Subspecific relationships and genetic structure in the spotted owl

Hierarchical genetic structure was examined in the three geographically-defined subspecies of spotted owl (Strix occidentalis) to define relationships among subspecies and quantify variation within and among regional and local populations. Sequences (522 bp) from domains I and II of the mitochondrial control region were analyzed for 213 individuals from 30 local breeding areas. Results confirmed significant differences between northern spotted owls and the other traditional geographically defined subspecies but did not provide support for subspecific level differences between California and Mexican spotted owls. Divergence times among subspecies estimated with a 936 bp portion of the cytochrome b gene dated Northern and California/Mexican spotted owl divergence time to 115,000–125,000 years ago, whereas California/Mexican spotted owl divergence was estimated at 15,000 years ago. Nested clade analyses indicated an association between California spotted owl and Mexican spotted owl haplotypes, implying historical contact between the two groups. Results also identified a number of individuals geographically classified as northern spotted owls (S. o. caurina) that contained haplotypes identified as California spotted owls (S. o. caurina). Among all northern spotted owls sampled (n=131), 12.9% contained California spotted owl haplotypes. In the Klamath region, which is the contact zone between the two subspecies, 20.3% (n=59) of owls were classified as California spotted owls. The Klamath region is a zone of hybridization and speciation for many other taxa as well. Analyses of population structure indicated gene flow among regions within geographically defined subspecies although there was significant differentiation among northern and southern regions of Mexican spotted owls. Among all areas examined, genetic diversity was not significantly reduced except in California spotted owls where the southern region consists of one haplotype. Our results indicate a stable contact zone between northern and California spotted owls, maintaining distinct subspecific haplotypes within their traditional ranges. This supports recovery efforts based on the traditional subspecies designation for the northern spotted owl. Further, although little variation was found between California and Mexican spotted owls, we suggest they should be managed separately because of current isolation between groups.     

Genetic diversity, structure, and demographic change in tanoak, Lithocarpus densiflorus (Fagaceae), the most susceptible species to sudden oak death in California

Knowledge of population genetic structure of tanoak (Lithocarpus densiflorus) is of interest to pathologists seeking natural variation in resistance to sudden oak death disease, to resource managers who need indications of conservation priorities in this species now threatened by the introduced pathogen (Phytophthora ramorum), and to biologists with interests in demographic processes that have shaped plant populations. We investigated population genetic structure using nuclear and chloroplast DNA (cpDNA) and inferred the effects of past population demographic processes and contemporary gene flow. Our cpDNA results revealed a strong pattern of differentiation of four regional groups (coastal California, southern Oregon, Klamath mountains, and Sierra Nevada). The chloroplast haplotype phylogeny suggests relatively deep divergence of Sierra Nevada and Klamath populations from those of coastal California and southern Oregon. A widespread coastal California haplotype may have resulted from multiple refugial sites during the Last Glacial Maximum or from rapid recolonization from few refugia. Analysis of nuclear microsatellites suggests two major groups: (1) central coastal California and (2) Sierra Nevada/Klamath/southern Oregon and an area of admixture in north coastal California. The low level of nuclear differentiation is likely to be due to pollen gene flow among populations during postglacial range expansion.     

Habitat Selection by American Martens in Coastal California

ABSTRACT We investigated habitat selection using single- and mixed-scale modeling at 2 spatial scales, stand and home range, by the only known population of American martens (Martes americana) remaining in the historical range of the Humboldt subspecies (M. a. humboldtensis) in California, USA. During 2000 and 2001, we sampled a 12 times 14 grid with 2-km spacing, using 2 sooted track plates at each grid point. We detected martens at 26 of the 159 grid points. We used resource selection probability functions and an information-theoretic method to model habitat at detection locations. At the stand scale, martens selected conifer-dominated stands with dense, spatially extensive shrub cover (x̄ = 74% cover, SE = 4) in the oldest developmental stage. At the home-range scale, martens selected the largest available patches (x̄ = 181 ha, SE = 14) of old-growth, old-growth and late-mature, or serpentine habitat. Mixed-scale models revealed that habitat characteristics from both scales best explained marten occurrence compared to one scale alone. Dense, spatially extensive shrub cover is a key habitat element for martens in coastal forests. Dense shrubs provide refuge from predators, cover for prey, and may also deter larger-bodied competitors. Managers can increase the likelihood of marten population persistence and encourage expansion in coastal forests by maintaining and restoring late-mature and old-growth, conifer-dominated forests with dense shrub cover in large, contiguous patches.     

