Conservation Genetics of the Common Snapping Turtle (Chelydra serpentina)

Previous studies of relationships among the subspecies of snapping turtles ( Chelydra serpentina } based on morphological and osteological characters have been inconclusive. We investigated relationships among the four currently recognized subspecies using restriction endonuclease fragment patterns of mtDNA and protein electrophoresis. Sixteen six-based recognizing restriction endonucleases yielded 90 variable fragments that define 11 different haplotypes. Individuals of the two North American subspecies, C. s. osceola and C. s. serpentina , are closely related, differing by a maximum of 0.5% sequence divergence. The Central American subspecies, C. s. rossignonii and C. s. acutirostris , are more distinct, both from each other (a minimum of 1.7% sequence divergence) and from the North American samples (an average of 4.45% sequence divergence). The degree of allozymic variation among the four subspecies was found to be limited and could not be used to diagnose the four recognized subspecies. The mtDNA data presented here support the species-level distinctness of C. s. rossignonii and C. s. acutirostris from each other and from a C. s serpentina-C. s. osceola complex. The recognition of three distinctive groups of Chelydra rather than one widespread polytypic species has important conservation implications because it focuses attention on the poorly known middle and South American species.     

Evolutionary Significant Units versus Geopolitical Taxonomy: Molecular Systematics of an Endangered Sea Turtle (genus Chelonia)

Abstract: Taxonomic rank is an important criterion in assessing the conservation priority of an endangered organism: the sole member of a distinct family will generally receive a higher priority than a semi-isolated population in a polytypic species. When cryptic evolutionary partitions are discovered in endangered species, these findings are heralded as a positive step in the conservation process. The opposite action, demoting the taxonomic rank of an endangered organism, can be resisted by the conservation community because it is perceived as detrimental to preservation efforts. We explore the arguments for and against the species status of the endangered black turtle ( Chelonia agassizii ) and contribute an additional data set based on DNA sequences of single-copy nuclear loci. These data are concordant with previous mtDNA surveys in indicating no evolutionary distinction between C. agassizii and adjacent green turtle ( C. mydas ) populations. Although the black turtle is morphologically identifiable at a low level, much of its distinction is based on size and color differences that are highly variable throughout the range of C. mydas . Thus the black turtle would be more accurately classified at the subspecific or population level. There is no strong scientific case available to defend the species status of C. agassizii , and yet that designation has persisted for over a century. We suggest that the maintenance of this name is based on geographical and political considerations, and we propose a pragmatic category for this type of taxonomy: the geopolitical species . Furthermore, we argue against the practice of preserving species status for conservation purposes. There are several good reasons to preserve the black turtle, including morphological diversity and the possibility that it is an incipient evolutionary lineage with novel adaptations; taxonomic rank, however, is not one of them.     

Effects of Roads on the Structure of Freshwater Turtle Populations

Abstract:  Road mortality has the potential to alter the structure of turtle populations because turtle populations are highly sensitive to additive sources of adult mortality. To address the issue, we captured painted turtles (   Chrysemys picta ; n = 174) and snapping turtles (   Chelydra serpentina ; n = 56) in 18 wetlands surrounded by low road density (≤1.5 km roads/km² of landscape) and 17 wetlands surrounded by high road density (>1.5 km/km²) in central New York in 2002. High road density was associated with male-biased sex ratios in painted turtles (74% vs. 54% males; p = 0.01) and snapping turtles (95% vs. 74% males; p = 0.08), whereas turtle morphology and abundance were not associated with road density. Disproportionate road mortality of females on nesting migrations is the most likely cause of skewed sex ratios.     

Adaptive Units for Conservation: Population Distinction and Historic Extinctions in the Island Scrub-Jay

Abstract:  The Island Scrub-Jay ( Aphelocoma insularis ) is found on Santa Cruz Island, California, and is the only insular bird species in the continental United States. We typed seven microsatellite loci and sequenced a portion of the mitochondrial DNA control region of Island Scrub-Jays and their closest mainland relative, the Western Scrub-Jay ( Aphelocoma californica ), to assess levels of variability and effective population size and to examine the evolutionary relationship between the two species. The estimated female effective population size, N _ef, of the Island Scrub-Jay was 1603 (90% confidence interval: 1481–1738) and was about 7.5% of the size of the mainland species. Island and Western Scrub-Jays have highly divergent control-region sequences, and the value of 3.14 ± 0.09% sequence divergence between the two species suggests a divergence time of approximately 151,000 years ago. Because the four northern Channel Islands were joined as one large island as recently as 11,000 years ago, extinctions must have occurred on the three other northern Channel islands, Santa Rosa, San Miguel, and Anacapa, highlighting the vulnerability of the remaining population. We assessed the evolutionary significance of four island endemics, including the Island Scrub-Jay, based on both genetic and adaptive divergence. Our results show that the Island Scrub-Jay is a distinct species of high conservation value whose history and adaptive potential is not well predicted by study of other island vertebrates.     

