Crossing the uncrossable: novel trans‐valley biogeographic patterns revealed in the genetic history of low‐dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California

Antrodiaetus riversi is a dispersal‐limited, habitat‐specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here, we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans‐valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans‐valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well‐recognized modern‐day and historical biogeographic barrier in California. For one clade, the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2–1.3 Ma. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans‐valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low‐dispersal biology of mygalomorph spiders, where ‘post‐event’ gene exchange rarely erases historical biogeographic signal.     

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.     

Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae)

Antrodiaetus riversi (Araneae, Antrodiaetidae) is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. This species occupies a disjunct distribution, with populations in the Sierra Nevada and Coast Ranges, separated by the inhospitable Central Valley. Previous studies of morphological and allozyme variation have suggested that these populations may constitute cryptic species. We investigated the phylogeography of A. riversi using both nuclear and mitochondrial DNA sequences, collected for a comprehensive population sample. These data reveal the presence of at least five species in the A. riversi complex - these species are deeply diverged, and genealogically exclusive in both nuclear and mitochondrial genomes. Each of these species is characterized by extreme population subdivision and deep phylogeographical structuring, consistent with minimal gene flow across the dissected Californian landscape. Three species are restricted to the Coast Ranges, one to high altitudes of the central Sierran Nevada, and one species is found in both ranges. These species have allopatric distributions, although species parapatry is hypothesized to occur in several areas. Species diversification appears to have pulsed in the Late Miocene/Early Pliocene, a timing consistent with biogeographical reconstructions for many Californian taxa, and a time of turbulent geological activity in the region.     

The advantages of going large: genome‐wide SNPs clarify the complex population history and systematics of the threatened western pond turtle

As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well‐studied declining species, the western pond turtle (Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller‐scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management.     

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.     

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus)

Background

The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats.

Methodology/Principal Findings

We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general “3 clade” structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism.

Conclusions/Significance

This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.     

Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Cricetidae) in the deserts of eastern California

The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year‐round, is a remnant of the mesic history of the southern Great Basin and Mojave deserts of eastern California. The history of voles in this region is a model for species‐edge population dynamics through periods of climatic change. We sampled voles from the eastern deserts of California and examined variation in the mitochondrial cytb gene, three nuclear intron regions, and across 12 nuclear microsatellite markers. Samples are allocated to two mitochondrial clades: one associated with southern California and the other with central and northern California. The limited mtDNA structure largely recovers the geographical distribution, replicated by both nuclear introns and microsatellites. The most remote population, Microtus californicus scirpensis at Tecopa near Death Valley, was the most distinct. This population shares microsatellite alleles with both mtDNA clades, and both its northern clade nuclear introns and southern clade mtDNA sequences support a hybrid origin for this endangered population. The overall patterns support two major invasions into the desert through an ancient system of riparian corridors along streams and lake margins during the latter part of the Pleistocene followed by local in situ divergence subsequent to late Pleistocene and Holocene drying events. Changes in current water resource use could easily remove California voles from parts of the desert landscape.     

Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii

Aim The salamander Ensatina eschscholtzii Gray is a classic example of a ring species, or a species that has expanded around a central barrier to form a secondary contact characterized by species‐level divergence. In the original formulation of the ring species scenario, an explicit biogeographical model was proposed to account for the occurrence of intraspecific sympatry between two subspecies in southern California (the ‘southern closure’ model). Here we develop an alternative ring species model that is informed by the geomorphological development of the California Coast Ranges, and which situates the point of ring closure in the Monterey Bay region of central coastal California (the ‘Monterey closure’ model). Our study has two aims. The first is to use phylogenetic methods to evaluate the two competing biogeographical models. The second is to describe patterns of phylogeographical diversity throughout the range of the Ensatina complex, and to compare these patterns with previously published molecular systematic data. Location Western North America, with a focus on the state of California, USA. Methods We obtained mitochondrial DNA sequence data from 385 individuals from 224 populations. A phylogeny was inferred using Bayesian techniques, and the geographical distributions of haplotypes and clades were mapped. The two biogeographical ring species models were tested against our Bayesian topology, including the associated Bayesian 95% credible set of trees. Results High levels of phylogeographical diversity were revealed, especially in central coastal and northern California. Our Bayesian topology contradicts the Monterey closure model; however, 0.08% of the trees in our Bayesian 95% credible set are consistent with this model. In contrast, the classic ring species biogeographical model (the southern closure model) is consistent with our Bayesian topology, as were 99.92% of the trees in our 95% credible set. Main conclusions Our Bayesian phylogenetic analysis most strongly supports the classic ring species model, modified to accommodate an improved understanding of the complex geomorphological evolution of the California Coast Ranges. In addition, high levels of phylogeographical diversity in central and northern California were identified, which is consistent with the striking levels of allozymic differentiation reported previously from those regions.     

