New species records and changes in abundance of waterfowl in northwest Greenland

Breeding populations of Nearctic and Palearctic waterfowl have undergone significant changes in abundance and distribution over the past 50 years. The Avanersuaq District in northwest Greenland is home to an assemblage of waterfowl from both geographic areas; however, minimal historic or current information is available on species abundance. In 2008 and 2009, we conducted field surveys in Greenland from 76.00° to 77.35°N for breeding and non-breeding waterfowl and have collected anecdotal field notes of avian observations over a 20-year period (1993–2012). During these periods, we documented the first observation of a Ross’s goose (Chen rossii) and the first confirmed breeding by lesser snow geese (Chen caerulescens caerulescens) in Greenland. Northern pintails (Anas acuta) were observed for the first time in northwest Greenland, and a previously unknown breeding location for brent geese (Branta bernicla hrota) was also identified. Local populations of greater snow (C. c.) and Canada geese (B. canadensis) have increased in size. The Booth Sound and Drown Bay wetland areas and many islands throughout the Avanersuaq District were identified as critical habitat for both breeding and non-breeding waterfowl. Further increases in waterfowl abundance, including more frequent rare and new visitors, are likely in the study area as breeding populations further south continue to increase and an ameliorating climate allows for a longer breeding season. These results will prove useful as a baseline for comparisons with future surveys.     

长江口水域鱼卵、仔稚鱼种类组成和数量的分布与变化

根据2005年4和11月、2006年4和9月在长江河口水域进行的鱼卵、仔稚鱼种类和数量调查,并结合1990年9月和1991年3月的历史数据,对该水域的鱼卵、仔稚鱼群落结构的种类组成和数量的季节变化作了研究,其结果共发现鱼卵、仔稚鱼36种(类),以海洋鱼类种类最多。秋季航次鱼卵、仔稚鱼的平均种类数和丰度均高于春季。河口咸淡水区鱼卵总数显著高于淡水区,而仔稚鱼总数略低于淡水区。与1990—1991年数据相比,2005—2006年春、秋季的鱼卵和仔稚鱼丰度均有所增加。1990、2006年秋季(9月)鱼卵、仔稚鱼种类组成差异较大,特别是翘嘴红鲌和太湖新银鱼丰度差异较大。这些都说明近20年来,长江河口水域鱼卵、仔稚鱼种类组成和数量均发生了明显的改变。     

Optimal design of butterfly occupancy surveys and testing if occupancy converts to abundance for sparse populations

Occupancy has several important advantages over abundance methods and may be the best choice for monitoring sparse populations. Here we use simulations to evaluate competing designs (number of sites vs. number of surveys) for occupancy monitoring, with emphasis on sparse populations of the endangered Karner blue butterfly (Lycaeides melissa samuelis Nabokov). Because conservation planning is usually abundance-based, we also ask whether detection/non-detection data may reliably convert to abundance, hypothesizing that occupancy provides a more dependable shortcut when populations are sparse. Count-index and distance sampling were conducted across 50 habitat patches containing variably sparse Karner blue populations. We used occupancy-detection model estimates as simulation inputs to evaluate primary replication tradeoffs, and used peak counts and population densities to evaluate the occupancy-abundance relationship. Detection probability and therefore optimal design of occupancy monitoring was strongly temperature dependent. Assuming a quality threshold of 0.075 root-mean square error for the occupancy estimator, the minimum allowable effort was 360 (40 sites?×?9 surveys) for spring generation and 200 (20 sites?×?10 surveys) for summer generation. A mixture model abundance estimator for repeated detection/non-detection data was biased low for high-density and low-density populations, suggesting that occupancy may not provide a reliable shortcut in abundance-based conservation planning for sparse butterfly populations.     

Estimating species trees from unrooted gene trees

In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.     

