There braches from the corwn were collected in November 2004, and methods previously described were carried out. By February 2005 somatic embryogenesis was obtained from leaves of the tree with percentages on induction ranging from 17 to 54% depending on the branch, which may show a novel source of variation that requires further study. Spontaneously matured somatic embryos germinated at 46% in average, and the first somatic seedlings from the Alfavaret's cork oak tree were obtained. Therefore, this study shows one of the most relevant applications of somatic embryogenesis: the plant regeneration of valuable genotypes for the in situ and ex situ conservation of forest genetic resources.

Census, reproductive biology, and germination of Astragalus gines-lopezii (Fabaceae), a narrow and endangered endemic species of SW Spain

Astragalus gines-lopezii Talavera, Podlech, Devesa & F.M.Vázquez (Fabaceae) is a threatened endemic species with a distribution restricted to a very small area in Badajoz Province (Extremadura Region, SW Spain) and only 2 populations are known. This species was catalogued in the ?Endangered? category in the 2008 Red List and the 2010 Threatened Spanish Vascular Flora List. Despite its status as an endangered species, at present very little is known about the distribution, census, and reproductive biology of this species. In this study we have carried out an exhaustive census of A. gines-lopezii , and we have evaluated the production of flowers, fruits, and seeds and the existence or not of intra- and interpopulation variability in seed germination. Results have highlighted the high reproductive capacity of this species on the basis of a high production of flowers, fruits, and seeds. Mechanical scarification of seeds was effective for increasing germination. Thus, initial germination (22%?60%) was increased to 97%?99% when seeds were rubbed with sandpapers. A high intra- and interpopulation variability in seed germination was found in this species. A. gines-lopezii produces seeds with different degrees of physical dormancy, varying this grade among different individuals within a population.

Conservation of endangered Lupinus mariae-josephae in its natural habitat by inoculation with selected, native Bradyrhizobium strains

Lupinus mariae-josephae is a recently discovered endemism that is only found in alkaline-limed soils, a unique habitat for lupines, from a small area in Valencia region (Spain). In these soils, L. mariae-josephae grows in just a few defined patches, and previous conservation efforts directed towards controlled plant reproduction have been unsuccessful. We have previously shown that L. mariae-josephae plants establish a specific root nodule symbiosis with bradyrhizobia present in those soils, and we reasoned that the paucity of these bacteria in soils might contribute to the lack of success in reproducing plants for conservation purposes. Greenhouse experiments using L. mariae-josephae trap-plants showed the absence or near absence of L. mariae-josephae-nodulating bacteria in ‘‘terra rossa’’ soils of Valencia outside of L. mariaejosephae plant patches, and in other ‘‘terra rossa’’ or alkaline red soils of the Iberian Peninsula and Balearic Islands outside of the Valencia L. mariae-josephae endemism region. Among the bradyrhizobia able to establish an efficient symbiosis with L. mariae-josephae plants, two strains, LmjC and LmjM3 were selected as inoculum for seed coating. Two planting experiments were carried out in consecutive years under natural conditions in areas with edapho-climatic characteristics identical to those sustaining natural L. mariae-josephae populations, and successful reproduction of the plant was achieved. Interestingly, the successful reproductive cycle was absolutely dependent on seedling inoculation with effective bradyrhizobia, and optimal performance was observed in plants inoculated with LmjC, a strain that had previously shown the most efficient behavior under controlled conditions. Our results define conditions for L. mariae-josephae conservation and for extension to alkaline-limed soil habitats, where no other known lupine can thrive.

Census, reproductive biology, and germination of Astragalus gines-lopezii (Fabaceae),a narrow and endangered endemic species of SW Spain.

Astragalus gines-lopezii Talavera, Podlech, Devesa & F.M.Vazquez (Fabaceae) is a threatened endemic species with a distribution restricted to a very small area in Badajoz Province (Extremadura Region, SW Spain) and only 2 populations are known.This species was catalogued in the "Endangered" category in the 2008 Red List and the 2010 Threatened Spanish Vascular Flora List. Despite its status as an endangered species, at present very little is known about the distribution, census, and reproductive biology of this species. In this study we have carried out anexhaustive census of A. gines-lopezii, and we have evaluated the production of flowers, fruits, and seeds and the existence or not of intra- and interpopulation variability in seed germination. Results have highlighted the high reproductive capacity of this species on the basis of a high production of flowers, fruits, and seeds. Mechanical scarification of seeds was effective for increasing germination. Thus, initial germination (22%-60%) was increased to 97%-99% when seeds were rubbed with sandpapers. A high intra- and interpopulation variability in seed germination was found in this species. A. gines-lopezii produces seeds with different degrees of physical dormancy, varying this grade among different individuals within a population.