Phylogeography of the Northern Alligator Lizard (Squamata,Anguidae): Hidden diversity in a western endemic

Western North America includes the California Floristic Province and the Pacific Northwest, biologically diverse regions highlighted by a complex topography, geology, climate and history. A number of animals span these regions and show distinctive patterns of dispersal, vicariance and lineage diversification. Examining phylogeographic patterns in the fauna of this area aids in our understanding of the forces that have contributed to the generation and maintenance of regional biodiversity. Here, we investigate the biogeography and population structure of the Northern Alligator Lizard (Elgaria coerulea), a wide‐ranging anguid endemic to western North America. We sequenced two mtDNA fragments (ND2 and ND4) for 181 individuals across the range of the species and analysed these data with phylogenetic approaches to infer population and biogeographic history, and date major divergences within the taxon. We further used Bayesian clustering methods to assess major patterns of population structure and performed ecological niche modelling (ENM) to aid in our interpretation of geographic structure and diversification of E. coerulea lineages. Our phylogeographic examination of E. coerulea uncovered surprising diversity and structure, recovering 10 major lineages, each with substantial geographic substructure. While some divergences within the species are relatively old (Pliocene, 5.3–2.6 mya), most intraspecific variation appears to be of more recent origin (Pleistocene, 2.6 mya‐11,700 ya). Current diversity appears to have arisen in the Sierra Nevada Mountains and spread west and north since the Pliocene. Finally, our ENMs suggest that much of the Coast Ranges in California provided ideal habitat during the Last Glacial Maxima (LGM) that has since contracted dramatically and shifted northwards, whereas significant portions of the Sierra Nevada were unsuitable during the LGM and have since become more suitable. Interestingly, E. coerulea shares a number of genetic boundaries with other sympatric taxa, suggesting common historical events and geomorphological features have shaped the biota of this region.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California

Identifying historic patterns of population genetic diversity and connectivity is a primary challenge in efforts to re‐establish the processes that have generated and maintained genetic variation across natural landscapes. The challenge of reconstructing pattern and process is even greater in highly altered landscapes where population extinctions and dramatic demographic fluctuations in remnant populations may have substantially altered, if not eliminated, historic patterns. Here, we seek to reconstruct historic patterns of diversity and connectivity in an endangered subspecies of woodrat that now occupies only 1–2 remnant locations within the highly altered landscape of the Great Central Valley of California. We examine patterns of diversity and connectivity using 14 microsatellite loci and sequence data from a mitochondrial locus and a nuclear intron. We reconstruct temporal change in habitat availability to establish several historical scenarios that could have led to contemporary patterns of diversity, and use an approximate Bayesian computation approach to test which of these scenarios is most consistent with our observed data. We find that the Central Valley populations harbour unique genetic variation coupled with a history of admixture between two well‐differentiated species of woodrats that are currently restricted to the woodlands flanking the Valley. Our simulations also show that certain commonly used analytical approaches may fail to recover a history of admixture when populations experience severe bottlenecks subsequent to hybridization. Overall our study shows the strength of combining empirical and simulation analyses to recover the history of populations occupying highly altered landscapes.     

