Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa

Re‐introduced African elephant (Loxodonta africana Blumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.     

盐度对红树植物海莲幼苗的生长和某些生理生态特性的影响

本文主要探讨了不同盐度海水砂培的海莲幼苗生长量和某些生理生态特性与盐度的相关效应。结果表明,生长基盐度20‰以上,海莲繁殖体的萌苗时间推迟,成活率降低;随着盐度的提高,幼苗高生长量降低,叶片变小;叶片叶绿素含量随盐度提高而提高,相反的叶片可溶性糖含量则降低,而叶片可溶性蛋白质含量变化不明显;叶片组织内氯含量随盐度提高而提高;随着盐度的提高,叶片蒸腾作用减弱,气孔导度降低。由此表明,海莲幼苗适宜生长的盐度范围在15‰以下,更高的盐度表现为生态抗盐适应性生长。     

Fun in facets: A flexible new tool for population genomics in R

The landscape of analytical tools for population genomics continues to evolve. However, these tools are scattered across programming languages, making them largely inaccessible for many biologists. In this issue of Molecular Ecology Resources, Hemstrom and Jones, 2022 (Mol Ecol Resour; 962) introduce a new R package, snpR. This package combines a large number of existing analyses, to provide a one-stop shop for population genomics. F-statistics, admixture analyses, effective population size inferences, genome-wide association studies (GWAS), and parentage analyses are all implemented natively within the package. A variety of third-party software can also be run without leaving the R environment. The authors pay particular attention to data structure – avoiding redundancy – and allowing analyses to be run across multiple sample or single-nucleotide polymorphism (SNP) groupings. Because of its great accessibility and wide range of analyses, snpR has the potential to become a favourite within the Molecular Ecology community.     

北京东灵山海拔梯度上辽东栎种群结构和空间分布

种群年龄结构和空间分布格局是种群生态学的核心研究内容.为了阐明辽东栎种群海拔梯度分布特点,在北京东灵山地区辽东栎海拔分布范围(1000～1800m)内调查10条样带,研究种群大小级结构和空间分布的变异.种群的平均胸径在海拔梯度上表现出两段式的分布特征,海拔1480m为两段分布的分界点,在每一段内随海拔增加平均胸径也增加, 这反映了海拔梯度上种群的不同发育历史.种群密度、种群的聚集程度、种群的结构在海拔梯度上的分布特征都与平均胸径分布相似,种群密度和聚集程度与平均胸径为负相关系,其分布趋势与平均胸径相反.总体上,东灵山海拔梯度上辽东栎种群还是比较稳定的.辽东栎种群结构和空间分布在海拔梯度上的分布特征是种群发育历史、物种特性、环境、干扰等因素在海拔梯度上综合作用的结果.     

内蒙古贺兰山冬春季岩羊种群现状及保护

为调查内蒙古贺兰山国家级自然保护区内岩羊（Pseudois nayaur alashanicus）的种群现状,通过样线法在2017、2018年冬季,2018、2019年春季进行了调查,利用R 4.0.3中的Distance 1.0.2对样线观测数据进行分析,估测保护区内岩羊的种群数量及密度,分析其种群结构。结果显示,调查共观测到岩羊6299只,其中,2018年冬季种群数量最高,约为2654（2230-3161）只（括号内为95%数量置信区间）,种群密度为3.921（3.293-4.668）只/km²。与2003年同季节的调查数据对比发现,保护区内岩羊的种群数量在15年间增长迅速,岩羊的种群密度累计增长了约53.17%,年平均增长3.54%。岩羊集群形式：混合群（88.03%,80.95%）为岩羊冬、春最主要的集群形式,且混合群的数量冬季多于春季,独羊出现的次数最低（1.99%,2.86%）,不同的集群类型在不同的季节的差异极显著（P<0.001）;岩羊平均群大小：春季为（13.439±12.085）只,冬季为（9.011±8.610）只,调查季节中集群大小多为1-10只,岩羊的不同季节的群大小差异极显著（P<0.001）。种群成体与幼体比在不同季节的变化范围为1.411-2.673,雌雄比在不同季节的变化范围为0.934-1.469,种群结构的季节性差异极显著（P<0.001）。集群类型、群大小及群组成的调查表明,不同季节间岩羊种群结构差异明显。     

