Population regulation and demography in a harvested freshwater crayfish from Madagascar

Despite advances in statistical techniques for investigating population dynamics based on mark–recapture data, the majority of our understanding about demography and regulation comes from relatively few taxa. Most proposed generalisations about the association between demography and variation in population size are based on data from vertebrates, there are few sufficiently detailed invertebrate studies to examine whether these generalisations are widely supported. The population biology of freshwater invertebrates is especially poorly known. We present a large-scale mark–recapture study of an endemic freshwater crayfish from Madagascar ( Astacoides granulimanus ). Variation in density, caused by difference in fishing pressure due to local taboos, allowed us to investigate density-dependent regulation. We found evidence of density dependence in fecundity operating through the proportion of reproductive females by size but no significant evidence of density dependence in growth. Using a prospective analysis based on the elasticities from a size-structured matrix model, we found that both recruitment rates and survival rates of large individuals were strongly associated with deterministic population growth – a result that differs from generalisations drawn from vertebrate studies. A central assumption in mark–recapture studies is that handling does not affect mortality. By treating the number of times an individual was captured as an individual covariate, easily done using the freeware program MARK, we were able to test for, and take account of, handling-induced mortality. Our results show interesting similarities, and important differences, to generalisations based on vertebrate studies and emphasise the importance of population studies on poorly known taxa.     

物种多样性与生态系统功能时间变异性的关系研究进展

近年来物种多样性的急剧丧失使得物种多样性与生态系统功能的时间变异性的关系及其机制问题的研究成为了生态学研究的一个热点。综述了物种多样性与群落集合性质变异性以及种群性质变异性的关系及其机制的最新研究成果：1、理论上探讨造成物种多样性与群落集合性质变异性负相关关系的机制包括：抽样效应、资源利用分化假说、统计平均效应、保险假说、种群变异性的均匀度效应等;但实验研究对理论预期的支持并不是普遍的;2．多样性与种群变异性之间的关系主要依赖于均值-方差尺度系数Z;理论上大部分自然群落是种群变异性应该随着多样性的增加而增加;但有研究表明：在变动环境中多样性对单个组分物种的种群水平有稳定性作用;而经验研究并不能得出多样性对种群变异性效应的清晰模式。讨论了目前的理论和实验研究中存在的和今后研究中需要认真思考的问题。     

Effect of population size on the prospect of species survival

Many recent studies have demonstrated a negative effect of small population size on single plant traits. However, not much is known about the actual consequences of reduced plant performance on the long-term prospect of species survival. I studied the effect of population size on population growth rate and survival probability in the rare perennial herbScorzonera hispanica occurring in fragmented grasslands. Its performance was measured using several traits related to reproduction in 21 populations ranging in size from 3 to 2475 plants. These data were then connected with data on full demography of the species from three of the studied populations. Two different matrix models differing in the number of transitions based on measurements in the populations differing in size were used to explore the relationship between population size and population growth rate. Both matrix models showed that despite the decline in seed production in small populations, population growth rate is never significantly different from one, and the populations could thus be expected to survive in the long run. Calculations of extinction probabilities that take into account demographic and environmental stochasticity, however, showed that populations below 100 flowering individuals have a high probability to become extinct. This demonstrates that demographic and environmental stochasticity is an important driver of the fate of small populations in this system. This study demonstrates that estimation of population growth rate can provide new insights into the effect of population size on population growth and survival. It also shows how matrix models enable the combination various pieces of information about the single populations into one overall measure, and may provide a useful tool for the standardization of studies on the effects of population size on population performance.     

Mitochondrial DNA and two perspectives on evolutionary genetics

This essay reviews comparative studies of animal mitochondrial DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two previous paths of progress in evolutionary biology. One path is that of those who worked far above the species level and were concerned with genealogical trees, time scales and the accumulation of new mutations on surviving molecular lineages. The other path is that of those who worked at and below the species level and were concerned mainly with population structure, migration and the frequencies of alleles that existed in an ancestral population. This fusion of paths is made possible by the high rate at which mutations accumulate on mtDNA lineages and by this molecule's uniparental and apparently haploid mode of inheritance. These properties make mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level. In addition, owing to its mode of inheritance, mtDNA is more sensitive to bottlenecks in population size and to population subdivision than are nuclear genes. Joint comparative studies of both mtDNA and nuclear DNA variability give us valuable insights into how effective population size has varied through time. Such studies also give insight into the conditions under which mtDNA from one species can colonize another species.     

