Estimating ancestral population sizes and divergence times

This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly >10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.     

Host-plant-mediated interaction between populations of a true omnivore and its herbivorous prey

Western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), are competitors with twospotted spider mites, Tetranychus urticae Koch (Acari: Tetranychidae), for plant resources and potential predators on spider mites when the opportunity arises. Which interaction predominates may depend on relative population densities and individual species’ responses to the plants on which they co‐occur. We examined interactions between populations of thrips and spider mites on several cultivars of two bedding plants: impatiens (Impatiens wallerana Hook.f) cultivars ‘Impulse Orange’ and ‘Cajun Carmine’, and ivy geranium [Pelargonium peltatum (L.) L’Her ex Aiton] cultivars ‘Sybil Holmes’ and ‘Amethyst 96’. Four combinations of thrips and mite numbers were studied: thrips alone, mites alone, and two densities of thrips and mites together. We compared population numbers after 4 weeks. Overall, mite numbers increased more rapidly than thrips did, but both species increased more rapidly on impatiens than on ivy geraniums. Between impatiens cultivars, thrips and mites increased more slowly on ‘Cajun Carmine’ (i.e., it was more resistant) than on ‘Impulse Orange’. On ivy geraniums, spider mites increased more slowly on ‘Sybil Holmes’ than on ‘Amethyst 96’ but the reverse was the case for thrips. Regardless of plant species or cultivar, thrips had a strong negative effect on spider mites whenever they co‐occurred, suppressing mite population growth by around 50% compared to when mites were alone. However, the effect of spider mites on western flower thrips depended on the quality of the plant species. On impatiens, thrips co‐occurring with spider mites increased slightly more than thrips alone did, while on ivy geranium mites had a small negative effect on thrips. Contrary to expectations, thrips had a larger negative impact on spider mites on plants that were more susceptible to thrips than they did on plants more resistant to thrips. We suggest that host plants mediate the interaction between an omnivore and its herbivorous prey not only by altering individual diet choice but by changing the relative population dynamics of each species.     

Absolute estimates of larval populations of culicid mosquitoes: comparison of 'capture-recapture', 'removal' and 'dipping' methods

• 1 Four sets of experiments were devised to evaluate the absolute size of aedine larval populations. Three methods were used and compared: ‘capture-recapture’, ‘removal’ and ‘dipping’ methods.
• 2 The results show that ‘dipping’ gives estimates of population size similar to those obtained with the two other methods, providing that a strict procedure is followed.
• 3 Since the ‘dipping’ technique is particularly easy, the results offer new possibilities for the study of population dynamics in Culicidae.

     

Comparative demographics of a Hawaiian forest bird community

Estimates of demographic parameters such as survival and reproductive success are critical for guiding management efforts focused on species of conservation concern. Unfortunately, reliable demographic parameters are difficult to obtain for any species, but especially for rare or endangered species. Here we derived estimates of adult survival and recruitment in a community of Hawaiian forest birds, including eight native species (of which three are endangered) and two introduced species at Hakalau Forest National Wildlife Refuge, Hawai?i. Integrated population models (IPM) were used to link mark–recapture data (1994–1999) with long‐term population surveys (1987–2008). To our knowledge, this is the first time that IPM have been used to characterize demographic parameters of a whole avian community, and provides important insights into the life history strategies of the community. The demographic data were used to test two hypotheses: 1) arthropod specialists, such as the ‘Akiapōlā‘au Hemignathus munroi, are ‘slower’ species characterized by a greater relative contribution of adult survival to population growth, i.e. lower fecundity and increased adult survival; and 2) a species’ susceptibility to environmental change, as reflected by its conservation status, can be predicted by its life history traits. We found that all species were characterized by a similar population growth rate around one, independently of conservation status, origin (native vs non‐native), feeding guild, or life history strategy (as measured by ‘slowness’), which suggested that the community had reached an equilibrium. However, such stable dynamics were achieved differently across feeding guilds, as demonstrated by a significant increase of adult survival and a significant decrease of recruitment along a gradient of increased insectivory, in support of hypothesis 1. Supporting our second hypothesis, we found that slower species were more vulnerable species at the global scale than faster ones. The possible causes and conservation implications of these patterns are discussed.     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

