Rediscovery of ‘lost’ treefrogs from the Oaxacan highlands of Mexico

The Oaxacan highlands of Mexico boast an exceptional diversity of stream-breeding treefrogs (Hylidae). Recent surveys in these regions have reported dramatic declines for entire stream-breeding communities, and many endemic species have not been seen in several decades and are feared to be extinct. In 2007 we conducted a rapid survey in two focal regions that were surveyed in 1970 and 2000; both prior to and subsequent to reported population declines. We report on extant populations of six species missing from recent surveys following declines, one of which (Plectrohyla thorectes) had not been seen in over 28 years and was feared to be extinct. We document new populations of Exerodonta abdivita, a species previously known only from its type locality and currently listed as data deficient. We make comparisons with historical records and note changes in species composition and abundance with recent work. Differences in species compositions among studies may reflect population declines and rebounds over relatively short periods. However, we argue that aspects of species natural history in combination with the variable nature of brief surveys may account for some of the observed differences, and are important factors to consider when inferring species declines.     

Patterns of Mass Mortality among Rocky Shore Invertebrates across 100 km of Northeastern Pacific Coastline

Mass mortalities in natural populations, particularly those that leave few survivors over large spatial areas, may cause long-term ecological perturbations. Yet mass mortalities may remain undocumented or poorly described due to challenges in responding rapidly to unforeseen events, scarcity of baseline data, and difficulties in quantifying rare or patchily distributed species, especially in remote or marine systems. Better chronicling the geographic pattern and intensity of mass mortalities is especially critical in the face of global changes predicted to alter regional disturbance regimes. Here, we couple replicated post-mortality surveys with preceding long-term surveys and historical data to describe a rapid and severe mass mortality of rocky shore invertebrates along the north-central California coast of the northeastern Pacific Ocean. In late August 2011, formerly abundant intertidal populations of the purple sea urchin (Strongylocentrotus purpuratus, a well-known ecosystem engineer), and the predatory six-armed sea star (Leptasterias sp.) were functionally extirpated from ~100 km of coastline. Other invertebrates, including the gumboot chiton (Cryptochiton stelleri) the ochre sea star (Pisaster ochraceus), and subtidal populations of purple sea urchins also exhibited elevated mortality. The pattern and extent of mortality suggest the potential for long-term population, community, and ecosystem consequences, recovery from which may depend on the different dispersal abilities of the affected species.     

Demographic parameters of sexes in an elusive insect: implications for monitoring methods

Estimating demographic parameters in rare species is challenging because of the low number of individuals and their cryptic behaviour. One way to address this challenge is to gather data from several regions or years through mark-release-recapture (MRR) and radio-tracking monitoring. However, the comparison of demographic estimates obtained using these methods has rarely been investigated. Using 5 years of intensive MRR and radio-tracking surveys of an elusive and endangered saproxylic insect, the hermit beetle (Osmoderma eremita), in two regions of France, we aimed to estimate population size at the adult stage for each sex separately and to assess differences in demographic parameter estimates between survey methods. We found that males were approximately three times more likely to be recaptured than females. Taking this into account, we determined that the sex ratio was male-biased in almost all populations, except in Malus trees, where it was female-biased. Temporal fluctuations of sex ratios were also detected in one region. The radio-tracking transmitter (450 mg) allowed only the largest individuals (>2 g) to be targeted. However, we found that, among non-equipped individuals, the larger males survived better than the smaller males. We also confirmed that transmitter-equipped individuals survived approximately 25 % better than non-equipped individuals. Extrapolating the estimates from radio-tracking surveys to the population scale may result in overly optimistic population projections. Our results revealed large temporal and spatial variations in population size and sex ratios. This knowledge is crucial for predicting the persistence of small populations in fragmented landscapes. This study also questioned the representativeness of radio-tracking surveys for insect species in estimating demographic parameters at the population scale.     

