The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex

The sheepshead minnow, Cyprinodon variegatus, is a widespread fish species that typically inhabits coastal tidal marsh and mangrove swamp environments, ranging from Cape Cod, Massaschusetts to northern Mexico and into the Caribbean. This wide range crosses several biogeographic boundaries which are coincident with genetic structuring within numerous species originating in the Pleistocene. In addition, the more northerly reaches of this species range have been further subject to the evolutionary consequences of Pleistocene glaciation due to local extinction and recolonization of formerly glaciated sites. C. variegatus thus provides an excellent vertebrate model system within which to test the extent of genetic differentiation among populations in a dominant coastal ecosystem and examine patterns of historical demography in populations distributed along a latitudinal gradient. Using mitochondrial control region and ND2 sequence data, we discovered monophyletic clades within C. variegatus with divergence times within the Pleistocene, and very low gene flow between most sites. Intraspecific genetic breaks appear to correspond broadly to biogeographic or oceanic boundaries. Pleistocene climate change appears to have had dramatic impacts on the size and distribution of populations within and near the glacial margins, but has also affected populations far from formerly glaciated regions.     

Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the Great Barrier Reef

Effective management of reef corals requires knowledge of the extent to which populations are open or closed and the scales over which genetic exchange occurs, information which is commonly derived from population genetic data. Such data are sparse for Great Barrier Reef (GBR) corals and other organisms, with the studies that are available being mostly based on a small number of sampling locations spanning only part of the GBR. Using 11 microsatellite loci, we genotyped 947 colonies of the reef-building coral Acropora millepora from 20 sites spanning almost the full length of the GBR (～12° of latitude and ～1550 km). The results show a major divide between the southernmost central to southern offshore populations and all other sampled populations. We interpret this divide as a signature of allopatric divergence in northern and southern refugia during the Pleistocene glaciations, from which the GBR was subsequently recolonized. Superimposed on this pattern is a cross-shelf genetic division, as well as a separation of inshore populations south of the Cape Clifton Front at ～21.5-22°S. Most inshore populations north of this, as well as mid-shelf populations in the northern and far northern GBR, are open, exchanging recruits frequently. In contrast, inshore populations south of the Cape Clifton Front and offshore populations in the central and southern GBR are largely self-seeding, at least within the spatial resolution that was achieved given our sampling intensity. Populations that have been impacted by recent disturbance events causing extensive coral mortality show no evidence of reduced genetic diversity.     

A cryptic genetic boundary in remnant populations of a long‐lived,bird‐pollinated shrub Banksia sphaerocarpa var. caesia (Proteaceae)

Plant species often exhibit genetic structure at multiple spatial scales. Detection of this structure may depend on the sampling strategy used. We intensively sampled a common, naturally patchy Banksia species within a 200 km² region, in order to assess patterns of genetic diversity and structure at multiple spatial scales. In total, 1321 adult shrubs from 37 geographical populations were genotyped using eight highly polymorphic microsatellite markers developed for the species. Genetic structure was detected at three spatial scales. First, we identified a stark and unexpected division of the landscape into two genetic subregions, one to the north‐east and one to the south‐west of the sampling grid. This differentiation was based on sudden, highly structured differences in common allele frequencies, the cause of which is unknown but that may relate to physical and reproductive barriers to gene flow, localised selection, and/or historical processes. Second, we observed genetic differentiation of populations within these subregions, reflecting previously described patterns of restricted pollen flow in this species. Finally, fine‐scale genetic structure, although weak, was observed within some of the populations (mean S_P = 0.01837). When feasible, intensive sampling may uncover cryptic patterns of genetic structure that would otherwise be overlooked when sampling at broader spatial scales. Further studies using a similar sampling strategy may reveal this type of discontinuity to be a feature of other south‐western Australian taxa and has implications for our understanding of evolution in this landscape as well as conservation into the future. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 241–255.     

Population genetic structure and history of fragmented remnant populations of the New England cottontail (<Emphasis Type="Italic">Sylvilagus transitionalis</Emphasis>)

The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species’ range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F _ST = 0.145; P < 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.     

Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei, Gobiidae), in coastal California

The tidewater goby, Eucyclogobius newberryi, inhabits discrete, seasonally closed estuaries and lagoons along approximately 1500 km of California coastline. This species is euryhaline but has no explicit marine stage, yet population extirpation and recolonization data suggest tidewater gobies disperse intermittently via the sea. Analyses of mitochondrial control region and cytochrome b sequences demonstrate a deep evolutionary bifurcation in the vicinity of Los Angeles that separates southern California populations from all more northerly populations. Shallower phylogeographic breaks, in the vicinities of Seacliff, Point Buchon, Big Sur, and Point Arena segregate the northerly populations into five groups in three geographic clusters: the Point Conception and Ventura groups between Los Angeles and Point Buchon, a lone Estero Bay group from central California, and San Francisco and Cape Mendocino groups from northern California. The phylogenetic relationships between and patterns of molecular diversity within the six groups are consistent with repeated, and sometimes rapid, northward and southward range expansions out of central California caused by Quaternary climate change. Plio-Pleistocene tectonism, Quaternary coastal geography and hydrography, and historical human activities probably also influenced the modern geographic and genetic structure of E. newberryi. The phylogeography of E. newberryi is concordant with phylogeographic patterns in several other coastal California taxa, suggesting common extrinsic factors have had similar effects on different species. However, there is no evidence of a phylogeographic break coincident with a biogeographic boundary at Point Conception.     

Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate

Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat distribution, and historical factors as important determinants of estuarine speciation and diversification.     

Across the highest mountain on earth: discordant phylogeographic patterns and recent dispersal of Tibetan stone loaches (Triplophysa) in the Himalayas

Phylogeographic congruence among co-distributed taxa is regarded as an inherent inference to vicariance events. Nonetheless, incongruent patterns of contemporary lineage divergence among taxa indicated that species differ in their response to common past events. To investigate the role of past events, ecological traits and lineage diversification time in shaping the contemporary phylogeographic patterns, comparative analyses were conducted for Tibetan stone loaches in the Himalayas using three gene markers and two ecological traits (depth of caudal peduncle in their length and presence/absence of posterior chamber of the air bladder). By a thorough sampling in two flanks of the Himalayas, the authors detected that phylogenetic breaks were spatially discordant and divergences of populations were also temporally asynchronous in co-distributed loaches. Estimated divergence time using fossil-calibrated node dating indicated that the Tibetan stone loaches colonised into the south flank of the Himalayas until the Pleistocene. The demographic expansions were also disconcerted between populations in north and south flanks, or east and west Himalayas. Ongoing gene flows between populations in north and south sides implied that the Himalayas do not strictly impede dispersal of cold-adapted species. The results highlight that the quaternary climatic oscillation, in conjunction with ecological traits and lineage diversification time, shaped contemporary phylogenetic patterns of stone loaches in the Himalayas and provide new insights into the biodiversity and composition of species in the Himalayas and surrounding region.     

Use of the 16S-23S rDNA internal transcribed spacer of Roseovarius crassostreae for epizootiological studies of juvenile oyster disease (JOD)

Juvenile oyster disease (JOD) in Crassostrea virginica is caused by the marine bacterium Roseovarius crassostreae. Although the 16S rRNA genes of the bacterial isolates exhibit little variation, 2 genetic signatures (GSI and GSII) may be discerned by Ava I digestion of the 16S-23S internal transcribed spacer (ITS). In this study we analyzed isolates from JOD epizootics throughout the northeastern USA (including affected adults for the first time) to better understand how oyster populations encounter and become affected by the pathogen. Isolates from a given epizootic usually had the same ITS signature; however, the involvement of both genetic signatures was occasionally detected, even within the same oyster. Sequencing was used to localize the variable Ava I site to a 100 bp region of low sequence identity, and detection of additional base changes resulted in the identification of 11 distinct genotypes. One genotype was found only in Martha's Vineyard, Massachusetts, USA and persisted in JOD survivors. Two genotypes were associated with Maine epizootics, and both were believed to be unique to that region until 2004, when one was detected in Martha's Vineyard among oysters that had survived colonization by the local genotype. Apparent competition between those 2 genotypes was also detected among a population of juveniles. Five genotypes were found only in New York, and the other 3 were isolated from both New York and from around Cape Cod, Massachusetts. Relationships between the geographic occurrence and phylogenetic relatedness of genotypes were compared with regional current patterns to identify possible mechanisms controlling their distribution.     