The importance of within-year repeated counts and the influence of scale on long-term monitoring of sage-grouse

Long-term population monitoring is the cornerstone of animal conservation and management. The accuracy and precision of models developed using monitoring data can be influenced by the protocols guiding data collection. The greater sage-grouse (Centrocercus urophasianus) is a species of concern that has been monitored over decades, primarily, by counting the number of males that attend lek (breeding) sites. These lek count data have been used to assess long-term population trends and for multiple mechanistic studies. However, some studies have questioned the efficacy of lek counts to accurately identify population trends. In response, monitoring protocols were changed to have a goal of counting lek sites multiple times within a season. We assessed the influence of this change in monitoring protocols on model accuracy and precision applying generalized additive models to describe trends over time. We found that at large spatial scales including >50 leks, the absence of repeated counts within a year did not significantly alter population trend estimates or interpretation. Increasing sample size decreased the model confidence intervals. We developed a population trend model for Wyoming greater sage-grouse from 1965 to 2008, identifying significant changes in the population indices and capturing the cyclic nature of this species. Most sage-grouse declines in Wyoming occurred between 1965 and the 1990s and lek count numbers generally increased from the mid-1990s to 2008. Our results validate the combination of monitoring data collected under different protocols in past and future studies—provided those studies are addressing large-scale questions. We suggest that a larger sample of individual leks is preferable to multiple counts of a smaller sample of leks. © 2011 The Wildlife Society.     

Hardy weinberg expectations in canine breeds: implications for genetic studies

Hardy-Weinberg equilibrium (HWE) is a useful indicator of genotype frequencies within a population and whether they are based on a valid definition of alleles and a randomly mating sample. HWE assumes a stable population of adequate size without selective pressures and is used in human genetic studies as a guide to data quality by comparing observed genotype frequencies to those expected within a population. The calculation of genetic associations in case-control studies assume that the population is "in HWE." Canine breed populations deviate away from many of the criteria for HWE, and if genetic markers are not in HWE, conventional statistical analysis cannot be performed. To date, little attention has been paid as to whether genetic markers in dog breeds are distributed in compliance to HWE. In this study, 109 single-nucleotide polymorphisms (SNPs) were genotyped from 13 genes in a cohort of 894 dogs encompassing 33 breeds. Analysis of the entire cohort of dogs revealed a significant deviation away from HWE for all SNPs tested (P < 0.00001); analysis of the cohort stratified by breed and subbreed indicated that the majority of the markers complied with HWE expectation. This suggests that canine case-control association studies will be valid if performed within defined breeds.     

Influence of volunteer wheat plant condition on movement of the wheat curl mite, Aceria tosichella, in winter wheat

The wheat curl mite (WCM), Aceria tosichella Keifer, is the vector of wheat streak mosaic virus and high plains virus which cause significant crop loss in winter wheat throughout the western Great Plains. Volunteer wheat emerging before harvest, as a result of severe hail, is the primary source of mites and virus that infect fall-planted winter wheat. Wind-borne movement of the WCM is of key importance in the spread and infection of the virus complex. Significant movement of WCM from wheat has been thought to be closely tied to the senescence or deterioration of the host. Results from field and greenhouse studies indicated that movement from un-vernalized winter wheat was not closely associated with the deterioration of the wheat host. Greenhouse studies showed no correlation between WCM movement and plant condition, but there was a highly significant relationship between WCM movement and mite population on the host plant. Field studies did not demonstrate increased movement associated with deteriorating un-vernalized winter wheat. However, healthier hosts which were able to support a larger population of mites were associated with increased movement. The main influence on the level of mite movement relates to the size of the source population and not the condition of the host plant, but plant condition appears to be a factor in limiting the increase of the WCM population.     

Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour

Subpopulation genetic structure was studied in a population of the short-lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep-sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub-populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.     

