Diurnal Habitat Use by Lower Keys Marsh Rabbits

Abstract: We used radiotelemetry to locate daytime forms of endangered Lower Keys marsh rabbits (LKMRs; Sylvilagus palustris hefneri) throughout their range so we could determine habitat characteristics of diurnal cover. We typically found forms (n = 1,298) of 36 rabbits in brackish wetlands in patches of saltmarsh or buttonwoods. In freshwater wetlands, forms (n = 54) were located most often in patches of freshwater hardwoods embedded in or adjacent to freshwater marshes. Forms (n = 942) in brackish wetlands were characterized by thick groundcover (>75%), whereas those (n = 42) in freshwater wetlands had both thick groundcover and canopy vegetation. The mean minimum convex polygon around forms of 15 rabbits was 1.4 ha (SD = 1.7), with smaller ranges characterized by thick bunchgrasses or clump-forming sedges. To increase the amount of annual space usable by LKMRs, managers should provide more saltmarsh habitat interspersed with buttonwoods and enhance ground cover in existing habitat.     

Spatial patch occupancy patterns of the Lower Keys marsh rabbit

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naïve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats. © 2011 The Wildlife Society.     

Population estimation and monitoring of an endangered lagomorph

We conducted the most intensive estimate of the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) metapopulation to date using pellet surveys and capture–recapture methodology. We livetrapped 83 rabbits, evaluated 5 closed population models, and selected the model that best represented the data. We considered the variation in behavioral response model the best model and correlated (r² = 0.913) its patch population estimates to patch pellet densities. From the prediction equation, we generated a range-wide metapopulation estimate of 317 rabbits, a western clade population of 257 rabbits, an eastern clade population of 25 rabbits, and translocated marsh rabbit populations of 35 and zero on Little Pine and Water keys, respectively. A subset of patches whose marsh rabbit subpopulations were last estimated in 1993 exhibited a 46% decline in abundance over 15 yr. Due to the low estimate of the eastern clade population, special effort should be initiated to avoid loss of genetic diversity. The prediction equation suffers from limited data at high pellet densities, patches with ≥5 pellets/m². Future studies should investigate if the slope of the regression is indeed near 1 by sampling patches across the range of pellet densities, especially those with ≥5 pellets/m². The equation provides managers a quick, efficient, and noninvasive method to estimate marsh rabbit abundance from pellet counts but the confidence of predicted rabbit densities from high pellet density patches is low. © 2011 The Wildlife Society     

Mitochondrial and nuclear DNA analyses reveal population differentiation in Brazilian Creole sheep

Using ND5 sequences from mtDNA and 10 nuclear markers, we investigated the genetic differentiation of two South American Creole sheep phenotypes that historically have been bred in different biomes in southern Brazil. In total, 18 unique mtDNA haplotypes were detected, none of which was shared between the two phenotypes. Bayesian analysis also indicated two different groups (k = 2). Thus, these varieties are supported as being genotypically distinct. This situation could have resulted either from geographical isolation, associated with differences in the cultural habits of sheep farmers and in the way that flocks were managed, or more likely, from the introduction of different stocks four centuries ago.     

Genetic Structure of Japanese Scallop Population in Hokkaido, Analyzed by Mitochondrial Haplotype Distribution

To examine the genetic structure of Japanese scallop populations (Mizuhopecten yessoensis) in Hokkaido prefecture, Japan, and compare it with those in the Aomori prefecture, we applied a method for lineage analysis based on sequence variation in a mitochondrial DNA segment (NcR2). After showing that there was a low probability of doubly uniparental inheritance of mitochondrial DNA in the scallop, we sequenced the NcR2 regions of 914 individuals from 15 populations (13 in Hokkaido and 2 in Aomori). In total, 103 different haplotypes were detected. Results of homogeneity tests for pairwise populations and the fixation indices indicated that significant heterogeneity (P < 0.0005) and structuring (pairwise fixation index F_ST = 0.1606–0.4444, P = 0.0000; fixation index among groups F_CT = 0.1549, P = 0.0078) could be inferred between the Hokkaido and Aomori groups, but not among populations within the groups. Moreover, heterogeneity of the haplotype distribution between populations of the 1980s and 1990s or 2000s at the 4 culturing areas was not observed (P > 0.05), and the haplotype diversity between them was not significant (P = 0.05), suggesting that the culture operations had not imparted a significant effect on the genetic structure during these periods.     

