Molecular Variation and Evolutionarily Significant Units in the Endangered Gila Topminnow

Determining evolutionarily significant units in endangered species is one of the most significant challenges facing conservation biology. Often genetic information has been used as the primary basis of recommendations for evolutionarily significant units, but these data should be evaluated carefully and used in conjunction with other information. The endangered Gila topminnow ( Poeciliopsis. o. occidentalis ) has been the subject of extensive conservation biology research and genetic investigation. We extended these data to highly variable genetic markers, examined variation in microsatellite loci, and compared it with previous measures of genetic diversity for the Gila topminnow from the four watersheds in Arizona in which they are still naturally extant. Fish from Monkey Spring were the most highly differentiated from the other populations. Overall, the amounts and patterns of genetic variation were consistent with known historical and physical differences among sites. The four watersheds are highly physically isolated from one another and differ in a number of important factors in their physical habitat, biota, and the life-history of the topminnows. Based on these geographic patterns and the genetic results, we recommend that the four watersheds all be managed and conserved separately.     

Using survival analysis to study translocation success in the Gila topminnow (Poeciliopsis occidentalis).

Translocation, the intentional release of captive-propagated and/or wild-caught animals into the wild in an attempt to establish, reestablish, or augment a population, is a commonly used approach to species conservation. Despite the frequent mention of translocation as an aid in threatened or endangered species recovery plans, translocations have resulted in the establishment of few sustainable populations. To improve the effectiveness of translocation efforts, it is essential to identify and adopt features that contribute to successful translocations. This study analyzed 148 translocations of the endangered Gila topminnow (Poeciliopsis occidentalis) to identify various factors that have significantly influenced translocation success. We quantified success as the "persistence time" of translocated populations and used survival analysis to interpret the role of several factors. The following factors affected persistence times of translocated populations: season in which the fish were translocated, habitat type of the translocation site, and genetic origin of the fish stocked. In general, factors associated with stocking, the population stocked, and the site of translocation can significantly affect the persistence of translocated populations and thus increase the probability of translocation success. For Gila topminnow, future translocations should be undertaken in late summer or fall (not early summer), should occur into ponds (not streams, wells, or tanks), and should generally utilize individuals from genetic lineages other than Monkey Spring. For other species, a key lesson emerging from this work is that life history attributes for each translocated species need to be considered carefully.     

Impact of Hybridization on a Threatened Trout of the Southwestern United States

Trouts native to the American Southwest provide an excellent example of the plight of endangered fishes from this region. The native species, Apache trout and Gila trout ( Oncorhynchus apache and O. gilae , respectively) have faced drastic reduction in habitat and detrimental interactions with introduced species, resulting in a dramatic decrease in numbers and sizes of populations. We used biochemical methods to identify diagnostic markers for the estimation of genetic relatedness and analysis of hybridization among native trouts and introduced cutthroat and rainbow trouts ( O. clarki and O. mykiss , respectively). Restriction endonuclease analysis of mitochondrial DNA (mtDNA) indicated that Apache and Gila trout were very similar to each other, and more similar to rainbow trout than cutthroat. Diagnostic allozyme marker loci indicated that Apache trout hybridized extensively with rainbows in four populations and provided no evidence for reproductive isolation between the forms. Analysis of mtDNA, however, indicated that introduced haplotypes were rare in these same individuals, identifying a bias in the direction of gene exchange between species. The potential reproductive isolation and lack of information concerning population structure necessitate further study of Apache trout to determine the appropriate management strategy for this threatened species. This case demonstrates that extreme care must be exercised when considering elimination of any contaminated population lest the unique genetic identity of the native taxon be lost forever.     