Availability bias in population survey of Northern Hudson Bay narwhal (Monodon monoceros)

Population estimates are important for the development of management plans of harvested species and thereby ultimately important for species sustainability. Aerial surveys are one of the methods used in preparing population estimates. For marine mammals, aerial population surveys require that animal biology is understood in order to account for availability bias. Availability bias in this case derives from animals that are invisible to the survey due to diving behavior. In order to understand diving behavior of the Northern Hudson Bay narwhal (Monodon monoceros), nine whales were tagged with satellite tracking devices in the Repulse Bay, Nunavut area in August 2006 (n = 5) and 2007 (n = 4). Of specific interest was time at depth of 0–2 m of water, the depth at which studies have shown that whales could be distinguished at the species level during an aerial survey. The proportion of time spent in 0–2 m of water can then be used to correct the population estimate from aerial survey. This research found that narwhals spent approximately 32 % of their time at the surface where they would be available to be seen by an aerial survey. This paper provides raw data that can be used to correct population survey estimates.     

Amplified fragment length polymorphism (AFLP) analysis of the genetic structure of the zebra mussel, Dreissena polymorpha, in the Mississippi River

1. We predicted that zebra mussel, Dreissena polymorpha (Pallas), genetic structure in the Mississippi River would follow a model of invasive species genetics, which predicts low genetic structure among populations of recently established species. This prediction was upheld in our previous genetic study using allozymes, however, one locus yielded anomalous results. 2. We employed amplified fragment length polymorphism (AFLP) analysis as a neutral marker to assess the amount of genetic structure within and among populations, and as a test of expected population structure from both invasion genetic theory, and the results from our previous study. 3. There was greater spatial differentiation, as measured by F_st, observed using AFLP's than for allozymes (P < 0.001). There was no evidence that AFLP variation conformed to an isolation by distance model, and genetic relationships of populations, as measured by AFLP markers, were not similar to those detected in our allozyme survey. 4. The lack of concordance between these two genetic marker systems probably reflects their differential responses to drift, migration, and selection occurring during this rapid invasion. Strong population structure is counter to predictions that populations of invasive species will not be differentiated, as with observations based on allozyme markers. Therefore, newly established species may require genetic surveys using multiple marker systems to evaluate population structure.     

Temporally Adaptive Sampling: A Case Study in Rare Species Survey Design with Marbled Salamanders (Ambystoma opacum)

Improving detection rates for elusive species with clumped distributions is often accomplished through adaptive sampling designs. This approach can be extended to include species with temporally variable detection probabilities. By concentrating survey effort in years when the focal species are most abundant or visible, overall detection rates can be improved. This requires either long-term monitoring at a few locations where the species are known to occur or models capable of predicting population trends using climatic and demographic data. For marbled salamanders (Ambystoma opacum) in Massachusetts, we demonstrate that annual variation in detection probability of larvae is regionally correlated. In our data, the difference in survey success between years was far more important than the difference among the three survey methods we employed: diurnal surveys, nocturnal surveys, and dipnet surveys. Based on these data, we simulate future surveys to locate unknown populations under a temporally adaptive sampling framework. In the simulations, when pond dynamics are correlated over the focal region, the temporally adaptive design improved mean survey success by as much as 26% over a non-adaptive sampling design. Employing a temporally adaptive strategy costs very little, is simple, and has the potential to substantially improve the efficient use of scarce conservation funds.     