Maximum-likelihood estimation of admixture proportions from genetic data

For an admixed population, an important question is how much genetic contribution comes from each parental population. Several methods have been developed to estimate such admixture proportions, using data on genetic markers sampled from parental and admixed populations. In this study, I propose a likelihood method to estimate jointly the admixture proportions, the genetic drift that occurred to the admixed population and each parental population during the period between the hybridization and sampling events, and the genetic drift in each ancestral population within the interval between their split and hybridization. The results from extensive simulations using various combinations of relevant parameter values show that in general much more accurate and precise estimates of admixture proportions are obtained from the likelihood method than from previous methods. The likelihood method also yields reasonable estimates of genetic drift that occurred to each population, which translate into relative effective sizes (N(e)) or absolute average N(e)'s if the times when the relevant events (such as population split, admixture, and sampling) occurred are known. The proposed likelihood method also has features such as relatively low computational requirement compared with previous ones, flexibility for admixture models, and marker types. In particular, it allows for missing data from a contributing parental population. The method is applied to a human data set and a wolflike canids data set, and the results obtained are discussed in comparison with those from other estimators and from previous studies.     

Spatial and temporal variability of aquatic habitat use by amphibians in a hydrologically modified landscape

1. Habitat loss is a major driver of biodiversity decline worldwide. Temporary waterbodies are especially vulnerable because they are sensitive both to human impact and to climatic variations. Pond‐breeding amphibians are often dependent on temporary waterbodies for their reproduction, and hence are sensitive to loss of temporary ponds. 2. Here we present the results of a 5‐year study regarding the use of temporary aquatic habitats by amphibians in a hydrologically modified area of Eastern Europe (Romania). The annual number of aquatic habitats varied between 30 and ～120. Each aquatic habitat was characterised by a number of variables such as: ‘type’ (pond, drainage ditch and archaeological ditch), ‘hydroperiod’ (number of weeks the ponds were filled in a given year), ‘depth’ (cm), ‘area’ (m²) and the density of predatory insects (‘predation’). The turnover rate for each amphibian species for each wetland was calculated based on the pond occupancy. 3. Eight amphibian species were recorded from the aquatic habitats. Hydroperiod was the most important variable, positively influencing wetland use by amphibians and their reproductive success. Most species preferred drainage ditches for reproduction, and the reproductive success was highest in this habitat type every year. For most of the species, the local extinction rate was higher than the colonisation rate in the first 4 years, but the situation reversed in the last year of the study when wetland use by amphibians sharply increased because of high rainfall. 4. This study confirms the importance for amphibians of maintaining and managing aquatic habitat diversity at small spatial scales. Man‐made aquatic habitats such as drainage ditches may be important habitats for amphibians, and this should be considered in restoration activities.     

Sex‐related variation in migration phenology in relation to sexual dimorphism: a test of competing hypotheses for the evolution of protandry

Timing of arrival/emergence to the breeding grounds is under contrasting natural and sexual selection pressures. Because of differences in sex roles and physiology, the balance between these pressures on either sex may differ, leading to earlier male (protandry) or female (protogyny) arrival. We test several competing hypotheses for the evolution of protandry using migration data for 22 bird species, including for the first time several monochromatic ones where sexual selection is supposedly less intense. Across species, protandry positively covaried with sexual size dimorphism but not with dichromatism. Within species, there was weak evidence that males migrate earlier because, being larger, they are less susceptible to adverse conditions. Our results do not support the ‘rank advantage’ and the ‘differential susceptibility’ hypotheses, nor the ‘mate opportunity’ hypothesis, which predicts covariation of protandry with dichromatism. Conversely, they are compatible with ‘mate choice’ arguments, whereby females use condition‐dependent arrival date to assess mate quality.     

Turnover patterns in fish versus macroinvertebrates — implications for conservation planning

Spatial patterns in taxonomic richness and turnover for fish and aquatic macroinvertebrates are compared to assess the relative usefulness of each taxonomic group in mapping biodiversity patterns. Fish and aquatic macroinvertebrate species data for sites down the longitudinal axes of nine rivers in four provinces along the eastern side of South Africa were analysed. Fish and aquatic macroinvertebrate data from previous studies and recent river surveys were used in analyses of species richness and turnover. Fish proved to be not useful for mapping biodiversity patterns, as measured by turnover, whereas aquatic macroinvertebrate species patterns exhibited predictable patterns of turnover with downstream distance. Average turnover rates could be decomposed into turnover of common (‘core’) species, which were accelerated by presence of rare and narrow-range species. Disruptions to the river continuum impacted on the rate of turnover. Consistent with other research on South African rivers, aquatic macroinvertebrate communities could be grouped into upland versus lowland assemblages, and also be defined by longitudinal zones. Fish biodiversity patterns should be viewed at a riverscape scale, whereas macroinvertebrate patterns are more easily discerned at a segment-reach scale, and applied to reflect connectivity and environmental gradients respectively.     

