Temporally adaptive acoustic sampling to maximize detection across a suite of focal wildlife species

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Characterization of opsin gene alleles affecting color vision in a wild population of titi monkeys (Callicebus brunneus)

The color vision of most platyrrhine primates is determined by alleles at the polymorphic X-linked locus coding for the opsin responsible for the middle- to long-wavelength (M/L) cone photopigment. Females who are heterozygous at the locus have trichromatic vision, whereas homozygous females and all males are dichromatic. This study characterized the opsin alleles in a wild population of the socially monogamous platyrrhine monkey Callicebus brunneus (the brown titi monkey), a primate that an earlier study suggests may possess an unusual number of alleles at this locus and thus may be a subject of special interest in the study of primate color vision. Direct sequencing of regions of the M/L opsin gene using feces-, blood-, and saliva-derived DNA obtained from 14 individuals yielded evidence for the presence of three functionally distinct alleles, corresponding to the most common M/L photopigment variants inferred from a physiological study of cone spectral sensitivity in captive Callicebus.     

Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity

DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species-level identification tool for taxonomy assessment. Trees play important roles in the conservation of many land ecosystems, the wood trade, and the definition of biogeographical processes; nevertheless, peculiar biological, evolutionary and taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions (trnh-psba, rbcL, rpoc1, matK) proposed by the Consortium for the Barcode of Life (CBOL) matched species taxonomy in a preliminary tree biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species in the main forest ecosystems. Fifty-two species were included in a floristic study. We obtained 73% total discrimination success, with trnH-psbA as the best performing marker and oaks as the least responsive plants to the markers used. A further taxon-based study of Quercus (thirty specimens, 12 species) revealed that this genus is refractory to barcoding (0% discrimination success), a probable consequence of low variation rate at the plastid genome level, hybridization, and the incidence of biogeography. We conclude that some species-rich tree genera in small geographical regions may prove exceptionally difficult to barcode. Until more efficient markers are developed, we recommend that improved and diversified sampling (multiple locations of sympatric and co-occurring congenerics) be embraced as a timely and important goal for the precise assessment of haplotype specificity to facilitate the productive application of barcoding in practice.     

Molecular analysis of dispersal in giant pandas

Although dispersal in the giant panda (Ailuropoda melanoleuca) is a demographic mechanism which can potentially counteract the negative effect of habitat fragmentation, little is known about dispersal in this species because of difficulties in observing individuals. Using data from faecal microsatellite genotyping, we compared the spatial distribution of giant pandas in two populations and the proximity of relatives in one key population to infer their dispersal pattern. We conclude that giant pandas exhibit female-biased dispersal because: (i) vAIc (variance of assignment index) for females was significantly larger than for males, suggesting that females comprise both 'local' and 'foreign' genotypes; (ii) the average spatial distance of related female dyads was significantly larger than that of males; (iii) larger r (relatedness), F(ST) (genetic variance among populations) and mAIc (mean of assignment index) values were found in males using the software FSTAT, although the differences were not significant; (iv) males set up territories neighbouring to their birth place; (v) significant population structure using microsatellites with a concomitant lack of mitochondrial structure was found in a previous study, possibly indicating more extensive female dispersal; and (vi) female-biased dispersal was strongly supported by evidence from concomitant ecological studies. Considering previous ecological data and life-history characteristics of the giant panda, female-biased dispersal is most likely to be due to competition for birth dens among females, inbreeding avoidance and enhancing inclusive fitness among related males.     