Use of Museum Specimens to Refine Historical Pronghorn Subspecies Boundaries

Endangered Sonoran (Antilocapra americana sonoriensis) and Peninsular (A. a. peninsularis) pronghorn persist largely because of captive breeding and reintroduction efforts. Recovery team managers want to re-establish pronghorn in their native range, but there is currently uncertainty regarding the subspecies status of extinct pronghorn populations that historically inhabited southern California, USA, and northern Baja California, Mexico. To address this uncertainty, we genotyped museum specimens and conducted phylogenetic and population genetic analyses of historical data in the context of 3 contemporary pronghorn populations. The historical northern Baja California pronghorn share the most ancestry with contemporary Peninsular pronghorn, whereas pronghorn in southern California share more ancestry with contemporary American (A. a. americana) pronghorn. For reintroductions into northern Baja California, the Peninsular subspecies is more appropriate based on museum genetic data. For reintroductions into Southern California, ecological and genetic factors are both important, as the subspecies most genetically related to historical populations (American) may not be well-adapted to the hot, low-elevation deserts of the reintroduction area. © 2019 The Wildlife Society.     

Conservation genetics of the fisher (Martes pennanti) based on mitochondrial DNA sequencing

Translocation of animals to re-establish extirpated populations or to maintain declining ones has often been carried out without genetic information on source or target populations, or adequate consideration of the potential effects of mixing genetic stocks. We consider the conservation status of the fisher (Martes pennanti) and evaluate the potential genetic consequences of past and future translocations on this medium-sized carnivore by examining population variation in mitochondrial control-region sequences. We sampled populations throughout the fisher's range in North America including five populations unaffected by translocations and two western populations that had received long-distance translocations. Twelve haplotypes showed little sequence divergence. Haplotype frequencies differed significantly among subspecies and between populations within subspecies. Analysis of molecular variance (amova) and neighbour-joining analyses of haplotype relationships revealed population subdivision similar to current subspecies designations, but which may reflect an isolation-by-distance pattern. Populations in Oregon and in Montana and Idaho received several translocations and each showed greater similarity to the populations where translocations originated than to adjacent populations. Additional sequences obtained from museum specimens collected prior to any translocations suggest historical gene flow among populations in British Columbia, Washington, Oregon, and California. Anthropogenic impacts in that region have greatly reduced and isolated extant populations in Oregon and California. Future translocations may be necessary to recover populations in Washington and portions of Oregon and California; our results indicate that British Columbia would be the most appropriate source population.     

Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of California

The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small F_ST values (?0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep‐water channel from the coastal sites, however, was significantly divergent (large F_ST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size.     

Inferring Geographic Isolation of Wolverines in California Using Historical DNA

ABSTRACT Delineating a species' geographic range using the spatial distribution of museum specimens or even contemporary detection-non-detection data can be difficult. This is particularly true at the periphery of a species range where species' distributions are often disjunct. Wolverines (Gulo gulo) are wide-ranging mammals with discontinuous and potentially isolated populations at the periphery of their range. One potentially disjunct population occurred in the Sierra Nevada Mountains, California, USA, and appears to have been extirpated by the 1930s. Many early 20th century naturalists believed that this population was connected to other populations occurring in the Cascade Range of northern California, Oregon, and Washington, USA, but a recent analysis of historical records suggests that California wolverines were isolated from other populations in North America. We used DNA extracted from museum specimens to examine whether California wolverines were isolated. Both nuclear and mitochondrial DNA data indicate that California wolverines were genetically distinct from extant populations, suggesting long-term isolation. We identified 2 new control region (mitochondrial DNA) haplotypes located only within California. We used these data and referenced sequences from the Rocky Mountains, USA, to make inferences regarding potential wolverine translocations into California. In addition, we used these genetic data to make inferences about wolverine conservation throughout western North America.     