Estimating surface growth rates from changes in curvature

The shape of a biological surface may be regarded as an observable. Here a method is given for deriving growth parameters from the change in shape of such a surface. Isotropy is assumed, and implies a conformal relationship between initial and final surfaces. One further assumption is necessary to specify the growth regime: in the case of radially symmetric surfaces, this is that the process is similarly symmetric; in the general case the assumption is that the Dirichlet integral of scale factors is miminized.     

Estimating bacterial diversity from clone libraries with flat rank abundance distributions

There are a number of parametric and non-parametric methods for estimating diversity. However all such methods employ either the proportional abundance of the most abundant taxon in a sample or require that a specific taxon is sampled more than once. Consequently, the available methods for estimating diversity cannot be applied to samples consisting entirely of singletons, which might be characteristic of some hyperdiverse communities. Here we present a non-parametric method that estimates the probability that a given number of unique taxa would be sampled from a community with a particular diversity. We have applied this approach to a well known data set of 100 unique clones from a sample of Amazonian soil (Borneman and Triplett (1997) Appl Environ Microbiol 63: 2647-2653) and determine the probability that this observation would be made from an environment of a given diversity. On this basis we can state this observation would be very unlikely (P = 0.006) if the soil diversity was less than 10(3), and quite unlikely (P = 0.6) if the diversity was less than 10(4), and probable (P = 0.95) if the diversity was about 10(5). There are essentially no contestable assumptions in our method. Thus we are able to offer almost unequivocal evidence that the bacterial diversity, of at least soils, is very large and a method that may be used to interpret samples consisting entirely of singletons from other hyperdiverse communities.     

Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness

Declines in species richness due to fertilization are typically rapid and associated with increases in aboveground production. However, in a long-term experiment examining the impacts of fertilization in an early successional community, we found it took 14 years for plant species richness to significantly decline in fertilized plots, despite fertilization causing a rapid increase in aboveground production. To determine what accounted for this lag in the species richness response, we examined several potential mechanisms. We found evidence suggesting the abundance of one functional group—tall species with long-distance (runner) clonality—drove changes in species richness, and we found little support for other mechanisms. Tall runner species initially increased in abundance due to fertilization, then declined dramatically and were not abundant again until later in the experiment, when species richness and the combined biomass of all other functional groups (non-tall runner) declined. Over 86 % of the species found throughout the course of our study are non-tall runner, and there is a strong negative relationship between non-tall runner and tall runner biomass. We therefore suggest that declines in species richness in the fertilized treatment are due to high tall runner abundance that decreases the abundance and richness of non-tall runner species. By identifying the functional group that drives declines in richness due to fertilization, our results help to elucidate how fertilization decreases plant richness and also suggest that declines in richness due to fertilization can be lessened by controlling the abundance of species with a tall runner growth form.     

Assessment of species diversity from species abundance distributions at different localities

We show how the spatial structure of species diversity can be analyzed using the correlation between the log abundances of the species in the communities, assuming that two communities at different localities can be described by a bivariate lognormal species abundance distribution. A useful property of this approach is that the log abundances of the species at two localities can be considered as samples from a bivariate normal distribution defined by only five parameters. The variances and the correlation can be estimated by maximum likelihood methods even if there is no information about the sampling intensity and the number of unobserved species. This method also enables estimation of over-dispersion in the sampling relative to a Poisson distribution that allows sampling adjustment of the estimate of β-diversity. Furthermore, we also obtain a partitioning of species diversity into additive components of α-, β- and γ-diversity. For instance, if the correlation between the log abundances of the species is close to one, the same species will be common and rare in the two communities and the β-diversity will be low. We illustrate this approach by analysing similarities of communities of rare and endangered species of oak-living beetles in south-eastern Norway. The number of recorded species was estimated to be only 48.1% of the total number of species actually present in these communities. The correlations among communities dropped rather quickly with distance with a scaling of order 200 km. This illustrates large spatial heterogeneity in species composition, which should be accounted for in the design of schemes of such devices for assessing species diversity in these habitat-types.     

