Phylogeny and biogeographic history of hake (genus Merluccius), inferred from mitochondrial DNA control-region sequences

 Phylogenetic analyses of the left domain of the mitochondrial DNA control-region sequence have been used to examine the relationships among species of the genus Merluccius (Rafinesque, 1810), and to compare these with hypotheses based on morphological, meristic and allozyme characters. Analysis of aligned sequences revealed that transition bias was much lower than in mammalian mtDNA, and that nucleotide composition of control-region sequences was biased toward A and T. We have roughly calibrated a molecular clock for the genus, based on the rise of the Isthmus of Panamá, which is believed to have created a barrier to dispersal between marine species of the Atlantic and Pacific Oceans. Our mtDNA-based phylogeny was highly congruent with allozyme-based phylogenies, but poorly so with a previously described phylogeny based on morphology. Specifically, our phylogeny resolved two well-supported principal clades, one of American (west Atlantic and east Pacific) species and the other of Euro–African (east Atlantic) species. This suggests an evolutionary history during which the ancestral lineage of Merluccius was divided between two geographic regions, with subsequent dispersal and vicariant events resulting in the evolution and distribution of extant taxa. However, the relationships between some taxa within the American clade could not be resolved. We suggest that this is consistent with an hypothesis of a rapid origin and radiation of these taxa. Received: 12 December 1998 / Accepted: 15 October 1999     

Incorporating geographical and evolutionary rarity into conservation prioritization

Key goals of conservation are to protect both species and the functional and genetic diversity they represent. A strictly species-based approach may underrepresent rare, threatened, or genetically distinct species and overrepresent widespread species. Although reserves are created for a number of reasons, including economic, cultural, and ecological reasons, their efficacy has been measured primarily in terms of how well species richness is protected, and it is useful to compare how well they protect other measures of diversity. We used Proteaceae species-occurrence data in the Cape Floristic Region of South Africa to illustrate differences in the spatial distribution of species and evolutionary diversity estimated from a new maximum-likelihood molecular phylogeny. We calculated species richness, phylogenetic diversity (i.e., summed phylogenetic branch lengths in a site), and a site-aggregated measure of biogeographically weighted evolutionary distinctiveness (i.e., an abundance weighted measure that captures the unique proportion of the phylogenetic tree a species represents) for sites throughout the Cape Floristic Region. Species richness and phylogenetic diversity values were highly correlated for sites in the region, but species richness was concentrated at a few sites that underrepresented the much more spatially extensive distribution of phylogenetic diversity. Biogeographically weighted evolutionary diversity produced a scheme of prioritization distinct from the other 2 metrics and highlighted southern sites as conservation priorities. In these sites, the high values of biogeographically weighted evolutionary distinctiveness were the result of a nonrandom relation between evolutionary distinctiveness and geographical rarity, where rare species also tended to have high levels of evolutionary distinctiveness. Such distinct and rare species are of particular concern, but are not captured by conservation schemes that focus on species richness or phylogenetic diversity alone.     

Phylogeny of Opsanus spp. (Batrachoididae) inferred from multiple mitochondrial-DNA sequences

 Species of the toadfish genus Opsanus are increasingly used as experimental organisms in biomedicine and evolutionary/ecological physiology. Despite their importance, little is known of the phylogenetic relationships among Opsanus species. DNA sequence data for portions of the mitochondrial 12S rRNA, cytochrome oxidase I and cytochrome b genes were generated and analyzed from the four recognized Opsanus species and three outgroup taxa. Results of these analyses indicate an evolutionarily rapid divergence of three lineages within the genus. O. beta and O. pardus were resolved within the same lineage, and could not be distinguished with these mitochondrial sequence data. These data and paleoclimatic theory support a hypothesis of speciation based on the formation of allopatric populations during periods of elevated water temperature in the northern Caribbean. Received: 6 July 1999 / Accepted: 15 March 2000     

Implications of Phylogenetic Studies for Conservation of Genetic Diversity in Shiitake Mushrooms