Acoustic estimation of wildlife abundance: methodology for vocal mammals in forested habitats

Habitat loss and hunting pressure threaten mammal populations worldwide, generating critical time constraints on trend assessment. This study introduces a new survey method that samples continuously and non‐invasively over long time periods, obtaining estimates of abundance from vocalization rates. We present feasibility assessment methods for acoustic surveys and develop equations for estimating population size. As an illustration, we demonstrate the feasibility of acoustic surveys for African forest elephants (Loxodonta africana cyclotis). Visual surveys and vocalizations from a forest clearing in the Central African Republic were used to establish that low‐frequency elephant calling rate is a useful index of elephant numbers (linear regression P < 0.001, r_adj.² = 0.58). The effective sampling area was 3.22 km² per acoustic sensor, a dramatic increase in coverage over dung survey transects. These results support the use of acoustic surveys for estimating elephant abundance over large remote areas and in diverse habitats, using a distributed network of acoustic sensors. The abundance estimation methods presented can be applied in surveys of any species for which an acoustic abundance index and detection function have been established. This acoustic survey technique provides an opportunity to improve management and conservation of many acoustically‐active taxa whose populations are currently under‐monitored.     

Latrine survey as a method to estimate the population size of Arabian gazelles (Gazella arabica)

Arabian gazelle (Gazella arabica) populations have been decimated in most parts of their original range. As a cryptic, crepuscular species, Arabian gazelles are difficult to observe, rendering monitoring programs for conservation purposes a challenging endeavour. Latrine mapping has been suggested as an effective, time- and cost-efficient tool to survey and estimate the abundance of gazelles in remote areas with low population densities. In the present study we collected data from five populations in Saudi Arabia to address the question of how population estimates can be inferred from such latrine counts and uncovered a non-linear relationship between both variables. Methodologies applied during the five surveys differed between study sites, so caution is required when interpreting our data. Still, given the immediate threat to the survival of the species, there is an urgent need to establish a time- and cost-efficient sampling method that will be vital for the conservation of remnant pockets of natural populations and for the proclamation of new protected areas in Saudi Arabia and other countries in the Middle East, and the present data are the only available source of information in this context.     

Habitat complexity and fish size affect the detection of Indo-Pacific lionfish on invaded coral reefs

A standard approach to improving the accuracy of reef fish population estimates derived from underwater visual censuses (UVCs) is the application of species-specific correction factors, which assumes that a species’ detectability is constant under all conditions. To test this assumption, we quantified detection rates for invasive Indo-Pacific lionfish (Pterois volitans and P. miles), which are now a primary threat to coral reef conservation throughout the Caribbean. Estimates of lionfish population density and distribution, which are essential for managing the invasion, are currently obtained through standard UVCs. Using two conventional UVC methods, the belt transect and stationary visual census (SVC), we assessed how lionfish detection rates vary with lionfish body size and habitat complexity (measured as rugosity) on invaded continuous and patch reefs off Cape Eleuthera, the Bahamas. Belt transect and SVC surveys performed equally poorly, with both methods failing to detect the presence of lionfish in >50 % of surveys where thorough, lionfish-focussed searches yielded one or more individuals. Conventional methods underestimated lionfish biomass by ~200 %. Crucially, detection rate varied significantly with both lionfish size and reef rugosity, indicating that the application of a single correction factor across habitats and stages of invasion is unlikely to accurately characterize local populations. Applying variable correction factors that account for site-specific lionfish size and rugosity to conventional survey data increased estimates of lionfish biomass, but these remained significantly lower than actual biomass. To increase the accuracy and reliability of estimates of lionfish density and distribution, monitoring programs should use detailed area searches rather than standard visual survey methods. Our study highlights the importance of accounting for sources of spatial and temporal variation in detection to increase the accuracy of survey data from coral reef systems.     