The effectiveness of two common sampling methods for assessing imperilled freshwater fishes

This study tested the hypothesis that the most common gear type used to sample fishes in wadeable systems, electrofishing, was more effective than another commonly used gear type, seining, for sampling fish species at risk. Five predictions were tested. At sites where species at risk were detected, (1) the probability of detecting the species at risk, (2) the probability of only one gear type detecting the species at risk and (3) the estimated catch per unit effort of the species at risk, was as high as, or higher, when using electrofishing than when using a seine. (4) The number of sample sites required to detect a species at risk within a watershed and (5) the number of subsections required to detect a species at risk within a site, were as low as, or lower, using electrofishing than the number required using a seine. Based on analyses of these measurements, electrofishing was a more effective gear type than seining for sampling fish species at risk, irrespective of the unit (presence or absence or catch per unit effort) or scale of measurement (watershed or site level). Dissolved oxygen, turbidity, specific conductivity and nitrate concentrations were measured at each site and did not account for the between gear differences. Selection of sampling gear can be a fundamental consideration for the assessment of fish species at risk, where, unlike common species, they may be particularly influenced by small population sizes, restricted geographic ranges and narrow habitat preferences. Resource managers must weigh differences in the risks of injury of fish species at risk against differences in the effectiveness of each gear type when deciding between gear types and the utility of the assessments they represent.     

A phylogenetic analysis of Diplodocoidea (Saurischia: Sauropoda)

Diplodocoidea includes some of the first well‐known sauropod dinosaurs, including such late 19^th century and early 20^th century discoveries as Apatosaurus, Diplodocus, and Dicraeosaurus. As a consequence of their long history of study, the basic set of suprageneric diplodocoid interrelationships is well resolved, and the diagnostic features of each genus are well established. However, intergeneric relationships are less resolved, including the relationships of putatively basal taxa like Amphicoelias and Haplocanthosaurus, the flagellicaudatan Suuwassea, and the highly specialized rebbachisaurids. For the rebbachisaurids, this uncertainty is coupled with a recent surge in the discovery of new taxa. Comparative cladistic methods demonstrate that character and taxon sampling need to be improved before greater phylogenetic resolution can be expected. Here, I present a new phylogenetic analysis that resolves many of the outstanding questions regarding the relationships within Diplodocoidea and examines palaeobiogeographical trends within the group. Suuwassea is recovered as a basal dicraeosaurid (the only Laurasian member of the group), and two distinct clades of rebbachisaurids are identified: a group closely allied with Nigersaurus and a clade associated with Limaysaurus. Amphicoelias, Amazonsaurus, and Haplocanthosaurus are provisionally placed as successively less‐derived taxa at the base of Diplodocoidea. A North American origin for Diplodocoidea and Flagellicaudata is hypothesized based on the geographical and temporal distribution of those taxa. Rebbachisaurid taxa demonstrate a South American/African vicariance pattern, but the timing of the event pre‐dates the proposed final rifting of those continents by c. 40 million years; the meaning of this discrepancy is uncertain. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 872–915.     

Comparative influence of spatial scale on beta diversity within regional assemblages of birds and butterflies

Aim We examined whether variation in species composition of breeding birds and resident butterflies in the Great Basin of North America depended on sampling grain (the smallest resolvable unit of study) and on the relative proximity of sampling units across the landscape. We also compared patterns between the two taxonomic groups with reference to their life‐history characteristics. Location Data for our analyses were collected from 1996 to 2003 in three adjacent mountain ranges in the central Great Basin (Lander and Nye counties, Nevada, USA): the Shoshone Mountains, Toiyabe Range and Toquima Range. Methods Data on species composition for both taxonomic groups were collecting using standard inventory methods for birds and butterflies in temperate regions. Data were compiled at three sampling grains, sites (average 12 ha), canyons (average 74 ha) and mountain ranges. For each sampling grain in turn, we calculated similarity of species composition using the Jaccard index. First, we investigated whether mean similarity of species composition among the three ranges differed as a function of the grain size at which data were compiled. Secondly, we explored whether mean similarity of species composition was greater for canyons within the same mountain range than for canyons within different mountain ranges. Thirdly, we examined whether mean similarity of species composition at the site level was different for sites within the same canyon, sites within different canyons in the same mountain range, and sites within canyons in different mountain ranges. We used a Bayesian model to analyse these comparisons. Results For both taxonomic groups, mean similarity of species composition increased as the sampling grain increased. The effect of spatial grain was somewhat greater for birds than for butterflies, especially when the intermediate sampling grain was compared with the smallest sampling grain. Similarity of species composition of butterflies at each sampling grain was greater than similarity of species composition of birds at the same grain. Mean similarity of species composition of both birds and butterflies at the canyon level and site level was affected by relative proximity of sampling locations; beta diversity increased as the relative isolation of sampling locations increased. Main conclusions The sensitivity of beta diversity to sampling grain likely reflects the effect of local environmental heterogeneity: as sampling grain increases, biotic assemblages appear more homogeneous. Although breeding birds in our study system have larger home ranges than resident butterflies, birds may have more specialized resource requirements related to vegetation structure and composition, especially at small sampling scales. The degree of variation in species composition of both taxonomic groups suggests that spatially extensive sampling will be more effective for drawing inferences about regional patterns of species diversity than intensive sampling at relatively few, smaller sites.     