Population dynamics of hypolimnetic rotifers in the Pluss-see (North Germany)

The hypolimnetic rotifer populations of the Pluss-see (Keratella hiemalis, Filinia terminalis, Filinia hofmanni) show similar patterns of changing population parameters indicating that they respond to particular environmental signals in the same way.     

The effective founder effect in a spatially expanding population

The gradual loss of diversity and the establishment of clines in allele frequencies associated with range expansions are patterns observed in many species, including humans. These patterns can result from a series of founder events occurring as populations colonize previously unoccupied areas. We develop a model of an expanding population and, using a branching process approximation, show that spatial gradients reflect different amounts of genetic drift experienced by different subpopulations. We then use this model to measure the net average strength of the founder effect, and we demonstrate that the predictions from the branching process model fit simulation results well. We further show that estimates of the effective founder size are robust to potential confounding factors such as migration between subpopulations. We apply our method to data from Arabidopsis thaliana. We find that the average founder effect is approximately three times larger in the Americas than in Europe, possibly indicating that a more recent, rapid expansion occurred.     

从文献看种群、种群生态及种群行为研究

通过维普中文期刊网和英文ScienceDirect数据库有关种群、种群生态和种群行为文献的查询,发现文献的发表量很不平衡,种群研究文献的年增长率远大于种群生态和种群行为。英文文献中关于种群行为研究的文献增长率高于种群生态,而中文文献正好相反。     

The macroecology of population dynamics: taxonomic and biogeographic patterns in population cycles

Regular cycles in population abundance are fascinating phenomena, but are they common in natural populations? How are they distributed among taxa? Are there differences between different regions of the world, or along latitudinal gradients? Using the new Global Population Dynamics Database we analysed nearly 700 long (25 + years) time series of animal field populations, looking for large-scale patterns in cycles. Nearly 30% of the time series were cyclic. Cycle incidence varied among taxonomic classes, being most common in mammal and fish populations, but only in fish did cycle incidence vary among orders. Cycles were equally common in European and North American populations, but were more common in Atlantic fish than Pacific fish. The incidence of cycles increased with latitude in mammals only. There was no latitudinal gradient in cycle period, but cycle amplitude declined with latitude in some groups of fish. Even after considering the biases in the data source and expected type I error, population cycles seem common enough to warrant ecological attention.     

Gene flow of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis

Population outbreaks of the coral-eating starfish, Acanthaster planci , are hypothesized to spread to many localities in the Indo-Pacific Ocean through dispersal of planktonic larvae. To elucidate the gene flow of A. planci across the Indo-Pacific in relation to ocean currents and to test the larval dispersal hypothesis, the genetic structure among 23 samples over the Indo-Pacific was analysed using seven highly polymorphic microsatellite loci. The F -statistics and genetic admixture analysis detected genetically distinct groups in accordance with ocean current systems, that is, the Southeast African group (Kenya and Mayotte), the Northwestern Pacific group (the Philippines and Japan), Palau, the North Central Pacific group (Majuro and Pohnpei), the Great Barrier Reef, Fiji, and French Polynesia, with a large genetic break between the Indian and Pacific Oceans. A pattern of significant isolation by distance was observed among all samples ( P =  0.001, r  = 0.88, n  = 253, Mantel test), indicating restricted gene flow among the samples in accordance with geographical distances. The data also indicated strong gene flow within the Southeast African, Northwestern Pacific, and Great Barrier Reef groups. These results suggest that the western boundary currents have strong influence on gene flow of this species and may trigger secondary outbreaks.     