Collision mortality has no discernible effect on population trends of North American birds

Avian biodiversity is threatened by numerous anthropogenic factors and migratory species are especially at risk. Migrating birds frequently collide with manmade structures and such losses are believed to represent the majority of anthropogenic mortality for North American birds. However, estimates of total collision mortality range across several orders of magnitude and effects on population dynamics remain unknown. Herein, we develop a novel method to assess relative vulnerability to anthropogenic threats, which we demonstrate using 243,103 collision records from 188 species of eastern North American landbirds. After correcting mortality estimates for variation attributable to population size and geographic overlap with potential collision structures, we found that per capita vulnerability to collision with buildings and towers varied over more than four orders of magnitude among species. Species that migrate long distances or at night were much more likely to be killed by collisions than year-round residents or diurnal migrants. However, there was no correlation between relative collision mortality and long-term population trends for these same species. Thus, although millions of North American birds are killed annually by collisions with manmade structures, this source of mortality has no discernible effect on populations.     

Estimation of nektonic insect populations

SUMMARY 1. A water column sampler is described for obtaining absolute population estimates of nektonic insects in shallow waters.
2. Relative population estimates were obtained for Corixidae (Hemip-tera) and Buenoa (Hemiptera: Notonectidae) using a standardized sweep net procedure and compared to absolute estimates from column samples. These two types of estimates were highly correlated among lakes.
3. Simultaneous prediction and tolerance intervals for predictions from linear regressions indicated that reliable absolute population estimates generally cannot be expected from relative estimates     

Decision analysis for the planning and assessment of ex situ management: An application to the endangered mahogany glider

Ex situ (‘off-site’) management refers to keeping species in artificial conditions away from their natural habitat and includes captive breeding facilities, botanical gardens and seed banks. There is scope for ex situ programmes to be more commonly used for supplementing or establishing wild populations. However, undertaking ex situ management comes with risks, costs and uncertainties, which must be assessed in the context of available in situ (‘on-site’) management options. The PACES (Planning and Assessment for Conservation through Ex situ management) tool tailors the principles of structured decision-making to the specific problem of assessing and comparing ex situ and in situ management options. We applied the PACES tool to the mahogany glider (Petaurus gracilis), a threatened arboreal marsupial endemic to north Queensland, Australia. Through an expert elicitation process, we predicted the likely benefits of an ex situ and two in situ management options, as compared to a baseline ‘do-nothing’ scenario. The ‘in situ plus’ alternative (where extra resources are dedicated to in situ management) was predicted to result in the largest population increase according to the participants' best estimates. However, this benefit came at a much larger cost than the ex situ alternative, and without the benefit of an ex situ insurance population. The PACES tool assessment allowed the Mahogany Glider Recovery Team to document and plan the financial costs, risks and benefits of potential future management options for the mahogany glider, laying a transparent basis for future assessment and decision-making.     

Screening effects in risk studies of thyroid cancer after the Chernobyl accident

In this article scenarios have been developed, which simulate screening effects in ecological and cohort studies of thyroid cancer incidence among Ukrainians, whose thyroids have been exposed to ¹³¹I in the aftermath of the Chernobyl accident. If possible, the scenarios were based on directly observed data, such as the population size, dose distributions and thyroid cancer cases. Two scenarios were considered where the screening effect on baseline cases is either equal to or larger than that of radiation-related thyroid cancer cases. For ecological studies in settlements with more than ten measurements of the ¹³¹I activity in the human thyroid in May–June 1986, the screening bias appeared small (<19%) for all risk quantities. In the cohort studies, the excess absolute risk per dose was larger by a factor of 4 than in the general population. For an equal screening effect on baseline and radiation-related cancer (Scenario 1) the excess relative risk was about the same as in the general population. However, a differential screening effect (Scenario 2) produced a risk smaller by a factor of 2.5. A comparison with first results of the Ukrainian–US-American cohort study did not give any indication that a differential screening effect has a marked influence on the risk estimates. The differences in the risk estimates from ecological studies and cohort studies were explained by the different screening patterns in the general population and in the much smaller cohort. The present investigations are characterized by dose estimates for many settlements which are very weakly correlated with screening, the confounding variable. The results show that under these conditions ecological studies may provide risk estimates with an acceptable bias.     

