Architectural specialization of the intrinsic thoracic limb musculature of the American badger (Taxidea taxus)

Evaluation of the relationships between muscle structure and digging function in fossorial species is limited. Badgers and other fossorial specialists are expected to have massive forelimb muscles with long fascicles capable of substantial shortening for high power and applying high out‐force to the substrate. To explore this hypothesis, we quantified muscle architecture in the thoracic limb of the American badger (Taxidea taxus) and estimated the force, power, and joint torque of its intrinsic musculature in relation to the use of scratch‐digging behavior. Architectural properties measured were muscle mass, belly length, fascicle length, pennation angle, and physiological cross‐sectional area. Badgers possess hypertrophied shoulder flexors/humeral retractors, elbow extensors, and digital flexors. The triceps brachii is particularly massive and has long fascicles with little pennation, muscle architecture consistent with substantial shortening capability, and high power. A unique feature of badgers is that, in addition to elbow joint extension, two biarticular heads (long and medial) of the triceps are capable of applying high torques to the shoulder joint to facilitate retraction of the forelimb throughout the power stroke. The massive and complex digital flexors show relatively greater pennation and shorter fascicle lengths than the triceps brachii, as well as compartmentalization of muscle heads to accentuate both force production and range of shortening during flexion of the carpus and digits. Muscles of most functional groups exhibit some degree of specialization for high force production and are important for stabilizing the shoulder, elbow, and carpal joints against high limb forces generated during powerful digging motions. Overall, our findings support the hypothesis and indicate that forelimb muscle architecture is consistent with specializations for scratch‐digging. Quantified muscle properties in the American badger serve as a comparator to evaluate the range of diversity in muscle structure and contractile function that exists in mammals specialized for fossorial habits. J. Morphol. 2013. © 2012 Wiley Periodicals, Inc.     

Pathogen and rodenticide exposure in American badgers (Taxidea taxus) in California

Urban and agricultural land use may increase the risk of disease transmission among wildlife, domestic animals, and humans as we share ever-shrinking and fragmented habitat. American badgers (Taxidae taxus), a species of special concern in California, USA, live in proximity to urban development and often share habitat with livestock and small peridomestic mammals. As such, they may be susceptible to pathogens commonly transmitted at this interface and to anticoagulant rodenticides used to control nuisance wildlife on agricultural lands. We evaluated free-ranging badgers in California for exposure to pathogens and anticoagulant rodenticides that pose a risk to wildlife, domestic animals, or public health. We found serologic evidence of badger exposure to Francisella tularensis, Toxoplasma gondii, Anaplasma phagocytophilum, canine distemper virus, and three Bartonella species: B. henselae, B. clarridgeiae, and B. vinsonii subsp. berkhoffii. Badger tissues contained anticoagulant rodenticides brodifacoum and bromadiolone, commonly used to control periurban rodent pests. These data provide a preliminary investigation of pathogen and toxicant exposure in the wild badger population.     

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul , which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure ( F _ST = 0.051–0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes ( N _e = 7–30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B.   exsul 's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.     

Fine-scale phenotypic change across a species transition zone in the genus neotoma: disentangling independent evolution from phylogenetic history

Zones of secondary contact between closely related species provide a rare opportunity to examine evidence of evolutionary processes that reinforce species boundaries and/or promote diversification. Here, we report on genetic and morphological variation in two sister species of woodrats, Neotoma fuscipes and N. macrotis, across a 30-km transition zone in the Sierra Nevada of California. We assessed whether these lineages readily hybridize, and whether their morphology suggests ecological interactions favoring phenotypic diversification. We combined measurements of body size and 11 craniodental traits from nine populations with genetic data to examine patterns of variation within and between species. We used phylogenetic autocorrelation methods to estimate the degree to which phenotypic variation in our dataset arose from independent evolution within populations versus phylogenetic history. Although no current sympatry or hybridization was evident, craniodental morphology diverged in both lineages near their distributional limits, whereas body size converged. The shift in craniodental morphology arose independently within populations whereas body size retained a strong phylogenetic signal, yet both patterns are consistent with expectations of phenotypic change based on different models of resource competition. Our findings demonstrate the importance of examining a suite of morphological traits across contact zones to provide a more complete picture of potential ecological interactions: competition may drive both diversification and convergence in different phenotypic traits.     

