Utility of Mitochondrial DNA Barcodes in Species Conservation

Abstract:  Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.     

Conservation Genetics of the Black Rhinoceros (Diceros bicornis), I: Evidence from the Mitochondrial DNA of Three Populations

Abstract: A drastic decline in the number of black rhinoceroses ( Diceros bicornis ), primarily as a result of poaching places this species in imminent danger of extinction. The remaining black rhinos are divided into small, isolated populations that are vulnerable to demographic extinction, disease epidemics, genetic drift and inbreeding. Some conservationists have suggested minimizing these threats by moving as many animals as possible from different isolated populations to a few safe "rhino sanctuaries." To examine the possible long-term genetic consequences of such a strategy, we focused our efforts on determining the level of genetic differences among the remaining black rhino populations by examining restriction fragment length polymorphisms of the rapidly evolving mitochondrial DNA molecule. The 23 black rhinos in our survey, including animals from three geographic regions and two named subspecies, showed very little mitochondrial DNA differentiation. Only 4 out of 18 restriction enzymes revealed any mtDNA polymorphism, and the average estimated percent sequence divergence between the four mtDNA genotypes observed as 0.17%. Mitochondrial DNA divergence between the two named subspecies, D. b. minor and D. b. michaeli , was estimated to be only 0.29%. These results indicate a very close genetic relationship among the black rhinos in our survey. Thus, the mitochondrial DNA data suggest that within national boundaries, the black rhino populations we sampled may be considered single populations for breeding purposes, which might increase the species' probability of survival.     

Mitochondrial DNA Phylogeography and the Conservation of Endangered Lesser Antillean Icterus Orioles

Abstract: Recent natural and anthropogenic disturbances have endangered two of the three oriole species endemic to single islands in the Lesser Antilles. The ongoing eruption of the Soufriere Hills volcano may have doomed the Montserrat Oriole (   Icterus oberi ), whereas high levels of nest parasitism by a cowbird threaten the Martinique Oriole (   I. bonana ). These orioles and related Antillean and Central American forms have been considered part of the Icterus dominicensis superspecies complex, but the taxonomic status of the different Antillean island populations has been long debated. To investigate levels of evolutionary differentiation among threatened Lesser Antillean orioles, we analyzed 2507 nucleotides of protein-coding mitochondrial DNA (mtDNA) sequence from orioles on Martinique, Montserrat, St. Lucia (   I. laudabilis ), Puerto Rico (   I. dominicensis dominicensis ), Mexico (   I. d. prosthemelas ), and three Icterus outgroup species. Phylogenetic analyses of the mtDNA data supported the monophyly of Antillean members of the I. dominicensis complex and identified a star-like pattern of relationship among them. Mitochondrial distances between the Antillean populations were large (4.5–5.8% nucleotide divergence) and suggested that the Lesser Antillean orioles have been isolated evolutionarily from one another since the late Pliocene. The oriole taxa on Montserrat, Martinique, and St. Lucia meet species criteria under the phylogenetic species concept and represent evolutionarily significant units. The impending extinction of the phylogenetically unique Montserrat oriole highlights the vulnerability of island endemics to habitat degradation followed by rare and unpredictable natural catastrophes.     

Regional Consequences of Local Population Demography and Genetics in Relation to Habitat Management in Gentiana pneumonanthe

Abstract:  A joint demographic and population genetics stage-based model for a subdivided population was applied to Gentiana pneumonanthe , an early successional perennial herb, at a regional (metapopulation) scale. We used numerical simulations to determine the optimal frequency of habitat disturbance (sod cutting) and the intensity of gene flow among populations of G. pneumonanthe to manage both population viability and genetic diversity in this species. The simulations showed that even small populations that initially had near-equal allele frequencies could, if managed properly through sod cutting every 6 to 7 years, sustain their high genetic variation over the long run without gene flow. The more the allele frequencies in the small populations are skewed, however, the higher the probability that in the absence of gene flow, some alleles will be lost and within-population genetic variation will decrease even under proper management. This implies that although local population dynamics should be the major target for management, regional dynamics become important when habitat fragmentation and decreased population size lead to the loss of local genetic diversity. The recommended strategy to improve genetic composition of small populations is the introduction of seeds or seedlings of nonlocal origin.     

Releasing Adults versus Young in Reintroductions: Interactions between Demography and Genetics

Abstract:  We integrated genetics and demography into population modeling in the context of species restorations, in which both the origin of released individuals and the management strategy may influence the success of introduction. Through an explicit individual-based simulation approach, we investigated the effects of the age of released individuals by exploring the relative merits of releasing juveniles or adults to establish populations. We included the effect of genetic variability responsible for inbreeding depression and mutational meltdown. Our general analysis uncovered an interaction between the age of founders and the extent of intrapopulation fitness variability, which substantially influenced the efficiency of selection in populations founded by juveniles and had subsequent positive consequences for long-term persistence compared with the case in which adults were released. We then applied the model to the case of the reintroduction of the Griffon Vulture ( Gyps fulvus fulvus ) to southern France, for which post-release data were available. The demographic aspects of this reintroduction were already analyzed and published, suggesting that it is more efficient to release adults than juveniles, despite an observed reduction of demographic parameters following the release of adults. In that context, the inclusion of genetic considerations qualitatively changes the conclusion, predicting reduced long-term extinction risk if juveniles rather than adults are released.     

Mitochondrial DNA Variation in Black Rhinoceros (Diceros bicornis): Conservation Management Implications

Cell cultures have been established from 33 individual black rhinoceroses. These were from wild populations from various localities in southern Africa and include representatives from three geographical regions (southwestern, south-central, and eastern) corresponding to currently accepted conservation units, and include individuals previously attributed to one of the four subspecies, Diceros b. minor, D. b. bicornis, D. b. michaeli , and D. b. chobiensis (du Toit et al. 1987). Comparative mitochondrial DNA restriction maps were constructed using 16 restriction enzymes. These showed in each case two site differences between representative individuals from any two of the above geographical regions. Maps were monomorphic within geographical regions and, therefore, have the potential to provide diagnostic markers. The map from a single individual attributed to the D. b. chobiensis subspecies was identical to other individuals (attributed to D. b. minor ) in the south-central geographical region. The low amount of genetic diversity implied by these few differences renders it unlikely that problems with outbreeding depression will arise if, given the continuing decline in numbers of black rhinoceroses, it becomes necessary to supplement wild or captive populations with individuals from a different conservation unit in order to avoid inbreeding depression.     

Conservation Genetics in the Management of Desert Fishes

Abstract: The status and security of fishes in North American deserts have steadily declined in this century due to man's activities in this naturally fragile region. We address genetic aspects of the population structure of desert fishes as applicable to conservation and recovery programs by developing two zoogeographic models of isolation and gene flow. In the Death Valley model populations are isolated, with no chance of natural gene flow among them. Genetic diversity within populations tends to be low, but genetic divergence among populations within a species is high. In the Stream Hierarchy model, a complicated hierarchical genetic structure exists and is a function of geographic proximity and connectivity of habitats. Within-habitat genetic diversity tends to be higher, and among-habitat differentiation lower, than in the Death Valley model. These two systems must be recognized as distinct and managed differently. We also suggest three areas of experimentation needed to better understand and manage genetic stocks of desert fishes: relationships between heterozygosity and fitness, experimental mixing of similar stocks to examine effects of increased heterozygosity, and analysis of the relative roles of genetic adaptation and phenotypic plasticity in local differentiation.