INTRASPECIFIC PHYLOGEOGRAPHY ACROSS THE POINT CONCEPTION BIOGEOGRAPHIC BOUNDARY

Recent studies of intraspecific phylogeography have suggested that the geographic location of genetic discontinuities, or phylogeographic breaks, may frequently coincide with biogeographic boundaries. The concordance is hypothesized to reflect similarity in the processes governing species boundaries and intraspecific lineage boundaries. This concordance has not, however, been widely tested. In the case of the Point Conception biogeographic boundary between the Oregonian and Californian marine biotas, only the supralittoral copepod Tigriopus californicus has been found to have a coincident phylogeographic break. Here I show that the apparent relationship between this break and Point Conception was, in fact, an artifact of insufficient geographic sampling. Mitochondrial DNA analyses of T. californicus populations between Morro Bay and San Diego reveal at least five equally deep phylogeographic breaks in the region (where only one biogeographic boundary is recognized). Limited nuclear DNA sequence data and allozyme data also support the occurrence of multiple genetic discontinuities along this geographic range. Lack of one-to-one correspondence between intraspecific phylogeography and biogeographic boundaries indicates that the processes affecting the genetic differentiation of populations of T. californicus differ from those responsible for determining species distributional limits at the Point Conception biogeographic boundary. A review of genetic data from other species also fails to provide evidence for concordance of biogeography and intraspecific phylogeography across Point Conception. I suggest that the concordance of phylogeography with biogeography will only be pronounced where the biogeographic boundary separates biotas that are phylogenetically related. The numerous cases of interspecific hybrid zones in the region of Cape Canaveral, for example, indicate that many sister-species pairs occur across this biogeographic boundary. Such hybrid zones are not common at Point Conception, and there appears to be no cases of intraspecific phylogeographic breaks associated with this well-recognized biogeographic boundary.     

Population structure of long‐finned pilot whales in the North Atlantic: a correlation with sea surface temperature?

The long-finned pilot whale, Globicephala melas, is a social, pelagic odontocete distributed widely in the cold temperate waters of the North Atlantic. Despite genetic, morphometric, physiological and observational studies, it remains unclear whether any population substructure exists. We have used eight highly polymorphic microsatellite loci to analyse samples from four disparate sampling sites: USA East Coast (Cape Cod), West Greenland, the Faeroe Islands and the UK. Our results indicate that substructure does exist, and is particularly pronounced between West Greenland and other sites. The magnitudes of the various pairwise comparisons do not support a simple isolation-by-distance model. Instead, the patterns of genetic differentiation suggest that population isolation occurs between areas of the ocean which differ in sea surface temperature. Such a mechanism is supported by the observation that temperature is a primary factor determining the relative distributions of two short-finned pilot whale (G. macrorhynchus) populations off the Pacific coast of Japan.     

Genetics and asexual reproduction of the sea anemone Metridium senile.

1. Metridium senile was studied for phosphohexose-isomerase variation at three locations on Cape Cod, Massachusetts: Woods Hole, Cape Cod Canal, and Barnstable Town Boat Harbor. 2. All three locations exhibited significant polymorphism for PHI. 3. Mapping of individual polyps was performed at Barnstable to analyze spatial distributions of clones and genotypes. 4. In Barnstable, PHI does not depart significantly from Hardy-Weinberg expectations at the time of establishment of new polyps, and establishment of larvae is spatially random with respect to PHI genotype. 5. Asexual reproduction was uses as a meausre of the relative success of different PHI genotypes. There are indications that not all genotypes are equally likely to produce large clones. 6. There is significant heterogeneity among the three locations with respect to PHI genotype frequencies, suggesting that there may be geographical differentiation of the populations. 7. Sessile, asexual organisms provide powerful tools for examining the dynamic aspects of genetic structure in natural populations.     

Limited phylogeographic structure in the flightless ground beetle, Calathus ruficollis, in southern California

The California Floristic Province is home to more than 8000 species of beetles, yet their geographical patterns of supra- and infraspecific diversity remain largely unexplored. In this paper, we investigate the phylogeography and population demographics of a flightless ground beetle, Calathus ruficollis (Coleoptera: Carabidae), in southern California. We sampled 136 specimens from 25 localities divided into 10 populations using a fragment of the mitochondrial cytochrome oxidase I gene. We tested several hypotheses, including the association of geography with particular clades and populations, the degree of differentiation among regions, and the expansion of populations. Parsimony and Bayesian phylogenetic analyses along with nested clade analysis and amova indicate a deep split between the southern Sierra Nevada population and populations south and west. This split corresponds closely to the split between subspecies C. ruficollis ignicollis (southern Sierra Nevada) and C. ruficollis ruficollis . Populations otherwise exhibit limited geographical structure, though F st values indicate some local differentiation. Mismatch distributions and Fu's F s indicate range expansion of several populations, suggesting that some structure may have been obscured by recent exchange. The population of C. ruficollis on Santa Cruz Island, which might have been expected to be isolated, shares several haplotypes with mainland populations, appearing to represent multiple colonizations.     

