Evaluating an icon of population persistence: the Devil's Hole pupfish

The Devil''s Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World''s most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000–20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360–2900 years (median 410–1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil''s Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.     

On the Bayesian estimation of a closed population size in the presence of heterogeneity and model uncertainty

Summary .   We consider the estimation of the size of a closed population, often of interest for wild animal populations, using a capture–recapture study. The estimate of the total population size can be very sensitive to the choice of model used to fit to the data. We consider a Bayesian approach, in which we consider all eight plausible models initially described by Otis et al. (1978, Wildlife Monographs 62, 1–135) within a single framework, including models containing an individual heterogeneity component. We show how we are able to obtain a model-averaged estimate of the total population, incorporating both parameter and model uncertainty. To illustrate the methodology we initially perform a simulation study and analyze two datasets where the population size is known, before considering a real example relating to a population of dolphins off northeast Scotland.     

Population size, weight distribution and food in a persistent population of the rare medicinal leech, Hirudo medicinalis

1. It is important for species recovery and conservation management projects to know the minimum viable population size for rare and endangered species, such as the medicinal leech, Hirudo medicinalis. Therefore, using a catch‐removal method, this study estimated every two years (1986, 1988, 1990, 1992) the total number of medicinal leeches in a tarn in the English Lake District, and the number of mature adults in the population. 2. Four samples were taken each year in June and July, when water temperatures exceeded 20 °C. Population size was estimated both by maximum likelihood and regression methods. All leeches were weighed alive and size groups were separated by polymodal frequency analysis. A small sample of the blood meal in each leech gut was taken before the leeches were returned to the tarn, and was used to estimate the proportion of mammalian and non‐mammalian blood in the meals. 3. Both methods of estimation produced similar values, increasing confidence in the population estimates. Values for the total population in June and July varied among years from 248 to 288, the maximum value being only 16% higher than the minimum. Values for the number of mature leeches varied from 48 to 58 (19–20% of the total population), and this was an estimate of the effective population size. 4. There were four size groups. The largest mature leeches (live weight >5 g) in group IV formed only 1% of the population, and the smallest (0.02–0.5 g) in group I 14–17%. Most leeches were in two overlapping groups of immature (64–67% of population) and mature (18%) leeches with size ranges of 0.4–3.4 g and 2.5–5 g respectively. The percentage of leeches in each size group was very consistent among years. Blood meals were found in 38–44% of the leeches in group I, 45–50% in group II, 70–75% in group III, and 100% in group IV, but mammalian blood was present only in larger mature leeches (>3.5 g). 5. Medicinal leeches were first detected in the tarn in 1980 and are still present in 2007, so the population has persisted for at least 27 years. Compared with minimum viable population sizes for other species, including many endangered species, values for this medicinal leech population are extremely low, but may be typical of some rare freshwater invertebrates in isolated habitats.     

A Predictive Bayesian Dose-Response Assessment for Evaluating the Toxicity of Carbon Nanotubes Relative to Crocidolite Using a Proposed Emergent Model

Carbon Nanotubes (CNTs) are a product of the nanotechnology revolution and show great promise in industrial applications. However, their relative toxicity is still not well understood and has drawn comparison to asbestos fibers due to their size and shape. In this study, a predictive Bayesian dose-response assessment was conducted with extremely limited initial dose-response data to compare the toxicity of long-fiber CNTs with that of crocidolite, an asbestos fiber associated with human mesothelioma. In the assessment, a new, theoretically derived emergent dose-response model was used and compared with the single-hit and multistage models. The multistage and emergent DRFs were selected for toxicity assessment based on two criteria: visual fit to several datasets, and a goodness-of-fit test using an available data-rich study with crocidolite. The predictive assessment supports previous concerns that long-fiber CNTs have toxicity comparable to crocidolite in intratracheal and intraperitoneal applications. Collection of further dose-response data on these materials is strongly recommended.     