Responses of breeding duck populations to changes in food supply

We describe the main results of a monitoring study at Lake Myvatn, northern Iceland, begun in 1975. The aims were to find factors that limit production of young and cause changes in density of breeding ducks of several species. We estimated numbers of ducks in spring, before nesting, numbers of ducklings produced, and numbers moulting. Chironomid and simuliid dipterans were monitored with window traps. In all duck species studied, production of young was correlated with food abundance. Reproductive performance determined subsequent changes in spring population density of Eurasian Wigeon, Tufted Duck, Greater Scaup, Common Scoter and Harlequin Duck. The spring population of Barrow's Goldeneye apparently did not respond to variation in reproductive success. Moulting numbers of male Tufted Duck were related to chironomid abundance, but not those of Scaup and Barrow's Goldeneye. Moulting numbers were not associated with previous reproductive output.     

Sex ratio and sexual dimorphism in mountain dioecious thuriferous juniper (Juniperus thurifera L., Cupressaceae)

Thuriferous juniper ( Juniperus thurifera L), a dioecious bush or tree is only found in isolated parts of the western Mediterranean: France, Spain, Algeria and Morocco. These mountain juniper stands are seriously endangered in Morocco as a result of intensive wood removal, and in Europe as a result of recolonization of stands by pines or oaks. Field studies were conducted to investigate sex ratio and sexual dimorphism, never previously examined, in eight different populations in the Atlas mountains and, for comparison, in one of two populations in the French Pyrenees. The sex ratio was female-biased for six of the eight Moroccan stands and especially for the oldest populations. The Pyrenean population showed a similar female-biased ratio. This particular sex ratio is possibly linked to cost of reproduction, paid by both males and females. Sex ratios can also be linked to population dynamics. Males begin to flower slightly younger than females, which explains their apparent dominance in young populations in Morocco or in a recolonization zone with young trees in the Pyrenees. Studies concerning sexual dimorphism in the western High Atlas sites showed no significant difference in phytomass between males and females. Females appear to be significantly taller but with a lower radial growth. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 237–244.     

The relevance of time series in molecular ecology and conservation biology

The genetic structure of a species is shaped by the interaction of contemporary and historical factors. Analyses of individuals from the same population sampled at different points in time can help to disentangle the effects of current and historical forces and facilitate the understanding of the forces driving the differentiation of populations. The use of such time series allows for the exploration of changes at the population and intraspecific levels over time. Material from museum collections plays a key role in understanding and evaluating observed population structures, especially if large numbers of individuals have been sampled from the same locations at multiple time points. In these cases, changes in population structure can be assessed empirically. The development of new molecular markers relying on short DNA fragments (such as microsatellites or single nucleotide polymorphisms) allows for the analysis of long‐preserved and partially degraded samples. Recently developed techniques to construct genome libraries with a reduced complexity and next generation sequencing and their associated analysis pipelines have the potential to facilitate marker development and genotyping in non‐model species. In this review, we discuss the problems with sampling and available marker systems for historical specimens and demonstrate that temporal comparative studies are crucial for the estimation of important population genetic parameters and to measure empirically the effects of recent habitat alteration. While many of these analyses can be performed with samples taken at a single point in time, the measurements are more robust if multiple points in time are studied. Furthermore, examining the effects of habitat alteration, population declines, and population bottlenecks is only possible if samples before and after the respective events are included.     