High levels of genetic variation in natural populations of marine lower invertebrates

The predictions of neutralist and selectionist hypotheses have been tested many times in the past, but mostly using data only from organisms such as vertebrates, with generally low to average heterozygosities. The more recent discovery of particularly high levels of genetic variation in marine sponges and coelenterates provides an opportunity to use data from such species to contribute further to the understanding of the determinants of heterozygosity in natural populations. Therefore, 23 species of sponges and coelenterates from temperate, tropical and boreal waters were analysed by gel electrophoresis for an average of 14.3 enzyme loci per species. Mean heterozygosity values for each species were unusually high, ranging between 0.106 and 0.401. The means and variances of the heterozygosity estimates showed reasonable correlation with neutralist predictions (with both the stepwise mutation and the infinite alleles models). Population sizes were generally difficult to estimate with any confidence, but, for one sponge species for which this was possible, levels of heterozygosity again were similar to neutralist predictions, although the same was not apparently true for three species of sea anemone. No differences were found between heterozygosity levels of tropical and temperate species of sponges and coelenterates, thus apparently contradicting the selectionist ‘trophic resource stability’ and ‘temporal environmental variation’ hypotheses. Conversely, however, the consistently high levels of genetic variation found in coelenterates and sponges may be argued to be related to common biological characteristics, such as sessile life, great evolutionary ‘age’, limited ability to disperse and probable low homoeostatic capability. Our results seem, overall, to agree well with neutralist expectations for species with large, stable population sizes. Also, the mean heterozygosities, their variances and the observed and expected proportions of polymorphic loci seem to fit well with predictions based on the neutralist hypothesis. However, the selectionist ‘environmental grain’ and the ‘shifting balance’ hypotheses fit the data equally well. As with much earlier work, the problems in distinguishing between the various predictions of selectionist or neutralist ideas make it both difficult and unwise to draw definite conclusions.     

Evaluating the potential of night spotlighting as a method for assessing species composition and brown trout abundance: a comparison with electrofishing in small streams

Direct counts of fish obtained by night spotlighting were compared with species composition and population estimates obtained from three-pass electrofishing obtained across 29 sites along small clear streams in the Otago region of New Zealand. The influence of habitat variables on the relative efficiency of each method was also examined. The same seven species of fishes were identified by both methods. Juvenile brown trout Salmo trutta were the only species present in sufficient numbers to allow comparison of abundance estimates using the two methods. A total of 777 brown trout were counted by spotlight and 803 brown trout were caught using electrofishing. Estimates of abundance obtained by spotlighting reflected population estimates obtained by three-pass electrofishing across most habitats. Electrofishing produced higher population estimates relative to spotlighting in fast-flowing turbulent riffle habitats, whereas counts obtained by spotlighting tended to be higher relative to electrofishing in slow-flowing pool habitats. The results suggest that spotlighting is an effective method for assessing fish composition and brown trout abundance in small clear water streams, although the extremes of water velocity may influence efficiency of both spotlighting and electrofishing.     

基于连续统去除法的水生植物提取及其时空变化分析——以官厅水库库区为例

光谱特征变量的筛选作为水生植物识别的重要手段之一, 在水生植物种类识别研究中应用广泛。该研究将实测光谱特征提取与多时相Landsat 8 OLI影像数据分析相结合, 找到一种有效识别不同种类水生植物的特征变量。在水生植物反射光谱特征分析中引入矿质分析中普遍使用的连续统去除法, 对光谱重采样结果作连续统去除处理后提取光谱吸收深度特征。采用单因素方差分析法对比7个光谱重采样波段和3个连续统去除吸收深度敏感波段, 发现经连续统去除处理的短波红外1波段(SWIR1CR)对于不同类型的水生植物区分效果最佳。将连续统去除法应用到遥感影像处理上, 发现SWIR1CR波段能较好区分沉水植物和挺水植物; 结合影像归一化植被指数和SWIR1CR波段可较好区分三类水生植物。结合特征波段筛选结果采用支持向量机分类方法, 得到水生植物的分类结果精度为86.33%, 对比全生长期12期影像提取的水生植物分布图, 发现水生植物主要分布于官厅水库库区南北岸浅水区, 水生植物面积最大时约占库区总面积的35.13%; 其中沉水植物年内生长分布变化幅度较大, 6月上旬开始迅速生长; 10月份水生植物开始衰减; 11月份水生植物占库区面积的20%, 沉水、浮水植物大幅衰减消失。     

