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 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.     

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.     

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.     

Conservation Genetics at the Species Boundary

Abstract: Conservation genetics has expanded its purview such that molecular techniques are now used routinely to prioritize populations for listing and protection and infer their historical relationships in addition to addressing more traditional questions of heterozygosity and inbreeding depression. Failure to specify whether molecular data are being used for diagnosis-related questions or for population viability questions, however, can lead either to misinterpretation of character data as adaptive information or to misinterpretation of frequency or distance data as diagnostic or historical information. Each of these misinterpretations will confound conservation programs. The character-based approach to delimiting phylogenetic species is both operationally and logically superior to "diagnostic" methods that involve distance- or frequency-based routines, which are unstable over time. Tree-based criteria for the diagnosis of conservation "units" are also inappropriate because they can depend on patterns inferred without reference to diagnostic characters. Intraspecific studies, conservation-related or otherwise, that adopt terminology and methods designed to infer nested hierarchic relationships confuse diagnosis with historical inferences by treating diagnoses as outcomes rather than as precursors to phylogeny reconstruction. A character-based diagnostic approach recognizes the analytical dichotomy between species hierarchies and population statistics and provides a framework for the understanding of each. No species concept, however, should be viewed as an absolute criterion for protecting populations, but as part of a framework from within which identification of protection and management goals can be achieved effectively and defensibly.     

Mitochondrial DNA Variability of the Gray Wolf: Genetic Consequences of Population Decline and Habitat Fragmentation

The gray wolf is a large, highly mobile predator whose original geographic range included most of the Northern Hemisphere. High rates of genetic exchange probably characterized even distantly-separated populations in the past, but recent population declines and habitat fragmentation have isolated previously contiguous populations, especially in the Old World. We examine mitochondrial DNA (mtDNA) variability among twenty-six populations of wolves from throughout their geographic range. We find eighteen mtDNA genotypes in gray wolves, seven of these are derived from hybridization with coyotes, four are confined to the New World, six are confined to the Old World and one is shared by both areas. Genetic differentiation among wolf populations is significant but small in magnitude. In the Old World, most localities have a single unique genotype, whereas in the New World several genotypes occur at most localities and three of the five genotypes are nearly ubiquitous. The pattern of genetic differentiation in the gray wolf contrasts with that of another large, highly vagile canid, the coyote, in which genetic differentiation among populations is not significant even among widely separated localities. We suggest that the difference between these two species reflects the rapid, recent increase in coyote numbers and expansion of their geographic range, and the coincident decline in gray wolf populations. Apparent genetic differences among extant wolf populations may be a recent phenomenon reflecting population declines and habitat fragmentation rather than a long history of genetic isolation.     

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.     

Mitochondrial DNA Variability in Italian and East European Wolves: Detecting the Consequences of Small Population Size and Hybridization

Abstract: The Italian wolf ( Canis lupus ) population has declined continuously over the last few centuries and become isolated as a result of the extermination of other populations in central Europe and the Alps during the nineteenth century. In the 1970s, approximately 100 wolves survived in 10 isolated areas in the central and southern Italian Apennines. Loss of genetic variability, as suggested by preliminary studies of mitochondrial DNA (mtDNA) sequences, hybridization with feral dogs, and the illegal release of captive, non-native wolves are considered potential threats to the viability of the Italian wolf population. We sequenced 546 base pairs of the mtDNA control region in a comprehensive set of Italian wolves and compared them to those of dogs and other wolf populations from Europe and the Near East. Our data confirm the absence of mtDNA variability in Italian wolves: all 101 individuals sampled across their distribution in Italy had the same, unique haplotype, whereas seven haplotypes were found in only 26 wolves from an outbred population in Bulgaria. Most haplotypes were specific either to wolves or dogs, but some east European wolves shared haplotypes with dogs, indicative of hybridization. In contrast, neither hybridization with dogs nor introgression of non-native wolves was detected in the Italian population. These findings exclude the introgression of dog genes via matings between male wolves and female dogs, the most likely direction of hybridization. The observed mtDNA monomorphism is the possible outcome of random drift in the declining and isolated Italian wolf population, which probably existed at low effective population size during the last 100–150 years. Low effective population size and the continued loss of genetic variability might be a major threat to the long-term viability of Italian wolves. A controlled demographic increase, leading to recolonization of the historical wolf range in Italy, should be enforced.     

