基于广义可加模型的昆虫种群动态非线性分析及R语言实现

昆虫种群受到气候、天敌和土壤等多种生态因子的综合作用,其动态具有复杂性、不确定性和非线性等特征。广义加性模型(generalized additive models,GAM)就是适用于响应变量与解释变量之间的关系是非线性或非单调的数据分析。本文以1973—1990年稻纵卷叶螟种群数量与降雨持续天数和降雨量的相关性分析为例,介绍了广义可加模型的应用及其R语言实现步骤,为研究昆虫种群动态及其驱动因子提供了有效的分析工具。     

On a log-linear approach to detecting ecological interactions in monitored populations

We discuss a log-linear model for series of regular bird counts taken at a number of survey sites. The model is parameterized in terms of annual growth rates rather than actual indices of abundance, as is more frequently done. This not only permits easy estimation of and inference about these rates, but also allows us to model the effects upon population growth of covariates, such as the local presence of a competitor or predator, which may themselves vary in space and over time. A recursive relationship permits the expected count at a site to be functionally dependent upon the expected count at the previous visit. We discuss the advantages of using this relationship, rather than replacing the latter with their observed counterparts, as has been used previously.     

Heterogeneous capture-recapture models with covariates: a partial likelihood approach for closed populations

In practice, when analyzing data from a capture-recapture experiment it is tempting to apply modern advanced statistical methods to the observed capture histories. However, unless the analysis takes into account that the data have only been collected from individuals who have been captured at least once, the results may be biased. Without the development of new software packages, methods such as generalized additive models, generalized linear mixed models, and simulation-extrapolation cannot be readily implemented. In contrast, the partial likelihood approach allows the analysis of a capture-recapture experiment to be conducted using commonly available software. Here we examine the efficiency of this approach and apply it to several data sets.     

探讨基于红外相机技术对大型猫科动物及其猎物的种群评估方法

红外相机技术的发展促进了对东北虎(Panthera tigris altaica)、东北豹(Panthera pardus orientalis)及其猎物种群的研究。本研究以珲春保护区春化和马滴达两个区域的监测结果为例, 介绍利用该技术对我国长白山区东北虎、东北豹及其猎物的种群评估方法, 包括监测位点的选择、相机的架设方式及参数设置、数据筛选、东北虎和东北豹体侧花纹个体识别方法、物种相对丰富度的计算以及捕食者与猎物丰富度关系模型的构建。最后就东北虎、东北豹体侧花纹个体识别技术的适用性、红外相机监测与传统调查方法的差异, 相机监测的误差进行了讨论。研究表明, 利用红外相机技术进行密度预测以及东北虎、东北豹个体自动识别技术还需继续完善。1对/25 km²的相机架设密度基本上满足对于珲春保护区春化至马滴达区域虎豹的监测强度要求, 但对于有蹄类则需要另外的监测方案。     

Spatial and habitat variation in aphid,butterfly, moth and bird phenologies over the last half century

Global warming has advanced the timing of biological events, potentially leading to disruption across trophic levels. The potential importance of phenological change as a driver of population trends has been suggested. To fully understand the possible impacts, there is a need to quantify the scale of these changes spatially and according to habitat type. We studied the relationship between phenological trends, space and habitat type between 1965 and 2012 using an extensive UK dataset comprising 269 aphid, bird, butterfly and moth species. We modelled phenologies using generalized additive mixed models that included covariates for geographical (latitude, longitude, altitude), temporal (year, season) and habitat terms (woodland, scrub, grassland). Model selection showed that a baseline model with geographical and temporal components explained the variation in phenologies better than either a model in which space and time interacted or a habitat model without spatial terms. This baseline model showed strongly that phenologies shifted progressively earlier over time, that increasing altitude produced later phenologies and that a strong spatial component determined phenological timings, particularly latitude. The seasonal timing of a phenological event, in terms of whether it fell in the first or second half of the year, did not result in substantially different trends for butterflies. For moths, early season phenologies advanced more rapidly than those recorded later. Whilst temporal trends across all habitats resulted in earlier phenologies over time, agricultural habitats produced significantly later phenologies than most other habitats studied, probably because of nonclimatic drivers. A model with a significant habitat‐time interaction was the best‐fitting model for birds, moths and butterflies, emphasizing that the rates of phenological advance also differ among habitats for these groups. Our results suggest the presence of strong spatial gradients in mean seasonal timing and nonlinear trends towards earlier seasonal timing that varies in form and rate among habitat types.     