Is relative abundance a good indicator of population size? Evidence from fragmented populations of a specialist butterfly (Lepidoptera: Lycaenidae)

A common task for conservation biologists and ecologists is to establish how many individuals there are in a population, usually within a defined area of habitat. Estimates of both absolute and relative population sizes are widely used in many aspects of population conservation and management. Mark–recapture studies are appropriate for estimating the absolute population sizes of a wide range of animals, in both open and closed populations, while relative abundances can be estimated from a variety of survey methods. Relative abundances are often used in a comparative way to compare both population size and fluctuations in abundance. Here, we used transect counts and capture–recapture studies to estimate the relative abundances and population sizes of a specialist butterfly, Theclinesthes albocincta (Lycaenidae) in three habitat fragments, over two consecutive years. The sizes of the three populations differed significantly between sites and were highly variable between years. One population was extremely small and is likely to become locally extinct. We found that estimates of relative abundance were highly correlated with estimates of population size (r ² = 0.88, P = 0.017) derived from the open population models. The combination of transect counts and capture–recapture studies used in this study appears to be a very informative tool for the conservation and management of this butterfly species and could be extended to other insects.     

Variation of Genetic Diversity in a Rapidly Expanding Population of the Greater Long-Tailed Hamster (Tscherskia triton) as Revealed by Microsatellites

Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984–1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.     

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.     

Genetics of the Shimokita macaque population suggest an ancient bottleneck

The macaque population of the Shimokita Peninsula represents the northernmost distribution of this species and is isolated from other populations in the Tohoku region of Japan. A previous protein-based study revealed a high level of genetic variability in this population and considerable differentiation from other populations. In order to reassess the genetic features of the Shimokita macaques, we examined 11 autosomal microsatellite loci and three Y chromosomal microsatellite loci. We observed considerable differentiation from other Japanese populations of macaques, but in contrast to the previous results, we observed significantly lower genetic variability in this population. There was a weak indication of a population bottleneck, suggesting a decay over time from an excess of heterozygotes that might be expected in the initial stages of a bottleneck. This may indicate that an ancient bottleneck occurred during the warm period after the last glacial period rather than a recent bottleneck due to hunting in modern times. The frequencies of private alleles were exceptionally high in the Shimokita population, suggesting that the difference in variability as determined in various studies was due to accidental sampling of marker loci with low power to resolve genetic variations in the protein-based studies. The assessments of interpopulation differentiation as determined using autosomal and Y chromosomal markers were highly correlated, and using both types of markers the Shimokita population was found to be the most differentiated of the study populations, probably due to infrequent gene flow with surrounding populations.     

Toxicological and biochemical characterizations of malathion sensitivity in two field populations of Oxya chinensis （Orthoptera： Acridoidea）

We evaluate comparative toxicity of malathion in the two populations of the grasshopper Oxya chinensis, collected from Daixian and Fanshi of Shanxi province, China. General esterases and acetylcholinesterase （ACHE） from the two populations were characterized and compared. LD50 of the Daixian population （7.58 μg/g body weight） was 2.02-fold higher than that of the Fanshi population （3.75μg/g body weight）. General esterase-specific activities in the Daixian population were 1.91,130 and 1.85-fold higher than those in the Fanshi population, when α-NA, α-NB and β-NA were used as a substrate, respectively. Kinetic studies of general esterase showed that Vmax values of general esterases hydrolyzing α-NA,α-NB and β-NA in the Daixian population were 2.15-, 1.12-, and 1.47-fold, respectively, higher than those in the Fanshi population. The AChE activity of the Fanshi population was 1.54-fold higher than that of the Daixian population. Kinetic analysis of AChE showed that significant differences were presented between the two populations in the Km values; and the Vmax value in the Fanshi population was higher than that in the Daixian population. Inhibition studies of AChE indicated that AChE from the Daixian population was 2.56-, 2.80-, and 2.29-fold less sensitive to inhibition by paraoxon, chlorpyrifos-oxon, and demeton-S-methyl, respectively, than that from the Fanshi population. These biochemical characterizations of general esterases and AChE were consistent with malathion bioassay in the two populations. It is inferred that the reduced sensitivity of altered AChE and increased general esterase activities play an important role in the differences of insusceptibility of Oxya chinensis to malathion between the two populations.     

Isolation and characterization of microsatellite loci in wheat stem sawfly Cephus cinctus and cross‐species amplification in related species

The wheat stem sawfly is an important insect pest of wheat that can cause significant damage to yield and grain quality. Five microsatellite loci were isolated and characterized in wheat stem sawfly, Cephus cinctus, to facilitate future population genetic studies and help delineate their geographical origin. These loci were found to be polymorphic with an expected heterozygosity ranging from 0.304 to 0.937 and an observed heterozygosity ranging from 0.05 to 0.65. Successful cross‐species amplification demonstrates the potential for these markers to provide a valuable tool for future population studies among related Cephus species.     