Fitness in the Endangered Gila Topminnow

The Gila topminnow (Poeciliopsis o. occidentalis) is a small, live-bearing, endangered fish extant in a maximum of nine locales in four separate watersheds in the United States. To determine if these populations differed in their fitness, we obtained samples from the four watersheds and examined them for four fitness correlates: survival, growth rate, fecundity, and bilateral asymmetry. Earlier research found that one population, Sharp Spring, had higher allozyme heterozygosity than the other three and had higher survival, growth rate, and fecundity and lower bilateral asymmetry than a sample from one of the other populations with no polymorphic allozyme loci, Monkey Spring. We also verified that Sharp Spring fish were polymorphic for the same allozyme loci whereas the Monkey Spring population was not. We did not, however, find positive associations of allozyme heterozygosity with the four fitness correlates for the four samples. Because the earlier study had much lower survival, it is likely that the differences resulted from differential response of the two populations to a stressful laboratory environment. Whether this unknown stress occurs in natural environments or its effect is predictive of other stresses remains unresolved. As a result, we concur with suggestions in the draft recovery plan that topminnows from nearby sources be used for reintroductions and that the Sharp Spring stock not be used outside the upper Santa Cruz River drainage.     

Patterns of Genetic Diversity in Remaining Giant Panda Populations

Abstract: The giant panda ( Ailuropoda melanoleuca ) is among the more familiar symbols of species conservation. The protection of giant panda populations has been aided recently by the establishment of more and better-managed reserves in existing panda habitat located in six mountain ranges in western China. These remaining populations are becoming increasingly isolated from one another, however, leading to the concern that historic patterns of gene flow will be disrupted and that reduced population sizes will lead to diminished genetic variability. We analyzed four categories of molecular genetic markers (mtDNA restriction-fragment-length polymorphisms [RFLP], mtDNA control region sequences, nuclear multilocus DNA fingerprints, and microsatellite size variation) in giant pandas from three mountain populations (Qionglai, Minshan, and Qinling) to assess current levels of genetic diversity and to detect evidence of historic population subdivisions. The three populations had moderate levels of genetic diversity compared with similarly studied carnivores for all four gene measures, with a slight but consistent reduction in variability apparent in the smaller Qinling population. That population also showed significant differentiation consistent with its isolation since historic times. From a strictly genetic perspective, the giant panda species and the three populations look promising insofar as they have retained a large amount of genetic diversity in each population, although evidence of recent population reduction—likely from habitat loss—is apparent. Ecological management to increase habitat, population expansion, and gene flow would seem an effective strategy to stabilize the decline of this endangered species.     

Post-Perturbation Genetic Changes in Populations of Endangered Virgin River Chubs

A 34-kilometer reach of the Virgin River, Utah-Arizona-Nevada, was poisoned with rotenone in an attempt to eradicate non-native red shiners ( Cyprinella lutrensis ), a species implicated in the decline of native fish populations in the American West. An error in detoxification resulted in lethal concentrations of piscicide passing through an additional 50 kilometers of stream. We used allozyme electrophoresis to analyze genetic variation among pre- and post-poison samples of endangered Virgin River chubs ( Gila seminuda ). Pre-poison samples indicated a single panmictic population in the river. In contrast, fish subsequently produced through natural recruitment in poisoned reaches exhibited deviations from the original pattern of genetic variation. A genetic bottleneck caused by severe reduction in the number of spawning adults was indicated. The altered pattern persisted 2.5 years post-poisoning, indicating unexpectedly slow recolonization from the unpoisoned reach upstream. Genetic variation among hatchery-produced young was similarly unrepresentative of the original pattern because of the small number of brood fish used in propagation. Because of their small numbers and/or restricted distribution, endangered species are particularly vulnerable to natural or anthropogenic catastrophes. Assessment of the genetic impact of such events is essential but requires that baseline data are available.     