Survival in northern microrefugia in an endemic Carpathian gammarid (Crustacea: Amphipoda)

Gammarus leopoliensis (Crustacea: Amphipoda) is considered a north‐eastern Carpathian endemic species and therefore can be regarded as an appropriate model for testing the hypothesis of Quaternary glacial survival in northern microrefugia. However, 250 km south, the south‐western Carpathians harbour populations that resemble phenotypically both G. leopoliensis and Gammarus kischineffensis, a similar species distributed east of the Carpathians. We used maximum‐likelihood and Bayesian methods to evaluate the phylogenetic relationships of these three taxa based on mitochondrial and nuclear markers, and quantitatively compared diversity patterns, phylogeography and divergence times among north‐eastern and south‐western Carpathian taxa. Results indicate that G. leopoliensis and the south‐western populations form together a strongly supported group (G. leopoliensis s.l.) which, along with G. kischineffensis, belongs to the Gammarus balcanicus clade. This group contains 12 lineages mainly of Pliocene age. G. leopoliensis consists of two widely distributed and recently expanded allopatric sister lineages that diverged from the southern ones ca. 4 Ma, indicating long‐term survival in northern microrefugia. The southern lineages are micro‐endemic and display a scattered distribution, suggesting a more ancient, relict pattern. We conclude that the contrasting diversity patterns between the disjunct distributional areas of G. leopoliensis s.l. reflect differential survival of lineages across the latitudinal gradient, offering a promising system for comparing the evolutionary ecology of lineages persisting in latitudinally disconnected microrefugia. These results fill an important gap in the knowledge of European gammarid biogeography and reveal that all Carpathian Gammarus taxa are ancient and diverse species complexes.     

Contemporary genetic structure of an endemic freshwater turtle reflects Miocene orogenesis of New Guinea

The island of New Guinea lies in one of the most tectonically active regions in the world and has long provided outstanding opportunity for studies of biogeography. Several chelid turtles, of clear Gondwanal origin, occur in New Guinea; all species except one, the endemic Elseya novaeguineae, are restricted to the lowlands south of the Central Ranges. Elseya novaeguineae is found throughout New Guinea. We use mitochondrial and nuclear gene variation among populations of E. novaeguineae throughout its range to test hypotheses of recent extensive dispersal versus more ancient persistence in New Guinea. Its genetic structure bears the signature of Miocene vicariance events. The date of the divergence between a Birds Head (Kepala Burung) clade and clades north and south of the Central Ranges is estimated to be 19.8 Mya [95% highest posterior density (HPD) interval of 13.3–26.8 Mya] and the date between the northern and southern clades is estimated to be slightly more recent at 17.4 Mya (95% HPD interval of 11.0–24.5 Mya). The distribution of this endemic species is best explained by persistent occupation (or early invasion and dispersal) and subsequent isolation initiated by the dramatic landform changes that were part of the Miocene history of the island of New Guinea, rather than as a response to the contemporary landscape of an exceptionally effective disperser. The driving influence on genetic structure appears to have been isolation arising from a combination of: (1) the early uplift of the Central Ranges and establishment of a north‐south drainage divide; (2) development of the Langguru Fold Belt; (3) the opening of Cenderawasih Bay; and (4) the deep waters of the Aru Trough and Cenderawasih Bay that come close to the current coastline to maintain isolation of the Birds Head through periods of sea level minima (?135 m). The dates of divergence of turtle populations north and south of the ranges predate the telescopic uplift of the central ranges associated with oblique subduction of the Australian Plate beneath the Pacific Plate. Their isolation was probably associated with earlier uplift and drainage isolation driven by the accretion of island terranes to the northern boundary of the Australian craton that occurred earlier than the oblique subduction. The opening of Cenderawasih Bay is too recent (6 Mya) to have initiated the isolation of the Birds Head populations from those of the remainder of New Guinea, although its deep waters will have served to sustain the isolation through successive sea level changes. The molecular evidence suggests that the Birds Head docked with New Guinea some time before the Central Ranges emerged as a barrier to turtle dispersal. Overall, deep genetic structure of the species complex reflects events and processes that occurred during Miocene, whereas structure within each clade across the New Guinea landscape relates to Pliocene and Pleistocene times. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 192–208.     

Hidden endemism,deep polyphyly,and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.     

