Range-wide Scale Research Articles

Population Genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across Multiple Spatial Scales

Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (Fst values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94–98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.

Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient

Studies addressing the variation of mating system between plant populations rarely account for the variability of these parameters between individuals within populations, although this variability is often non-negligible. Here, we propose a new direct method based on paternity analyses (Mixed Effect Mating Model) to estimate individual migration (mi ) and selfing rates (si ) together with the pollen dispersal kernel. Using this method and the KINDIST approach, we investigated the variation of mating system parameters within and between three populations of Fagus sylvatica along an elevational gradient. Among the mother trees, si varied from 0% to 48%, mi varied from 12% to 86% and the effective number of pollen donors (Nepi ) varied from 2 to 364. The mating patterns differed along the gradient, the top population showing higher m and lower s, and a trend to higher Nep than the bottom populations. The phenological lag shaped long-distance pollen flow both within population (by increasing mi at mother-tree level) and between populations (by increasing m at high elevation). Rather than the mate density, the canopy density was detected as a major mating system determinant within population; it acted as a barrier to pollen flow, decreasing the proportion of long-distance pollen flow and increasing si . Overall, the effects of ecological factors on mating system were not the same within vs. between populations across the gradient, and these factors also differed from those traditionally found to shape variation at range-wide scale, highlighting the interest of multiscale approaches.

Effects of Landscape-Scale Environmental Variation on Greater Sage-Grouse Chick Survival.

Effective long-term wildlife conservation planning for a species must be guided by information about population vital rates at multiple scales. Greater sage-grouse (Centrocercus urophasianus) populations declined substantially during the twentieth century, largely as a result of habitat loss and fragmentation. In addition to the importance of conserving large tracts of suitable habitat, successful conservation of this species will require detailed information about factors affecting vital rates at both the population and range-wide scales. Research has shown that sage-grouse population growth rates are particularly sensitive to hen and chick survival rates. While considerable information on hen survival exists, there is limited information about chick survival at the population level, and currently there are no published reports of factors affecting chick survival across large spatial and temporal scales. We analyzed greater sage-grouse chick survival rates from 2 geographically distinct populations across 9 years. The effects of 3 groups of related landscape-scale covariates (climate, drought, and phenology of vegetation greenness) were evaluated. Models with phenological change in greenness (NDVI) performed poorly, possibly due to highly variable production of forbs and grasses being masked by sagebrush canopy. The top drought model resulted in substantial improvement in model fit relative to the base model and indicated that chick survival was negatively associated with winter drought. Our overall top model included effects of chick age, hen age, minimum temperature in May, and precipitation in July. Our results provide important insights into the possible effects of climate variability on sage-grouse chick survival.

Allozyme and phenotypic variation in beech (Fagus sylvatica L.): Are there any links?

Allozymes are generally considered neutral markers, although there is evidence of adaptive significance of some allozyme markers in many tree species. Nevertheless, as shown by numerous studies, geographical distribution of variation at allozyme loci reflects mainly non-selective processes and phenomena such as colonization, gene flow and founder/bottleneck effects. On the other hand, neutral processes also affect genes controlling quantitative phenotypic traits such as growth and tree architecture. Basic question arising with all gene-marker studies aiming at gene conservation is whether neutral markers can provide any relevant and useful information, i.e. to what extent they reflect variation at genes controlling quantitative and fitness-related traits. This study focuses on potential concordances/discordances in spatial patterns of allozyme and quantitative phenotypic variation. We found that on the range-wide scale, there is no association between phenotypic variation in growth and adaptive traits and neutral allelic richness, but an association with neutral gene diversity. Populations with a high diversity at allozyme loci tend to exhibit also a high intra-population variance of phenotypic traits.

A State-Based National Network for Effective Wildlife Conservation

State wildlife conservation programs provide a strong foundation for biodiversity conservation in the United States, building on state wildlife action plans. However, states may miss the species that are at the most risk at rangewide scales, and threats such as novel diseases and climate change increasingly act at regional and national levels. Regional collaborations among states and their partners have had impressive successes, and several federal programs now incorporate state priorities. However, regional collaborations are uneven across the country, and no national counterpart exists to support efforts at that scale. A national conservation-support program could fill this gap and could work across the conservation community to identify large-scale conservation needs and support efforts to meet them. By providing important information-sharing and capacity-building services, such a program would advance collaborative conservation among the states and their partners, thus increasing both the effectivenes...

