Effects of the landscape on boreal toad gene flow: does the pattern–process relationship hold true across distinct landscapes at the northern range margin?

Understanding the impact of natural and anthropogenic landscape features on population connectivity is a major goal in evolutionary ecology and conservation. Discovery of dispersal barriers is important for predicting population responses to landscape and environmental changes, particularly for populations at geographic range margins. We used a landscape genetics approach to quantify the effects of landscape features on gene flow and connectivity of boreal toad (Bufo boreas) populations from two distinct landscapes in south-east Alaska (Admiralty Island, ANM, and the Chilkat River Valley, CRV). We used two common methodologies for calculating resistance distances in landscape genetics studies (resistance based on least-cost paths and circuit theory). We found a strong effect of saltwater on genetic distance of CRV populations, but no landscape effects were found for the ANM populations. Our discordant results show the importance of examining multiple landscapes that differ in the variability of their features, to maximize detectability of underlying processes and allow results to be broadly applicable across regions. Saltwater serves as a physiological barrier to boreal toad gene flow and affects populations on a small geographic scale, yet there appear to be few other barriers to toad dispersal in this intact northern region.     

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

An enhanced conformational sampling method, multicanonical molecular dynamics (McMD), was applied to the ab intio folding of the 57-residue first repeat of human glutamyl- prolyl-tRNA synthetase (EPRS-R1) in explicit solvent. The simulation started from a fully extended structure of EPRS-R1 and did not utilize prior structural knowledge. A canonical ensemble, which is a conformational ensemble thermodynamically probable at an arbitrary temperature, was constructed by reweighting the sampled structures. Conformational clusters were obtained from the canonical ensemble at 300 K, and the largest cluster (i.e., the lowest free-energy cluster), which contained 34% of the structures in the ensemble, was characterized by the highest similarity to the NMR structure relative to all alternative clusters. This lowest free-energy cluster included native-like structures composed of two anti-parallel α-helices. The canonical ensemble at 300 K also showed that a short Gly-containing segment, which adopts an α-helix in the native structure, has a tendency to be structurally disordered. Atomic-level analyses demonstrated clearly that inter-residue hydrophobic interactions drive the helix formation of the Gly-containing segment, and that increasing the hydrophobic contacts accompanies exclusion of water molecules from the vicinity of this segment. This study has shown, for the first time, that the free-energy landscape of a structurally well-ordered protein of about 60 residues is obtainable with an all atom model in explicit water without prior structural knowledge.     

Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi-strata capture-recapture models, to infer changes in mobility over time in seven sympatric, forest-dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post-fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest-dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.     

The value of DNA sequence data for studying landscape genetics

In a recent Opinion article in Molecular Ecology, Wang (2010) emphasizes the fact that current patterns of genetic differentiation among populations reflect processes that have acted over temporal scales ranging from contemporary to ancient. He draws a sharp distinction between the fields of phylogeography (as the study of historical processes) and landscape genetics (which he restricts to very recent processes). Wang characterizes DNA sequence data as being inappropriate for the study of contemporary population processes and further states that studies which only include mitochondrial DNA or chloroplast DNA data cannot be considered part of landscape genetics. In this response, we clarify the generally accepted view that DNA sequence data can be analysed with methods that separate contemporary and historical processes. To illustrate this point, we summarize the study of Vandergast et al. (2007), which Wang mischaracterizes as being confused in terms of temporal scale. Although additional focus should be placed on the important issue of correct data interpretation, we disagree strongly with the implication that contemporary and historic processes cannot be separated in the analyses of DNA sequence data.     

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.     

Comparison of tree sprouting in three regeneration stages of an evergreen broadleaved forest in a karst landscape, SW China

Little is known about the role of tree sprouting in the regeneration of karst forest communities. In Shilin Stone Forest Geographical Park, southwestern China, all genets with the largest stem ?3 cm DBH (diameter at breast height) and/or stumps ?3 cm BD (basal diameter) were identified and number of sprouts counted in 10 transects (10 m × 100 m) in each of three evergreen broadleaved forest stands representing three regeneration stages (about 10, 20, and 30 years old). Species with >10 genets accounted for 72.4% of the 76 species, and all of them showed evidence of sprouting. One-third to two-thirds of the genets in the three forests were sprouting, with an average of 4.0–5.7 sprouts per sprouting genet. Sprouting capability (sprouting genets/total genets) and intensity (sprouts per sprouting genet) differed significantly among the three forest stages. More than 90% of the damaged genets were sprouting. The number of sprouts in a non-damaged genet was determined by intrinsic sprouting ability, and the number of sprouts in damaged genets was determined by stump size. As the forest developed, percentage of damaged genets increased, the portion of shoots ≥3 cm DBH co-existing in a genet decreased, and the portion of shoots <3 cm DBH sprouted from damaged genet increased. Thus the role of sprouting changed from contributing recruitment in the young stage to persistence in the later stage.     

