Estimation of capture probabilities using generalized estimating equations and mixed effects approaches

Modeling individual heterogeneity in capture probabilities has been one of the most challenging tasks in capture–recapture studies. Heterogeneity in capture probabilities can be modeled as a function of individual covariates, but correlation structure among capture occasions should be taking into account. A proposed generalized estimating equations (GEE) and generalized linear mixed modeling (GLMM) approaches can be used to estimate capture probabilities and population size for capture–recapture closed population models. An example is used for an illustrative application and for comparison with currently used methodology. A simulation study is also conducted to show the performance of the estimation procedures. Our simulation results show that the proposed quasi‐likelihood based on GEE approach provides lower SE than partial likelihood based on either generalized linear models (GLM) or GLMM approaches for estimating population size in a closed capture–recapture experiment. Estimator performance is good if a large proportion of individuals are captured. For cases where only a small proportion of individuals are captured, the estimates become unstable, but the GEE approach outperforms the other methods.     

Postlogging Succession and Habitat Usage of Shrubland Birds

ABSTRACT In the first decades after logging, the vegetation structure of harvested areas changes rapidly due to succession. For shrubland birds, many of which specialize on regeneration of specific ages, the changing vegetation structure makes determining how much habitat is available for individual species difficult. We conducted a meta-analysis to determine how populations of shrubland birds in the eastern United States and Canada respond to succession in the first 20 years after timber harvest. Based on those results, we used the area under the abundance-time regression curves to estimate the proportion of regenerating forest actually used by each bird species. Of the 28 species for which we had sufficient data, 14 showed significant changes in abundance over time. For 6 species, abundance was highest immediately after logging and decreased thereafter. Abundances of 7 other species were initially low, peaked roughly 10 years after harvest, and declined thereafter. Based on these results, shrubland birds would be expected to occupy a mean of just 53% (SD = 17%) of regenerating forests up to 20 years old. Thus, current estimates of habitat availability for shrubland birds may be too high by a factor of 2. Our findings also suggest that managed openings should be maintained on longer rotations than are currently used, providing habitat for birds that prefer older regeneration.     

Effects of overexpression of NAPRTase,NAMNAT, and NAD synthetase in the NAD(H) biosynthetic pathways on the NAD(H) pool,NADH/NAD+ ratio,and succinic acid production with different carbon sources by metabolically engineered Escherichia coli

Escherichia coli BA002, the ldhA and pflB deletion strain, cannot utilize glucose anaerobically due to the inability to regenerate NAD⁺. To regulate NAD(H) pool size and NADH/NAD⁺ ratio, overexpression of the enzymes in the NAD(H) biosynthetic pathways in BA002 was investigated. The results clearly demonstrate that the increased NAD(H) pool size and the decreased NADH/NAD⁺ ratio improved the glucose consumption and cell growth, which improved succinic acid production. When the pncB and the nadD genes were co-overexpressed in CA102, the ratio of NADH/NAD⁺ was decreased from 0.60 to 0.12, and the concentration of NAD(H) was the highest among that of all the strains. Moreover, the dry cell weight (DCW), glucose consumption, and the concentration of succinic acid in CA102 were also the highest. Based on the sufficient NAD⁺ supply after gene modification in the NAD(H) biosynthetic pathways, reductive carbon sources with different amounts of NADH can further change the distribution of metabolites. When sorbitol was used as a carbon source in CA102, the byproducts were lower than those of glucose fermentation, and the yield of succinic acid was increased.     

Clonal diversity and structure related to habitat of the marine angiosperm Thalassia testudinum along the Atlantic coast of Mexico

The clonal structure of the tropical seagrass Thalassia testudinum was studied at 16 sites along the Mexican Atlantic coast, situated in back-reef, shallow coastal and lagoon habitats. Thalassia testudinum was highly clonal, with an overall average clonal richness (R) of 0.55. The largest genet found in this study extended throughout the sampling area (∼230 m), with an estimated max age almost reaching 600 years. Lagoons with higher nutrient availability reflected by nutrient content of leaves (mean leaf C:N ratio 11.4) and lower hydrodynamic regimes reflected by the percentage of fine sediments (on average 23%), sustained larger genets of T. testudinum (mean of the largest genets over populations was 167.3 m) than the shallow coastal areas (C:N 12.3, 6.2% fine sediment, mean largest genet 10.3 m) and the more oligotrophic back-reefs (C:N 16.3, 2.7% fine sediment, mean largest genet 6.5 m). Population genetic analysis showed different levels of clonality, genotypic diversity and spatial genetic relatedness for this seagrass per habitat, with the lagoons presenting much lower levels of clonal diversity than the other two habitats.     