Growth and persistence of a recent invader <Emphasis Type="Italic">Carcinus maenas</Emphasis> in estuaries of the northeastern Pacific

During the summer of 1998 a new year class of the invasive European green crab, Carcinus maenas, appeared in Oregon and Washington estuaries as well as in northern California, USA, and on Vancouver Island, Canada. This invader was first discovered in San Francisco Bay almost a decade earlier and by 1995 it had spread to northern California. The coast-wide colonization event we studied in 1998 (El Niño cohort) was correlated with unusually strong north flowing coastal currents from September 1997 to April 1998. Larval transport by ocean currents from established populations to the south appeared to be the mechanism for the colonization. Crabs from the 1998-year class grew faster than counterparts from Maine and Europe, averaging 14 mm in carapace width in June, and 46 mm by September 1998. By the end of their second summer, males ranged from 52 to 80 mm in carapace width, and by fall of 2000 some males attained a carapace width of over 90 mm. The life span for C. maenasit in Oregon, Washington and British Columbia is estimated to be similar as in Europe and Maine: 4–6 years. Even though the initial colonists (98-year class) are dying of senescence, and coastal currents have not been favorable for larval transport from source populations in California, green crabs do persist in Oregon and Washington estuaries. It appears that local reproduction and recruitment in some years is high enough to keep this population from going extinct.     

Genetic variation in two widespread species of salamanders,Taricha granulosa and Taricha torosa

Two species of the genus Taricha are widely distributed. T. granulosa ranges from southern Alaska to central California. T. torosa is comprised of two described subspecies, T. t. torosa, which occupies much of the coast ranges of California, and T. t. sierrae, which inhabits the western slopes of the Sierra Nevada Mountains. A starch gel electrophoretic survey for genetic variation at 34 loci in four population samples of T. granulosa and at 40 loci in five population samples of T. torosa reveals differences among these taxa both in amounts of intrapopulational variability and in patterns of geographic variation. Average observed heterozygosity is 9.6%±0.3% in T. granulosa, 3.3%±0.5% in T. t. torosa, and 7.2%±1.2% in T. t. sierrae. Average numbers of alleles per locus and proportions of polymorphic loci are also highest in T. granulosa, intermediate in T. t. sierrae, and lowest in T. t. torosa. Oregon and California granulosa are genetically nearly as different as the subspecies of torosa, but geographic variation is continuous in the former. T. torosa on the other hand is comprised of three distinct gene pools—T. t. sierrae and northern and southern races of T. t. torosa. Strikingly different amounts of intrapopulational genetic variation and patterns of geographic variation may be explained by steadystate species differences, but historical causes may also exist.This work was supported by AEC Research Contract AT(04-3)34 and NSF Grant GB-42246 to F. J. Ayala and by an NIH predoctoral traineeship administered by the Department of Genetics, U.C. Davis.     