Changes in phenology and abundance of suction-trapped Diptera from a farmland site in the UK over four decades

1. Recently documented insect declines have caused major concerns and an increased interest in studies using long-term population-monitoring data. 2. Samples from a 12.2-m suction trap were used to examine trends in phenology and abundance of Diptera over four decades. 3. The timing of peak flight has advanced by an average of 17 days, from 23 July in 1974 to 6 July in 2014. 4. The abundance of flies has decreased by 37% over the studied period (from April to September), and peak abundance has decreased by 48%. The flight period has started earlier in recent years, and in 2014, the number of flies was higher in spring until the 31st of May than in 1974. Possible causes and impacts of these changes are discussed.     

Factors determining nest-site selection of surface-nesting seabirds: a case study on the world's largest pelagic bird,the Wandering Albatross (Diomedea exulans)

Several factors may drive bird nest-site selection, including predation risk, resource availability, weather conditions and interaction with other individuals. Understanding the drivers affecting where birds nest is important for conservation planning, especially where environmental change may alter the distribution of suitable nest-sites. This study investigates which environmental variables affect nest-site selection by the Wandering Albatross Diomedea exulans, the world's largest pelagic bird. Here, wind characteristics are quantitatively investigated as a driver of nest-site selection in surface-nesting birds, in addition to several topographical variables, vegetation and geological characteristics. Nest locations from three different breeding seasons on sub-Antarctic Marion Island were modelled to assess which environmental factors affect nest-site selection. Elevation was the most important determinant of nest-site selection, with Wandering Albatrosses only nesting at low elevations. Distance from the coast and terrain roughness were also important predictors, with nests more generally found close to the coast and in flatter terrain, followed by wind velocity, which showed a hump-shaped relationship with the probability of nest occurrence. Nests occurred more frequently on coastal vegetation types, and were absent from polar desert vegetation (generally above c. 500 m elevation). Of the variables that influence Wandering Albatross nest location, both vegetation type and wind characteristics are likely to be influenced by climate change, and have already changed over the last 50 years. As a result, the availability of suitable nest-sites needs to be considered in light of future climate change, in addition to the impacts that these changes will have on foraging patterns and prey distribution. More broadly, these results provide insights into how a wide range of environmental variables, including wind, can affect nest-site selection of surface-nesting seabirds.     

Demographic and spatial responses of resident bird populations to the arrival of migratory birds within an urban environment

Long-distance migration allows many bird species to overcome the severe climatic changes that occur in seasonal environments. Migration is highly demanding, and given its cyclical nature, we currently know that it has substantial effects on the population parameters of migratory birds during both breeding and wintering seasons. However, the potential effects of the presence of migratory birds in their wintering grounds on populations of resident birds have remain largely unexplored. Here, we propose the hypothesis that migratory birds negatively affect the habitat occupancy and population abundance of resident birds because of the arrival of numerous individuals during the most limiting months of the year. Here, we studied different species of migratory and resident birds that coexist during winter in an urban ecological reserve located within Mexico City. We used single-species multiseason occupancy models, two-species occupancy models, and distance sampling techniques to evaluate changes in occupancy and population density of resident bird species during three consecutive winters. We found an aggregation pattern between two resident species (Psaltriparus minimus and Thryomanes bewickii) with three migratory warblers (Cardellina pusilla, Setophaga coronata and Setophaga townsendi). Thus, our results provide evidence of the formation of mixed-species flocks in our study area. We also conclude that resident birds experience different demographic and behavioral processes during winter that not necessarily result from interspecific interactions with migratory birds.     

The probability of germination and establishment in discrete density-dependent plant populations with a seed bank: a correction formula

The effect of ignoring a seed bank in unstructured population models of annual plants is investigated under the assumption of ecological equilibrium. It is demonstrated that if delayed germination is an important life-history strategy and seed mortality in the seed bank is relatively low then it is important to take the effect of the seed bank into account. A formula that corrects the probability of germination and establishment in unstructured population models of annual plants for the effect of a seed bank is derived. This correction formula may be used in order to apply plant ecological data to a number of published unstructured plant ecological models.     

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.     

