Mapping aquatic faunal exchanges across the Sunda shelf,South-East Asia,using distributional and genetic data sets from the cyprinid fish Barbodes gonionotus (Bleeker, 1850)

The islands of Sumatra, Java and Borneo and mainland South-East Asia are encompassed by a shallow marine shelf, the Sunda shelf. The striking faunal similarities between countries bordering the Sunda shelf have been attributed to faunal exchanges across the shelf during Pleistocene glacial maxima when sea levels fell by up to 120 m and the shelf was exposed and drained by large river systems which connected many of today's rivers. The widespread distribution of fish species reflecting extensive faunal exchange across the area is predicted to be observed within species through the broad geographic distribution of genetic lineages. Here I report a discontinuous species distribution across the region for the cyprinid fish, Barbodes gonionotus. Mitochondrial DNA control region sequence and nuclear locus data from populations sampled across the species range, suggest that the present species distribution largely reflects faunal exchanges early in the Pleistocene and that these two regional population groupings have subsequently diverged in isolation. However, the mtDNA data present some evidence for limited genetic dispersal during more recent Pleistocene low sea levels. These results broadly confirm previous work from a catfish species and suggest that freshwater faunal exchanges may have been limited across the region during the Pleistocene despite extended periods during which the Sunda shelf was exposed.     

Phylogenetic divergence in a desert fish: differentiation of speckled dace within the Bonneville, Lahontan, and upper Snake river basins

Historical events have had a great impact on the biogeography of fishes of western North America. We examined the genetic variation of the speckled dace ( Rhinichthys osculus ) to determine the effects on this species of extensive hydrological changes during the last 10 million years in the Bonneville and Lahontan basins of the Great Basin and the upper Snake River Basin. Eight hundred sixty-nine base pairs of the mitochondrial gene cytochrome b were sequenced from 97 individuals representing 22 populations within these 3 basins, as well as from 2 individuals of longnose dace ( Rhinichthys cataractae ) that served as outgroups. Additionally, 13 speckled dace sequences representing 3 Bonneville populations were used from GenBank. Phylogenetic relationships were reconstructed using maximum parsimony and maximum likelihood criteria. Analysis of molecular variance was used to determine population structure and to estimate the amount of gene flow across the community boundaries. Three distinct clades were reconstructed representing the Lahontan Basin, the northern Bonneville and upper Snake River basins, and the southern Bonneville Basin. Additionally, most of the population structuring was explained by variation among basins (65.33%). Speckled dace demonstrated high genetic variation. As hypothesized, the northern and southern Bonneville specimens formed separate clades; however, the southern Bonneville clade was basal to a sister clade formed by the northern Bonneville/upper Snake River and Lahontan clades. These relationships indicate that Pliocene connections between the Snake, Lahontan, and Bonneville drainages, rather than more recent Pleistocene connections, best explain population structuring in speckled dace.     

Preliminary report on the genetic structure of Glyphoglossus molossus (Anura: Microhylidae) from the Khorat Plateau,north-eastern Thailand

Glyphoglossus molossus, is one of the most economically important amphibians in the Khorat Plateau, north-eastern Thailand. It is categorised as a near-threatened species by IUCN due to over-exploitation. Here, we examined the genetic structure of G. molossus using partial mitochondrial cytochrome-b gene sequences from specimens collected at 11 localities. The sequence analysis revealed the presence of 15 haplotypes, 5 of which are shared by 2 or more populations, and 10 haplotypes that are confined to a single population. The relatively low haplotype (h) and nucleotide (π) diversities suggest that the Phu Phan Mountain Range is not high enough to act as an effective dispersal barrier between the Sakon Nakhon and Khorat Basins. However, AMOVA and phylogenetic analyses based on Maximum likelihood (ML) and Bayesian inference (BI) strongly supported the presence of two genetically divergent clades, Sakon Nakhon Basin and the northern part of the Khorat Basin (clade A) and the southern part of the Khorat Basin (clade B). These two lineages are separated by substantial geographical distance, which has putatively resulted in a reduction of gene flow. Further studies, with more extensive genetic sampling, especially from throughout the species range will aid in better interpreting our results.     