PHYLOGEOGRAPHY OF SPOTTED OWL (STRIX OCCIDENTALIS) POPULATIONS BASED ON MITOCHONDRIAL DNA SEQUENCES: GENE FLOW,GENETIC STRUCTURE,AND A NOVEL BIOGEOGRAPHIC PATTERN

Mitochondrial DNA control region sequences of spotted owls (Strix occidentalis) allowed us to investigate gene flow, genetic structure, and biogeographic relationships among these forest-dwelling birds of western North America Estimates of gene flow based on genetic partitioning and the phylogeography of haplotypes indicate substantial dispersal within three long-recognized subspecies. However, patterns of individual phyletic relationships indicate a historical absence of gene flow among the subspecies, which are essentially monophyletic. The pattern of haplotype coalescence enabled us to identify the approximate timing and direction of a recent episode of gene flow from the Sierra Nevada to the northern coastal ranges. The three subspecies comprise phylogenetic species, and the northern spotted owl (S. o. caurina) is sister to a clade of California (S. o. occidentalis) plus Mexican spotted owls (S o lucida); this represents a novel biogeographic pattern within birds. The California spotted owl had substantially lower nucleotide diversity than the other two subspecies; this result is inconsistent with present patterns of population density A causal explanation requires postulating a severe bottleneck or a selective sweep, either of which was confined to only one geographic region.     

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911–1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F _ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F _ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F _ST = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F _ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F _CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F _SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.     

Limited realized dispersal and introgressive hybridization influence genetic structure and conservation strategies for brown rockfish, <Emphasis Type="Italic">Sebastes auriculatus</Emphasis>

Understanding patterns of connectivity among marine fish populations with demersal adults and pelagic larvae is critical for effective conservation of west coast rockfishes. The brown rockfish (Sebastes auriculatus) occurs in nearshore habitat and is common from northern Baja California, Mexico to northern California, rare off the outer coast of Oregon and Washington and again common in the inland waters of Puget Sound, Washington. Here we examine patterns of microsatellite DNA diversity from throughout the species’ range as an indirect measure of long-term trends in larval dispersal. Genetic divergence was large and highly significant over all populations (F _ST=0.056, P<0.0001), and was significantly correlated with geographic distance when considering coastal populations. The best estimates of mean coastal dispersal distance were on the order of 10 km or less per generation. Diversity was relatively low in the Puget Sound, suggesting that Puget Sound rockfish populations experienced a post-glacial founder effect followed by genetic isolation and low effective population size. Puget Sound individuals appeared to have recent mixed ancestry as a result of introgression with S. maliger and S. caurinus. Genetic isolation of Puget Sound fish provides a basis for consideration as a Distinct Population Segment (DPS) under the provisions of the Endangered Species Act. We recommend that coastal brown rockfish fisheries be managed at regional rather than coast-wide scales, and that design of marine reserve networks considers the surprisingly low realized dispersal distance of some species with high dispersal potential.     

Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (Centrocercus urophasianus phaios) subspecies of Sage-grouse using mitochondrial control-region sequence data

The status of Sage-grouse (Centrocercusurophasianus) is of increasing concern, aspopulations throughout its range havecontracted as a result of habitat loss anddegradation. Historically, Sage-grouse wereclassified into two subspecies: eastern(C. u. urophasianus) and westernSage-grouse (C. u. phaios) based onslight differences in coloration noted amongeight individuals sampled from Washington,Oregon, and California. We sequenced a rapidlyevolving portion of the mitochondrial controlregion in 332 birds from 16 populations. Although our sampling area covers the proposedboundary between the eastern and westernsubspecies, no genetic evidence to support thedelineation of these subspecies was found. However, a population straddling southwesternNevada and eastern California was found tocontain an unusually high proportion of uniquehaplotypes, consistent with its geneticisolation from other Sage-grouse populations. Of additional interest was the lack ofdiversity in the two populations sampled fromWashington, one of which contained only asingle haplotype. We suggest that multiplelines of evidence are valuable for theformulation of conservation strategies andhence the southwestern Nevada/easternCalifornia population merits furthermorphological, behavioral, and molecular investigation.     