Variation in larval black fly populations at three sites in a stream system over five years (Diptera:Simuliidae)

Five years of monthly samples taken from three sites in the Broad Cove River, two at lake outlets and one a kilometer downstream from an outlet were analyzed. Considerable variations in the population of each species between sites and years were observed. Fluctuations in the populations were not always consistent from site to site or between species at the same site from one year to the next. As all sites were on the same stream and within 3 km of each other with only slight altitude differences climatic factors were not a major factor producing variations observed between sites. Also the previous years population level did not appear to be directly related to the following seasons population level. Apparently localized conditions at a site were exerting a marked influence on the larval simuliid population at each site.     

Agricultural land use and Skylark Alauda arvensis: a case study linking a habitat association model to spatially explicit change scenarios

The development of forward scenarios is a useful method of envisaging the environmental implications of potential changes in land use, as a tool for policy development. In this paper, a spatially explicit case study is used to provide insight into the environmental impacts of Common Agricultural Policy reform on Skylark Alauda arvensis, a species which is widespread on arable farmland, breeds in crops and has declined in recent decades. A generalized linear mixed model was used to estimate Skylark breeding population densities in different crops, using survey data collected from farms in the east of England, supplemented by the literature. Model outputs were then used to predict Skylark densities in an East Anglian Joint Character Area dominated by arable cropping. Predicted densities were mapped at field level using GIS, based on actual cropping derived from Integrated Administration and Control System data collected for the administration of subsidy payments. Three future scenarios were then created, based on expert opinion of potential changes in cropping over the next 5 years, and potential changes in Skylark density mapped on the basis of the predicted changes in cropping patterns. Overall, Skylark densities were predicted to decrease on average by 11–14% under ‘market‐led’ (increasing wheat and oilseed rape, reduced set‐aside) and ‘energy crop’ (5% area under short rotation coppice) scenarios, but remained virtually unchanged under an ‘environment‐led’ (diverse cropping) scenario. The ‘market‐led’ scenario is closest to short‐term agricultural trajectories, but wider cultivation of biomass energy crops as modelled under the ‘energy crop’ scenario could occur in the medium term if energy policies are favourable. Appropriate mitigation strategies therefore need to be implemented if a continued decline in the Skylark population on lowland arable farmland is to be averted. The results provide a readily accessible visualization of the potential impacts of land‐use change for policy‐makers; similar techniques could be applied to visualize effects of changes arising through other drivers, including climate change.     

Opening the door to greater phylogeographic inference in Southeast Asia: Comparative genomic study of five codistributed rainforest bird species using target capture and historical DNA

Indochina and Sundaland are biologically diverse, interconnected regions of Southeast Asia with complex geographic histories. Few studies have examined phylogeography of bird species that span the two regions because of inadequate population sampling. To determine how geographic barriers/events and disparate dispersal potential have influenced the population structure, gene flow, and demographics of species that occupy the entire area, we studied five largely codistributed rainforest bird species: Arachnothera longirostra, Irena puella, Brachypodius atriceps, Niltava grandis, and Stachyris nigriceps. We accomplished relatively thorough sampling and data collection by sequencing ultraconserved elements (UCEs) using DNA extracted from modern and older (historical) specimens. We obtained a genome‐wide set of 753–4,501 variable loci and 3,919–18,472 single nucleotide polymorphisms. The formation of major within‐species lineages occurred within a similar span of time (0.5–1.5 mya). Major patterns in population genetic structure are largely consistent with the dispersal potential and habitat requirements of the study species. A population break across the Isthmus of Kra was shared only by the two hill/submontane insectivores (N. grandis and S. nigriceps). Across Sundaland, there is little structure in B. atriceps, which is a eurytopic and partially frugivorous species that often utilizes forest edges. Two other eurytopic species, A. longirostra and I. puella, possess highly divergent populations in peripheral Sunda Islands (Java and/or Palawan) and India. These species probably possess intermediate dispersal abilities that allowed them to colonize new areas, and then remained largely isolated subsequently. We also observed an east–west break in Indochina that was shared by B. atriceps and S. nigriceps, species with very different habitat requirements and dispersal potential. By analyzing high‐throughput DNA data, our study provides an unprecedented comparative perspective on the process of avian population divergence across Southeast Asia, a process that is determined by geography, species characteristics, and the stochastic nature of dispersal and vicariance events.     