Genetic structuring at a fine scale in the russet-crowned motmot ( Momotus mexicanus ) in a tropical dry forest in central Mexico

Because of their high dispersal abilities, birds are expected to manifest marked genetic structuring only at relatively large geographic scales. However, it is not well known how factors like nest site fidelity in a largely resident species could limit gene flow and increase genetic structuring in birds. In this study we use RAPD markers to estimate genetic structuring in a strongly sedentary species of the American tropics, the Russet crowned Motmot ( Momotus mexicanus ), within a tropical dry forest in central Mexico. Genetic structuring was assessed among 3 populations separated by a mean distance of only 25 km. We report that 12.9% of the total genetic variation is explained by differences among sites, which is quite high for a bird at this geographic scale. We propose that high nest site fidelity, brought on by a scarcity of suitable nest substrates, may be responsible for high genetic structuring in this species.     

Biochemical differentiation in the Idaho ground squirrel, Spermophilus brunneus (Rodenta: Scuridae)

Spermophilus brunneus is restricted to a 90 × 125-km area of west central Idaho, with two distinct (northern and southern) groups of populations within this limited range. Morphological differences in pelage length and coloration, external and cranial measurements, and bacula suggest that these groups are either very distinct subspecies or species. We used starch-gel electrophoresis to estimate the amount of genetic differentiation accompanying these morphological differences by assaying genetic variation at 31 loci in the two geographic groups. Fifteen loci were polymorphic (13 in the northern group, 12 in the southern), and mean heterozygosity (H) was high (12.3% northern and 10.8% southern). Nei's genetic distance (0.057) is in the range usually associated with subspecific differences. However, Jaccard's association coefficient (0.893) is about the same as that found between several ground squirrel taxa currently recognized as species. The high levels of heterozygosity suggest that S. brunneus is a neoendemic rather than a paleoendemic species.     

Post-pleistocene dispersal in the Mexican vole ( Microtus mexicanus ): an example of an apparent trend in the distribution of southwestern mammals

The present distribution of the Mexican vole ( Microtus mexicanus ) is not entirely the product of post-Pleistocene forest fragmentation and extinction; recent dispersal also is indicated. Literature records further suggest that this phenomenon may reflect a general pattern of northward range expansion in many southwestern mammal species.     

Genetic structure in striped skunks ( Mephitis mephitis ) on the Southern High Plains of Texas

Genetic variation within populations reflects population-level social and demographic processes and influences how a population behaves as an evolutionary unit. We examined partitioning of genetic variation in striped skunks ( Mephitis mephitis ) from the Southern High Plains of Texas during 1994-1995. Sixty-nine male and 35 female skunks were sampled on four 12.8-km 2 study plots. Plot centers ranged from 17.6 to 61.6 km apart. We used multi-locus DNA fingerprinting with 2 probes, pV47 and CTTxAGG, to test 3 hypotheses: (1) females are more genetically similar to other females than males are to other males on the same plot (indicating greater female philopatry than male philopatry), (2) genetic similarity is greater within plots than among plots (indicating partitioning of genetic variation in space), and (3) genetic similarity of males decreases as the distance separating males increases (indicating geographic distance affects rates of gene flow). In general, males on a plot had lower average genetic similarity than females. Genetic similarity within plots was not different from genetic similarity among plots for males or for females. Genetic similarity of males did not decrease with increasing distance among plots. The lack of geographical genetic structure in striped skunks suggests at the scale of this study (< 60 km) that gene flow of biparentally inherited genes is not distance-mediated. However, the higher similarity values for females than for males on the same plot supports an effect of male-biased dispersal and female philopatry on partitioning of genetic variation between sexes.     

Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region – Greece

The brown bear (Ursus arctos) in Greece is considered endangered but little is known about the genetic status and the exact size of local populations. Non-invasive genetic sampling was used in this study to investigate the genetic diversity and genetic structure of the brown bear population in the Kastoria region (northwest Macedonia, Greece) and to estimate its population size. Estimation of demographic parameters was based on innovative, well-evaluated methods that can provide estimates from a single sampling session. DNA was extracted from hairs, scat and blood samples and subsequent amplification of 10 microsatellite loci allowed the identification of a minimum number of 75 living bears in the study area while the mark–recapture-based analysis resulted in a point estimation of 219 individuals. Relatively high diversity values, lack of heterozygosity deficiency as well as estimated effective population size, support the Kastoria bear population having good conservation status.     

Comparative genetic differentiation study of three coexisting mangrove crabs in western Atlantic

ABSTRACT

A multispecies approach may reveal the factors influencing the genetic differentiation of coexisting species along a wide geographic area. Our aim was to compare the genetic differentiation of mangrove crabs coexisting along the western Atlantic in order to verify if there are common barriers, using two mitochondrial DNA markers to quantify genetic differentiation, variance and diversity. In addition, we included a mismatch distribution to check demographic history. Our data revealed that species with similar pelagic larval duration had either high genetic differentiation or the absence of genetic structure. These results can be explained by factors that contribute to genetic differentiation, such as the presence of large estuarine areas (acting as barriers), ocean currents, and larval behaviour. Also, historical events that promoted the isolation of some areas in the past, such as glacial cycles during the Pleistocene, could have caused the observed high levels of genetic divergence in some species.     

Strong genetic differentiation among neighboring populations of a locally endemic primrose

Maguire primrose is a locally endemic plant of northern Utah, USA, with a total known range of less than 20 km 2 . A previous study found evidence for strong differentiation among local populations at 4 allozyme loci. Here we reexamined populations using 165 AFLP loci and found further evidence of unusually strong genetic structure. We also found an apparently fixed nucleotide difference between populations for a noncoding region of chloroplast DNA, mirroring the patterns seen for AFLP loci. Furthermore, we tested the hypothesis that the current population structure is the result of breeding barriers between plants from different populations. We made controlled hand-pollinated crosses and found that interpopulation crosses did not set significantly fewer seeds than intrapopulation crosses. Thus, we found no evidence of breeding barriers to explain these genetic patterns. However, we did note a relatively short overlap in flowering time, suggesting that phenology is a more feasible explanation for genetic differentiation than pollen-stigma incompatibility. Our study emphasizes that even locally endemic plants can house measurable genetic differences over a short geographic scale.     

Mitochondrial DNA genetic variation and phylogeography of the recently described vole species Proedromys liangshanensis Liu,Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae)

A vole species, Proedromys liangshanensis Liu, Sun, Zeng and Zhao, 2007 Liu, SY, Sun, ZY, Zeng, ZY and Zhao, EM. 2007. A new vole (Cricetidae: Arvicolinae: proedromys) from the Liangshan Mountains of Sichuan province. China. J Mammal., 88(5): 1170–1178.  [Google Scholar] (Rodentia: Arvicolinae), which is endemic to the Liangshan Mountains, Sichuan, China, was reported in 2007. The species is restricted to a narrow range because of its weak dispersal ability and habitat specificity, and only lives in fir and spruce forests with abundant grass. In this study, the genetic diversity and phylogeographical structure of 42 P. liangshanensis were examined based on analysis of a partial mitochondrial DNA control region. The results revealed low genetic diversity in the P. liangshanensis populations. Twelve nucleotide haplotypes were defined in the 42 collected individuals, and were divided into two major phylogenetic clades, which were obviously related to geographic pattern. Estimates of gene flow (Nm?=?0.09) also revealed a genetic divergence between the Jinyang and Meigu populations. Species-specific traits, habitat specificity and geographic events contributed to the genetic divergence of the new vole. ?These authors contributed equally to this work.      