Mitochondrial DNA sequence diversity in three ethnic populations from the South-west Iran: a preliminary study

To investigate the genetic structure of human populations in the South-west region of Iran, mitochondrial first hypervariable DNA sequences were obtained from 50 individuals representing three different ethnic groups from Khuzestan Province. Studied groups were Shushtari Persians and Chahar Lang Bakhtiyaries from Indo-European-speaking populations and Bani Torof Arabs from Semitic-speaking linguistic families. Genetic analysis of mtDNA data showed high similarity of Chahar Lang Bakhtiyaries with other Iranian Indo-European-speaking populations while Shushtaries and Bani Torofs had a closer affinity with Semitic-speaking groups rather than to other Iranian populations. The relationship of Chahar Lang Bakhtiyaries and Bani Torof Arabs with their neighbor populations can be explained by linguistic and geographic proximity. Whereas, the greater similarity of Shushtari Persians with West Asian Arabs is probably according to high gene flow between them. This article represents a preliminary study of three major ethnic groups of South-west Iran which investigates the potential genetic substructure of the region.     

Population subdivision among desert bighorn sheep (Oviscanadensis) ewes revealed by mitochondrial DNA analysis

We used behavioural observations and mitochondrial DNA (mtDNA) sequence analysis to examine demographic and genetic structure within and among home-range groups of desert bighorn sheep (Oviscanadensis) ewes in the Peninsular Ranges of southern California, USA. We identified substantial genetic variation in the first 515 bp of the mtDNA control region and determined that seven haplotypes were distributed in a nonrandom fashion among these ewe subpopulations. Although a significant (P < 0.01) amount of mtDNA variation (33%) was partitioned among home-range groups, we did not find strong evidence for matrilineal substructuring within these groups. Based on analyses of molecular variance, and comparisons of behavioural associations and distances between centres of activity, we concluded that within a given home-range group, bighorn sheep ewes generally associate with other ewes based on their availability rather than their matrilineal relationships. Our results also supported the conclusion that multiple ewe subpopulations exist within the Peninsular Ranges, and that these subpopulations are the most basic demographic and genetic units.     

红腹锦鸡线粒体DNA控制区结构和遗传变异研究

红腹锦鸡(Chrysolophus pictus)是中国特有珍稀鸟类,仅见于中国中部和西部的山地,为国家二级重点保护动物.采用聚合酶链式反应和直接测序的方法测定了采自湖南新宁县和龙山县的28只红腹锦鸡线粒体DNA控制区序列.在获得的1 123 bp的碱基序列中,碱基含量为T 32.79%、C 26.07%、A 26.62%和G14.52%,共检测出20个多态性核苷酸变异位点,其中简约信息位点11个.对比其它已报导的雉类控制区结构,对红腹锦鸡控制区结构进行了分析,识别了其高变Ⅰ区、中间保守Ⅱ区和保守Ⅲ区,找到了与终止相关的序列TAS以及保守序列(F、E、D、C).28个样本共发现11种单倍型,其中单倍型hap1和hap2的比例很高.新宁种群的遗传多样性比龙山种群的高,两个种群存在基因流较频繁,未出现明显遗传分化.     

Mitochondrial DNA analysis distinguishes between British populations of the whitefish

The whitefish Coregonus lavaretus is confined to two Scottish lochs and four English and one Welsh lake in the British Isles. Restriction fragment length polymorphisms (RFLPs) in the mitochondrial (mt) DNA have been used to analyse variability within and between populations. The 14 restriction enzymes employed in this study examined approximately 3% of the mt genome and revealed 15 haplotypes among 156 fish. Haplotype diversity within populations was generally low except for the Welsh population where nine haplotypes were found among 30 fish examined. The haplotypes clustered into three distinct groups corresponding to Scottish, English and Welsh populations. No haplotypes were shared among the three groups. Possible alternative explanations for these findings are introgression from another species, stochastic lineage sorting from a polymorphic ancestral gene pool and/or separate colonizations following the last glaciation.     