Dynamics of a northern fulmar (Fulmarus glacialis) population at the southern limit of its range in Europe

In the context of global changes, defining the source–sink dynamics of populations of emblematic species, such as seabirds, within the limits of their distribution range is often crucial to optimize the priorities of surveys and conservation management, especially in protected areas. However, ringing is often not possible and only simple survey methods, such as the ‘apparently occupied sites’ method, can be utilized by managers of protected areas and threatened species. Using data collected between 1997 and 2005, we investigated the population dynamics of the northern fulmar (Fulmarus glacialis) at the southern limit of its range on the western French coast, which hosts increasing populations. Using a robust design spatial occupancy model, we estimated the proportion of occupied nests, the rates of nest colonization, nest extinction and the population growth rates of four colonies of the largest population (Ouessant Island). The estimated annual growth rate was high (average 1.049). A deterministic population dynamics model indicated that the observed rapid increase of Ouessant populations cannot be explained by their intrinsic dynamics, which suggested an important role for immigration. Different demographic scenarios provide several lines of evidence that the large northern fulmar population in this Man and Biosphere Reserve is a sink population. The strong increase in a population located at the limits of the species distributional range implies that it functions as a population sink. Inexpensive effective survey methods could allow investigation of the demographic status of seabird populations and provide relevant information for the hierarchization of conservation priorities.     

Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes)

Assessing levels and patterns of population genetic variation is an important step for evaluating rare or endangered species and determining appropriate conservation strategies. This is particularly important for ensuring the preservation of novel genetic variation in wild relatives of crops, which could provide beneficial alleles for plant breeding and improvement. In this study, we evaluate the population genetics of Helianthus niveus ssp. tephrodes (the Algodones sunflower), which is an endangered, wild relative of cultivated sunflower (H. annuus L.). This rare sunflower species is native to the sand dunes of the Sonoran Desert in southern California, southwestern Arizona, and northern Mexico and is thought to harbor beneficial alleles for traits related to drought tolerance. We genotyped nine populations of this species with a set of simple-sequence repeat markers derived from expressed sequence tags (EST-SSRs) and investigated levels of genetic diversity and population structure, in H. niveus ssp. tephrodes. We also compared our results to findings from five related sunflower species that have been analyzed with these same markers, including annuals and perennials that range from rare to widespread. The Algodones sunflower harbors lower levels of standing genetic variation, but similar levels of population structure as compared to other sunflower species. We also discovered that a disjunct population from northern Mexico was genetically distinct from populations elsewhere in the range. Given the occurrence of such a genetically unique population, our recommendations include population surveys of the southern portion of the range in hopes of bolstering the existing germplasm collection.     

Forest-cutting rapidly improves the demographic status of Paeonia officinalis, a species threatened by forest closure

In the Mediterranean region, the spread and densification of woodlands and shrublands subsequent to rural depopulation is a critical issue for the conservation of open-habitat plant species. Our objective was to assess the effectiveness of forest management to reduce the negative impact of forest closure on the persistence of a protected herbaceous perennial species Paeonia officinalis. Using demographic surveys from 2003 to 2008 in a woodland, open and managed habitat clear-cutted for the aim of our study, we assessed the effect of forest opening on plant performance and population dynamics. In addition, we performed a shading experiment on reproductive plants to mimic canopy closure and study its impact on plant growth and fecundity. Based on quadrat surveys and matrix models, we showed that forest cutting induced a rapid increase in plant performance and population asymptotic growth rate. Indeed, within 2 years, plant size, flower, seed and ovule numbers as well as the plant stage distribution, asymptotic growth rates and elasticity patterns shifted from values similar to those in the woodland habitat to values similar to those in the open habitat. Similarly, artificially shaded reproductive plants regressed within 2 years towards the vegetative stage. For perennial plants which have a stage in their life-cycle which allows for individual survival under unfavourable conditions such as the vegetative stage for P. officinalis, such demographic plasticity may be fundamental for their long-term persistence in temporally heterogeneous environments. Our study highlights the need to mix an experimental approach with a mid-term demographic survey in order to design efficient conservation management strategies for declining populations of rare species.     

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species

Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.     