Species richness and California voles in an annual and a perennial grassland

Populations of a common burrowing rodent, Microtus californicus (the California vole), thrive in ungrazed or lightly grazed grasslands in coastal California. Two sites ungrazed by livestock, one dominated by native perennial grasses and another dominated by invasive annuals, were evaluated over 2 consecutive years for the relationship between plant species richness and location of M. californicus burrow entrances (burrows). Plant species and burrows were sampled as present or absent in contiguous 1-m 2 quadrats on a 100-m 2 grid. Quadrats with burrows averaged significantly more plant species than quadrats without them (11.3 vs. 9.9 species, P < 0.001). Burrows found in 1996 were not correlated with species richness in 1995, suggesting that voles affect richness rather than seek it out. Vole burrow locations showed significant clumping on the annual site and trended toward clumping on the perennial site in both 1995 and 1996. Because voles seem to create a clumped pattern with their burrow entrances, the associated increase in plant species richness may have a strong effect on the overall structure of the plant community. A quantitative comparison of the 2 sites showed that the plant matrix of the perennial site contained flora of the annual site. This similarity in plant species composition may allow for similar treatment of our 2 types of sites and potentially other California grasslands. Undetected increases in vole populations with livestock grazing reduction may account for the erratic results from grasslands management research and the inconsistent success of derived management practices.     

Comparison of distribution and habitat characteristics between an endemic and a wide-ranging cryptic species of Peromyscus on the Baja California Peninsula

Peromyscus eva and Peromyscus fraterculus are 2 morphologically similar species of the Peromyscus eremicus group occurring on the Baja California Peninsula. Due to the similarity between these 2 species, their ranges have been greatly confused; consequently, the specific habitat characteristics for each group are not well known. The goal of this study was to assess distribution ranges and characteristics of preferred habitats for P. eva and P. fraterculus in more detail. We identified taxonomy of individuals by evaluating genetic patterns produced by restriction fragment length polymorphisms (RFLPs). We evaluated the banding pattern generated by Alu I and Bam HI restriction enzymes in an 850-bp cytochrome b fragment. Consistent differences in number and size of fragments allowed for discrimination of individuals to species. The heterogeneity and evenness indexes showed that the microhabitat of P. fraterculus contained less-diverse soil types and is more homogeneous than the microhabitat of P. eva. In the state of Baja California Sur, P. eva occurs exclusively in the flat areas along the Pacific coast from the Vizcaino Desert to the south, including Margarita Island, with one small population in the Loreto area adjacent to Carmen Island. The habitats occupied by P. eva were heterogeneous (areas with friable, soft sandy soil and a low percentage of small stones). Peromyscus fraterculus occurs mostly in Baja California Norte, with some populations distributed in Baja California Sur, particularly in the western areas of the Vizcaino Desert along the mountain range, in the gulf side of the peninsula south of the city of La Paz, and in a small area on the eastern side of Sierra de Las Cruces. This species was mostly found on hard soil with high medium-size stone content.     

Hybridization between a rare and introduced Oenothera along the north Pacific Coast

Interspecific hybridization has increasingly become regarded as a serious threat to the genetic integrity and persistence of rare plants. Oenothera glazioviana (Onagraceae) is a horticultural species that has escaped cultivation and now threatens the narrow Pacific coastal endemic O. wolfii with hybridization. Reports of morphologically intermediate and ecologically aggressive forms prompted this investigation into the extent of hybridization over the range of O. wolfii . In particular, this study identifies populations of pure and hybrid origins. We used multivariate methods to characterize the morphological variation of Oregon and northern California coastal Oenothera populations. Putatively pure O. wolfii and O. glazioviana individuals do not overlap in many floral characteristics. We found morphologies ranging between the 2 species in northern California populations, however, supporting the inference of hybridization. Remote O. wolfii populations in Oregon were smaller in almost all characters, and discriminant analysis was able to distinguish the rare species from both hybrids and O. glazioviana . However, 5 of 10 O. wolfii populations overlapped significantly with hybrid populations for individual traits and composite morphology, and trait values outside the range of O. wolfii were discovered in 2 populations previously considered to be pure. We also discuss the morphological evidence in light of these species’ chromosomal complexes and environmental factors.     