We consider the impact of recent molecular phylogenetic analyses on conservation issues for shiitake mushrooms. Bused on mating compatibility, shiitake has been considered a single species, Lentinula edodes sensu lato . Phylogenetic analyses of ribosomal RNA internal transcribed spacers (Hibbett et al. 1995), however, suggest that shiitake is composed of four distinct lineages. Thus, under a phylogenetic species concept, four species of shiitake should be recognized. A classification of shiitake based on a phylogenetic species concept would convey information about evolutionary relationships and distribution of genetic variation, whereas a classification based on a biological species concept would lack such information. This is a clear case in which new insights into phylogenetic relationships can be used to target areas for conservation action and formulate international agricultural policies. At the heart of our argument is the belief that the basic units of both taxonomy and conservation should be unique evolutionary lineages of organisms identified through phylogenetic studies.     

Designatable Units for Status Assessment of Endangered Species

Abstract:  Species status assessment and the conservation of biological diversity may require defining units below the species level to portray probabilities of extinction accurately and to help set priorities for conservation efforts. What those units should be has been debated in the scientific literature largely in terms of evolutionarily significant units (ESUs), but this discourse has had little impact on government policy with regard to status assessment. As with species concepts, the variously proposed ESU concepts have not been resolvable into a single approach. The need for a practicable procedure to identify infraspecific entities for status assignment is the motivation behind employing designatable units (DUs). In aid of a policy to prevent elements of biodiversity from becoming extinct or extirpated, DUs are determined during the process of resolving a species' conservation status according to broadly applicable guidelines. The procedure asks whether putative DUs are distinguishable based on a reliably established taxonomy or a well-corroborated phylogeny, compelling evidence of genetic distinction, range disjunction, and/or biogeographic distinction as long as extinction probabilities also differ. The language of the DU approach avoids wording that implies value judgments concerning evolutionary importance or significance. Because species conservation status assessment is not science but, rather, the use of science to further policy, DUs contribute to a precautionary approach to listing whereby status may be assessed even though knowledge of systematic relationships below the species level may be lacking or unresolved. The pragmatic approach of using DUs has been adopted by the Committee on the Status of Endangered Wildlife in Canada for status assessment of species under the Canadian Species at Risk Act.     

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.     

Specimen‐Based Modeling,Stopping Rules,and the Extinction of the Ivory‐Billed Woodpecker

Abstract: Assessing species survival status is an essential component of conservation programs. We devised a new statistical method for estimating the probability of species persistence from the temporal sequence of collection dates of museum specimens. To complement this approach, we developed quantitative stopping rules for terminating the search for missing or allegedly extinct species. These stopping rules are based on survey data for counts of co‐occurring species that are encountered in the search for a target species. We illustrate both these methods with a case study of the Ivory‐billed Woodpecker (Campephilus principalis), long assumed to have become extinct in the United States in the 1950s, but reportedly rediscovered in 2004. We analyzed the temporal pattern of the collection dates of 239 geo‐referenced museum specimens collected throughout the southeastern United States from 1853 to 1932 and estimated the probability of persistence in 2011 as <6.4 × 10^?5, with a probable extinction date no later than 1980. From an analysis of avian census data (counts of individuals) at 4 sites where searches for the woodpecker were conducted since 2004, we estimated that at most 1–3 undetected species may remain in 3 sites (one each in Louisiana, Mississippi, Florida). At a fourth site on the Congaree River (South Carolina), no singletons (species represented by one observation) remained after 15,500 counts of individual birds, indicating that the number of species already recorded (56) is unlikely to increase with additional survey effort. Collectively, these results suggest there is virtually no chance the Ivory‐billed Woodpecker is currently extant within its historical range in the southeastern United States. The results also suggest conservation resources devoted to its rediscovery and recovery could be better allocated to other species. The methods we describe for estimating species extinction dates and the probability of persistence are generally applicable to other species for which sufficient museum collections and field census results are available.     