An Integrated Framework to Estimate Seabird Population Numbers and Trends

Generating trend and population estimates from bird count data is challenging and a variety of factors have to be taken into account. We present an integrative statistical approach for estimating population numbers and trends for seabirds at sea. The method allows for the integration of bird-count data from different sources and sampling schemes: offshore observer-based line transect and digital strip transect surveys and land-based point counts; the estimation of log-linear and highly nonlinear trends; the prediction of population numbers for predefined sub-areas, years, or seasons; and investigations of the effects of various environmental and detection-related covariates on bird count numbers. We applied the approach to count data for great black-backed gulls (Larus marinus) in the German part of the North Sea and Baltic Sea from 1990–2016. Count data were collected by observer-based offshore ship and aerial surveys, offshore digital aerial surveys, and point counts from the shore. The detectability of great black-backed gulls was affected by the sea state (the condition of the sea surface, characterized by wave height, wave form, foam, and spray) and survey method. Digital and observer-based aerial surveys detected only 59–77% of the abundance recorded by ship-based surveys. Great black-backed gulls are mainly present in German waters in winter, when they account for 3–4% of the European population. Their core distributional areas are mainly in deeper offshore waters where they are relatively dispersed, with several concentrations probably connected to fishing activity. Great black-backed gulls have undergone substantial declines, with the most pronounced decreases of >90% in the offshore waters of the German part of the North Sea. Breeding numbers at important European breeding sites do not show similar declines, suggesting that the trends observed in the sea areas might indicate a shift in the distribution or habitat use and a decreasing importance of marine areas for European great black-backed gulls. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Spatial genetic and morphologic structure of wolves and coyotes in relation to environmental heterogeneity in a Canis hybrid zone

Eastern wolves have hybridized extensively with coyotes and gray wolves and are listed as a ‘species of special concern’ in Canada. However, a distinct population of eastern wolves has been identified in Algonquin Provincial Park (APP) in Ontario. Previous studies of the diverse Canis hybrid zone adjacent to APP have not linked genetic analysis with field data to investigate genotype‐specific morphology or determine how resident animals of different ancestry are distributed across the landscape in relation to heterogeneous environmental conditions. Accordingly, we studied resident wolves and coyotes in and adjacent to APP to identify distinct Canis types, clarify the extent of the APP eastern wolf population beyond the park boundaries and investigate fine‐scale spatial genetic structure and landscape–genotype associations in the hybrid zone. We documented three genetically distinct Canis types within the APP region that also differed morphologically, corresponding to putative gray wolves, eastern wolves and coyotes. We also documented a substantial number of hybrid individuals (36%) that were admixed between 2 or 3 of the Canis types. Breeding eastern wolves were less common outside of APP, but occurred in some unprotected areas where they were sympatric with a diverse combination of coyotes, gray wolves and hybrids. We found significant spatial genetic structure and identified a steep cline extending west from APP where the dominant genotype shifted abruptly from eastern wolves to coyotes and hybrids. The genotypic pattern to the south and northwest was a more complex mosaic of alternating genotypes. We modelled genetic ancestry in response to prey availability and human disturbance and found that individuals with greater wolf ancestry occupied areas of higher moose density and fewer roads. Our results clarify the structure of the Canis hybrid zone adjacent to APP and provide unique insight into environmental conditions influencing hybridization dynamics between wolves and coyotes.     

Climate change and bird phenology: a long-term study in the Iberian Peninsula

Many studies in recent years have demonstrated long‐term temporal trends in biological parameters that can only be explained by climate change. Bird phenology has received great attention, as it studies one of the most conspicuous, popular, and easily observable phenomena in nature. There are many studies of long‐term changes in spring arrival dates, most of which concur with earlier records from the last few decades. However, few data are available for autumn departures or length of stays. Furthermore, existing data offer an equivocal picture. In this study, we analysed a huge database of about 44 000 records for five trans‐Saharan bird species (Ciconia ciconia, Cuculus canorus, Apus apus, Hirundo rustica and Luscinia megarhynchos). Data were collected from over 1300 sites around Spain during the period 1944–2004. Common spring arrival patterns were found in all species. Spring arrival dates have tended to advance since the mid‐1970s. Current dates are similar to those from the 1940s (except for C. ciconia). Thus, the advance of spring migration over the last three decades could be seen as a return to the initial timing of arrival dates, after abnormally delayed arrivals during the 1970s. A strong negative relationship with temperature in Spain at arrival time was observed in all species. A negative relationship with the Sahel Index (a measurement of precipitation in the African Sahel area during the rainy season) for the previous year was also found in C. canorus, A. apus and H. rustica. Regarding autumn departures, all species showed common interdecadal fluctuations, but only H. rustica is leaving earlier Spain at present. All species departed earlier in years that had higher temperatures during their reproductive period. However, only for H. rustica the relation between Spanish temperatures at departure time and the last sightings of individuals was significant. A heterogeneous temporal response for the length of stay was also found: C. ciconia increased, A. apus did not change and H. rustica decreased its stay. This is the first study, based on an extensive bird phenology observational network covering a large region, that shows the most complete and thorough analysis available for the Mediterranean region.     