Population structure and ecological effects of the crayfish Pacifastacus leniusculus in Castle Lake, California

The recent appearance of the ""California crayfish,"" Pacifastacus leniusculus , in Castle Lake, California, and interest in its potential impacts on the lake ecosystem provided motivation for a study of the population structure and habitat use of this species and its effects on aquatic macrophytes. Mark-recapture studies indicated that the total number of adult (3 + yr or older) crayfish in the lake was ca 10,100 individuals, yielding an estimate of lakewide crayfish density in preferred crayfish habitats of 0.13 adults m -2 . Using mean body mass of individuals, we estimated that ambient biomass density was 5.9 g m -2 . Length-weight relationships determined for captured individuals were sex dependent, with males having greater body mass for a given carapace length. Length-frequency and weight-frequency diagrams indicated that P. leniusculus reaches larger sizes in Castle Lake than do populations of P. leniusculus in ultraoligotrophic Lake Tahoe. Population-wide, males were significantly larger in both carapace length and body mass than females. We also examined sex dependence of interhabitat differences in crayfish body size by comparing animals trapped in rocky areas with those from areas with macrophytes and soft sediments. No significant differences in overall body size were found between habitats, but a significant habitat-sex interaction term occurred because the sex-dependent size differences were more pronounced in sediment than in rocky areas. Exclosure and enclosure experiments indicated that crayfish had large but differential impacts on Castle Lake macrophyte species, as the abundance of two of the dominant species ( Chara sp., Potamogeton richardsonii ) declined in the presence of crayfish and, in one case, increased in exclosures. These effects occurred via both consumptive and nonconsumptive mechanisms. These studies indicate that and expanding population of P. leniusculus in Castle Lake may be producing sizable impacts on the littoral zone habitat.     

Influence of yellow starthistle ( Centaurea solstitialis ) on small mammals in central California

Yellow starthistle ( Centaurea solstitialis ) is native to Europe and Asia and has quickly invaded disturbed grasslands and rangelands in the western United States. The purpose of our study was to determine the effects of starthistle on rodents at Beale Air Force Base, Yuba County, California, by examining rodent species diversity, species abundance, age structure, and reproductive condition among locations with low, medium, and high percent cover and height of starthistle. Listed in decreasing order of abundance, the rodents were house mouse ( Mus musculus ), California vole ( Microtus californicus ), deer mouse ( Peromyscus maniculatus ), western harvest mouse ( Reithrodontomys megalotis ), and roof rat ( Rattus rattus ). Indices of diversity did not differ among starthistle cover categories. Regression analyses showed that Reithrodontomys megalotis was more abundant in high-cover starthistle plots, with 90.5% of captures occurring in at least 40% starthistle cover. Significant differences were found in capture rates, reproduction, and age between season only. To manage for all rodent species, an area with medium percent cover and height of starthistle will likely provide adequate protective cover.     

The Sex Ratio of Orange-flanked Bush-robins (Aves: Passeriformes: Muscicapidae) from a Winter Population in Central China