池州森林生态系统服务价值评估与分析

池州市是国家首个生态经济示范区,《中国21世纪议程》试点地之一,生态安徽建设试点市.基于LY/T1721-2008《森林生态系统生态服务价值评估规范》,采用实证研究、调查研究、文献研究等方法,估算了池州市森林生态系统生态服务价值.结果表明:2009年,池州市森林生态系统生态服务价值为443.30亿元,林果等实物产品价值...     

不同经营措施对黄龙山辽东栎林的影响

以黄龙山林区蔡家川林场的辽东栎群落为研究对象,以未采伐为对照,采取皆伐、间伐30%、间伐15%三种经营措施,在进行自然恢复6年后,对辽东栎林建群种径级结构、群落物种多样性、土壤养分水分状况进行了对比分析,以探讨不同经营措施对黄土高原南部辽东栎(Quercus liaotungensis)林群落多样性的影响.结果表明:不同经营措施实施后建群种径级结构、群落物种多样性、土壤养分水分等指标均与未采伐林地有差异;经过间伐30%的林地,建群种径级结构、群落物种多样性、土壤养分水分等指标均有显著增加;间伐15%林地上述指标均有增加,但不显著;皆伐后的林地相对未采伐林地,建群种径级结构、群落物种多样性、土壤养分水分等指标降低.间伐与皆伐措施后比较,间伐措施的林地建群种个体生长发育良好,林下有大量幼苗,林地物种多样性丰富,土壤养分水分相对优越;皆伐措施的辽东栎建群种个体发育不良,缺乏足够数量的幼苗,林分物种多样性、土壤水分养分相对较差.未来该地区辽东栎林经营管理中,应以近自然经营措施为主,尽量减少对灌草层破坏,完善群落复层结构;间伐强度拟定为30%,尽量间伐劣质木、病虫木,促进群落向异龄方向发展.     

秦岭宁陕县森林植被碳储量与碳密度特征

以秦岭南坡中段宁陕县林区2003年二类森林调查资料为基础,采用政府间气候变化委员会(IPCC)推荐使用的森林碳储量估算方法,从森林类型、林种、年龄和林分起源的角度,对该林区森林植被碳储量和碳密度进行估算。结果显示:(1)宁陕县森林植被碳储量为12.31Tg(1Tg=1×1012 g),平均碳密度为66.36Mg/hm2(1Mg=1×106 g),其各乡镇森林植被碳储量和碳密度在空间上的分布不平衡。(2)各森林类型中针叶林总碳储量为0.71Tg,平均碳密度为64.11 Mg/hm2,阔叶林总碳储量为11.61Tg,占宁陕县总碳储量的94.3%,碳密度为67.65Mg/hm2。(3)各林种中防护林碳储量最大(8.13Tg),占宁陕县总碳储量的66%,特种用途林碳密度最大(81.43Mg/hm2)。(4)不同林分起源中,天然林碳储量为12.231Tg,占宁陕县总碳储量的99.3%,人工林碳储量较小。(5)不同年龄森林中未成熟森林(包括幼龄林、中龄林和近熟林)碳储量为12.13Tg,占总碳储量的98.5%,近熟林碳密度最大(80.14Mg/hm2),幼龄林碳密度最小(39.85Mg/hm2)。研究表明,宁陕县森林具有较大的固碳能力和固碳潜力,其森林面积和蓄积是决定森林碳储量大小的重要因子,而森林碳密度的大小与森林类型、年龄组成和林分起源方式密切相关。     

泽陆蛙(Fejervarya limnocharis)两性异形的个体发育和雌体繁殖

2010年3月下旬-7月上旬于浙江富阳市农田采集680只泽陆蛙(Fejervarya limnocharis),研究了泽陆蛙成体和幼体的个体大小和局部形态特征的两性异形;通过解剖雌体获得窝卵数、测量抱对个体获得形态数据,研究了雌体大小与生育力关系以及抱对两性个体体形大小的相关性.结果表明:捕获个体中,雌性和雄性成体的最小体长分别为33mm和30 mm;雄性成体个体数显著超过雌性成体,两性幼体个体数无显著差异;两性成体头部大小、四肢长随体长呈同速增长,眼径和体重随体长呈异速增长,两性幼体所有被检形态特征均随体长呈同速增长;雌性成体平均体长显著大干雄性成体,去除体长差异的影响后发现,除眼径无显著的两性差异外,其余被检形态特征均为雌性大于雄性;幼体除雌性体重大于雄性外,其余被检形态特征均无两性差异;窝卵数与雌体大小(体长和体重)呈显著的正相关;两性抱对个体的体长无显著相关性;泽陆蛙雄性成体体形小于雌性成体的个体大小两性异形模式可能决定于驱使雄性向较大体形发展的进化驱动力相对较弱,雌性增大体形可增加繁殖输出,故向较大体形发展的进化驱动力相对较强;除体重外,其余被检形态特征的两性异形均形成于性成熟之后.