Genetic assessment of the population connectivity of the red urchin (Strongylocentrotus franciscanus)

A set of five microsatellite genetic markers was used to examine connectivity among populations of the red urchin, Strongylocentrotus franciscanus, collected from five locations in California and two locations in British Columbia, Canada. Consistent with previous studies, there was little evidence of differentiation among the California populations. However, significant divergence (FST=0.039), as well as isolation by distance (IBD) (R2=0.2815, p=0.024), was observed between the California and British Columbia populations. These results show for the first time that, on a range wide scale, populations of red urchins are genetically divergent. Although the detected differentiation is low, it suggests that even the estimated 7–19month planktonic larval duration of this species fails to homogenize the gene pool across the species range.

Population genetic structure and geographic differentiation in the hot spring snake Thermophis baileyi (Serpentes, Colubridae): Indications for glacial refuges in southern-central Tibet

The endangered hot spring snake (Thermophis baileyi) is endemic to the Tibetan Plateau and restricted to a few sites at high altitudes (>3500ma.s.l.). Its strong preference for habitats with hot springs might be an early adaptation to the cooling climate during the plateau uplift. Some of these thermal sites may have been free of ice during the last glacial maximum (LGM) serving as refuges for the snake. To test this and to examine the population genetic structure data of 12 microsatellites and mitochondrial DNA were obtained from 153 individuals from 12 sites across the plateau. Four of the microsatellite loci were newly developed for this study. The results suggest that T. baileyi has at least two genetically diverse clades in Tibet, which developed during the Pleistocene and expanded after the LGM. Accordingly, the existence of separate glacial refuges on the central plateau can be assumed. Analyses of the genetic variation indicated a high level of geographic differentiation and population structure on a regional as well as on a range-wide scale. The study shows that, apart from the phylogeographic signatures, the diversification of current Thermophis populations is caused by (a) a limited dispersal due to mountain ranges, (b) a strong preference for hot springs and (c) the insular distribution of suitable habitats on the plateau. The present data should be taken into account in necessary monitoring and management plans for T. baileyi.

Predicting patch occupancy in fragmented landscapes at the rangewide scale for an endangered species: an example of an American warbler.

AIM: Our objective was to identify the distribution of the endangered golden-cheeked warbler (Setophaga chrysoparia) in fragmented oak-juniper woodlands by applying a geoadditive semiparametric occupancy model to better assist decision-makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning. LOCATION: Texas, USA. METHODS: We used repeated double-observer detection/non-detection surveys of randomly selected (n = 287) patches of potential habitat to evaluate warbler patch-scale presence across the species breeding range. We used a geoadditive semiparametric occupancy model with remotely sensed habitat metrics (patch size and landscape composition) to predict patch-scale occupancy of golden-cheeked warblers in the fragmented oak-juniper woodlands of central Texas, USA. RESULTS: Our spatially explicit model indicated that golden-cheeked warbler patch occupancy declined from south to north within the breeding range concomitant with reductions in the availability of large habitat patches. We found that 59% of woodland patches, primarily in the northern and central portions of the warbler's range, were predicted to have occupancy probabilities ≤0.10 with only 3% of patches predicted to have occupancy probabilities >0.90. Our model exhibited high prediction accuracy (area under curve = 0.91) when validated using independently collected warbler occurrence data. MAIN CONCLUSIONS: We have identified a distinct spatial occurrence gradient for golden-cheeked warblers as well as a relationship between two measurable landscape characteristics. Because habitat-occupancy relationships were key drivers of our model, our results can be used to identify potential areas where conservation actions supporting habitat mitigation can occur and identify areas where conservation of future potential habitat is possible. Additionally, our results can be used to focus resources on maintenance and creation of patches that are more likely to harbour viable local warbler populations.

Differentiation of reproductive and competitive ability in the invaded range of Senecio inaequidens: the role of genetic Allee effects, adaptive and nonadaptive evolution

Genetic differentiation in the competitive and reproductive ability of invading populations can result from genetic Allee effects or r/K selection at the local or range-wide scale. However, the neutral relatedness of populations may either mask or falsely suggest adaptation and genetic Allee effects. In a common-garden experiment, we investigated the competitive and reproductive ability of invasive Senecio inaequidens populations that vary in neutral genetic diversity, population age and field vegetation cover. To account for population relatedness, we analysed the experimental results with 'animal models' adopted from quantitative genetics. Consistent with adaptive r/K differentiation at local scales, we found that genotypes from low-competition environments invest more in reproduction and are more sensitive to competition. By contrast, apparent effects of large-scale r/K differentiation and apparent genetic Allee effects can largely be explained by neutral population relatedness. Invading populations should not be treated as homogeneous groups, as they may adapt quickly to small-scale environmental variation in the invaded range. Furthermore, neutral population differentiation may strongly influence invasion dynamics and should be accounted for in analyses of common-garden experiments.