Conservation Genetics of the Endangered Isle Royale Gray Wolf

Abstract. The small group of wolves on Isle Royale has been studied for over three decades as a model of the relationship between large carnivores and their prey. During the last ten years the population declined from 50 individuals to as few as 12 individuals. The causes of this decline may be food shortages, disease, or reduced genetic variability. We address the issues of genetic variability and relationships of Isle Royale wolves using allozyme electrophoresis, mtDNA restriction-site analysis, and multilocus hypervariable minisatellite DNA analysis (genetic fingerprinting). Our results indicate that approximately 50% of the allozyme heterozygosity has been lost in the island population, a decline similar to that expected if no immigration had occurred from the mainland. The genetic fingerprinting data indicate that the seven sampled Isle Royale wolves are as similar as captive populations of siblings. Surprisingly, the Isle Royale wolves have an mDNA genotype that is very rare on the mainland, being found in only one of 144 mainland wolves ThFF suggests that the remaining Isle Royale wolves areprobably derived from a single female founder     

Genetics, Taxonomy, and Conservation of the Threatened California Gnatcatcher

Abstract: The California Gnatcatcher (   Polioptila californica ) has become a flagship species in the dispute over development of southern California's unique coastal sage scrub habitat, a fragile, geographically restricted ecosystem with high endemism. One aspect of the controversy concerns the status of the subspecies of this bird in southern California coastal sage scrub that is currently listed as threatened under the U.S. Endangered Species Act. To investigate the recent population history of this species and the genetic distinctiveness of subspecies and to inform conservation planning, we used direct sequencing of mitochondrial DNA (mtDNA) for 64 individuals from 13 samples taken throughout the species' range. We found that coastal sage scrub populations of California Gnatcatchers are not genetically distinct from populations in Baja California, which are dense and continuously distributed throughout the peninsula. Rather, mtDNA sequences from this species contain the signatures of population growth and support a hypothesis of recent expansion of populations from a southern Baja California refugium northward into the southern coastal regions of California. During this expansion, stochastic events led to a reduction in genetic variation in the newly occupied range. Thus, preservation of coastal sage scrub cannot be linked to maintaining the genetic diversity of northern gnatcatcher populations, despite previous recognition of subspecies. Our study suggests that not all currently recognized subspecies are equivalent to evolutionarily significant units and illustrates the danger of focusing conservation efforts for threatened habitats on a single species.     

Conservation Genetics of North American Freshwater Mussels Amblema and Megalonaias

Freshwater bivalves are among the most endangered groups of organisms in North America. Efforts to protect the declining mussel fauna are confounded by ambiguities associated with recognition of distinct evolutionary entities or species. This, in part, is due to the paucity of reliable morphological characters for differentiating taxa. We have employed allozymes and DNA sequence data to search for diagnosably distinct evolutionary entities within two problematic genera of unionid mussels, Amblema and Megalonaias. Within the genus Amblema three species are recognized based on our DNA sequence data for the mitochondrial 16S rRNA and allozyme data (Amblema neislerii, A. plicata, and A. elliotti). Only one taxonomically distinct entity is recognized within the genus Megalonaias—M. nervosa. Megalonaias boykiniana of the Apalachicolan Region is not diagnosable and does not warrant specific taxonomic status. Interestingly, Megalonaias from west of the Mississippi River, including the Mississippi, exhibited an allozyme and mtDNA haplotype frequency shift suggestive of an east-west dichotomy. The results of this study eliminate one subspecies of Amblema and increase the range of A. plicata. This should not affect the conservation status of "currently stable" assigned to A. plicata by Williams et al. (1993). The conservation status of A. elliotti needs to be reexamined because its distribution appears to be limited to the Coosa River System in Alabama and Georgia.