Extraction of aquatic plants based on continuous removal method and analysis of its temporal and spatial changes—A case study of Guanting Reservoir

光谱特征变量的筛选作为水生植物识别的重要手段之一, 在水生植物种类识别研究中应用广泛。该研究将实测光谱特征提取与多时相Landsat 8 OLI影像数据分析相结合, 找到一种有效识别不同种类水生植物的特征变量。在水生植物反射光谱特征分析中引入矿质分析中普遍使用的连续统去除法, 对光谱重采样结果作连续统去除处理后提取光谱吸收深度特征。采用单因素方差分析法对比7个光谱重采样波段和3个连续统去除吸收深度敏感波段, 发现经连续统去除处理的短波红外1波段(SWIR1CR)对于不同类型的水生植物区分效果最佳。将连续统去除法应用到遥感影像处理上, 发现SWIR1CR波段能较好区分沉水植物和挺水植物; 结合影像归一化植被指数和SWIR1CR波段可较好区分三类水生植物。结合特征波段筛选结果采用支持向量机分类方法, 得到水生植物的分类结果精度为86.33%, 对比全生长期12期影像提取的水生植物分布图, 发现水生植物主要分布于官厅水库库区南北岸浅水区, 水生植物面积最大时约占库区总面积的35.13%; 其中沉水植物年内生长分布变化幅度较大, 6月上旬开始迅速生长; 10月份水生植物开始衰减; 11月份水生植物占库区面积的20%, 沉水、浮水植物大幅衰减消失。     

Effects of errors in range maps on estimates of historical species richness of mammals in Canadian national parks

Aim Tests for faunal relaxation in reserves, particularly for mammals, have relied on comparisons of current species richness with estimates of species richness derived from historical range maps. However, any range map reflects the extent of occurrence of species and not necessarily the area of occupancy. Thus, estimates of historical species richness might be prone to error introduced by ‘false positives’, that is, a species might be considered to have been present in locations where it actually was not. The effect of such ‘false positives’ could bias statistical tests of faunal relaxation to type I error, and result in estimates of the extent of faunal relaxation in reserves greater than was actually the case. We evaluated the potential for errors in historical range maps to generate inflated estimates of historical species richness of mammals at sites that are reserves today. Location Canadian national parks in the Canadian portion of the Alleghenian‐‐Illinoian mammal province in south‐eastern Canada (the maritime region and parts of southern Québec, Ontario and Manitoba). Methods The effect of varying levels of error in range maps on estimates of historical species richness was tested using geographical information systems (GIS)‐based statistical sampling of simulated historical ranges. Species’ areas of occupancy were simulated to be only 25%, 75% and 95% of published historical species ranges. For each reserve, estimates of historical species richness from these simulated species ranges were then compared with similar, previously published estimates of richness based on published historical species ranges. Results Previous estimates of historical species richness for reserves were inversely and linearly related to the degree of inaccuracy of species ranges. If species ranges were, on average, 5% smaller than the accepted ranges, then estimates of historical species richness agreed with previous estimates in c. 90% of cases. However, if historical ranges were, on average, 25% smaller than those used in previous analyses, then previous historical estimates of species richness may be overestimates in c. 40% of cases. Main conclusions Estimates of the extent of faunal relaxation in reserves that use historical range maps to quantify past species richness appear to be sensitive to even small errors in the degree to which range maps may overestimate ‘area of occupancy’.     

Do plant communities exist? Evidence from scaling‐up local species‐area relations to the regional level

Abstract. One long tradition in ecology is that discrete communities exist, at least in the sense that there are areas of relatively uniform vegetation, with more rapid change in species composition between them. The alternative extreme view is the Self‐similarity concept – that similar community variation occurs at all spatial scales. We test between these two by calculating species‐area curves within areas of vegetation that are as uniform as can be found, and then extrapolating the within‐community variation to much larger areas, that will contain many ‘communities’. Using the Arrhenius species‐area model, the extrapolations are remarkably close to the observed number of species at the regional/country level. We conclude that the type of heterogeneity that occurs within ‘homogeneous’ communities is sufficient to explain species richness at much larger scales. Therefore, whilst we can speak of ‘communities’ for convenience, the variation that certainly exists at the ‘community’ level can be seen as only a larger‐scale manifestation of micro‐habitat variation.