Iwao’s patchiness regression through the origin: biological importance and efficiency of sampling applications

Iwao’s mean crowding-mean density relation can be treated both as a linear function describing the biological characteristics of a species at a population level, or a regression model fitted to empirical data (Iwao’s patchiness regression). In this latter form its parameters are commonly used to construct sampling plans for insect pests, which are characteristically patchily distributed or overdispersed. It is shown in this paper that modifying both the linear function and statistical model to force the intercept or lower functional limit through the origin results in more intuitive biological interpretation of parameters and better sampling economy. Firstly, forcing the function through the origin has the effect of ensuring that zero crowding occurs when zero individuals occupy a patch. Secondly, it ensures that negative values of the intercept, which do not yield an intuitive biological interpretation, will not arise. It is shown analytically that sequential sampling plans based on regression through the origin should be more efficient compared to plans based on conventional regression. For two overdispersed data sets, through-origin based plans collected a significantly lower sample size during validation than plans based on conventional regression, but the improvement in sampling efficiency was not large enough to be of practical benefit. No difference in sample size was observed when through-origin and conventional regression based plans were validated using underdispersed data. A field researcher wishing to adopt a through-origin form of Iwao’s regression for the biological reasons outlined above can therefore be confident that their sampling strategies will not be affected by doing so.     

Distinguishing area and habitat heterogeneity effects: a simulation test of the MacNally and Watson (1997) protocol

Distinguishing the roles that different factors, such as sampling effects and habitat heterogeneity, play in generating species‐area curves continues to be difficult in many communities. A recent response to this challenge is the proposal of a ‘zoom’ protocol in which species richness and habitat heterogeneity are sampled in successively larger units (transects or quadrats). The utility of this approach requires that there be justifiable, predictable and unambiguous relationships between richness and heterogeneity. Results of computer simulations that I have done to test the predicted relationships demonstrate, however, that the predicted patterns were not always observed and, on occasion, more complex relationships were observed in their place. While the development of such protocols may increase our understanding of species‐area curves, they are unlikely ever to pronounce unambiguously on their causes.     

利用ISSR分子标记构建濒危植物水青树核心种质

基于全国26个居群的174份水青树Tetracentron sinense种质,利用14条ISSR引物,采用UPGMA聚类法进行多次逐步聚类,利用三种取样策略(随机取样策略、位点优先取样策略和偏离度取样策略)构建初始核心种质,并将各遗传多样性指标进行比较分析,从而确定构建水青树核心种质的最佳方法。利用14条ISSR引物扩增出180个条带,其观测等位基因数(Na)、有效等位基因数(Ne)、Nei’s基因多样性指数(H)与Shannon信息指数(I)分别为1.6944、1.3912、0.2321和0.3509,说明水青树具有较低的遗传多样性。采用位点优先取样策略构建的核心种质各遗传多样性指数均大于随机取样策略和偏离度取样策略。利用位点优先取样策略构建了78 份核心种质资源,保留了44.83%原种质样品,遗传多样性指数Na、Ne、H和I的保留率分别为98.69%、100.01%、99.27%和98.67%,比较完好地保留了原种质的遗传多样性和遗传变异。因此,位点优先取样策略是构建水青树核心种质的最佳取样策略。