Extreme streams: species persistence and genomic change in montane insect populations across a flooding gradient

The ecological and evolutionary consequences of extreme events are poorly understood. Here, we tested predictions about species persistence and population genomic change in aquatic insects in 14 Colorado mountain streams across a hydrological disturbance gradient caused by a one in 500‐year rainfall event. Taxa persistence ranged from 39 to 77% across sites and declined with increasing disturbance in relation to species' resistance and resilience traits. For taxa with mobile larvae and terrestrial adult stages present at the time of the flood, average persistence was 84% compared to 25% for immobile taxa that lacked terrestrial adults. For two of six species analysed, genomic diversity (allelic richness) declined after the event. For one species it greatly expanded, suggesting resilience via re‐colonisation from upstream populations. Thus, while resistance and resilience traits can explain species persistence to extreme disturbance, population genomic change varies among species, challenging generalisations about evolutionary responses to extreme events at landscape scales.     

Environmental dependence of population dynamics and height growth of a subalpine conifer across its vertical distribution: an approach using high‐resolution aerial photographs

Many studies have reported shifts in the altitudinal ranges of plant species in response to recent global warming. However, most studies of tree species have been conducted on a small scale and have focused on tree line ecotones by examining tree rings and age structure on account of the long life spans of the trees. To examine the impact of climate change on forest dynamics at a regional scale, we investigated differences in the population density and canopy height of a Japanese subalpine coniferous species, Abies mariesii, between 1967 and 2003 by analysis of high‐resolution aerial photographs of the Hakkoda Mountains, Honshu, Japan. In 712 plots within the photographs we analyzed which environmental variables (including elevation, aspect, wetness, and distance from moorlands) account for these changes. The population density of A. mariesii decreased below 1000 m a.s.l. and increased above 1300 m a.s.l. It also increased around moorlands, which may provide refugia at low elevations. The rate of increase in canopy height was lowest on the southeastern slopes and on the periphery of the moorlands. The distinct changes in the population density of A. mariesii at its distribution limits probably reflect the responses of the population to climatic changes during three decades. Areas surrounding the moorlands may offer refugia in spite of the poor growing conditions there.     

Linking root morphology, longevity and function to root branch order: a case study in three shrubs

Root branching order supports a powerful approach to understanding complex root systems; however, how the pattern of root morphological characteristics, tissue carbon (C) and nitrogen (N) concentrations, and root lifespan are related to anatomical features of variable root orders for mature shrubs (～19 years old) in sandy habitats is still unclear. In this study, these relationships were investigated for three typical shrubs in Horqin Sand Land, Northeast China. Root diameter, individual root length, tissue carbon concentration, C:N ratio, root lifespan, root cross-sectional area (CSA), stele CSA, proportion of stele in root CSA, mean xylem vessel CSA and the number of xylem vessels all increased with root order for the three shrubs, while specific root length and nitrogen concentration decreased with root order. The combined root biomass of the first two orders accounted for more than 63% of the first–fourth order root biomass for all the three shrubs. Proportion of stele to root CSA and number of xylem vessels of third-order root segments were significantly higher than that of the first two orders, and third-order roots showed secondary development with a continuous cork layer. All first-order and most second-order roots exhibited primary development, had an intact cortex, a lower proportion of stele to root CSA, and a smaller number of vessels. Our research suggests that the first two order roots of shrubs in sandy habitats are responsible mainly for absorption, and that they play a major role in root turnover and C and N flux in the soil organic matter pool due to their high proportion of biomass and N concentration, as well as their short lifespan.