Population Structure and Cryptic Evolutionary Units in the Alligator Snapping Turtle

The alligator snapping turtle (  Macroclemys temminckii ) is a long-lived, slow-growing chelydrid turtle found in Gulf of Mexico drainages from Florida to Texas (U.S.A.). Populations are thought to be depleted throughout the range due in part to an increased harvest in the 1960s through 1980s. To identify population and evolutionary units, 420 base pairs were sequenced within the mitochondrial DNA control region of 158 specimens from 12 drainages. Results indicate substantial phylogeographic structuring and strong population-level separations among river drainages. Eight of 11 haplotypes were observed to be river-specific, providing diagnostic markers for most drainages. Three partitions are resolved in the mtDNA genealogy, corresponding to the eastern, central, and western portion of the species' range. These separations coincide with recognized biogeographic provinces. The population structure by river system indicates that many drainages are distinct management units, with the Suwannee River lineage possibly deserving special attention, based on the criterion of genetic distinctiveness. The partitioning of M. temminckii into river-specific populations illustrates the management framework and conservation challenges that apply to a broad array of riverine species. Drainage-specific molecular markers may be used to identify the geographic origin of turtle products in the marketplace.     

Identifying conservation priorities for threatened Eastern Himalayan mammals

To augment mammal conservation in the Eastern Himalayan region, we assessed the resident 255 terrestrial mammal species and identified the 50 most threatened species based on conservation status, endemism, range size, and evolutionary distinctiveness. By using the spatial analysis package letsR and the complementarity core‐area method in the conservation planning software Zonation, we assessed the current efficacy of their protection and identified priority conservation areas by comparing protected areas (PAs), land cover, and global ecoregion 2017 maps at a 100 × 100 m spatial scale. The 50 species that were most threatened, geographically restricted, and evolutionarily distinct faced a greater extinction risk than globally nonthreatened and wide‐ranging species and species with several close relatives. Small, medium‐sized, and data‐deficient species faced extinction from inadequate protection in PAs relative to wide‐ranging charismatic species. There was a mismatch between current PA distribution and priority areas for conservation of the 50 most endangered species. To protect these species, the skewed regional PA distribution would require expansion. Where possible, new PAs and transboundary reserves in the 35 priority areas we identified should be established. There are adequate remaining natural areas in which to expand current Eastern Himalayan PAs. Consolidation and expansion of PAs in the EH requires strengthening national and regional transboundary collaboration, formulating comprehensive regional land‐use plans, diversifying conservation funding, and enhancing information sharing through a consolidated regional database.     

Using cumulative human-impact models to reveal global threat patterns for seahorses

Understanding threats acting on marine organisms and their conservation status is vital but challenging given a paucity of data. We studied the cumulative human impact (CHI) on and conservation status of seahorses (Hippocampus spp.)—a genus of rare and data-poor marine fishes. With expert knowledge and relevant spatial data sets, we built linear-additive models to assess and map the CHI of 12 anthropogenic stressors on 42 seahorse species. We examined the utility of indices of estimated impact (impact of each stressor and CHI) in predicting conservation status for species with random forest (RF) models. The CHI values for threatened species were significantly higher than those for nonthreatened species (category based on International Union for Conservation of Nature Red List). We derived high-accuracy RF models (87% and 96%) that predicted that 5 of the 17 data-deficient species were threatened. Demersal fishing practices with high bycatch and pollution were the best predictors of threat category. Major threat epicenters were in China, Southeast Asia, and Europe. Our results and maps of CHI may help guide global seahorse conservation and indicate that modeling and mapping human impacts can reveal threat patterns and conservation status for data-poor species. We found that for exploring threat patterns of focal species, species-level CHI models are better than existing ecosystem-level CHI models.     