ALPHA-CHAIN HEMOGLOBIN POLYMORPHISMS ARE CORRELATED WITH ALTITUDE IN THE DEER MOUSE,PEROMYSCUS MANICULATUS

In deer mouse (Peromyscus maniculatus) populations in the western United States, alpha-globin haplotype frequency, beta-globin haplotype frequency, and base-line blood oxygen affinity (measured after acclimation to low altitude) show strong correlations with native altitude. The correlations improve when an average regional altitude is substituted for the local altitude at collection sites. This substitution roughly compensates for the effects of gene exchange between populations in areas of highly variable topography. When subspecific effects are removed with covariate analyses a significant (P < 0.05) relationship remains only for alpha-globin haplotype frequency and altitude. Thus, alpha-globin haplotype frequency, beta-globin haplotype frequency, and base-line blood oxygen affinity may be explained by either subspecific or altitudinal effects, but subspecific effects explain a larger proportion of the variance. Part of the subspecific effect may be attributable to an underlying relationship of subspecies with altitude. The analyses for the alpha-globins in conjunction with other data on the effects of alpha-globins on blood oxygen affinity and whole-animal physiological performance are consistent with the hypothesis that the frequency of the alpha-globins evolved in response to selection resulting from the stress of high-altitude hypoxia.     

Mitochondrial DNA and plumage evolution in the white wagtail Motacilla alba

We analyzed sequences of two mitochondrial DNA (mtDNA) gene regions (control region and ND2) totaling 1477 base‐pairs from 232 specimens of the white wagtail Motacilla alba obtained from 27 localities throughout Eurasia. Although overall haplotype diversity was relatively low (0.79) and the most common haplotype was shared by 45% of individuals, belonging to six subspecies, a high level of population differentiation was detected. The mtDNA tree revealed three clades: (1) most individuals from Krasnodar (belonging to M. a. alba subspecies), (2) all individuals from Almaty and some from Primor'e (belonging to M. a. personata, M. a. lugens and M. a. leucopsis subspecies), and (3) the remaining individuals (representing all subspecies and all localities except Almaty). We suggest that these three clades represent historically isolated populations that relatively recently came into secondary contact in Krasnodar and Primor'e. None of the six subspecies were reciprocally monophyletic in the mtDNA tree. The Krasnodar population appeared to receive immigrants from other localities, but distinctive haplotypes from this locality did not appear elsewhere, suggesting asymmetric gene flow. Signatures of recent gene flow between northern populations were detected, and there was no evidence of isolation by distance within the northern group of populations. Mismatch distributions for most localities were consistent with population expansions. We also analyzed 12 male plumage characters from 93 study skins sampled from 24 populations. Phylogenetic trees resulting from separate genetic and morphological analyses were incongruent. Plumage evolution seems to be under strong sexual or natural selection, which favors particular phenotypes in various areas irrespective of the mitochondrial background. Dispersal events at different evolutionary times could have obscured the effects of earlier isolation events. The mtDNA data does not support species status for M. a. lugens and M. a. personata, which shared haplotypes with other subspecies of M. alba. We recommend that M. lugens and M. personata are placed as junior synonyms of M. alba.     

A non-invasive genetic method to identify the sympatric mustelids pine marten (<Emphasis Type="Italic">Martes martes</Emphasis>) and stone marten (<Emphasis Type="Italic">Martes foina</Emphasis>): preliminary distribution survey on the northern Iberian Peninsula

The closely related mustelids European pine marten (Martes martes) and stone marten (Martes foina) sympatrically inhabit a large area of Europe. However, given our limited knowledge of their bioecological relationships, their extremely elusive behaviour and the fact that their faeces cannot be distinguished on the basis of morphology alone, it is very difficult to monitor their populations. In this study, we describe a reliable non-invasive polymerase chain reaction (PCR)–restriction fragment length polymorphism (PCR-RFLP) method for distinguishing between M. martes and M. foina based on the analysis of deoxyribonucleic acid extracted from faeces samples. The method was specifically designed to avoid possible interference from potential prey mammals and other sympatric carnivores. The procedure consists of PCR amplifying a mitochondrial D-loop region followed by digesting the resulting 276-bp-long amplicons with the restriction enzymes HaeIII and RsaI. To assess the efficiency of this technique, we conducted a preliminary field study across the potential sympatric distribution areas of both marten species in the northern Iberian Peninsula. Out of 359 faeces samples collected, we identified 80 as specimens from the stone marten and 235 from the pine marten. Unequivocal species identification was thus possible in 88% of the faeces samples collected. These findings reveal the combined use of non-invasive genetic sampling and GIS technology to be a reliable and cost-effective procedure for improving our knowledge of the spatial distributions of sympatric marten species. This protocol could also be used to identify and improve information gaps, to develop effective research and management programmes and in population and landscape genetics studies of marten species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population genetic structure and conservation of marbled murrelets (<Emphasis Type="Italic">Brachyramphus marmoratus</Emphasis>)