Habitat factors affecting site occupancy and relative abundance of four-horned antelope

The four-horned antelope is endemic to the Indian sub-continent. It was formerly distributed widely in deciduous forests throughout its range, but the current distributional patterns of this low-density species are largely unknown and conservation efforts are hampered by the lack of information on species–habitat relationships. We investigated the habitat factors influencing four-horned antelope occurrence and abundance in Bandipur National Park, an important four-horned antelope conservation site in India. Detection/non-detection data, collected under a systematic sampling framework, were used to test a priori hypotheses incorporating covariates believed to influence occurrence and abundance. The best fitting models for four-horned antelope occurrence and relative abundance reveal that the tree-savanna deciduous habitat sub-type, characterized by relatively open habitats with a lower tree density and a high degree of deciduousness, is most preferred by the species. Four-horned antelope conservation efforts in Bandipur National Park and other reserves should be focused on areas typified by tree-savanna habitats. Four-horned antelope occurrence was negatively related to the alien weed Lantana camara . The prolific spread of this weed in Indian deciduous forests is a likely threat.     

Relative changes in krill abundance inferred from Antarctic fur seal

Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ(13)C) and nitrogen (δ(15)N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ(15)N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ(15)N values indicated decreasing krill availability. This is agreement with direct observation for the past ～30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators.     

Extinction, colonization, and species occupancy in tidepool fishes

Despite the increasing sophistication of ecological models with respect to the size and spatial arrangement of habitat, there is relatively little empirical documentation of how species dynamics change as a function of habitat size and the fraction of habitat occupied. In an assemblage of tidepool fishes, I used maximum-likelihood estimation to test whether models which included habitat size provided a better fit to empirical data on extinction and colonization probabilities than models that assumed constant probabilities over all habitats. I found species differences in how extinction and colonization probabilities scaled with habitat size (and hence local population size). However, there was little evidence for a relationship between extinction and colonization probabilities and the fraction of occupied tidepools, as assumed in simple metapopulation models. Instead, colonization and extinction were independent of the fraction of occupied tidepools, favoring a MacArthur-Wilson island-mainland model. When I incorporated declines in extinction probability with tidepool volume in a simple simulation model, I found that predicted occupancy could change greatly, especially when colonization was low. However, the predicted fraction of occupied patches in the simulation model changed little when I incorporated the range of values reported here for extinction and colonization and the rate at which they scale with habitat size. Quantifying extinction and colonization patterns of natural populations is fundamental to understanding how species are distributed spatially and whether metapopulation models of species occupancy provide explanatory power for field populations. Received: 14 March 1997 / Accepted: 21 September 1997     

Clonal growth and plant species abundance

Background and Aims

Both regional and local plant abundances are driven by species'' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden.

Methods

Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates.

Key Results

After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level.

Conclusions

Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden performance parameters provide a practical approach to assessing the roles of clonal growth morphological traits (and LHS traits) for large sets of species.     

Modeling species dispersal with occupancy urn models

Models for species dispersal make various simplifications to facilitate analysis, such as ignoring spatial correlations or assuming equal probability of colonization among all sites within a dispersal neighborhood. Here we introduce a variation of the basic contact process (BCP) which allows us to separate the number of offspring produced from the neighborhood size, which are confounded in the original BCP. We then use classical results arising from probability models involving placing balls in urns to study our modified BCP, obtaining bounds for the critical value of the survival probability needed for the population to persist. We also use the probability urn calculations with a local-dispersal mean-field approximation to estimate equilibrium population density. These methods are able to include features such as unequal dispersal probabilities to different sites in the neighborhood, e.g., as would arise when dispersers have a fixed rate of mortality per distance traveled from the parent site. We also show how urn models allow one to generalize these results to two species competing for space.     