Time energy budgets and food use of Atlantic brant across their wintering range

We conducted extensive behavioral and food sampling of Atlantic brant (Branta bernicla hrota) across their winter range and used time–activity budgets for brant to determine daily energy expenditure (DEE). Sampling occurred 1 December–31 May 2006–2008 in 11,225-km2 sites between Rhode Island and Virginia containing important estuarine and upland habitat. To calculate DEE we used instantaneous scan sampling to estimate time–activity budgets. We also determined foods eaten by brant and energy density of food plants. Last, we quantified body condition of brant, which differed among years, months, regions, and ages, and sexes. Overall DEE for brant was 1,530 ± 64 kJ/day. There was considerable variation in time–activity budgets among years, months, regions, habitat, tide, temperature, and time-of-day, but we detected no significant difference in DEE of brant between years or among regions. However, DEE in January (2,018 ± 173 kJ/day) was nearly double the DEE of brant in May (1,048 ± 137 kJ/day). Brant spent their time feeding (32.3%), swimming (26.2%), resting (16.2%), and flying (14.5%). The percent of brant foreguts sampled contained macroalgae (53%) eelgrass (Zostera marina; 18%), salt marsh cordgrass (Spartina alterniflora; 17%), and terrestrial grass (Poa. sp.) and clover (Trifollium sp.; 9%). Energy density differed by vegetation type: macroalgae (12.6 ± 0.1 kJ/g), eelgrass (14.1 ± 0.1 kJ/g), new-growth salt marsh cordgrass (16.9 ± 0.2 kJ/g), and terrestrial grass and clover (17.7 ± 0.1 kJ/g). Atlantic brant exhibited behavioral plasticity thereby allowing modification of daily activity budgets to meet seasonally varying energetic requirements associated with wintering and spring staging. Recognizing a variable DEE can be used along with eventual estimates of food biomass and total metabolizable energy on the landscape to calculate carrying capacity (goose use days) on state, region, or range-wide scales. © 2011 The Wildlife Society.

Contrasting genetic variation and differentiation on Hainan Island and the Chinese mainland populations of Dacrycarpus imbricatus (Podocarpaceae)

Dacrycarpus imbricatus is a vulnerable conifer in China whose geographical distribution encompasses large island but small mainland populations, providing a framework for contrasting the patterns of population genetic composition. In this study, seven populations on Hainan Island and the Chinese mainland were sampled throughout its distribution range and assessed using ISSR. The results did not show significant differences neither in genetic variation nor in genetic differentiation between the island and the mainland populations ( P > 0.05). Severe bottlenecks were identified at population, island/mainland as well as range-wide scales. A relatively high level of variation but a low degree of differentiation was revealed. Ecological and life traits were suggested to play main roles in the shaping of genetic variation pattern. Of them long generation times could have exerted a lagging effect on both the genetic variation and differentiation. Our findings may contribute to establish management practices.

Regional Variation in mtDNA of the Lesser Prairie-Chicken

Cumulative loss of habitat and long-term decline in the populations of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) have led to concerns for the species' viability throughout its range in the southern Great Plains. For more efficient conservation past and present distributions of genetic variation need to be understood. We examined the distribution of mitochondrial DNA (mtDNA) variation in the Lesser Prairie-Chicken across Kansas, Colorado, Oklahoma, and New Mexico. Throughout the range we found little genetic differentiation except for the population in New Mexico, which was significantly different from most other populations. We did, however, find significant isolation by distance at the rangewide scale (r = 0.698). We found no relationship between haplotype phylogeny and geography, and our analyses provide evidence for a post-glacial population expansion within the species that is consistent with the idea that speciation within Tympanuchus is recent. Conservation actions that increase the likelihood of genetically viable populations in the future should be evaluated for implementation.