濒危植物脱皮榆种群结构与分布格局研究

对山西南部中条山和霍山脱皮榆的种群结构与分布格局进行了研究,其中根据大小结构图和存活曲线分析脱皮榆种群动态,应用扩散系数、聚集指数、平均拥挤度、聚块性指数、聚集强度、Cassie指数(1/K)、Poisson分布和负二项分布的χ2拟合检验等方法研究分布格局.结果表明,脱皮榆种群幼苗个体比例较大,总体上近于增长型种群.脱皮榆分布格局呈聚集型,这主要与物种本身的生物学和生态学特性密切相关,同时受群落内生境异质性的影响.图2表2参14     

Microsatellite Analysis of Population Structure in the Endangered Hawaiian Monk Seal

Abstract: The endangered Hawaiian monk seal breeds at six locations in the northwestern Hawaiian Islands. To determine whether significant genetic differentiation exists among these sites, we used microsatellite loci to examine the monk seal population structure at the five largest breeding colonies. Of 27 loci isolated from other seal species, only 3 were polymorphic in an initial screening of one individual from each breeding site. Only two alleles were found at each of these 3 loci in samples of 46–108 individuals. This extremely low variation is consistent with other measures of genetic variability in this species and is probably the result of a recent severe population bottleneck, combined with a long-term history of small population sizes. Although the smallest monk seal subpopulation in this study ( Kure Atoll) showed some evidence of heterozygote deficit, possibly indicative of inbreeding, the next smallest ( Pearl and Hermes Reef) had an apparent excess of heterozygous individuals. Genetic differentiation was detected between the two subpopulations at extreme ends of the range ( Kure and French Frigate Shoals). This trend was significant only at the microsatellite locus for which we had the largest sample size ( Hg6.3: R _ST = 0.206, p = 0.002; allelic goodness of fit G _h = 15.412, p < 0.005). French Frigate Shoals is the source population for translocated animals that have been released primarily at Kure Atoll. Differentiation between these sites consisted of allele frequency differences (with the same allele predominant in each location at all three loci), rather than the preservation of alternative alleles. Although the translocations have had positive demographic effects, we recommend continued genetic monitoring of both the source and recipient populations because translocated individuals are now entering the breeding population.     

空心莲子草入侵对土壤AM真菌生物量和群落结构的影响——以湖北省典型区域为例

土壤丛枝菌根(Arbuscular mycorrhizal,AM)真菌具有维持植被稳定性和多样性的重要作用.为了解空心莲子草入侵过程中与AM真菌的相互作用,采用脂肪酸甲酯(FAMEs)和基于18S rDNA的PCR-DGGE方法对湖北咸宁、仙桃和武汉三地空心莲子草(Alternanthera philoxeroides)入侵前后土壤AM真菌的生物量和群落结构进行了比较分析.结果发现,基于FAMEs表征的AM真菌生物量在空心莲子草入侵后变化不大,仅仙桃地区显著增加(P<0.05).尽管DGGE图谱显示咸宁、仙桃和武汉三地AM真菌优势类群的群落结构均发生了明显演替,但群落间物种组成差异的多样性指数βWH在2.55-2.73之间、群落多样性指数H′在1.22-1.38之间,变化均不大.结果表明,空心莲子草入侵所形成的植物更替明显改变了AM真菌优势类群的结构,但对AM真菌的生物量和多样性影响很小.     

Spatial Structure and Population Extinction: A Study with Drosophila Flies

Abstract: The total amount of habitat and also its distribution and subdivision affect the extinction probability of a resident population Two species of Drosophila are studied in spatial configurations of a single large habitat patch, single small habitat patches, and two small but connected habitat patches in which a low rate of migration, roughly one fly per generation, is possible. The single large habitat patch shows the lowest extinction rate lower than the combined rate of two small patches of the same total size. For one of the species, the "corridor" between the pair of small patches seems to produce a "rescue effect" that lowers extinction rates, probably due to a decrease in the coefficient of variation in fluctuations of the population sire in this coupled system. The systems seem to have been influenced by demographic stochasticity, based on the relationship of population size to extinction probability.     