Conflicts in maintaining biodiversity at multiple scales

Biodiversity consists of multiple scales, including functional diversity in ecological traits, species diversity and genetic diversity within species, and is declining across the globe, largely in response to human activities. While species extinctions are the most obvious aspect of this, there has also been a more insidious loss of genetic diversity within species. While a vast literature concerns each of these scales of biodiversity, less is known about how different scales affect one another. In particular, genetic and species diversity may influence each other in numerous ways, both positively and negatively. However, we know little about the mechanism behind these patterns. In this issue of Molecular Ecology, Nestmann et al. (2011) experimentally explore the effect of species and functional diversity and composition of grassland plant communities on the genetic structure of one of the component species. Increasing species richness led to greater changes in the genetic composition of the focal populations over 4 years, primarily because of genetic drift in smaller population sizes. However, there were also genetic changes in response to particular plant functional groups, indicating selective differences driven by plant community composition. These results suggest that different levels of biodiversity can trade-off in communities, which may prove a challenge for conservation biologists seeking to preserve all aspects of biodiversity.     

Formulation and estimation of the effective size of stage-structured populations in Fritillaria camtschatcensis, a perennial herb with a complex life history

The effective population size (Ne) is formulated based on a stage-structured population model and is estimated for two populations of Fritillaria camtschatcensis (L.) Ker-Gawl. (Liliaceae), a perennial, mainly clonally reproducing herb. Plants in these populations change life-history stages year by year, either upward or downward across three unambiguously identifiable stages: one-leaf, nonflowering; multileaf nonflowering; and multileaf, flowering stages. Plants of all stages produce clonal progeny (bulblets) each year, and death of plants occurs only in the first stage. The populations are nearly at equilibrium in both population size and stage structure. Ne is estimated to be 20-30% of the census population size (N), leading to the prediction that a population size of about 20,000 or more will be needed to conserve the normal level of the gene diversity (Ne > or = 5000). With the current demographic pattern of this species, accelerated growth of the first-stage plants with reduced survival of the second- and third-stage plants will increase both the annual (Ny/N) and generation time (Ne/N) effective sizes of population.     

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Advancing technologies have facilitated the ever‐widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F_ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity‐based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration‐specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context‐dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non‐human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high‐throughput technologies in population genetics.     

16 Years of breed management brings substantial improvement in population genetics of the endangered Cleveland Bay Horse

The consequences of poor breed management and inbreeding can range from gradual declines in individual productivity to more serious fertility and mortality concerns. However, many small and closed groups, as well as larger unmanaged populations, are plagued by genetic regression, often due to a dearth in breeding support tools which are accessible and easy to use in supporting decision‐making. To address this, we have developed a population management tool (BCAS, Breed Conservation and Management System) based on individual relatedness assessed using pedigree‐based kinship, which offers breeding recommendations for such populations. Moreover, we demonstrate the success of this tool in 16 years of employment in a closed equine population native to the UK, most notably, the rate of inbreeding reducing from more than 3% per generation, to less than 0.5%, or that attributed to genetic drift, as assessed over the last 16 years of implementation. Furthermore, with adherence to this program, the long‐term impact of poor management has been reversed and the genetic resource within the breed has grown from an effective population size of 20 in 1994 to more than 140 in 2020. The development and availability of our BCAS for breed management and selection establish a new paradigm for the successful maintenance of genetic resources in animal populations.     

Population history in Arabidopsis halleri using multilocus analysis

A. halleri is a psuedometallophyte with a patchy distribution in Europe and is often spread by human activity. To determine the population history and whether this history is consistent with potential human effects, we surveyed nucleotide variation using 24 loci from 12 individuals in a large A. halleri population. The means of total and silent nucleotide variation (θ_W) are within the range expected for the species. The population genetic neutrality tests Tajima’s D and Wall’s B had significant composite results rejecting panmixia, and Approximate Bayesian Computation analysis revealed that a subdivision model better explained the variation than the standard neutral model, refugia (or admixture), bottleneck or change of population size models. A categorical regression analysis further supports the subdivision model, and under the subdivision model, the neutrality tests are no longer significant. The best support was for two source populations, a situation consistent with the mixing of two populations possibly mediated by human activity. This scenario might limit the genetic diversity and adaptive potential of the population. The non‐neutral population variation described here should be considered in bioinformatic searches for adaptation.