Population genetic variation, differentiation and bottlenecks of Dacrydium pectinatum (Podocarpaceae) in Hainan Island, China: implications for its conservation

Island populations provide an ideal natural experiment with which to study the forces driving population evolution. Seventeen populations of Dacrydium pectinatum de Laubenfels on Hainan Island, China, were sampled throughout its distribution range and then assessed using inter-simple sequence repeats (ISSR) markers. Population genetic parameters were estimated by Bayesian approaches as well as conventional methods. Genetic bottleneck signatures were further dissected by performing three heterozygosity excess tests and the mode-shift indicator test. Compared with other coniferous species, a relatively high level of genetic variation and a low degree of differentiation was revealed in D. pectinatum. In addition, severe bottlenecks were identified at local, regional as well as range-wide scale. Ecological and life-history traits were suggested to play major roles in the shaping of the genetic variation pattern. In particular, long life span could have exerted a lagging effect on both the genetic variation and differentiation of extant populations. Our findings may contribute to improving management practices for the restoration of D. pectinatum.

Black Pine Snake (Pituophis melanoleucus lodingi): Spatial Ecology and Associations between Habitat Use and Prey Dynamics

Abstract As remaining longleaf pine forests become increasingly fragmented, wildlife management becomes a daunting task, especially for rare and relatively unstudied taxa such as the Black Pine Snake (Pituophis melanoleucus lodingi). Appropriate management for P. m. lodingi depends on our understanding of the ecology of this subspecies; consequently, there were two main objectives of this study: to address questions of spatial ecology for P. m. lodingi on a rangewide scale; and to employ small mammal trapping within home ranges of telemetered snakes to investigate the relationship between prey density and spatial ecology. Pituophis melanoleucus lodingi exhibited large home ranges (MCP, Minimum Convex Polygon home ranges, were 92–396 ha), frequently crossed roads, and average (nonzero) movement distance for these snakes was 338 m per location event. Core home ranges of telemetered P. m. lodingi were characterized by significantly greater abundances of hispid cotton rats (Sigmodon hispidus) and significantl...

Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation

Fossil pollen records indicate that Hippophaë rhamnoides (Sea Buckthorn) was widespread on late- and early postglacial raw soils throughout much of central and northern Europe, but that Early Holocene reforestation restricted populations to northern coastal habitats, or along mountain streams in the Alps, Pyrenees, and Carpathians. We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA-restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic structure, and expansion demographic history of this dioecious and wind-pollinated shrub at its range-wide scale in Europe and Asia Minor. Four major Chsi phylogroups of unresolved relationships were identified with estimated divergences approximately 172,000 years ago. Large-scale phylogeographic structures of nuclear and cytoplasmic markers were congruent in identifying (i) southeastern Europe as the most likely source of colonization into central Europe and Scandinavia, and (ii) the area just north of the Alps as a contact zone between populations from the Alps and the east/central European-Scandinavian lineage. Coalescence-based analyses (i.e. nested clade analysis and mismatch distributions) of Chsi variation were able to detect at least four major episodes of population growth, all within about the last 40,000 years. In particular, these analyses identified a nearly synchronized timing of population expansions in various parts of the species' range in central-eastern Europe/Asia Minor, most likely correlating with the Younger Dryas Stadial ( approximately 13,000-11,600 years ago). It remains to be established whether the phylogeographic history of H. rhamnoides, and particularly its rapid response to the rapid environmental changes of the Younger Dryas cold snap, is unique to the species, or whether it is shared with other cold-tolerant shrub (or grassland) species known from late-glacial raw soils in Europe.

MONITORING THE ABUNDANCE OF BIRD POPULATIONS

LARGE-SCALE, LONG-TERM PROGRAMS to monitor bird abundance have provided the foundation for many of our most successful programs to study and conserve bird populations (Brown et al. 2001, Williams et al. 2002, Kushlan et al. 2002, Rich et al. 2004, U.S. Fish and Wildlife Service 2004). Those programs help identify species at risk and limiting factors, suggest and help evaluate management approaches, and document recovery at the regional and rangewide scale. It is difficult to think of a major wildlife issue for which monitoring has not provided essential information. Yet despite the critical role of bird monitoring programs, many of them are poorly designed and coordinated, and many improvements could be made at relatively low cost. In a welcome addition to the bird-monitoring literature, Conway and Gibbs (2005) describe improved methods for surveying secretive marsh birds. Their study is notable because it is based on >16,000 point counts contributed, at the authors' request, by 15 cooperators working on 12 species in 10 states. Only by recruiting collaborators (they wrote to more than 100 authors) could Conway and Gibbs have compiled such a large and spatially extensive database on that relatively unknown group of birds. Their specific question was whether secretive marsh birds are best monitored by broadcasting calls, listening passively, or doing both. Most of their collaborators used both methods, so Conway and Gibbs (2005) used differences in numbers recorded during passive and active periods, thereby excluding extraneous sources of variation such as site, observer, and weather. They also adjusted results to enable comparison of numbers that would have been recorded with periods of equal duration. They compared number recorded per