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of F _ST or Φ_ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.     

High genetic diversity in the blue-listed British Columbia population of the purple martin maintained by multiple sources of immigrants

To assess genetic diversity in the blue-listed purple martin (Progne subis) population in British Columbia, we analysed mitochondrial control region sequences of 93 individuals from British Columbia and 121 individuals collected from seven localities of the western and eastern North American subspecies P. s. arboricola and P. s. subis, respectively. Of the 47 haplotypes we detected, 34 were found exclusively in western populations, and 12 were found only in eastern populations. The most common eastern haplotype (25) was also found in three nestlings in British Columbia and one in Washington. Another British Columbia nestling had a haplotype (35) that differed by a C to T transition from haplotype 25. Coalescent analysis indicated that these five nestlings are probably descendents of recent immigrants dispersing from east to the west, because populations were estimated to have diverged about 200,000–400,000 ybp, making ancestral polymorphism a less likely explanation. Maximum likelihood estimates of gene flow among all populations detected asymmetrical gene flow into British Columbia not only of rare migrants from the eastern subspecies in Alberta but also a substantial number of migrants from the adjacent Washington population, and progressively lower numbers from Oregon in an isolation-by distance pattern. The influx of migrants from different populations is consistent with the migrant-pool model of recolonization which has maintained high genetic diversity in the small recovering population in British Columbia. Thus, the risk to this population is not from genetic erosion or inbreeding following a severe population crash, but from demographic stochasticity and extinction in small populations.     

Hierarchical genetic structure in fragmented populations of the Little Pocket Mouse (Perognathus longimembris) in Southern California

The geographic genetic structure, based onsequence variation of an 810 base pair fragmentof the mitochondrial cytochrome b gene,is described for populations of five subspeciesof the Little Pocket Mouse, Perognathuslongimembris, from Southern California. Oneof these, P. l. pacificus (Pacific PocketMouse), is listed as Endangered by the U.S.Federal Government. Sixty-two uniquehaplotypes were recovered from 99 individualssampled. Phylogenetic analyses of thesevariants do not identify regionallyreciprocally monophyletic lineages concordantwith the current subspecies designations, butmost haplotypes group by subspecies in networksgenerated by either statistical parsimony ormolecular variance parsimony. Moreover, asubstantial proportion of the total pool ofhaplotype variation is attributed to thesesubspecies, or to local populations withingeographic segments of each, indicating theirrelative evolutionary independence. The pooledextant populations of the endangered PacificPocket Mouse exhibit the same levels ofnucleotide and haplotype diversity as other,presumptively less-impacted populations ofadjacent subspecies, although the sample fromDana Point, Orange County, has markedly lowhaplotype diversity in comparison to allothers. These populations also show a geneticsignature of population expansion rather thanone of decline. Both pieces of evidence are atodds with current empirical populationestimates, which reinforces the fact thatpresent-day patterns of genetic diversity arethe product of coalescent history and will notnecessarily reflect recent anthropogenic, orother, perturbations. Comparison of haplotypevariation within and among extant populationsof the Pacific Pocket Mouse with those obtainedfrom museum samples collected more than 70years ago suggests that the pattern ofpopulation differentiation and diversity was inplace before the post-World War II exponentialurbanization of Southern California.