On plotting species abundance distributions

1. There has been a revival of interest in species abundance distribution (SAD) models, stimulated by the claim that the log-normal distribution gave an underestimate of the observed numbers of rare species in species-rich assemblages. This led to the development of the neutral Zero Sum Multinomial distribution (ZSM) to better fit the observed data. 2. Yet plots of SADs, purportedly of the same data, showed differences in frequencies of species and of statistical fits to the ZSM and log-normal models due to the use of different binning methods. 3. We plot six different binning methods for the Barro Colorado Island (BCI) tropical tree data. The appearances of the curves are very different for the different binning methods. Consequently, the fits to different models may vary depending on the binning system used. 4. There is no agreed binning method for SAD plots. Our analysis suggests that a simple doubling of the number of individuals per species in each bin is perhaps the most practical one for illustrative purposes. Alternatively rank-abundance plots should be used. 5. For fitting and testing models exact methods have been developed and application of these does not require binning of data. Errors are introduced unnecessarily if data are binned before testing goodness-of-fit to models.     

Gap-crossing movements predict species occupancy in Amazonian forest fragments

In fragmented landscapes, species persistence within isolated habitat patches is governed by a myriad of species life‐history, habitat patch and landscape characteristics. We investigated the inter‐specific variation in non‐forest gap‐crossing abilities of an entire tropical forest‐dependent avifauna. We then related this measure of dispersal ability to species life‐history characteristics and occupancy data from 31 variable‐sized forest patches sampled within the same fragmented forest landscape. A total of 5436 gap‐crossing movements of 231 forest‐dependent bird species were observed across ten linear forest gaps of varying widths, adjacent to large areas of undisturbed forest. Species persistence in isolated fragments was strongly linked to gap‐crossing ability. The most capable gap‐crossers were medium to large‐bodied species in the large insectivore, frugivore and granivore guilds, matching the most prevalent subset of species in small forest patches. However, some competent gap‐crossing species failed to occur in small patches, and minimum forest‐patch area requirements were more important in determining patch occupancy for these species. Narrow forest gaps (4–70 m) created by roads and power‐lines may become territory boundaries, thereby eliminating home‐range gap‐crossing movements for many forest species, but permit rarer dispersal events. Wider gaps (>70 m) may inhibit gap‐crossing behaviour for all but the most vagile species. Although patch size and quality may be the most important factors in structuring species assemblages in forest fragments, our results show that the degree of patch isolation and permeability of the surrounding matrix also explain which species can persist in forest isolates. Reducing the number and width of forest‐dividing gaps; maintaining and/or creating forest corridors and increasing matrix permeability through the creation and maintenance of ‘stepping‐stone’ structures will maximise the species retention in fragmented tropical forest landscapes.     

Estimating the uptake of traffic-derived NO2 from 15N abundance in Norway spruce needles

The ¹⁵N ratio of nitrogen oxides (NO_x) emitted from vehicles, measured in the air adjacent to a highway in the Swiss Middle Land, was very high [δ¹⁵N(NO₂) = +5.7‰]. This high ¹⁵N abundance was used to estimate long-term NO₂ dry deposition into a forest ecosystem by measuring δ¹⁵N in the needles and the soil of potted and autochthonous spruce trees [Picea abies (L.) Karst] exposed to NO₂ in a transect orthogonal to the highway. δ¹⁵N in the current-year needles of potted trees was 2.0‰ higher than that of the control after 4 months of exposure close to the highway, suggesting a 25% contribution to the N-nutrition of these needles. Needle fall into the pots was prevented by grids placed above the soil, while the continuous decomposition of needle litter below the autochthonous trees over previous years has increased δ¹⁵N values in the soil, resulting in parallel gradients of δ¹⁵N in soil and needles with distance from the highway. Estimates of NO₂ uptake into needles obtained from the δ¹⁵N data were significantly correlated with the inputs calculated with a shoot gas exchange model based on a parameterisation widely used in deposition modelling. Therefore, we provide an indication of estimated N inputs to forest ecosystems via dry deposition of NO₂ at the receptor level under field conditions. Received: 7 November 1997 / Accepted: 16 September 1998