Effects of Population Size, Mating System, and Evolutionary Origin on Genetic Diversity in Spiranthes sinensis and S. hongkongensis

Hong Kong once supported more than 109 species of wild orchids, of which approximately 30% were endemic. Most of the local wild orchids have now become rare or endangered. I conducted a comparative study of genetic diversity in two closely related terrestrial orchids, an allotetraploid, Spiranthes hongkongensis , and its diploid progenitor, S. sinensis , to assess the effects of the population bottleneck associated with the origin of the polyploid and to investigate the relationships between number of breeding individuals, mating system, and level of isozyme variation in their populations. Nearly complete genetic uniformity was observed both within and among populations of S. hongkongensis . In contrast, S. sinensis had high levels of genetic variation for all of the genetic parameters examined. Regression analysis of population size and several components of genetic diversity in S. sinensis revealed that, among various measures of within-population variation, the proportion of polymorphic loci ( P ) and average number of alleles per locus ( A ) or per polymorphic locus ( A _p ) were the most sensitive to population size ( R ² = 0.942, p = 0.001; R ² = 0.932, p = 0.002; and R ² = 0.923, p = 0.002 respectively). The highly negative correlation ( r = −0.999, p < 0.01) between population size and the mean frequency of private alleles in pairwise population comparisons, p (1), indicated that population size may also be used to predict the extent of population differentiation caused by random genetic drift. Conservation of genetic diversity in S. sinensis could be maximized by protecting several of both large and small populations, whereas fewer populations may be needed to achieve this goal for S. hongkongensis.     

北京松山油松种群结构及空间分布格局

研究了北京松山自然保护区天然油松(Pinus tabulaeformisr)林的树冠结构和个体胸径,通过Ripley's K函数探讨了油松种群不同层次个体(幼树、小树和大树)的空间分布及空间关系,并探讨了地形(海拔高度、坡度)对油松种群空间分布的影响.结果表明,油松种群的胸径分布呈双峰型,应用Weibull函数拟合效果较好;树冠分布呈倒J型;胸径与冠幅存在显著的指数关系.油松种群呈聚集分布,但随高度增Jm(幼树→树→大树)聚集强度逐渐减弱,枯立木在样地内呈随机分布.枯立木与油松大树在1 m、5 m和13～18 m距离为显著正相关,幼树与小树在2～4 m和6～18 m距离呈显著正相关.海拔高度与油松种群呈正相关,坡度与幼树分布呈正相关,与小树和大树分布呈负相关.图5表2参24     

给水生物预处理反应器的细菌种群多样性和群落结构

提取一生产性规模的给水生物预处理反应器中生物膜样品的总DNA,构建细菌16S rDNA克隆文库,并通过16S rDNA序列的系统发育分析,对生物膜中的细菌种群多样性和群落结构进行了研究.实验结果表明,给水生物膜反应器中的细菌种群多样性十分丰富;生物膜中的细菌分别属于10个主要类群,其中α-Proteobacteria是克隆文库中的最大细菌类群,占克隆子总数的32.28%,其次是β-Proteobacteria;与Rhodobacter系统关系密切的细菌是克隆文库中所占比例最大的一个菌属,占克隆子总数的12.6%;反应器中与硝化作用有关的是Nitrosomonas和Nitrospira属的细菌.研究结果表明,给水生物预处理反应器中的细菌群落结构和废水生物处理反应器中的细菌群落结构是有所差异的.图1表1参13     

Cryptic multiple hypotheses testing in linear models: overestimated effect sizes and the winner's curse

Fitting generalised linear models (GLMs) with more than one predictor has become the standard method of analysis in evolutionary and behavioural research. Often, GLMs are used for exploratory data analysis, where one starts with a complex full model including interaction terms and then simplifies by removing non-significant terms. While this approach can be useful, it is problematic if significant effects are interpreted as if they arose from a single a priori hypothesis test. This is because model selection involves cryptic multiple hypothesis testing, a fact that has only rarely been acknowledged or quantified. We show that the probability of finding at least one ‘significant’ effect is high, even if all null hypotheses are true (e.g. 40% when starting with four predictors and their two-way interactions). This probability is close to theoretical expectations when the sample size (N) is large relative to the number of predictors including interactions (k). In contrast, type I error rates strongly exceed even those expectations when model simplification is applied to models that are over-fitted before simplification (low N/k ratio). The increase in false-positive results arises primarily from an overestimation of effect sizes among significant predictors, leading to upward-biased effect sizes that often cannot be reproduced in follow-up studies (‘the winner's curse’). Despite having their own problems, full model tests and P value adjustments can be used as a guide to how frequently type I errors arise by sampling variation alone. We favour the presentation of full models, since they best reflect the range of predictors investigated and ensure a balanced representation also of non-significant results.