Cryptic diversity within the endemic prehensile‐tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level

The deciphering of the process of genetic differentiation of species with insular distributions is relevant for biogeographical and conservation reasons. Despite their importance as old gondwanic islands and part of the western Indian Ocean biodiversity hotspot, little is known about the genetic structure of taxa from the Seychelles Islands. We have examined the patterns of structure and isolation within Urocotyledon inexpectata (Reptilia: Geckkonidae), an endemic species from this archipelago. Genetic diversity was screened from populations across the archipelago for both mitochondrial and nuclear genes. Gene genealogies and model‐based inference were used to explore patterns and timings of isolation between the main lineages. High levels of genetic diversity were found for the mitochondrial and some of the nuclear markers. This species harbours at least two highly differentiated lineages, exclusively distributed across the northern and southern groups of the islands. The main split between these was dated back to the Miocene–late Pliocene, but isolation events throughout the Pliocene and Pleistocene were also inferred. Migration between groups of islands was apparently nonexistent, except for one case. The low dispersal capabilities of this species, together with the intrinsic fragmented nature of its geographical distribution, seem to have resulted in highly structured populations, despite the cyclic periods of contact between the different island groups. These populations may currently represent more than one species, making U. inexpectata another example of a morphologically cryptic lineage with deep genetic divergence within gekkonids. The observed patterns suggest a hypothetical biogeographic scenario (of a main north–south phylogeographic break) for the Seychelles that can be further tested with the exploration of the phylogeographic structure of other Seychellois taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 177–191.     

Distribution of mitochondrial haplotypes (cytb) in Polish populations of Emys orbicularis (L., 1758)

The European pond turtle, Emys orbicularis, inhabits a wide distribution area in the western Palaearctic. Polish populations of pond turtle represent the nominotypical subspecies Emys orbicularis orbicularis. The mitochondrial DNA haplotype (cytb gene) variation among 131 turtles from 26 locations in five regions of Poland was investigated. Five haplotypes belonging to three distinct lineages were identified. Two clades (I and II) were represented by two haplotypes each, while the other clade (IV) was represented by one haplotype. Three haplotypes were reported for the first time in E. orbicularis. The eastern part of Poland is inhabited exclusively by turtles bearing haplotype Ia. The remaining four sequence variants were recorded in western Poland where only the IIb haplotype is considered endemic. The distribution of the other haplotypes in western Poland could thus reflect past introductions or accidental releases. The authors regarded the two locations (Drzeczkowo and Karpicko) that were first included in the western Poland populations as autochthonous catchment areas of haplotype Ia.     

Biogeographical contingency and the evolution of tropical anchovies (genus Cetengraulis) from temperate anchovies (genus Engraulis)

Aim Similar regimes of selection in different geographical settings can deterministically produce similar adaptive morphologies. We tested the hypothesis that the evolutionary trajectories of fish in upwelling zones can be altered by biogeographic contingencies in the biological and physical environment. Location Eastern Pacific and western Atlantic oceans. Methods We estimated phylogenetic relationships among eastern Pacific temperate anchovies (genus Engraulis) and tropical anchovies (genus Cetengraulis) with neighbour‐joining and Bayesian tree analysis of a 521‐bp segment of mitochondrial DNA cytochrome b. Available sequences for five additional engraulid taxa were included to establish polarity of the tree. Bayesian estimates (BEAST) of time to most recent common ancestor (TMRCA) for the nodes in the phylogeny were calibrated with divergence between Cetengraulis edentulus and Cetengraulis mysticetus precipitated by the rise of the Panama Isthmus 2.8–3.2 Ma. Results Neighbour‐joining and Bayesian trees indicate that South American Engraulis anchoita (Argentina) and Engraulis ringens (Chile) together are basal sister taxa to the California anchovy (Engraulis mordax) and Old World anchovies (Engraulis japonicas, Engraulis australis, Engraulis capensis and Engraulis encrasicolus). The two tropical species of Cetengraulis are sister‐taxa to Californian E. mordax, even though their phenotypes and ecologies differ markedly. A relaxed molecular clock indicates a TMRCA between Californian E. mordax and Cetengraulis at about 4.2 Ma (3.0–6.3 Ma 95% highest probability density). Main conclusions The TMRCA between the California anchovy, E. mordax, and tropical Cetengraulis coincides with the formation of the Gulf of California, which provided opportunities for allopatric isolation during climate oscillations. Mid‐Pliocene warming (3.1–2.9 Ma) may have trapped ancestors of Cetengraulis in the Gulf of California, where they evolved digestive tract morphologies to exploit inshore tropical habitats with low plankton productivities. While populations of several other temperate fishes have become isolated in the Gulf of California, few of these derived species show strong adaptive shifts from temperate sister taxa or range expansions into the tropical provinces of the western Atlantic and eastern Pacific.     