Body size of insular carnivores: evidence from the fossil record

Aim Our goals here are to: (1) assess the generality of one aspect of the island rule – the progressive trend towards decrease in size in larger species – for fossil carnivores on islands; (2) offer causal explanations for this pattern and deviations from it – as far as fossil carnivores are concerned; and (3) estimate the speed of this trend. Location Oceanic and oceanic‐like islands world‐wide. Methods Body size estimates of fossil insular carnivores and of their phylogenetically closest mainland relative were obtained from our own data and the published literature. Our dataset consisted of 18 species from nine islands world‐wide. These data were used to test whether the body size of fossil insular carnivores varies as a function of body size of the mainland species in combination with characteristics of the island ecosystem. Results Dwarfism was observed in two canid species. Moderate decrease in body mass was observed in one hyena species. Gigantism was observed in one otter species. Moderate body mass increase was observed in two otter species, one galictine mustelid and perhaps one canid. Negligible or no change in body mass at all was observed in five otter species, three galictine mustelids and one genet. Size changes in teeth do not lag behind in comparison to skeletal elements in the dwarfed canids. The evolutionary speed of dwarfism in a canid lineage is low. Main conclusions Size change in fossil terrestrial insular carnivores was constrained by certain ecological conditions, especially the availability of prey of appropriate body size. When such alternative prey was not available, the carnivores retained their mainland size. The impact of competitive carnivores seems negligible. The case of (semi‐)aquatic carnivores is much less clear. The species that maintained their ancestral body mass may have changed their diet, as is evidenced by their dentition. Among the otters, one case of significant size increase was observed, perhaps best explained as being due to it entering the niche of an obligate aquatic otter. Dwarfism was not observed in otters. The island rule seems to apply to fossil carnivores, but with exceptions. The dependency of the island rule on resource availability is emphasized by the present study.     

More food,less habitat: how necromass and leaf litter decomposition combine to regulate a litter ant community

1. In brown food webs of the forest floor, necromass (e.g. insect carcasses and frass) falling from the canopy feeds both microbes and ants, with the former decomposing the homes of the latter. In a tropical litter ant community, we added necromass to 1 m² plots, testing if it added as a net food (increasing ant colony growth and recruitment) or destroyer of habitat (by decomposing leaf litter). 2. Maximum, but not mean, colony growth rates were higher on +food plots. However, neither average colony size, nor density was higher on +food plots. In contrast, +food plots saw diminished availability of leaf litter and higher microbial decomposition of cellulose, a main component of the organic substrate that comprises litter habitat. 3. Furthermore, necromass acted as a limiting resource to the ant community only when nest sites were supplemented on +food plots in a second experiment. Many of these +food +nest plots were colonised by the weedy species Wasmannia auropunctata. 4. Combined, these results support the more food–less habitat hypothesis and highlight the importance of embedding studies of litter ant ecology within broader decomposer food web dynamics.     

基于粪便DNA的马鹿种群数量和性比

为分析黑龙江省完达山林区马鹿种群生存状态,制定科学有效地保护措施,从分子水平研究了种群数量和性比。2006、2007两年冬季跟踪马鹿足迹链,于五泡林场共搜集210份粪便,以成功提取DNA的167份作为分析样本。通过多态性较高的7个微卫星位点进行了基因分型分析,显示167份粪便DNA分属66只个体。基于非损伤性标志重捕法,统计出林场内马鹿数量2a平均47(39—60)只,密度0.302(0.251—0.386)只/km2,与2002年大样方法调查结果相比有减无增。SRY基因性别鉴定显示,种群雌雄性比1.00∶2.00(22♀,44♂),存在较多雄性个体,分析认为偷猎是导致性比失衡的最主要原因。数量的持续下降和性比失衡提示完达山林区马鹿种群数量的恢复需要更好地保护工作。     

Nest groups of wild bonobos at Wamba: selection of vegetation and tree species and relationships between nest group size and party size

We examined the location of nest groups, spatial distribution of nests within a nest group, and attributes of individual nests of wild bonobos at Wamba, Democratic Republic of Congo. We also examined the seasonal factors influencing nesting behavior and compared the nest group size with the 1 hr party size during daytime. We defined a nest group to be a cluster of nests that were built in the same evening and found within 30 m from the other nearest nest. Examination of the largest gap within a nest group suggested that 30 m was an acceptable cutoff value. Monthly rainfall or fruit abundance did not significantly influence the monthly mean nest group size. Nests were built in the swamp forest for as many as 13% observation days, suggesting the need for reevaluation of the use of swamp forest by bonobos. The use of swamp forest was influenced not by seasonal rainfall or fruit abundance, but by the fruiting of specific species. Preferred tree species for building nests accounted for 19.8% of standing trees, which suggested that the selection of sleeping sites was not largely restricted by the distribution of specific species. The mean 1 hr party size was almost identical through the day and was similar to the mean nest group size. Parties of bonobos sometimes split into smaller nest groups, especially when feeding on non‐preferred fruits during fruit scarcity. By contrast, when feeding on preferred fruits while ranging in large parties, they often aggregated to form even larger nest groups. When sleeping in small‐ or middle‐sized nest groups, they tended to aggregate the next morning. These tendencies may reflect the gregarious nature of bonobos who prefer to range or sleep together as far as circumstances allow. Am. J. Primatol. 72:575–586, 2010. © 2010 Wiley‐Liss, Inc.     

利用离心法进行土壤颗粒分级

按照离心机Mandal RC5C的转子尺寸,根据Stocks公式对Anderson和Tiessen的土壤颗粒分级方法中的离心时间重新设定,用新设计出的土壤颗粒分级方法对3种黄土高原的土壤(黄绵土、灰褐土、黑垆土)和2种加拿大北美大草原的土壤(典型褐灰钙土、典型黑灰钙土)进行了分组,其结果与吸管法所得的结果相吻合,表明这一分级方法的分析误差小、适用的土壤范围广,可用于土壤有机质、土壤中N、P、S等元素在不同粒径中分布等研究,同时,讨论了利用超声波进行土壤颗粒分散技术的使用条件,建议针对特定土壤应对能量输入进行矫正。