Mitochondrial DNA distributions indicate colony propagation by single matri-lineages in the social spider Stegodyphus dumicola (Eresidae)

Colony-dwelling social spiders of the genus Stegodyphus are characterized by high colony turnover, within-colony mating, inbreeding and skewed sex ratios. These phenomena may purge genetic variation from the entire species gene pool. Social Stegodyphus have previously been discussed as ecologically unstable and evolutionary dead ends. We investigated the distribution and age (sequence divergence) of mitochondrial DNA variation for inferences of colony propagation, colony discreteness and maintenance of genetic variation in the social spider S. dumicola . In contrast to our expectations, we found abundant mtDNA variation, consisting of 15 haplotypes belonging to four haplotype lineages. Lineage divergence ranged between 2.75 and 6% for the gene ND1. Nearly all colonies (86%) were monomorphic and even neighbour colonies showed fixed differences. Simulations show that genetic drift in multifounder colonies cannot alone explain monomorphism within colonies. Haplotypes in polymorphic colonies and from neighbouring colonies were always genealogically similar. Monomorphism and the genealogical pattern among colonies suggest 'clonal' colony propagation involving single matrilineages. The divergence of haplotype lineages and distribution of haplotypes imply that colony turnover is not high enough to purge genetic variation in the species gene pool, and that S. dumicola as a species is old enough to question the instability (in ecological time) of a social spider.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 591–600.     

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

Population decline in red-legged kittiwakes(Rissa brevirostris) over recent decadeshas necessitated the collection of informationon the distribution of genetic variation withinand among colonies for implementation ofsuitable management policies. Here we present apreliminary study of the extent of geneticstructuring and gene flow among the threeprincipal breeding locations of red-leggedkittiwakes using the hypervariable Domain I ofthe mitochondrial control region. Geneticvariation was high relative to other species ofseabirds, and was similar among locations.Analysis of molecular variance indicated thatpopulation genetic structure was statisticallysignificant, and nested clade analysissuggested that kittiwakes breeding on BeringIsland maybe genetically isolated from thoseelsewhere. However, phylogeographic structurewas weak. Although this analysis involved onlya single locus and a small number of samples,it suggests that red-legged kittiwakes probablyconstitute a single evolutionary significantunit; the possibility that they constitute twomanagement units requires furtherinvestigation.     

线粒体DNA多态性在海洋动物群体遗传结构研究中的应用

线粒体DNA( mtDNA)分析在揭示物种亲缘关系、遗传比较、系统进化和遗传结构等领域的研究中得到了广泛的应用,尤其是在海洋动物的遗传结构研究中发挥了重要的作用.介绍线粒体DNA的结构特征、多态性研究方法,并对其在海洋动物群体遗传结构研究中的应用进行了综述.     

鳜类鱼类的线粒体DNA控制区结构及其系统发育分析

鳜类为低等鲈形目鱼类,是东亚特有类群。然而,关于其系统位置、分类以及一些物种的有效性等尚有争议。采用PCR扩增直接测序的方法,获得了鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜、中国少鳞鳜线粒体DNA控制区基因的序列。对比其他已报道鱼类控制区的结构识别序列,对鳜类鱼类控制区的结构进行了分析,识别了终止序列区、中央保守区和保守序列区,并找到了DNA复制终止相关的序列ETAS和中央保守区的保守序列CSB-F、CSB-E、CSB-D以及保守序列区的保守序列CSB1、CSB2、CSB3。几种鳜鱼间共有191个变异位点,其中,终止序列区的变异最高,占总变异的61．3％,中央保守区和保守序列区占总变异的38．7％。这一结果可为全面了解鱼类线粒体DNA控制区的结构特征提供资料。同时,利用高度变异的控制区序列,以鲈科和错科作为外群,使用邻接法和最大简约法构建了这几种鳜鱼的系统发育树。结果表明：鳜类为一单系类群,鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜构成一支鳜鱼群,其中,鳜与大眼鳜为姐妹种;中国少鳞鳜为另一支少鳞鳜群;长体鳜未单独成一支,而是聚入鳜鱼群内,应更名为Siniperca roulei。研究结果支持将现生鳜类分为两个类群的观点。     

Structure of the Mitochondrial DNA Control Region of the Sinipercine Fishes and Their Phylogenetic Relationship

The mitochondrial DNA control region of Siniperca chuatsi, S. kneri, S. scherzeri, S. obscura, S. undulata, Coreosiniperca roulei and Coreoperca whiteheadi were amplified by PCR amplification and directly sequenced. The mtDNA control region of the sinipercine fishes could be separated into three domains, namely, the terminal associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended terminal associated sequence (ETAS), three conserved sequence blocks (CSB-F, CSB-E, CSB-D) in the central conserved sequence domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were also identified. The phylogenetic relationships among these sinipercine fishes were constructed through neighbor-joining and maximum parsimony methods using Percidae and Serranidae as outgroups. Results showed that sinipercine fishes were a monophyletic group, with Siniperca forming one group, and Coreoperca forming another group. Coreosiniperca roulei did not form an independent group but was merged into the genus Siniperca. Thus it should be renamed as Siniperca roulei.     