National Responsibilities in European Species Conservation: a Methodological Review

Abstract: One particular challenge in reducing the loss of biodiversity by 2010, as agreed on at the Earth Summit in 2002, is to assign conservation tasks to geographic or administrative entities (e.g., countries or regions) on different geographical scales. To identify conservation tasks, it is imperative to determine the importance of a specific area for the global survival of a species. So far, these national or subnational responsibilities for the conservation of species have been included differently in methods prioritizing conservation. We reviewed how 12 European and 3 non‐European methods determined national conservation responsibilities and evaluated the international importance of a biological population. Different countries used different methodologies, which made a direct comparison of assessments of national responsibilities among countries extremely difficult. Differences existed in the importance criteria used. Criteria included population decline, range reduction, rarity status, degree of isolation of a population, endemism, proportional distribution, and geographic location. To increase comparability, it is imperative to develop criteria for which data are generally available and to standardize the methodology among countries. A standardized method would allow conservation decisions to be based on the conservation status of a species and on the responsibility of a geographic or administrative entity for the survival of a species. We suggest that such a method should use a scalable index of proportional distribution, taxonomic status, and the distribution pattern of a taxon or species as key elements. Such a method would allow for the creation of hierarchical lists and would be highly relevant for parts of the world with multiple political jurisdictions or state unions and for nations with regional governmental structures. Conservation priorities could then be reasonably set by combining national responsibility assessments with the international conservation status of a species.     

When Are Peripheral Populations Valuable for Conservation?

A great deal of effort is spent protecting geographically peripheral populations of widespread species. We consider under what conditions it is appropriate to expend resources to protect these populations. The conservation value of peripheral populations depends upon their genetic divergence from other conspecific populations. Peripheral populations are expected to diverge from central populations as a result of the interwoven effects of isolation, genetic drift, and natural selection. Available empirical evidence suggests that peripheral populations are often genetically and morphologically divergent from central populations. The long-term conservation of species is likely to depend upon the protection of genetically distinct populations. In addition, peripheral populations are potentially important sites of future speciation events. Under some circumstances, conservation of peripheral populations may be beneficial to the protection of the evolutionary process and the environmental systems that are likely to generate future evolutionary diversity.     

Biochemical genetic evidence supporting the taxonomic separation ofLoligo edulis andLoligo chinensis (Cephalopoda: Teuthoidea) from the genusLoligo

Confusion abounds regarding the relative generic status of many member species of the squid family Loliginidae. A taxonomie reorganisation within the family has been proposed in whichLoligo species from the Indo-Pacific possessing photophores on the ink sac, includingLogligo edulis andLoligo chinensis, are removed to the newly created genusPhotololigo. This system of classification has not however gained general acceptance, and some authors have continued to refer to these species asLoligo. Here biochemical genetic data gathered using allozyme electrophoresis are presented supporting the assertion thatL. edulis andL. chinensis should indeed be positioned in a genus distinct from that characterised by the type speciesLoligo vulgaris vulgaris. Cluster analysis of allele frequency data from 22 putative enzyme-coding loci suggests thatL. edulis andL. chinensis are as genetically distant fromL. vulgaris vulgaris as are members of the confamilial generaAlloteuthis, Uroteuthis andSepioteuthis, and as such warrant separate generic status. We conclude that the genusPhotololigo is valid.     

Conservation threats and the phylogenetic utility of IUCN Red List rankings in Incilius toads

Phylogenetic analysis of extinction threat is an emerging tool in the field of conservation. However, there are problems with the methods and data as commonly used. Phylogenetic sampling usually extends to the level of family or genus, but International Union for Conservation of Nature (IUCN) rankings are available only for individual species, and, although different species within a taxonomic group may have the same IUCN rank, the species may have been ranked as such for different reasons. Therefore, IUCN rank may not reflect evolutionary history and thus may not be appropriate for use in a phylogenetic context. To be used appropriately, threat‐risk data should reflect the cause of extinction threat rather than the IUCN threat ranking. In a case study of the toad genus Incilius, with phylogenetic sampling at the species level (so that the resolution of the phylogeny matches character data from the IUCN Red List), we analyzed causes of decline and IUCN threat rankings by calculating metrics of phylogenetic signal (such as Fritz and Purvis’ D). We also analyzed the extent to which cause of decline and threat ranking overlap by calculating phylogenetic correlation between these 2 types of character data. Incilius species varied greatly in both threat ranking and cause of decline; this variability would be lost at a coarser taxonomic resolution. We found far more phylogenetic signal, likely correlated with evolutionary history, for causes of decline than for IUCN threat ranking. Individual causes of decline and IUCN threat rankings were largely uncorrelated on the phylogeny. Our results demonstrate the importance of character selection and taxonomic resolution when extinction threat is analyzed in a phylogenetic context.     