INVITED REVIEW: Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations

AbstractPlants offer excellent models to investigate how gene flow shapes the organization of genetic diversity. Their three genomes can have different modes of transmission and will hence experience varying levels of gene flow. We have compiled studies of genetic structure based on chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear markers in seed plants. Based on a data set of 183 species belonging to 103 genera and 52 families, we show that the precision of estimates of genetic differentiation (GST) used to infer gene flow is mostly constrained by the sampling of populations. Mode of inheritance appears to have a major effect on GST. Maternally inherited genomes experience considerably more subdivision (median value of 0.67) than paternally or biparentally inherited genomes (∼0.10). GST at cpDNA and mtDNA markers covary narrowly when both genomes are maternally inherited, whereas GST at paternally and biparentally inherited markers also covary positively but more loosely and GST at maternally inherited markers are largely independent of values based on nuclear markers. A model‐based gross estimate suggests that, at the rangewide scale, historical levels of pollen flow are generally at least an order of magnitude larger than levels of seed flow (median of the pollen‐to‐seed migration ratio: 17) and that pollen and seed gene flow vary independently across species. Finally, we show that measures of subdivision that take into account the degree of similarity between haplotypes (NST or RST) make better use of the information inherent in haplotype data than standard measures based on allele frequencies only.

West Nile virus and wildlife health.

West Nile virus and wildlife health.

Molecular genetic structure suggests limited larval dispersal in grass rockfish, Sebastes rastrelliger

The grass rockfish (Sebastes rastrelliger Jordan and Gilbert, 1880) is a non-migratory, benthic, near shore species distributed along rocky reefs and sea grass beds. It occurs from Baja California, Mexico, to Oregon, USA, spanning the Oregonian and Californian biogeographic provinces. In California this fish receives intense fishing pressure from an expanding and loosely regulated live-fish fishery. It is not known whether or by what mechanism larvae and juveniles are retained locally or dispersed widely during the early life-history phase. Tissue samples of S. rastrelliger were collected between 1996 and 2001 from 405 adult fish at eight sites (42.70°N; 124.50°W to 32.67°N; 117.25°W) spanning the species’ range. Individuals were surveyed for polymorphism at six microsatellite loci. Allele frequency heterogeneity was not significant among all sites (FST=0.001; P=0.18), nor in pairwise comparisons, but a clear correlation of genetic and geographic distance was detected (P=0.019). Fit of genetic and geographic distance was stronger within biogeographic provinces than at a range-wide scale, suggesting that populations north and south of the Point Conception biogeographic boundary are not in equilibrium with respect to migration and genetic drift. Estimates of mean coastal dispersal distances associated with the isolation-by-distance relationship are on the order of 10 km generation−1. Such limited dispersal in a species with a pelagic early life history suggests active retention mechanisms near the shore. This has important implications for coastal management zones and design of marine reserves.

ENVIRONMENTAL CORRELATES OF GEOGRAPHIC VARIATION IN BODY SIZE OF THE EASTERN COTTONTAIL (SYLVILAGUS FLORIDANUS)

Geographic variation in body size of Sylvilagus floridanus was investigated from 3 climatically different and disjunct regions of the range of this species (region 1, northeastern United States and southern Canada; region 2, southeastern United States; region 3, southwestern United States and northern Mexico). On a rangewide scale, body size decreased from east to west and less strongly north to south, consistent with Bergmann's rule, and was associated most strongly with variability in winter precipitation. On a regional scale, body size decreased from northwest to southeast in region 1 and southwest to northeast in region 3. We detected no trend in region 2. Large body size in region 1 was found in cold and dry environments. Body size in region 3 increased with cooler and wetter summer environments, high elevations, and low variability in winter precipitation. Bergmann's rule was supported within region 1 but not in region 2 or 3. Directions and magnitudes of trends in body size appear to depend on severity of climate; the 2 most climatically stressful regions (1 and 3) had stronger climatic correlations than region 2.