云南保山猪线粒体DNA D-loop区序列初步分析 Primary Analysis of Mitochondrial DNA D-loop Region Sequence in Baoshan Pig

摘要：为了解云南保山猪(Baoshan pig)的遗传多样性及其遗传背景,我们测定了19个个体线粒体DNA D-loop高变区I 15 363～15 801片段序列438 bp。检测到10种单倍型,包括8个多态位点,其中5次T/C转换、1次G/A转换、1次G/C颠换和1次A/T颠换,其A、T、G、C碱基的平均含量分别为35.4%、26.9%、13.2%和24.5%,A+T含量(62.3%)明显高于G+C含量(37.7%)。对于保山猪的保种及其持续利用有着重要的理论指导意义。 Abstract:To investigate the genetic diversity and genetic data of Baoshan pig in Yunnan province,the mitochondrial DNA D-loop hypervariable segment I sequences 15 363～15 801 (438 bp) in 19 individuals of Baoshan pig were sequenced.Ten mitochondrial haplotypes were identified in the samples,with 8 sites showing polymorphism,which were 5 T/C and 1 G/A transitions,1 G/C and 1 A/T transversions.The contents of A,T,G and C were 35.4%,269%,13.2% and 24.5%,respectively.The content of A+T (62.3%) was significantly higher than that of G+C (37.3%).It will be of importance to conservation and sustainable utilization in Baoshan pig.     

Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations

This study describes complete control region sequences of mitochondrial DNA (mtDNA) from 117 Ethiopian cattle from 10 representative populations, in conjunction with the available cattle sequences in GenBank. In total, 79 polymorphic sites were detected, and these defined 81 different haplotypes. The haplotype and nucleotide diversity of Ethiopian cattle did not vary among the populations studied. All mtDNA sequences from Ethiopian cattle converged into one main maternal lineage (T1) that corresponds to African Bos taurus cattle. According to the results of this study, no zebu mtDNA haplotypes have been found in Ethiopia, where the most extensive hybridization took place on the African continent.     

Mitochondrial DNA variability of the pipefish Syngnathus abaster

This study provides data on the genetic structuring of the pipefish Syngnathus abaster in the western Mediterranean and Adriatic Seas. A total of 109 specimens were collected in brackish‐water biotopes. The control region and three other regions of the mitochondrial genome were analysed. The most relevant result was the high genetic structuring found by Bayesian inference (BI), maximum likelihood (ML) and network analyses, which were consistent in showing three well‐separated clusters of S. abaster populations. Furthermore, BI and ML did not support the monophyly of the taxon S. abaster. These results suggest the occurrence of a species complex in the study area, whose differentiation may have occurred since the Pleistocene. The results also show a very high genetic variability at the inter‐population level, with no shared haplotypes among sites. Evolutionary forces due to the fragmented nature of the brackish‐water habitats may account for the high genetic divergence found among the groups and populations. Finally, although dispersal by rafting over long distances may occasionally occur, this study suggests linear stepping‐stone model of colonization to be most likely. The complexity of the results obtained suggests that further studies are needed to elucidate the phylogeny of S. abaster.     

日本落叶松群体的叶绿体SSR分析

利用叶绿体微卫星（cpSSR）分子标记对日本国内的7个日本落叶松（Larix kaempferi）群体遗传结构进行了研究。11对cpSSR引物中筛选出的3对多态性引物,共产生10个长度不同片段,在197个样品中组合出现10个不同的单倍型（haplotype）。各群体的单倍型差异较大。cpSSR基因座揭示了日本落叶松的遗传变异：平均等位基因数A=3.33,平均有效等位基因数NE=1.20,基因多样度HE=0.17,群体间变异占总群体变异的5.37%,遗传变异主要来自于群体内个体间。Abstract: Genetic structure of seven populations in Larix kaempferi in Japan was studied by use of cpSSR markers. Ten different length fragments in and ten different kinds of haplotypes were reduced in 197 samples based on 3 pairs of polymorphic primers screened from 11 pairs of primers. There were significant variant haplotypes among the populations. The genetic variation in the populations of Larix kaempferi was detected by using cpSSR with the number of average loci A=3.33, the number of average efficient loci NE=1.20, gene diversity HE=0.17 and 5.37% variation from different populations. The genetic variation was mainly from individuals in population.     

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus‐I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus‐II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus‐I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus‐II haplotypes from North and Central America indicates that the C. acutus‐II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive‐bred individuals for conservation strategies until further genetic information is available.