Assessing the importance of artificial nest‐sites in the population dynamics of endangered Northern Aplomado Falcons Falco femoralis septentrionalis in South Texas using stochastic simulation models

Habitat availability might be the most important determinant of success for a species reintroduction programme, making investigation of the quality and quantity of habitat needed to produce self‐sustaining populations a research priority for reintroduction ecologists. We used a stochastic model of population dynamics to predict whether attempts to improve existing breeding territories using artificial nest platforms improved the population growth rate and persistence of a reintroduced population of Northern Aplomado Falcons Falco femoralis septentrionalis in South Texas. We further assessed whether the creation of new territories, i.e. conversion of entire areas to suitable habitat and not simply the erection of nest platforms, would lead to a subsequent increase in the nesting population. Our model was able to reproduce several characteristics of the wild population and predicted the number of breeding pairs per year strikingly well (R² = 0.97). Simulations revealed that the addition of nest platforms improved productivity such that the population would decline to extinction without them but is stable since their installation. Moreover, the model predicted that the increase in productivity due to nest platforms would cause the population to saturate available breeding territories, at which point the population would contain a moderate proportion of non‐territorial birds that could occupy territories if new ones become available. Population size would therefore be proportional to the increase in available territories. Our study demonstrates that artificial nest‐sites can be an effective tool for the management of reintroduced species.     

Model selection and parameter estimation for ion channel recordings with an application to the K + outward-rectifier in barley leaf

We present a statistical method, and its accompanying algorithms, for the selection of a mathematical model of the gating mechanism of an ion channel and for the estimation of the parameters of this model. The method assumes a hidden Markov model that incorporates filtering, colored noise and state-dependent white excess noise for the recorded data. The model selection and parameter estimation are performed via a Bayesian approach using Markov chain Monte Carlo. The method is illustrated by its application to single-channel recordings of the K⁺ outward-rectifier in barley leaf.Acknowledgement The authors thank Sake Vogelzang, Bert van Duijn and Bert de Boer for their helpful advice and useful comments and suggestions.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Coalescent-based estimation of population parameters when the number of demes changes over time

We expand a coalescent-based method that uses serially sampled genetic data from a subdivided population to incorporate changes to the number of demes and patterns of colonization. Often, when estimating population parameters or other parameters of interest from genetic data, the demographic structure and parameters are not constant over evolutionary time. In this paper, we develop a Bayesian Markov chain Monte Carlo method that allows for step changes in mutation, migration, and population sizes, as well as changing numbers of demes, where the times of these changes are also estimated. We show that in parameter ranges of interest, reliable estimates can often be obtained, including the historical times of parameter changes. However, posterior densities of migration rates can be quite diffuse and estimators somewhat biased, as reported by other authors.     

Evaluating the current condition of a threatened marine mammal population: Estimating northern sea otter (Enhydra lutris kenyoni) abundance in southwest Alaska

We estimated density and abundance of the threatened southwest Alaska distinct population segment of northern sea otters (Enhydra lutris kenyoni) in two management units. We conducted aerial surveys in Bristol Bay and South Alaska Peninsula management units in 2016, and modeled sea otter density and abundance with Bayesian hierarchical distance sampling models and spatial environmental covariates (depth, distance to shore, depth × distance to shore). Spatial environmental covariates substantially impacted sea otter group density in both management units, but effects sizes differed between the two management units. Abundance (9,733 otters, 95% CrI 6,412–17,819) and density (0.82 otters/km², 95% CrI 0.54–1.49) estimates for Bristol Bay indicated a moderate population size. In contrast, abundance (546 otters, 95% CrI 322–879) and density (0.06 otters/km², 95% CrI 0.03–0.09) estimates indicated a relatively low population size in South Alaska Peninsula. Overall, our results highlight the importance of accounting for the detection process in monitoring at-risk species to reduce the uncertainty associated with making conclusions about population declines.     

Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model

The role of past climatic change in shaping the distributions of tropical rain forest vertebrates is central to long-standing hypotheses about the legacy of the Quaternary ice ages. One approach to testing such hypotheses is to use genetic data to infer the demographic history of codistributed species. Population genetic theory that relates the structure of allelic genealogies to historical changes in effective population size can be used to detect a past history of demographic expansion or contraction. The fruit bats Cynopterus sphinx and C. brachyotis (Chiroptera: Pteropodidae) exhibit markedly different distribution patterns across the Indomalayan region and therefore represent an exemplary species pair to use for such tests. The purpose of this study was to test alternative hypotheses about historical patterns of demographic expansion and contraction in C. sphinx and C. brachyotis using a coalescent-based analysis of microsatellite variation. Specifically, we used a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters. The results revealed strong evidence for population contraction in both species. Evidence for a population contraction in C. brachyotis was expected on the basis of biogeographic considerations. However, similar evidence for population contraction in C. sphinx does not support the hypothesis that this species underwent a pronounced range expansion during the late Quaternary. Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale.     

Analysis of capture-recapture models with individual covariates using data augmentation

Summary .  I consider the analysis of capture–recapture models with individual covariates that influence detection probability. Bayesian analysis of the joint likelihood is carried out using a flexible data augmentation scheme that facilitates analysis by Markov chain Monte Carlo methods, and a simple and straightforward implementation in freely available software. This approach is applied to a study of meadow voles ( Microtus pennsylvanicus ) in which auxiliary data on a continuous covariate (body mass) are recorded, and it is thought that detection probability is related to body mass. In a second example, the model is applied to an aerial waterfowl survey in which a double-observer protocol is used. The fundamental unit of observation is the cluster of individual birds, and the size of the cluster (a discrete covariate) is used as a covariate on detection probability.     

Disentangling the effect of genes, the environment and chance on sex ratio variation in a wild bird population

Sex ratio theory proposes that the equal sex ratio typically observed in birds and mammals is the result of natural selection. However, in species with chromosomal sex determination, the same 1 : 1 sex ratio is expected under random Mendelian segregation. Here, we present an analysis of 14 years of sex ratio data for a population of song sparrows (Melospiza melodia) on Mandarte Island, at the nestling stage and at independence from parental care. We test for the presence of variance in sex ratio over and above the binomial variance expected under Mendelian segregation, and thereby quantify the potential for selection to shape sex ratio. Furthermore, if sex ratio variation is to be shaped by selection, we expect some of this extra-binomial variation to have a genetic basis. Despite ample statistical power, we find no evidence for the existence of either genetic or environmentally induced variation in sex ratio, in the nest or at independence. Instead, the sex ratio variation observed matches that expected under random Mendelian segregation. Using one of the best datasets of its kind, we conclude that female song sparrows do not, and perhaps cannot, adjust the sex of their offspring. We discuss the implications of this finding and make suggestions for future research.     

Transience in the humpback whale population of New Caledonia and implications for abundance estimation

A phenomenon of transience in the humpback whale population breeding in New Caledonia has been highlighted in recent analyses. We used these data to illustrate the risk of flawed inference when transience is not properly accounted for in abundance estimation of resident populations. Transients are commonly defined as individuals that pass through the sampling area once, i.e., have a null probability of being caught again, and therefore induce heterogeneity in the detection process. The presence of transients can lead to severe bias in the estimation of abundance and we demonstrate how to correct for this feature when estimating abundance of resident populations. In New Caledonia, very different conclusions about the number of resident whales in the southern lagoon between 1999 and 2005 are obtained when the abundance estimate accounts for the transient whales. Without correction, the estimates of the abundance were up to twice as high across all years compared to the estimates of the resident population when a correction for transients had been incorporated. Having reliable population estimates when assessing the status of endangered species is essential in documenting recovery and monitoring of population trends. Therefore, we encourage researchers to account for transients when reporting abundances of resident populations.     

Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia

Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.     