Population decline but increased distribution of an invasive ant genotype on a Pacific atoll

Populations of invasive species are often studied when their effects are perceived as a problem. Yet observing the dynamics of populations over longer time periods can highlight changes in effects on invaded communities, and assist with management decisions. In this study we revisit an invasion of the yellow crazy ant (Anoplolepis gracilipes) in the Tokelau archipelago to determine if the distribution and abundance of the ant has changed ~7 years after surveys completed in 2004. We were particularly interested in whether populations of a previously identified invasive haplotype (D) had increased in distribution and abundance, as this haplotype was implicated in negative effects on resident ant communities. Indeed, haplotype D populations have become more widespread since the initial survey, more likely owing to new introductions or movement by humans, rather than intrinsic characteristics of the haplotype. We also found that despite no significant change in the abundance of A. gracilipes overall, haplotype D populations have declined in abundance. Residents of the Tokelau atolls no longer consider the ant to be a pest as they did 7 years ago, when populations of this ant interfered with their food production and many other aspects of daily life. We observed no significant differences between A. gracilipes invaded and uninvaded communities, which suggests that the ant is at a level of abundance below which significant negative ecological effects may occur. Population declines of invasive species are not infrequent, and understanding these population dynamics, particularly the underlying mechanisms promoting population declines or stabilisation, should be a high priority for invasion ecology.     

Testing for hybridization and assessing genetic diversity in Morelet’s crocodile (Crocodylus moreletii) populations from central Veracruz

Among the loss of genetic diversity due to population declines, population fragmentation and habitat loss, hybridization also stands as a threat to Morelet’s crocodile (Crocodylus moreletii) populations. Genetic surveys in Belize and the Yucatan Peninsula have detected evidence of hybridization with the American crocodile (C. acutus). Admixture between these two species is most likely driven by human-mediated translocations. Along the central gulf coast of Mexico, C. moreletii populations are presumed to be purebred. To test this, we use nine microsatellite loci and sequence data from the mitochondrial control region to detect if C. acutus alleles have introgressed into populations of C. moreletii from central Veracruz. In 2010, C. moreletii was transferred from Appendix I to II of CITES based on a whole species demographic analysis, which indicated that populations had recovered across its range. Our study shows that populations in central Veracruz are purebred, although they exhibit low levels of genetic diversity most likely caused by inbreeding. Our data also suggest there is fragmentation among populations of C. moreletii, which may lead to further loss of genetic variation. Due the purity and low genetic diversity of C. moreletii populations from central Veracruz, we recommend increased protection and active management practices that take genetic data into account.     

Efficient mitigation of founder effects during the establishment of a leading-edge oak population

Numerous plant species are shifting their range polewards in response to ongoing climate change. Range shifts typically involve the repeated establishment and growth of leading-edge populations well ahead of the main species range. How these populations recover from founder events and associated diversity loss remains poorly understood. To help fill this gap, we exhaustively investigated a newly established population of holm oak (Quercus ilex) growing more than 30 km ahead of the nearest larger stands. Pedigree reconstructions showed that plants belong to two non-overlapping generations and that the whole population originates from only two founder trees. The four first-generation trees that have reached maturity showed disparate mating patterns despite being full-sibs. Long-distance pollen immigration was notable despite the strong isolation of the stand: 6 per cent gene flow events in acorns collected on the trees (n = 255), and as much as 27 per cent among their established offspring (n = 33). Our results show that isolated leading-edge populations of wind-pollinated forest trees can rapidly restore their genetic diversity through the interacting effects of efficient long-distance pollen flow and purging of inbred individuals during recruitment. They imply that range expansions of these species are primarily constrained by initial propagule arrival rather than by subsequent gene flow.     