How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna

Background

The species boundaries of some venerids are difficult to define based solely on morphological features due to their indistinct intra- and interspecific phenotypic variability. An unprecedented biodiversity crisis caused by human activities has emerged. Thus, to access the biological diversity and further the conservation of this taxonomically muddling bivalve group, a fast and simple approach that can efficiently examine species boundaries and highlight areas of unrecognized diversity is urgently needed. DNA barcoding has proved its effectiveness in high-volume species identification and discovery. In the present study, Chinese fauna was chosen to examine whether this molecular biomarker is sensitive enough for species delimitation, and how it complements taxonomy and explores species diversity.

Methodology/Principal Findings

A total of 315 specimens from around 60 venerid species were included, qualifying the present study as the first major analysis of DNA barcoding for marine bivalves. Nearly all individuals identified to species level based on morphological traits possessed distinct barcode clusters, except for the specimens of one species pair. Among the 26 individuals that were not assigned binomial names a priori, twelve respectively nested within a species genealogy. The remaining individuals formed five monophyletic clusters that potentially represent species new to science or at least unreported in China. Five putative hidden species were also uncovered in traditional morphospecies.

Conclusions/Significance

The present study shows that DNA barcoding is effective in species delimitation and can aid taxonomists by indicating useful diagnostic morphological traits, informing needful revision, and flagging unseen species. Moreover, the BOLD system, which deposits barcodes, morphological, geographical and other data, has the potential as a convenient taxonomic platform.     

Moose body mass variation revisited: disentangling effects of environmental conditions and genetics

Large-scale geographical variation in phenotypic traits within species is often correlated to local environmental conditions and population density. Such phenotypic variation has recently been shown to also be influenced by genetic structuring of populations. In ungulates, large-scale geographical variation in phenotypic traits, such as body mass, has been related to environmental conditions and population density, but little is known about the genetic influences. Research on the genetic structure of moose suggests two distinct genetic lineages in Norway, structured along a north-south gradient. This corresponds with many environmental gradients, thus genetic structuring provides an additional factor affecting geographical phenotypic variation in Norwegian moose. We investigated if genetic structure explained geographical variation in body mass in Norwegian moose while accounting for environmental conditions, age and sex, and if it captured some of the variance in body mass that previously was attributed to environmental factors. Genetic structuring of moose was the most important variable in explaining the geographic variation in body mass within age and sex classes. Several environmental variables also had strong explanatory power, related to habitat diversity, environmental seasonality and winter harshness. The results suggest that environmental conditions, landscape characteristics, and genetic structure should be evaluated together when explaining large-scale patterns in phenotypic characters or life history traits. However, to better understand the role of genetic and environmental effects on phenotypic traits in moose, an extended individual-based study of variation in fitness-related characters is needed, preferably in an area of convergence between different genetic lineages.     

Species–area and species–sampling effort relationships: disentangling the effects