A Markov chain Monte Carlo strategy for sampling from the joint posterior distribution of pedigrees and population parameters under a Fisher-Wright model with partial selfing

A simple population genetic model is presented for a hermaphrodite annual species, allowing both selfing and outcrossing. Those male gametes (pollen) responsible for outcrossing are assumed to disperse much further than seeds. Under this model, the pedigree of a sample from a single locality is loop-free. A novel Markov chain Monte Carlo strategy is presented for sampling from the joint posterior distribution of the pedigree of such a sample and the parameters of the population genetic model (including the selfing rate) given the genotypes of the sampled individuals at unlinked marker loci. The computational costs of this Markov chain Monte Carlo strategy scale well with the number of individuals in the sample, and the number of marker loci, but increase exponentially with the age (time since colonisation from the source population) of the local population. Consequently, this strategy is particularly suited to situations where the sample has been collected from a population which is the result of a recent colonisation process.     

Spatial and temporal variation of genetic diversity and estimation of effective population sizes in Atlantic salmon (Salmo salar, L.) populations from Asturias (Northern Spain) using microsatellites

Rivers in Asturias (northern Spain) constitute the southern limit of the distribution of Atlantic salmon (Salmo salar L.) in Europe, a biological resource facing one of the more serious challenges for conservation today. In this work, eight microsatellite loci have been used to analyse samples collected in 1993 and 1999 from four Asturian rivers (Esva, Narcea, Sella, and Cares), obtaining information about the temporal and the spatial genetic variation in these populations and, in addition, estimations of their effective population sizes. The temporal analysis revealed a general decrease in all the estimated genetic variability parameters when samples from 1993 (mean A ₍₁₉₉₃₎ = 6.47, mean H _O(1993) = 0.472, mean H _E(1993) = 0.530) were compared with those obtained in 1999 (mean A ₍₁₉₉₉₎ = 6.16, mean H _O(1999) = 0.460, mean H _E(1999) = 0.490). This reduction was particularly notable for the case of the Esva river. Our results pointed to a pattern of spatial genetic differentiation inside the Asturian region (F _{ST (1993)} = 0.016 P < 0.01; F _{ST (1999)} = 0.023 P < 0.01). Using the standard Temporal Method we found estimates of N _e^{^} _(Esva) = 75.1 (33.2–267.2); N _e^{^} _(Cares) = 96.6 (40.0–507.5), N _e^{^} _(Sella) = 106.5 (39.1–9396.4) and N _e^{^} _(Narcea) = 113.9 (42.0–3693.3). The use of likelihood-based methods for the N _e^{^} estimations improved the results (smaller CIs) for the Esva and Cares rivers (N _e^{^} _(Esva) = 63.9 (32.3–165.3); N _e^{^} _(Cares) = 76.4 (38.8–202.0) using a Maximum likelihood approach) and suggested the presence of larger populations for the Sella and Narcea rivers (N _e^{^}≈200). These results showed that the Asturian Atlantic salmon populations (in particular Esva and Cares river populations) could be close to the conservation genetic borderline for avoiding inbreeding depression although we discuss some implications of the analysis of temporal genetic change in populations with overlapping generations.     

Past and future demographic dynamics of alpine species: limited genetic consequences despite dramatic range contraction in a plant from the Spanish Sierra Nevada

Anthropogenic global climate change is expected to cause severe range contractions among alpine plants. Alpine areas in the Mediterranean region are of special concern because of the high abundance of endemic species with narrow ranges. This study combined species distribution models, population structure analyses and Bayesian skyline plots to trace the past and future distribution and diversity of Linaria glacialis, an endangered narrow endemic species that inhabits summits of Sierra Nevada (Spain). The results showed that: (i) the habitat of this alpine‐Mediterranean species in Sierra Nevada suffered little changes during glacial and interglacial stages of late Quaternary; (ii) climatic oscillations in the last millennium (Medieval Warm Period and Little Ice Age) moderately affected the demographic trends of L. glacialis; (iii) future warming conditions will cause severe range contractions; and (iv) genetic diversity will not diminish at the same pace as the distribution range. As a consequence of the low population structure of this species, genetic impoverishment in the alpine zones of Sierra Nevada should be limited during range contraction. We conclude that maintenance of large effective population sizes via high mutation rates and high levels of gene flow may promote the resilience of alpine plant species when confronted with global warming.