Can the introduction of Xenopus laevis affect native amphibian populations? Reduction of reproductive occurrence in presence of the invasive species

Biological invasions are regarded as a form of global change and potential cause of biodiversity loss. Xenopus laevis is an anuran amphibian native to sub-Saharan Africa with strong invasive capacity, especially in geographic regions with a Mediterranean climate. In spite of the worldwide diffusion of X. laevis, the effective impact on local ecosystems and native amphibian populations is poorly quantified. A large population of X. laevis occurs in Sicily and our main aim of this work was to assess the consequences of introduction of this alien species on local amphibian populations. In this study we compare the occurrence of reproduction of native amphibians in ponds with and without X. laevis, and before and after the alien colonization. The results of our study shows that, when X. laevis establishes a conspicuous population in a pond system, the populations of Discoglossus pictus, Hyla intermedia and Pelophylax synklepton esculentus show clear signs of distress and the occurrence of reproduction of these native amphibians collapses. In contrast, the populations of Bufo bufo do not appear to be affected by the alien species. Since the Sicilian population of X. laevis shows a strong dispersal capacity, proportionate and quick interventions become necessary to bound the detriment to the Sicilian amphibians populations.     

Contrasting patterns of genetic structure and evolutionary history as revealed by rnitochondrial DNA and nuclear gene-enzyme variation betweenDrosophila melanogaster andDrosophila simulans

Drosophila melanogaster and its sibling speciesD. simulans have a cosmopolitan distribution. Studies on nuclear gene-enzyme variation from natural populations of these species reveal that the two have almost equal overall heterozygosity, yetD. simulans populations are significantly less differentiated. However, it is not clear whether this difference in population structure represents a difference in the genetic strategy with which they respond to the same adaptive challenges, or is the result of difference in species history. To help answer this question, we have undertaken an intensive survey of restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) fromD. simulans; the results are compared with those fromD. melanogaster. We surveyed 69 isofemale lines ofD. simulans from four continents and seven lines from the Seychelles Islands. Ten restriction enzymes detected 104 restriction sites in the continental mtDNAs, of which only threeHinf1 sites were variable and account for fourHlnf1 (restriction variants) haplotypes. These four variants were all found in geographically distant locations. By contrast, twenty-three haplotypes were observed inD. melanogaster, many of which were observed in only one population. It would seem, therefore, that these two species have had different histories. Specifically, cosmopolitan populations ofD: simulans are probably products of a comparatively recent expansion from a source population in Africa. These results do not negate differences in their genetic strategy of adaptation, but they do show the importance of historical contingency in the present-day pattern of geographic variation.     

Volunteer surveys as a means of inferring trends in garden mammal populations

• 1 Habitats associated with humans, and gardens in particular, may prove to be important for populations of certain mammal species. However, means for measuring change in these populations are lacking.
• 2 This paper uses power analyses to examine the potential for mammal observation data, gathered through an extensive volunteer‐based survey of garden birds, to provide measures of population change within garden habitats at both national and regional levels.
• 3 Analyses show that this survey protocol has sufficient power to detect a decline in presence of between 5% and 40% at the national level for 20 of the 24 species included in this study. These results demonstrate that data from volunteer surveys allow the annual monitoring of garden use by a range of mammal species within Britain, and highlight the wider potential of such schemes worldwide.

     

Genetic consequences of intensive conservation management for the Mauritius parakeet

For conservation managers tasked with recovering threatened species, genetic structure can exacerbate the rate of loss of genetic diversity because alleles unique to a sub-population are more likely to be lost by the effects of random genetic drift than if a population is panmictic. Given that intensive management techniques commonly used to recover threatened species frequently involve movement of individuals within and between populations, managers need to be aware not only of pre-existing levels of genetic structure but also of the potential effects that intensive management might have on these patterns. The Mauritius parakeet (Psittacula echo) has been the subject of an intensive conservation programme, involving translocation and reintroduction that has recovered the population from less than 20 individuals in 1987 to approximately 500 in 2010. Analysis of genotype data derived from 18 microsatellite markers developed for this species reveals a clear signal of structure in the population before intensive management began, but which subsequently disappears following management intervention. This study illustrates the impacts that conservation management can have on the genetic structure of an island endemic population and demonstrates how translocations or reintroductions can benefit populations of endangered species by reducing the risk of loss of genetic diversity.