A Review of the Petition Process for the Endangered Species Act

The Endangered Species Act of 1973 (ESA) is an exceptionally powerful law which requires the involvement of many stake holders, including government and non-government professionals. This project reviewed the requirements of the ESA and the expectations of the USFWS and referenced them to the actions taken by the petitioner in the preparation of the petition for the black-tailed prairie dog. The study has shown the knowledge required by the petitioner to submit an effective petition and also the importance of communicating this knowledge so that the federal agencies may make sound decisions when deciding to protect a species and its habitat. This research can be used as a preliminary reference for beginning the process for future petitions.

The Adequacy of Wildlife Management on an Endangered Species: A Design Template for Ecosystems Management in Alabama

The Alabama beach mouse (ABM) was listed an an endangered species in 1985. The ABM has been cited as being minimally managed since its listing. The Sierra Club points out the lack of Primary Consituent Elements (PCE) that are required by the Endangered Species Act of 1973. While traditional habitat status is mired in legal and bureaucratic delays, effective management remains less than optimal. Ecosystem management presents with it, new observable and technological tools that may present a panacea in the ABM's paradox. This Capstone looks at the possible implementation of an ecosystems management alternative in aiding the persistence of a small isolated and endangered species.

Avoiding Extinction: An Evaluation of Short-Term Recovery Recommendations for the Endangered Rio Grande Silvery Minnow

The endangered Rio Grande silvery minnow (Hybognathus amarus; RGSM) is nearing extinction and requires immediate recovery actions. In a draft report to the Middle Rio Grande Program, a Program Advisory Panel (PAP) recommended 34 short-term recovery measures to be implemented within the next five years, and 21 long-term recovery actions. However, these recommendations need further analysis to determine if and how the actions could be implemented. This project evaluated short-term recommendations provided by the PAP to identify the most effective and rank the relative importance of the actions. These recommendations were divided into 7 recovery categories: population augmentation (5 recommendations); hydrologic regimen (4 recommendations); physical habitat (3 recommendations); biological component of habitat (2 recommendations); population monitoring (6 recommendations); monitoring, analysis, and modeling (12 recommendations); and information and planning (2 recommendations). Each recommendation was evaluated for its potential to produce anticipated recovery progress for the RGSM based on assessments of the degree of feasibility, cost effectiveness, and associated potential consequences if fully implemented. In addition, other alternatives in a range of options were also considered where applicable. In each case, recommendations were evaluated from on-site visits, interviews with researchers and resource managers, and literature review. Based on the research findings, three major groupings of the recovery categories were identified: natural aspects of recovery, program aspects of recovery, and emergency measures. At least one recovery category within each major grouping was considered important by the respondents, which indicates that each grouping is of high importance in relation to the situation at hand. However, actions within each grouping have varying priorities given constraints on available resources, time, and budget. An integrated approach that accounts for the complexity of the river system and the species itself was considered the best approach to avoid extinction while ensuring long-term sustainability. Results of these analyses were provided directly to the PAP for their review, and it is anticipated that project results could advance implementation of the most appropriate immediate recovery actions needed to prevent extinction of the RGSM.

Analysis of the Convention on International Trade in Endangered Species (CITES) and the Endangered Species Act (ESA) and Its Effects on Giant Panda Conservation

The giant panda, Ailuropoda melanoleuca is an endangered species that is protected under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the Endangered Species Act (ESA). Numerous factors have led to a decline in giant panda populations in China including habitat loss from human activity, poaching, panda inbreeding and a low reproductive rate. This capstone analyzes the effects of CITES and ESA as policies for the protection of panda populations and their habitat. CITES and ESA provide some protection for panda populations in the United States. However, these policies do not address panda habitat protection in China.

Short-Term Effects of a Wildfire on the Endangered Dupont's Lark Chersophilus duponti in an Arid Shrub-Steppe of Central Spain

In Europe, Dupont’s Lark Chersophilus duponti is a threatened open-habitat bird. Prescribed burning has sometimes been proposed for its conservation, but without evidence of its effectiveness. To evaluate the short-term effects of a summer wildfire on this species, we performed several transect counts in the burnt and unburnt parts of a shrubsteppe in central Spain. The same transects were counted within a three-year interval prior to the fire and were repeated during the first two springs after the fire. We also measured the vegetation during the first two springs after the fire. In the burnt area, we observed a decrease of about 85–100% in Dupont’s Lark abundance, and about 7–15% in the control area. The disappearance of the scrub cover after fire and its slow regeneration, as well as the large increase in grass cover during the second year, may explain the decrease in this habitat-specialist bird species. Fire should be avoided in areas occupied by the Dupont’s Lark, as its negative effects in the short-term may cause local extinctions. However, prescribed burning may be used in neighboring areas to create new open habitats that may be subsequently colonized by this species.