Mitochondrial phylogeography of the killifish Aphanius fasciatus (Teleostei, Cyprinodontidae) reveals highly divergent Mediterranean populations

We studied the genetic structure of the Mediterranean killifish Aphanius fasciatus. Analysis of the sequence variation in a 372-bp portion of the mitochondrial control region in 623 fish from 27 sampling sites along the species’ distributional range (Tyrrhenian coast, Sardinia, Sicily, Adriatic coast, Malta, Tunisia, and Greece) yielded 120 distinct haplotypes. Most of the haplotypes are unique, and only 15 % are shared among different populations. The high F _ST value (=0.80) suggests a strong population genetic structuring. The phylogenetic analysis based on Bayesian inference, maximum likelihood and maximum parsimony, and the median-joining network show a sharp separation of the Southeastern Sicilian populations (belonging to the Hyblean region) and of the fluvial Tunisian population of Rio Melah from the others. The Adriatic, the Eastern Sicilian, and the Greek populations are well differentiated, while the group of populations from the Central-Western Mediterranean does not show a clear pattern of differentiation. Our findings indicate that the current genetic structuring of A. fasciatus reflects historical geographical patterns occurring within the Mediterranean basin from the Late Miocene to the Pleistocene. The presence of divergent evolutionary entities in the Hyblean region and the Tunisian Rio Melah supports their inclusion as target areas for the conservation of A. fasciatus.     

一株中度嗜盐菌的分离及生物学特性

从我国内蒙古吉兰泰盐湖的样品中分离得到一株中度嗜盐细菌菌株JLT-01,研究了其形态和特性.结果显示:该菌株为杆状,革兰氏阴性,无芽孢,无荚膜,无鞭毛;最适培养温度为30℃,最适生长pH值7.5,最适生长盐度10%~12%(m/V),最适生长Mg2+浓度3.0%(m/V);能利用葡萄糖、蔗糖、半乳糖作为唯一碳源生长.脂肪酸成分分析表明在JLT-01中主要脂肪酸为C16:0与C18:1ω9c,含量分别为26.39%和20.30%.Tm法测定该菌的(G+C)含量(摩尔分数)为52.3%.以该菌的16S rRNA基因序列为基础构建了系统发育树;16S rRNA基因序列的序列同源性比对表明该菌与海杆菌属Marinobacter lipolyticus SM19T的同源性为98.0%,与Marinobacter属内其它菌株的同源性在96.0%~99.0%之间.DNA-DNA杂交实验分析显示:JLT-01与M.lipolyticus DSM15157的杂交率小于70%.结果表明,菌株JLT-01是海杆菌属的一个新菌株.     

Threatened Species and the Potential Loss of Phylogenetic Diversity: Conservation Scenarios Based on Estimated Extinction Probabilities and Phylogenetic Risk Analysis

Abstract: New species conservation strategies, including the EDGE of Existence (EDGE) program, have expanded threatened species assessments by integrating information about species' phylogenetic distinctiveness. Distinctiveness has been measured through simple scores that assign shared credit among species for evolutionary heritage represented by the deeper phylogenetic branches. A species with a high score combined with a high extinction probability receives high priority for conservation efforts. Simple hypothetical scenarios for phylogenetic trees and extinction probabilities demonstrate how such scoring approaches can provide inefficient priorities for conservation. An existing probabilistic framework derived from the phylogenetic diversity measure (PD) properly captures the idea of shared responsibility for the persistence of evolutionary history. It avoids static scores, takes into account the status of close relatives through their extinction probabilities, and allows for the necessary updating of priorities in light of changes in species threat status. A hypothetical phylogenetic tree illustrates how changes in extinction probabilities of one or more species translate into changes in expected PD. The probabilistic PD framework provided a range of strategies that moved beyond expected PD to better consider worst‐case PD losses. In another example, risk aversion gave higher priority to a conservation program that provided a smaller, but less risky, gain in expected PD. The EDGE program could continue to promote a list of top species conservation priorities through application of probabilistic PD and simple estimates of current extinction probability. The list might be a dynamic one, with all the priority scores updated as extinction probabilities change. Results of recent studies suggest that estimation of extinction probabilities derived from the red list criteria linked to changes in species range sizes may provide estimated probabilities for many different species. Probabilistic PD provides a framework for single‐species assessment that is well‐integrated with a broader measurement of impacts on PD owing to climate change and other factors.     