Utility of North Atlantic Right Whale Museum Specimens for Assessing Changes in Genetic Diversity

Abstract: We examined six historical specimens of the endangered North Atlantic right whale ( Eubalaena glacialis ) using DNA isolated from documented baleen plates from the late nineteenth and early twentieth centuries. Sequences from the mitochondrial DNA (mtDNA) control region from these samples were compared with those from a near-exhaustive survey (269 of approximately 320 individuals) of the remaining right whales in the western North Atlantic Ocean. Our results suggest that there has been only relatively modest change in maternal lineage diversity over the past century in the North Atlantic right whale population. Any significant reduction in genetic variation in the species most likely occurred prior to the late nineteenth century. One historical specimen was from the last documented female capable of propagating one of the maternal lineages in the population today; no females in the existing population have been found to carry this mtDNA haplotype. Analysis of the only specimens from the eastern North Atlantic right whale population ever to be examined revealed that eastern and western North Atlantic right whales may not have been genetically differentiated populations. Loss of gene diversity experienced by North Atlantic right whales over the last century has been modest, and the six decades of protection have been successful in maintaining much of the maternal lineage diversity that was present in the late nineteenth century.     

Comparisons of Genetic Diversity in the Endangered Adenophora lobophylla and Its Widespread Congener, A. potaninii

Abstract: Starch-gel electrophoresis was used to examine the levels and distribution of genetic diversity in two Adenophora species: the narrow endangered Adenophora lobophylla and its widespread congener, A. potaninii . Based on allozyme variation at 18 putative loci, we measured high levels of genetic variability both in the endangered and the widespread species, with 83.3% of the loci being polymorphic. The mean expected heterozygosity within populations (   H _ep  ) and within species (   H _es  ) were 0.234 and 0.244 for A. potaninii and were as high as 0.210 and 0.211 for A. lobophylla . There was higher differentiation among populations in A. potaninii (   F _ST = 0.155) than in A. lobophylla (   F _ST = 0.071). The high levels of genetic diversity in the present allozyme survey are consistent with the morphological variation observed in these species and may be attributed to high outcrossing rates in the Adenophora species. In addition, A. lobophylla was identified as a distinct species on the basis of Nei's genetic distances and thus should be given a high priority for protection. It is noteworthy that the endangered A. lobophylla maintains much higher genetic diversity than most endemic or narrowly distributed plant species in spite of its restricted distribution. We hypothesize that A. lobophylla has become endangered for ecological and stochastic reasons, including habitat destruction or environmental changes, mud slides, and human disturbance such as grazing and mowing. Consequently, habitat protection is of particular importance for conserving this endangered species.     

Managing a protected marine area for the conservation of critically endangered vaquita (Phocoena sinus Norris, 1958) in the Upper Gulf of California

We analysed fisheries trends in the northern region of the Gulf of California, within the Biosphere Reserve of the Upper Gulf of California and Colorado Delta River and the Vaquita Refuge Area, and suggest measures to protect the vaquita, Phocoena sinus. We compiled and analysed catch reports of artisanal fishermen in the three fishing communities of the Upper Gulf of California (San Felipe in the State of Baja California, and Golfo de Santa Clara and Puerto Peñasco in the State of Sonora) from 1995 to 2007. This information was categorised with respect to geographic information systems, and all fishing sites within two marine protected areas in the region were identified. In addition, from a survey based on direct interviews with artisanal fishermen in each of the three ports, we identified that 23% of fishermen will continue fishing despite on-going fishing buy-out programmes in the region. We suggest several specific courses of action to decrease the fishing impact on this critically endangered cetacean. However, given the critical situation of this critically endangered species, it is very uncertain whether enforcing a no-take zone within the biosphere reserve and the Vaquita Refuge Area, or even a wider fishing moratorium, will be enough to save this endangered species from extinction.     