Stock composition of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) encountered in marine and estuarine environments on the U.S. Atlantic Coast

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) is a large, anadromous fish native to the Atlantic Coast of North America. Although this species once supported important fisheries, centuries of exploitation and habitat degradation have resulted in dramatic declines, presumed extirpation in some rivers, and ultimately listing under the U.S. Endangered Species Act (ESA). Under the ESA, Atlantic sturgeon are listed as five separate Distinct Population Segments (DPSs), which form the basis for federal management. Despite state and federal protections Atlantic sturgeon still face significant threats to their recovery, including fisheries bycatch mortality, marine construction, dredging, dams, and vessel strikes. However, because subadult and adult Atlantic sturgeon migrate extensively across estuarine and marine environments and frequently form mixed-stock aggregations in non-natal habitats, it can be difficult to determine how these threats impact specific populations and DPSs. To better understand ontogenetic shifts in habitat use and stock-specific exposure to anthropogenic threats, we performed a mixed-stock analysis of 1704 Atlantic sturgeon encountered across the U.S. Atlantic Coast. Collections made north of Cape Cod, MA and south of Cape Hatteras, NC were dominated by individuals from regional stocks; however, we found extensive stock mixing in the mid-Atlantic region, particularly in coastal environments where individuals from all five DPSs were commonly observed. Subadults and adults that were encountered in offshore environments had moved, on average, 277 km from their natal source; however, 23% were sampled over 500 km from their natal river suggesting long-distance movements are relatively common in these age classes. Overall, our work highlights that Atlantic sturgeon populations are vulnerable to threats over vast areas and emphasizes the need for continued genetic monitoring to track recovery progress.

     

Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole‐rat,Heterocephalus glaber

The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole‐rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole‐rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long‐held view is that the original genetic studies were based on limited sampling from the species’ geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species—rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole‐rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole‐rat populations south of the Athi River reflects a founder event, rather than a consequence of this species’ unusual mating system.     

Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae)

Aim Based on extensive range‐wide sampling, we address the phylogeographical history of one of the most widespread and taxonomically complex sedges in Europe, Carex nigra s. lat. We compare the genetic structure of the recently colonized northern areas (front edge) and the long‐standing southern areas (rear edge), and assess the potential genetic basis of suggested taxonomic divisions at the rank of species and below. Location Amphi‐Atlantic, central and northern Europe, circum‐Mediterranean mountain ranges, central Siberia, Himalayas. Methods A total of 469 individuals sampled from 83 populations, covering most of the species’ range, were analysed with amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) markers. Bayesian clustering, principal coordinates analysis, and estimates of diversity and differentiation were used for the analysis of AFLP data. CpDNA data were analysed with statistical parsimony networks and maximum parsimony and Bayesian inference of phylogenetic trees. Results Overall genetic diversity was high, but differentiation among populations was limited. Major glacial refugia were inferred in the Mediterranean Basin and in western Russia; in addition, there may have been minor refugia in the North Atlantic region. In the southern part of the range, we found high levels, but geographically quite poorly structured genetic diversity, whereas the levels of genetic diversity varied among different areas in the north. North American populations were genetically very similar to the European populations. Main conclusions The data are consistent with extensive gene flow, which has obscured the recent history of the taxon. The limited differentiation in the south probably results from the mixing of lineages expanding from several local refugia. Northward post‐glacial colonization resulted in a leading‐edge pattern of low diversity in the Netherlands, Belgium, Scotland and Iceland, whereas the observed high diversity levels in Fennoscandia suggest broad‐fronted colonization from the south as well as from the east. The patterns found in the American populations are consistent with post‐glacial colonization, possibly even with anthropogenic introduction from Europe. Our data also suggest that the tussock‐forming populations of C. nigra, often referred to as a distinct species (Carex juncella), represent an ecotype that has originated repeatedly from different populations with creeping rhizomes.     