Genetic and phenotypic variation in a colourful treefrog across five geographic barriers

Aim Understanding the patterns and processes underlying phenotype in a polytypic species provides key insights into microevolutionary mechanisms of diversification. The red‐eyed treefrog, Agalychnis callidryas, exhibits strong regional differentiation in colour pattern, corresponding to five admixed mitochondrial DNA clades. We evaluated spatial diversity patterns across multiple, putative barriers to examine the fine‐scale processes that mediate phenotypic divergence between some regions while maintaining homogeneity between others. Location We examined patterns of phenotypic diversification among 17 sites that span five putative biogeographic barriers in lower Central America (Costa Rica and Panama). Methods We tested the extent to which genetic distance (F_ST) derived from six multilocus nuclear genotypes covaried with measures of phenotypic distance (leg coloration) within and between biogeographic regions. We used linear regression analyses to determine the role of geographic and genetic factors in structuring spatial patterns of phenotypic diversity. Results The factors that best explained patterns of phenotypic diversity varied among biogeographic regions. We identified one geographic barrier that impeded gene exchange and resulted in concordant phenotypic divergence across the Continental Divide, isolating Caribbean and Pacific populations. Across Caribbean Costa Rican populations, one barrier structured phenotypic but not genetic diversity patterns, indicating a role for selection. In other regions, the putative barriers had no determining effect on either genetic or leg colour structure. Main conclusions The processes mediating the distribution and diversification of colour pattern in this polytypic, wide‐ranging treefrog varied among biogeographic regions. Spatially varying selection combined with the isolating effects of geographic factors probably resulted in the patchy distribution of colour diversity across Costa Rican and Panamanian populations.     

Multilocus phylogeography of the flightless darkling beetle Nyctoporis carinata (Coleoptera: Tenebrionidae) in the California Floristic Province: deciphering an evolutionary mosaic

The California Floristic Province (CFP) is considered a global biodiversity hotspot because of its confluence of high species diversity across a wide range of threatened habitats. To understand how biodiversity hotspots such as the CFP maintain and generate diversity, we conducted a phylogeographic analysis of the flightless darkling beetle, Nyctoporis carinata, using multiple genetic markers. Analyses of both nuclear and mitochondrial loci revealed an east–west genetic break through the Transverse Ranges and high genetic diversity and isolation of the southern Sierra Nevada Mountains. Overall, the results obtained suggest that this species has a deep evolutionary history whose current distribution resulted from migration out of a glacial refugium in the southern Sierra Nevada via the Transverse Ranges. This finding is discussed in light of similar genetic patterns found in other taxa to develop a foundation for understanding the biodiversity patterns of this dynamic area. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 424–444.     

Survival and Causes of Mortality of Head-Started Western Pond Turtles on Pierce National Wildlife Refuge,Washington

ABSTRACT The western pond turtle (Actinemys marmorata) is a species of conservation concern over much of its range and is listed as endangered in Washington State. From 2000 to 2004, we used radiotelemetry to document survival and mortality factors of head-started western pond turtles (n = 68) released into Pierce National Wildlife Refuge in southwestern Washington. Survival estimates for first year and older turtles ranged from 86% to 97% and overlapping confidence intervals indicated no detectible differences among age classes or among years. Subadult turtles released at ≥90-mm carapace length apparently avoided capture by most aquatic predators, indicating that terrestrial predators should be the focus of research and management where predation on larger age-classes is a concern. High annual survival combined with the documented nesting by ≥7-year-old female head-started turtles in Washington suggest that recruitment of adults is being achieved; however, head-starting is only practical as an interim solution and strategies for effective removal of aquatic predators must be developed and implemented where natural recruitment is inadequate to maintain populations.