Developing a Sampling Strategy for Baptisia arachnifera Based on Allozyme Diversity

We analyzed the amount and distribution of genetic variation in Baptisia arachnifera Duncan to develop a sampling strategy for ex situ research. Baptisia arachnifera is an endangered plant species endemic to the coastal plain of Georgia (U.S.) where all populations are within 16 km of each other. A reduction in numbers of individuals has been observed during the last 50 years. Baptisia arachnifera was polymorphic at 24% of the 37 loci examined with an average of 1.32 alleles per locus. The genetic diversity index was relatively low ( H_e = 0.097) as expected for endemic species. Populations were in Hardy-Weinberg equilibrium, suggesting that the species is outcrossing. Consistent with this conclusion is the observation that the majority (approximately 90%) of the genetic variation present in the species is found within individual populations. Indirect evidence of gene flow between populations was detected (   Nm = 2.35). The close proximity of the populations and the recent reduction in population sizes suggest that the populations surveyed may be fragments of a once more continuous gene pool. Based on the observed distribution of genetic diversity among populations (G_ST = 0.096), sampling two populations would capture 99% of the allozyme diversity surveyed. Allozyme data were used to determine which 2 of the 10 populations surveyed should be sampled to maximize the ex situ conservation of genetic diversity. Although the paper-producing companies that own most of the land where Baptisia arachnifera occurs are modifying their harvesting techniques, the species could become extinct without more effective management and preservation efforts.     

Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River

The finless porpoise (Neophocaena phocaenoides) inhabits a wide range of tropical and temperate waters of the Indo-Pacific region. Genetic structure of finless porpoises in Chinese waters in three regions (Yangtze River, Yellow Sea, and South China Sea) was analyzed, including the Yangtze finless porpoise which is widely known because of its highly endangered status and unusual adaptation to freshwater. To assist in conservation and management of this species, ten microsatellite loci were used to genotype 125 individuals from the three regions. Contrary to the low genetic diversity revealed in previous mtDNA control region sequence analyses, relatively high levels of genetic variation in microsatellite profiles (H _E = 0.732–0.795) were found. Bayesian clustering analysis suggested that finless porpoises in Chinese waters could be described as three distinct genetic groups, which corresponded well to population “units” (populations, subspecies, or species) delimited in earlier studies, based on morphological variation, distribution, and genetic analyses. Genetic differentiation between regions was significant, with F _ST values ranging from 0.07 to 0.137. Immigration rates estimated using a Bayesian method and population ancestry analyses suggested no or very limited gene flow among regional types, even in the area of overlap between types. These results strongly support the classification of porpoises in these regions into distinct evolutionarily significant units, including at least two separate species, and therefore they should be treated as different management units in the design and implementation of conservation programmes.     

Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge<Emphasis Type="Italic"> Crambe crambe</Emphasis> (Poecilosclerida)

Crambe crambe is a common encrusting sponge found in the Mediterranean and Atlantic littoral. An analysis of a partial sequence (535 bp) of the mitochondrial DNA (mtDNA) gene cytochrome oxidase subunit I (COI) was conducted in an attempt to determine population structure in this species. This is the first study of population genetics using this kind of marker in the phylum. Samples (N=86) were taken in eight populations separated by distances from 20 to 3,000 km, spanning from the western Mediterranean to the Atlantic. Low variability of this gene was found, as only two haplotypes were identified, along with low nucleotide diversity (=0.0006). However, the different frequencies found among populations revealed genetic structure and low gene flow between close populations, as expected from the dispersal biology of the species. The low variability found in sponges is in agreement with reports on cnidarians and points to a high conservation of mtDNA in diploblastic phyla.     

元江流域干热河谷草地植物群落结构特征与相似性分析

选择元江干热河谷典型草地群落,采用标准样地调查法,对流域上、中、下游干热河谷草地植物群落的分布特征、群落结构、种群习性等特征开展研究,结果表明：（1）元江流域上游祥云和中下游红河干热河谷草地群落中出现的植物种类最多,元江流域干热河谷草地植物群落是以灌木为主、多年生草本为辅的结构类型。（2）元江流域干热河谷草地群落中,扭黄茅（Heteropogon contortus）为优势种群,次优种群随流域环境的改变而不同。（3）元江流域干热河谷草地植物群落之间的相似性系数均在0.00～0.25之间,处于极不相似水平,种群的扩散受流域河谷通道作用影响较小。（4）种群的扩散和定居受海拔高度的影响,随着海拔高度的变化,植物群落的组成也发生变化,形成不同的群落结构。     