The sex ratio of a population is an important demographic parameter, but compared with breeding populations, the sex ratios of avian winter populations have received relatively little attention. The orange-flanked bush-robin (Tarsiger cyanurus) is a migratory species whose plumage is sexually dimorphic with delayed plumage maturation wherein first-year males show female-like plumage. We investigated the sex ratio of an orange-flanked bush-robin population wintering in Dongzhai National Nature Reserve located in central China. The results show that most (> 85%) orange-flanked bush-robins of this population have female-like plumage, implying that the population sex ratio might be female-biased. However, genetic analysis revealed that most (c. 70%) individuals with female-like plumage were males, resulting in a significantly male-biased population sex ratio. Among the individuals with female-like plumage, the males were found to have significantly longer wings and tails than females, but the accuracy of a discriminant analysis employing the two morphological traits to sex them was low. The results suggest that a genetic method is a more appropriate way to sex those orange-flanked bush-robins with female-like plumage and more importantly, one needs to be cautious when using the morphology of individuals to infer the sex ratio of a population for species like orange-flanked bush-robins.     

Diversity and dispersal history of the talitrids (Crustacea: Amphipoda: Talitridae) of Bermuda

Five taxa of talitrid amphipods were found in the archipelago of Bermuda, of which three were recorded there for the first time. Four of these are supralittoral wrack generalists: Platorchestia monodi BOLD:AAB3402, (a unique Molecular Operational Taxonomic Unit according to the Barcode Index Number system), a related species recognized by molecular methods, Platorchestia platensis BOLD:AAA2949, Mexorchestia carpenteri carpenteri BOLD:AAC1491 and Tethorchestia antillensis; and one a terrestrial leaf-litter generalist: Talitroides alluaudi. A key is provided to discriminate between the formally described talitrids of Bermuda. Dispersal mechanisms from the American continent to Bermuda were considered for all taxa based on species distributions along the North American Atlantic coast and also investigated by molecular methods, using genetic population differentiation and haplotype network analysis based on the barcode region of cytochrome c oxidase subunit I gene. For P. monodi BOLD:AAB3402 the genetic results suggest that some dispersal events occurred before human colonization of Bermuda but are equivocal about the source population and therefore the direction of dispersal. Some very recent synanthropic dispersal is possible with this species. For the other two species studied genetically, P. platensis BOLD:AAA2949 and M. c. carpenteri BOLD:AAC1491, the small population samples analysed support dispersal to Bermuda from the American mainland, before human occupation of Bermuda, although the available sample size was limited for these species. The available limited direct, non-genetic evidence supports synanthropic transport for Talitroides alluaudi. Platorchestia monodi BOLD:AAB3402 is found in the same wrack habitat as P. platensis BOLD:AAA2949 on Bermuda, apparently without interbreeding. No evidence was found that driftwood specialist talitrids had become established in Bermuda.     

Role of three rodents in forest nitrogen fixation in western Oregon: another aspect of mammal-mycorrhizal fungus-tree mutualism

To determine the role of the California red-backed vole ( Clethrionomys califonicus ), the northern flying squirrel ( Glaucomys sabrinus ), and the deer mouse ( Peromyscus maniculatus ) in the nitrogen cycle of forest stands in western Oregon, bacterial colonies were isolated and purified from feces, and their nitrogen-fixing ability measured by acetylene-reduction assay. The ability of the bacterial species Azospirillum &nbsp; sp. to withstand freezing was also tested. Fecal extracts were used to test whether fecal pellets can provide the nutrients necessary for growth of the bacteria. All the feces tested contained viable nitrogen-fixing bacteria, and both species can survive drying and one can survive freezing. Azospirillum colonies grew well on liquid medium but required yeast extract for growth and nitrogenase activity. Fecal extracts from flying squirrels and chickarees ( Tamiasciurus douglasi ) were as effective as the yeast. The results suggest another link in the chain of mutualism that unites small mammals, mycorrhizal fungi, and forest trees.     

Genetics, environment, and subspecies differences: the case of Polites sabuleti (Lepidoptera: Hesperiidae)

Circumstantial evidence is presented that suggests the Mourning Cloak undergoes regular seasonal up- and downslope movements in northern California. The species breeds at low elevations in spring and then disappears until autumn; its disappearance coincides with the appearance of fresh individuals in the Sierra Nevada alongside obvious hibernators.&nbsp;