Species numbers tend to increase with both the area surveyed (species–area relationship, SAR) and the number of samples taken (species–sampling effort relationship, SSER). These two relationships differ in their nature and underlying mechanisms but are not clearly distinguished in field studies. To discriminate the effects of area (spatial extent) and sampling effort (SE) on species richness, several models explicitly involving both variables were proposed and tested against 13 datasets from marine micro‐, meio‐ and macrobenthos. A combination of power SSER and piecewise power SAR terms was found to have the best fit. The effects of area and SE were both significant, but the former one was noticeably weaker. The SSERs were roughly linear in log‐log space, whereas the SARs demonstrated scale‐dependent behavior with a noticeable threshold (slope breakpoint). Species richness was almost area‐independent below this threshold (the “small area effect”, SAE) but followed typical power‐law SAR beyond the threshold. This effect was similar to the “small island effect” but occurred for arbitrarily delineated areas within continuous habitats. Parameters of the SAR curves depended on organism size. The upper limit of the SAE increased from microorganisms to meiofauna to macrofauna. Also, SAR curves for unicellular groups had significantly lower slopes. SAE is supposed to indicate a spatial range of statistical homogeneity in species composition. Its upper limit corresponds to the characteristic size of a local community (a single habitat occupied by a common species pool). Interpretations of SAR and SSER parameters in terms of α‐ and β‐diversity are proposed. Both SAR and SSER slopes obtained from univariate regressions are overestimated. This upward bias depends on sampling design, decreasing for SAR but increasing for SSER with more unequally spaced samples. Both spatial extent and sampling effort should be taken into account to disentangle properly their effects on diversity.     

Growth strategies of tropical tree species: disentangling light and size effects

An understanding of the drivers of tree growth at the species level is required to predict likely changes of carbon stocks and biodiversity when environmental conditions change. Especially in species-rich tropical forests, it is largely unknown how species differ in their response of growth to resource availability and individual size. We use a hierarchical bayesian approach to quantify the impact of light availability and tree diameter on growth of 274 woody species in a 50-ha long-term forest census plot in Barro Colorado Island, Panama. Light reaching each individual tree was estimated from yearly vertical censuses of canopy density. The hierarchical bayesian approach allowed accounting for different sources of error, such as negative growth observations, and including rare species correctly weighted by their abundance. All species grew faster at higher light. Exponents of a power function relating growth to light were mostly between 0 and 1. This indicates that nearly all species exhibit a decelerating increase of growth with light. In contrast, estimated growth rates at standardized conditions (5 cm dbh, 5% light) varied over a 9-fold range and reflect strong growth-strategy differentiation between the species. As a consequence, growth rankings of the species at low (2%) and high light (20%) were highly correlated. Rare species tended to grow faster and showed a greater sensitivity to light than abundant species. Overall, tree size was less important for growth than light and about half the species were predicted to grow faster in diameter when bigger or smaller, respectively. Together light availability and tree diameter only explained on average 12% of the variation in growth rates. Thus, other factors such as soil characteristics, herbivory, or pathogens may contribute considerably to shaping tree growth in the tropics.     

Fine-scale effects of fire on non-woody species in a southern Amazonian seasonal wetland

Wetlands Ecology and Management - Grasslands and wetlands are non-forested highly biodiverse ecosystems. Although fire is a major factor controlling and maintaining biodiversity in different...     

Population genetics of the American eel (Anguilla rostrata): FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

We performed population genetic analyses on the American eel (Anguilla rostrata) with three main objectives. First, we conducted the most comprehensive analysis of neutral genetic population structure to date to revisit the null hypothesis of panmixia in this species. Second, we used this data to provide the first estimates of contemporary effective population size (N_e) and to document temporal variation in effective number of breeders (N_b) in American eel. Third, we tested for statistical associations between temporal variation in the North Atlantic Oscillation (NAO), the effective number of breeders and two indices of recruit abundance. A total of 2142 eels from 32 sampling locations were genotyped with 18 microsatellite loci. All measures of differentiation were essentially zero, and no evidence for significant spatial or temporal genetic differentiation was found. The panmixia hypothesis should thus be accepted for this species. N_b estimates varied by a factor of 23 among 12 cohorts, from 473 to 10 999. The effective population size N_e was estimated at 10 532 (95% CI, 9312–11 752). This study also showed that genetically based demographic indices, namely N_b and allelic richness (Ar), can be used as surrogates for the abundance of breeders and recruits, which were both shown to be positively influenced by variation during high (positive) NAO phases. Thus, long‐term genetic monitoring of American glass eels at several sites along the North American Atlantic coast would represent a powerful and efficient complement to census monitoring to track demographic fluctuations and better understand their causes.     

Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change

Landscape genetics seeks to determine the effect of landscape features on gene flow and genetic structure. Often, such analyses are intended to inform conservation and management. However, depending on the many factors that influence the time to reach equilibrium, genetic structure may more strongly represent past rather than contemporary landscapes. This well‐known lag between current demographic processes and population genetic structure often makes it challenging to interpret how contemporary landscapes and anthropogenic activity shape gene flow. Here, we review the theoretical framework for factors that influence time lags, summarize approaches to address this temporal disconnect in landscape genetic studies, and evaluate ways to make inferences about landscape change and its effects on species using genetic data alone or in combination with other data. Those approaches include comparing correlation of genetic structure with historical versus contemporary landscapes, using molecular markers with different rates of evolution, contrasting metrics of genetic structure and gene flow that reflect population genetic processes operating at different temporal scales, comparing historical and contemporary samples, combining genetic data with contemporary estimates of species distribution or movement, and controlling for phylogeographic history. We recommend using simulated data sets to explore time lags in genetic structure, and argue that time lags should be explicitly considered both when designing and interpreting landscape genetic studies. We conclude that the time lag problem can be exploited to strengthen inferences about recent landscape changes and to establish conservation baselines, particularly when genetic data are combined with other data.     

The NH(2)-terminal propeptides of fibrillar collagens: highly conserved domains with poorly understood functions.

The impetus for this review comes from the recent finding that the absence of the majority of the non-triple-helical sequence in the NH(2)-terminal propeptide (N-propeptide) of the pro alpha 1(I) collagen chain fails to generate a significant phenotype in the mouse (Bornstein et al., J. Biol. Chem., 277:2605-2613, 2002). This result is in apparent conflict with those of numerous studies in vitro that have implicated the N-propeptide in a number of processes that are involved in the biogenesis, maturation and function of type 1 collagen. To seek an explanation for this discrepancy, the sequences of the highly conserved, 55-57-amino acid, cysteine-rich repeats (CRR), which constitute the majority of the globular domains in the N-propeptides, were compared among 13 vertebrate species. Surprisingly, the CRR in mice and rats differs substantially from those in other mammalian species. Indeed, the CRR in birds, fish and amphibia are more similar to those of other mammals than are the CRR in rodents. This finding raises the possibility that the mutant mouse, which lacks exon 2 that encodes the CRR in the N-propeptide, might not be an appropriate model in which to study the function of the N-propeptide in other mammals. Alternatively, compensation, possibly by procollagens II or III, could account for the mild phenotype of the exon 2-deleted mouse. Yet another possibility is that the CRR plays a developmental role in the mouse, akin to that recently proposed for the N-propeptide in type IIA procollagen, rather than a function in collagen biogenesis. Some support for the latter possibility is provided by the observation that, on one background, the breeding of heterozygous exon 2-deleted mice generated homozygous mutants at less than the expected frequency. Experiments to examine these possibilities are proposed.     

Why replication is important in landscape genetics: American black bear in the Rocky Mountains

We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation, altitude, variation in elevation and road coverage. In all but one of the study areas, isolation by landscape resistance was more supported than IBD suggesting gene flow is likely influenced by elevation, forest cover, and roads. However, the landscape features influencing gene flow varied among study areas. Using subsets of loci usually gave models with the very similar landscape features influencing gene flow as with all loci, suggesting the landscape features influencing gene flow were correctly identified. To test if the cause of the variability of supported landscape features in study areas resulted from landscape differences among study areas, we conducted a limiting factor analysis. We found that features were supported in landscape models only when the features were highly variable. This is perhaps not surprising but suggests an important cautionary note - that if landscape features are not found to influence gene flow, researchers should not automatically conclude that the features are unimportant to the species' movement and gene flow. Failure to investigate multiple study areas that have a range of variability in landscape features could cause misleading inferences about which landscape features generally limit gene flow. This could lead to potentially erroneous identification of corridors and barriers if models are transferred between areas with different landscape characteristics.     