Phylogenetic relationships, biogeography and speciation in the avian genus Saxicola

The avian genus Saxicola is distributed throughout Africa, Asia, Europe and various islands across Oceania. Despite the fact that the group has great potential as a model to test evolutionary hypotheses due to the extensive variability in life history patterns recorded between and within species, the phylogenetic relationships among species and subspecies of this genus are poorly understood. We undertook a systematic investigation of the relationships within this genus with three main objectives in mind, (1) to test the monophyly of the genus; (2) to ascertain geographical origin and dispersal sequence; and (3) to test for monophyly within the most morphologically diverse species, S. torquata and S. caprata. We studied sequence data from the mitochondrial cytochrome b gene from 11 of the 12 recognized species and 15 of the 45 described subspecies. Four clades, two exclusively Asian, one Eurasian, and the fourth encompassing Eurasia and Africa, were identified. Based on our analyses, monophyly of the genus Saxicola is not supported and an Asian origin for the genus can be inferred. Results from DIVA analyses, tree topology and nodal age estimates suggest independent colonisation events from Asia to Africa and from Asia to the Western Palearctic, with the Sahara desert acting as a natural barrier for S. torquata. Subspecies and populations of S. torquata are not monophyletic due to S. tectes, S. dacotiae and S. leucura grouping within this complex. Subspecies and populations of S. caprata are monophyletic. Importantly, within S. torquata and S. caprata, slight morphological traits and plumage colour pattern differences used to recognize subspecies are indicative of the greater cryptic diversification that has occurred within this genus.     

Dispersal routes and habitat utilization of juvenile Atlantic bluefin tuna, Thunnus thynnus, tracked with mini PSAT and archival tags

Between 2005 and 2009, we deployed 58 miniature pop-up satellite archival tags (PSAT) and 132 implanted archival tags on juvenile Atlantic bluefin tuna (age 2-5) in the northwest Atlantic Ocean. Data returned from these efforts (n?=?26 PSATs, 1 archival tag) revealed their dispersal routes, horizontal and vertical movements and habitat utilization. All of the tagged bluefin tuna remained in the northwest Atlantic for the duration observed, and in summer months exhibited core-use of coastal seas extending from Maryland to Cape Cod, MA, (USA) out to the shelf break. Their winter distributions were more spatially disaggregated, ranging south to the South Atlantic Bight, northern Bahamas and Gulf Stream. Vertical habitat patterns showed that juvenile bluefin tuna mainly occupied shallow depths (mean=?5-12 m, sd?=?15-23.7 m) and relatively warm water masses in summer (mean=?17.9-20.9°C, sd=?4.2-2.6°C) and had deeper and more variable depth patterns in winter (mean=?41-58 m, sd=?48.9-62.2 m). Our tagging results reveal annual dispersal patterns, behavior and oceanographic associations of juvenile Atlantic bluefin tuna that were only surmised in earlier studies. Fishery independent profiling from electronic tagging also provide spatially and temporally explicit information for evaluating dispersals rates, population structure and fisheries catch patterns.     

Genetic population structure of Tectura paleacea: implications for the mechanisms regulating population structure in patchy coastal habitats

The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California - Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near shore marine environments.     

Phylogeography of a stream-dwelling frog (Pseudacris cadaverina) in southern California

Recent phylogeographic studies of animal taxa in California have revealed common geographic patterns of evolutionary divergence and genetic diversity that are generally attributable to landscape influences. However, there remains a paucity of knowledge on the evolution of freshwater taxa in southern California. Here, we investigate phylogeographic patterns in a stream-dwelling frog (Pseudacris cadaverina). Two hundred and twenty-one individuals were collected from 46 populations across the species’ range in southern California. Using 1100 bp of sequence data from cytochrome b and tRNA-Glu, we conducted phylogenetic analyses, analysis of molecular variance, and nested clade phylogeographic analysis to gain insight into the factors contributing to the distribution of genetic diversity in P. cadaverina. We tested for evidence of two putative phylogeographic breaks and tested hypotheses that genetic diversity in this species is partitioned into (1) major watersheds, (2) mountain ranges, and (3) coastal and desert regions. Our results suggest that the eastern Transverse Ranges are the center of origin for extant P. cadaverina lineages and that the observed genetic structure in this species was established during the Pleistocene Epoch. There is strong support for three major haplotype groups and a Transverse Range break in P. cadaverina that is concordant with breaks found in numerous other taxa. The distribution of genetic diversity in P. cadaverina is due in large part to the separation of populations into different major watersheds and mountain ranges. Gene flow appears to be generally limited among disjunct populations throughout the region and some desert populations have been isolated by historical habitat fragmentation.