Aligning science and policy to achieve evolutionarily enlightened conservation

There is increasing recognition among conservation scientists that long‐term conservation outcomes could be improved through better integration of evolutionary theory into management practices. Despite concerns that the importance of key concepts emerging from evolutionary theory (i.e., evolutionary principles and processes) are not being recognized by managers, there has been little effort to determine the level of integration of evolutionary theory into conservation policy and practice. We assessed conservation policy at 3 scales (international, national, and provincial) on 3 continents to quantify the degree to which key evolutionary concepts, such as genetic diversity and gene flow, are being incorporated into conservation practice. We also evaluated the availability of clear guidance within the applied evolutionary biology literature as to how managers can change their management practices to achieve better conservation outcomes. Despite widespread recognition of the importance of maintaining genetic diversity, conservation policies provide little guidance about how this can be achieved in practice and other relevant evolutionary concepts, such as inbreeding depression, are mentioned rarely. In some cases the poor integration of evolutionary concepts into management reflects a lack of decision‐support tools in the literature. Where these tools are available, such as risk‐assessment frameworks, they are not being adopted by conservation policy makers, suggesting that the availability of a strong evidence base is not the only barrier to evolutionarily enlightened management. We believe there is a clear need for more engagement by evolutionary biologists with policy makers to develop practical guidelines that will help managers make changes to conservation practice. There is also an urgent need for more research to better understand the barriers to and opportunities for incorporating evolutionary theory into conservation practice.     

Use of Congeneric Assessment to Reveal the Linked Genetic Histories of Two Threatened Fishes in the Murray‐Darling Basin,Australia

Abstract: The intensely regulated Murray‐Darling Basin in southeastern Australia is the nation's most extensive and economically important river system, and it contains fragmented populations of numerous fish species. Among these is the Murray hardyhead (Craterocephalus fluviatilis), a species listed as endangered (International Union for Conservation of Nature Red List) in the mid‐1990s prior to its acute decline with the progression of a severe drought that began in 1997. We compared the genetic structure of Murray hardyhead with 4 congeneric species (Darling hardyhead[C. amniculus], Finke hardyhead[C. centralis], Lake Eyre hardyhead[C. eyresii], and unspecked hardyhead[C. stercusmuscarum]), selected on the basis of their taxonomic or biological similarity to Murray hardyhead, in order to affirm species boundaries and test for instances of introgressive hybridization, which may influence species ecology and conservation prospects. We used allozyme (52 loci) and mtDNA markers (1999 bp of ATPase and cytochrome b) to provide a comparative genetic assessment of 139 Murray hardyhead, which represented all extant and some recently extirpated populations, and 71 congeneric specimens from 12 populations. We confirmed that Murray hardyhead and Darling hardyhead are taxonomically distinct and identified a number of potential conservation units, defined with genetic criteria, in both species. We also found allozyme and mtDNA evidence of historic genetic exchange between these 2 allopatric species, apparently involving one population of each species at the geographic edge of the species’ ranges, not in the most proximate populations sampled. Our results provide information on species boundaries and offer insight into the likely causes of high genetic diversity in certain populations, results which are already being used to guide national recovery planning and local action. Given the prevalence of incorrect taxonomies and introgression in many organismal groups, we believe these data point to the need to commence genetic investigations of any threatened species from an initially broad taxonomic focus.     

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.