The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland

The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.     

Development of polymorphic microsatellites for the invasive Asian fish tapeworm Schyzocotyle acheilognathi

We describe the development of ready-to-use set of fifteen polymorphic microsatellite markers to benefit future population biology and phylogeographic studies on the invasive Asian fish tapeworm Schyzocotyle acheilognathi. The microsatellite loci were selected from partial Illumina shotgun genome sequences of three parasite specimens and their universality tested on a set of 12 geographically distant populations of the parasite. Particularly low levels of heterozygosity have been detected in the Chinese population pointing towards possible hidden population structure that deserves further attention in future population genetic studies.     

Utility of Microcosm Studies for Predicting Phylloplane Bacterium Population Sizes in the Field

Population sizes of two ice nucleation-active strains of Pseudomonas syringae were compared on leaves in controlled environments and in the field to determine the ability of microcosm studies to predict plant habitat preferences in the field. The P. syringae strains investigated were the parental strains of recombinant deletion mutant strains deficient in ice nucleation activity that had been field tested for their ability to control plant frost injury. The population size of the P. syringae strains was measured after inoculation at three field locations on up to 40 of the same plant species that were studied in the growth chamber. There was seldom a significant relationship between the mean population size of a given P. syringae strain incubated under either wet or dry conditions in microcosms and the mean population size which could be recovered from the same species when inoculated in the field. Specifically, on some plant species, the population size recovered from leaves in the field was substantially greater than from that species in a controlled environment, while for other plant species field populations were significantly smaller than those observed under controlled conditions. Population sizes of inoculated P. syringae strains, however, were frequently highly positively correlated with the indigenous bacterial population size on the same plant species in the field, suggesting that the ability of a particular plant species to support introduced bacterial strains is correlated with its ability to support large bacterial populations or that indigenous bacteria enhance the survival of introduced strains. Microcosm studies therefore seem most effective at assessing possible differences between parental and recombinant strains under a given environmental regime but are limited in their ability to predict the specific population sizes or plant habitat preferences of bacteria on leaves under field conditions.     

Environmental stochasticity and population dynamics of large herbivores: a search for mechanisms

Recently, the results from several long-term individual-based population studies of ungulates have been published. One major conclusion is that the population dynamics of ungulates in predator-free environments is strongly influenced by a combination of stochastic variation in the environment, and population density. Both density dependence and environmental stochasticity operate through changes in life history traits, correlated with variation in body weight. This generates delays in the response of the population to changes in environment. In the absence of predation, a stable equilibrium is therefore unlikely to exist between an ungulate population and its food resources. This thorough understanding of the mechanisms generating population fluctuations suggests that studies of ungulates will provide an important source for examining effects of long-term changes in the environment, for instance, resulting from a climatic change.     

Seasonal population dynamics and the genetic structure of the mosquito vector Aedes aegypti in São Paulo,Brazil

Population genetic studies of insect vectors can generate knowledge to improve epidemiological studies focused on the decrease of pathogen transmission. In this study, we used nine SNPs across the Aedes aegypti genome to characterize seasonal population variations of this important dengue vector. Mosquito samples were obtained by ovitraps placed over Botucatu SP from 2005 to 2010. Our data show that, regardless of the large variation in mosquito abundance (deduced from the number of eggs obtained from ovitraps), the effective population size remained stable over the years. These results suggest that Ae. aegypti is able to maintain a sufficiently large active breeding population during the dry season to keep genetic frequencies stable. These results open new perspectives on mosquito survey and control methods.     

Freezer anthropology: new uses for old blood

Archived blood fractions (plasma, settled red cells, white cells) have proved to be a rich and valuable source of DNA for human genetic studies. Large numbers of such samples were collected between 1960 and the present for protein and blood group studies, many of which are languishing in freezers or have already been discarded. More are discarded each year because the usefulness of these samples is not widely understood. Data from DNA derived from 10-35-year-old blood samples have been used to address the peopling of the New World and of the Pacific. Mitochondrial DNA haplotypes from studies using this source DNA support a single wave of migration into the New World (or a single source population for the New World), and that Mongolia was the likely source of the founding population. Data from Melanesia have shown that Polynesians are recent immigrants into the Pacific and did not arise from Melanesia.