Genetic Analysis of the Endangered Island Endemic Malacothamnus fasciculatus (Nutt.) Greene var. nesioticus (Rob.) Kearn. (Malvaceae)

Isozyme, randomly amplified polymorphic DNA, and ribosomal DNA analyses were used to evaluate the genetic distinctness and diversity of the endangered island endemic Malacothamnus fasciculatus var. nesioticus (Santa Cruz Island bush mallow). Analysis of amplified DNA profiles and electrophoretic data indicates that var. nesioticus is genetically distinct from other varieties within the species. No isozyme or amplified DNA variation was detected among individuals of nesioticus populations, but restriction site analysis of ribosomal DNA revealed the presence of three closely related genotypes within one of the nesioticus populations. Apparent clonal structuring was found in both nesioticus populations and in one mainland population, var. nuttallli . Results from these analyses provide the background necessary for the design of conservation efforts with recovery goals that insure the long-term survival of Malacothamnus fasciculatus var. nesioticus .     

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations.     

Low Genetic Variability in the Hawaiian Monk Seal

The Hawaiian monk seal (   Monachus schauinslandi) is a critically endangered species that has failed to recover from human exploitation despite decades of protection and ongoing management efforts designed to increase population growth. The seals breed at five principal locations in the northwestern Hawaiian islands, and inter-island migration is limited. Genetic variation in this species is expected to be low due to a recent population bottleneck and probable inbreeding within small subpopulations. To test the hypothesis that small population size and strong site fidelity has led to low within-island genetic variability and significant between-island differentiation, we used two independent approaches to quantify genetic variation both within and among the principal subpopulations. Mitochondrial control region and tRNA gene sequences (359 base pairs) were obtained from 50 seals and revealed very low genetic diversity (0.6% variable sites), with no evidence of subpopulation differentiation. Multilocus DNA fingerprints from 22 individuals also indicated low genetic variation in at least some subpopulations (band-sharing values for "unrelated" seals from the same island ranged from 49 to 73%). This method also provided preliminary evidence of population subdivision (  F'_st estimates of 0.20 and 0.13 for two adjacent island pairs). Translocations of seals among islands may therefore have the potential to relieve local inbreeding and possibly to reduce the total amount of variation preserved in the population. Genetic variation is only one of many factors that determine the ability of an endangered species to recover. Maintenance of existing genetic diversity, however, remains an important priority for conservation programs because of the possibility of increased disease resistance in more variable populations and the chance that inbreeding depression may only be manifest under adverse environmental conditions.     

Mitochondrial DNA variation and population structure in the spiny lobster Panulirus argus

Adult spiny lobsters (Panulirus argus) were collected from nine locations throughout the tropical and subtropical northwest Atlantic Ocean and examined for mitochondrial DNA (mtDNA) variation. 187 different mtDNA haplotypes were observed among the 259 lobsters sampled. Haplotype diversity was calulated to be 0.986 and mean nucleotide sequence-diversity was estimated to be 1.44%; both of these values are among the highest reported values for a marine species. Analysis of molecular variance (AMOVA) and phenetic clustering both failed to reveal any evidence of genetic structure within and among populations of P. argus. The present data are consistent with high levels of gene flow among populations of P. argus resulting from an extended planktonic larval stage and strong prevailing ocean currents.     

Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations

Predicting and preventing outbreaks of infectious disease in endangered wildlife is problematic without an understanding of the biotic and abiotic factors that influence pathogen transmission and the genetic variation of microorganisms within and between these highly modified host communities. We used a common commensal bacterium, Campylobacter spp., in endangered Takahe (Porphyrio hochstetteri) populations to develop a model with which to study pathogen dynamics in isolated wildlife populations connected through ongoing translocations. Takahe are endemic to New Zealand, where their total population is approximately 230 individuals. Takahe were translocated from a single remnant wild population to multiple offshore and mainland reserves. Several fragmented subpopulations are maintained and connected through regular translocations. We tested 118 Takahe from 8 locations for fecal Campylobacter spp. via culture and DNA extraction and used PCR for species assignment. Factors relating to population connectivity and host life history were explored using multivariate analytical methods to determine associations between host variables and bacterial prevalence. The apparent prevalence of Campylobacter spp. in Takahe was 99%, one of the highest reported in avian populations. Variation in prevalence was evident among Campylobacter species identified. C. sp. nova 1 (90%) colonized the majority of Takahe tested. Prevalence of C. jejuni (38%) and C. coli (24%) was different between Takahe subpopulations, and this difference was associated with factors related to population management, captivity, rearing environment, and the presence of agricultural practices in the location in which birds were sampled. Modeling results of Campylobacter spp. in Takahe metapopulations suggest that anthropogenic management of endangered species within altered environments may have unforeseen effects on microbial exposure, carriage, and disease risk. Translocation of wildlife between locations could have unpredictable consequences including the spread of novel microbes between isolated populations.     

Relationship of Genetic Variation to Population Size in Wildlife

Genetic diversity is one of three levels of biological diversity requiring conservation. Genetic theory predicts that levels of genetic variation should increase with effective population size. Soulé (1976) compiled the first convincing evidence that levels of genetic variation in wildlife were related to population size, but this issue remains controversial. The hypothesis that genetic variation is related to population size leads to the following predictions: (1) genetic variation within species should be related to population size; (2) genetic variation within species should be related to island size; (3) genetic variation should be related to population size within taxonomic groups; (4) widespread species should have more genetic variation than restricted species; (5) genetic variation in animals should be negatively correlated with body size; (6) genetic variation should be negatively correlated with rate of chromosome evolution; (7) genetic variation across species should be related to population size; (8) vertebrates should have less genetic variation than invertebrates or plants; (9) island populations should have less genetic variation than mainland populations; and (10) endangered species should have less genetic variation than nonendangered species. Empirical observations support all these hypotheses. There can be no doubt that genetic variation is related to population size, as Soulé proposed. Small population size reduces the evolutionary potential of wildlife species.     

Evolutionary Significant Units versus Geopolitical Taxonomy: Molecular Systematics of an Endangered Sea Turtle (genus Chelonia)

Abstract: Taxonomic rank is an important criterion in assessing the conservation priority of an endangered organism: the sole member of a distinct family will generally receive a higher priority than a semi-isolated population in a polytypic species. When cryptic evolutionary partitions are discovered in endangered species, these findings are heralded as a positive step in the conservation process. The opposite action, demoting the taxonomic rank of an endangered organism, can be resisted by the conservation community because it is perceived as detrimental to preservation efforts. We explore the arguments for and against the species status of the endangered black turtle ( Chelonia agassizii ) and contribute an additional data set based on DNA sequences of single-copy nuclear loci. These data are concordant with previous mtDNA surveys in indicating no evolutionary distinction between C. agassizii and adjacent green turtle ( C. mydas ) populations. Although the black turtle is morphologically identifiable at a low level, much of its distinction is based on size and color differences that are highly variable throughout the range of C. mydas . Thus the black turtle would be more accurately classified at the subspecific or population level. There is no strong scientific case available to defend the species status of C. agassizii , and yet that designation has persisted for over a century. We suggest that the maintenance of this name is based on geographical and political considerations, and we propose a pragmatic category for this type of taxonomy: the geopolitical species . Furthermore, we argue against the practice of preserving species status for conservation purposes. There are several good reasons to preserve the black turtle, including morphological diversity and the possibility that it is an incipient evolutionary lineage with novel adaptations; taxonomic rank, however, is not one of them.