Fine-scale urbanization affects Odonata species diversity in ponds of a megacity (Paris,France)

Current developments in urban ecology include very few studies focused on pond ecosystems, though ponds are recognized as biodiversity hotspots. Using Odonata as an indicator model, we explored changes in species composition in ponds localized along an urban gradient of a megacity (Paris, France). We then assessed the relative importance of local- and landscape-scale variables in shaping Odonata α-diversity patterns using a model-averaging approach. Analyses were performed for adult (A) and adult plus exuviae (AE) census data. At 26 ponds, we recorded 657 adults and 815 exuviae belonging to 17 Odonata species. The results showed that the Odonata species assemblage composition was not determined by pond localization along the urban gradient. Similarly, pond characteristics were found to be similar among urban, suburban and periurban ponds. The analyses of AE census data revealed that fine-scale urbanization (i.e., increased density of buildings surrounding ponds) negatively affects Odonata α-diversity. In contrast, pond localization along the urban gradient weakly explained the α-diversity patterns. Several local-scale variables, such as the coverage of submerged macrophytes, were found to be significant drivers of Odonata α-diversity. Together, these results show that the degree of urbanization around ponds must be considered instead of pond localization along the urban gradient when assessing the potential impacts of urbanization on Odonata species diversity. This work also indicates the importance of exuviae sampling in understanding the response of Odonata to urbanization.     

The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander (Plethodon mississippi)

In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual''s dispersal distance, for low‐mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal‐limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite‐based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum‐likelihood population effects models that assessed the nature and strength of their relationship with each of five land‐use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best‐fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land‐use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.     

Conservation genetics and phylogeography of the poorly known Middle Eastern terrapin Mauremys caspica (Testudines: Geoemydidae)

The West Asian stripe-necked terrapin Mauremys caspica is widespread throughout the Middle East—a region for which only few phylogeographic studies are available. Due to landscape alteration, pollution and intensification of water management, M. caspica is increasingly threatened. However, genetic diversity among and within populations is poorly known, impeding the identification of management units. Using a nearly rangewide sampling, we analyzed 14 microsatellite loci and mtDNA sequences in order to gain insight into the population structure and history of M. caspica. In agreement with a previous study, we found two clusters of mitochondrial haplotypes, with one cluster distributed in the east and the other in the west of the range. However, our microsatellite data suggested a more pronounced geographical structuring. When null alleles were coded as recessive with structure 2.3.2, three clusters were revealed, with one cluster matching roughly the range of the western mitochondrial cluster, and the composite ranges of the two other microsatellite clusters correspond to the distribution of the eastern mitochondrial cluster. Naïve structure analyses without correction for null alleles were congruent with respect to the two eastern microsatellite clusters, but subdivided the western cluster into two units, with an additional geographical divide corresponding to the ‘Anatolian diagonal’—a well-known high mountain barrier impeding exchange between western and eastern taxa. In naïve analyses, the westernmost microsatellite cluster (from Central Anatolia) is quite isolated from the others, and its distinctness is also supported by fixation indices resembling the values among the other three clusters. One of the two eastern clusters is distributed in the Caucasus region plus Iran, and terrapins from Saudi Arabia and Bahrain constitute the second eastern cluster, supporting the view that these endangered populations are native. Coalescent-based analyses of our microsatellite data reveal for all four clusters bottlenecks 4,000–20,000 years ago, suggesting that climatic fluctuations of the Late Pleistocene and Holocene played an important role in shaping current genetic diversity. We propose that each of the four identified clusters, including the Central Anatolian one, should be treated as a distinct management unit. The presence of non-native terrapins in the animal trade of Bahrain highlights the danger of genetic pollution of the endangered Arabian populations. Further sampling is needed to elucidate the situation in southern and central Iran and Iraq. Our results confirm that genetic data do not support the validity of any of the three morphologically defined subspecies of M. caspica, and we propose that their usage be abandoned.