Population size influences amphibian detection probability: implications for biodiversity monitoring programs

Monitoring is an integral part of species conservation. Monitoring programs must take imperfect detection of species into account in order to be reliable. Theory suggests that detection probability may be determined by population size but this relationship has not yet been assessed empirically. Population size is particularly important because it may induce heterogeneity in detection probability and thereby cause bias in estimates of biodiversity. We used a site occupancy model to analyse data from a volunteer-based amphibian monitoring program to assess how well different variables explain variation in detection probability. An index to population size best explained detection probabilities for four out of six species (to avoid circular reasoning, we used the count of individuals at a previous site visit as an index to current population size). The relationship between the population index and detection probability was positive. Commonly used weather variables best explained detection probabilities for two out of six species. Estimates of site occupancy probabilities differed depending on whether the population index was or was not used to model detection probability. The relationship between the population index and detectability has implications for the design of monitoring and species conservation. Most importantly, because many small populations are likely to be overlooked, monitoring programs should be designed in such a way that small populations are not overlooked. The results also imply that methods cannot be standardized in such a way that detection probabilities are constant. As we have shown here, one can easily account for variation in population size in the analysis of data from long-term monitoring programs by using counts of individuals from surveys at the same site in previous years. Accounting for variation in population size is important because it can affect the results of long-term monitoring programs and ultimately the conservation of imperiled species.     

A sophisticated species conservation strategy for <Emphasis Type="Italic">Nyssa yunnanensis</Emphasis>, a species with extremely small populations in China

Conservation of plant species with extremely small populations (PSESP) is a focus of wild plant conservation in China at present. A relevant strategy for PSESP conservation requires improvement from previous programs for rare and endangered plants and national key protected plants. An integrated strategy for PSESP conservation of the Nyssa yunnanensis was initiated and applied over a 7-year period (2009–2015). Here, we reviewed the processes to implement the strategy: resource inventory, formulation of conservation action plan (CAP), in situ conservation, seedling propagation, near situ conservation, ex situ conservation and scientific research. Major concerns and technical requirements for each action are described and further analyzed within a broad scope to conserve PSESPs. A detailed resource inventory that highlights both the change in population status and the participation of local residents is recommended before the formulation of the CAP. Techniques for determination of the area of a mini-reserve is developed for in situ conservation of N. yunnanensis. Near situ conservation is a novel approach whereby establishing new viable population in contiguous areas with a similar climate, habitat and community, in which techniques for seedling preparation, soil preparation, and early management are introduced. A population-based species conservation strategy for N. yunnanensis may aid additional PSESP conservation, so as to contribute to overall wild plant conservation.     

Strategies for establishing and using genome resource banks to protect genetic diversity in conservation breeding programs

Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but there are few guidelines for integrating GRBs into established breeding programs. Here we present basic guidelines, focusing on strategies for the collection, maintenance, and use of semen GRBs for protecting genetic diversity. These guidelines should be applied in the context of the specific purposes and roles of a breeding program's GRB, which will differ among species depending on vulnerability to loss and the status of rescue and conservation efforts. We recommend establishing up to three types of collections: (1) a National Reserve to preserve a species' genetic diversity, to be used only as a last resort; (2) a Savings Account to be used periodically to invigorate a genetically depauperate population; and (3) a Checking Account to be used as a regular part of the breeding program. We present methods for identifying donors to maximize genetic diversity in a GRB, as well as strategies for maintaining and optimally using GRBs.     

Interactions of target population size,population parameters,and program management on viability of captive populations

When established conservation programs expand and evolve, management practices may become inconsistent with program goals. In the past decade, the American Zoo and Aquarium Association expanded species conservation programs by increasing the number of Species Survival Plans (SSP) and establishing more than 300 new Population Management Plan (PMP) programs. However, limited space in captive breeding facilities forces a competition among SSPs and less intensively managed PMPs. Regional Collection Plans establish priorities and allocate space accordingly by setting target population size for each species; species of high conservation priority (SSPs) are allocated space at the expense of lower priority species (PMPs). Because population size and genetic composition interact to impact population viability, target population size is a significant factor to a population’s prospects for long‐term survival. We examined four population parameters (current population size, target population size, current gene diversity, and mean generation time) for 46 mammalian SSPs and 17 PMPs. Relative to SSPs, PMPs combine smaller current and target population sizes, lower levels of current gene diversity, and shorter mean generation times than SSPs. Thus, the average PMP population can expect to lose gene diversity more rapidly than the average SSP population. PMPs are projected to lose 10% or more of their founding gene diversity, within only 2 years. In contrast, the average SSP population is projected to lose 10% in 40 years. Populations with small current or target population sizes require intensive management to avoid extinction. More intensive genetic management of populations typically designated as PMPs, through recruitment of potential founders and equalization of founder representation, could increase gene diversity and improve viability. Less rigorous population management should be reserved for populations whose long‐term survival is either secure or that can be readily replenished from the wild. Because PMP populations need intense genetic management similar to that currently in effect for SSPs, there should be neither a management‐level distinction between programs nor an arbitrary difference in space allocated to programs. Zoo Biol 20:169–183, 2001. © 2001 Wiley‐Liss, Inc.     

Egyptian tortoise conservation: A community‐based,field research program developed from a study on a captive population

Local community participation and ex situ conservation has the potential to assist the recovery of the endangered Egyptian tortoise, Testudo kleinmanni. We initiated an in situ community‐based conservation and research program from a captive population of T. kleinmanni. We used a captive population of the Egyptian tortoise to train a member of the local community as a research technician and used his indigenous tracking skills and knowledge of the area to collect activity and dietary data on 28 captive tortoises. We overcame problems with illiteracy by creating a data sheet based on symbols and numbers. This data sheet allowed us to use the indigenous knowledge of various people from the community, and employ them in the future. Our local community approach to data collection, in conjunction with a craft program, made the conservation of the Egyptian tortoise more rewarding to the local community by providing a more sustainable form of income than collecting animals for the pet trade. Our multidimensional approach (local community participation as research technicians, craft program, and trust building) for gaining local support eventually led to the rediscovery of wild Egyptian tortoises in North Sinai, which was significant, as this species was presumed extinct in Egypt. We have now shifted our focus to in situ conservation, using the research and local capacity building template developed from this captive population study. Our template can be used by zoos and conservation organizations with small budgets and collections of native species in natural habitats to create similar captive research programs that can be applied to in situ conservation. Zoo Biol 26:397–406, 2007. © 2007 Wiley‐Liss, Inc.     

Known knowns and unknowns in biology

Here we present a knowledge‐data framework based on the politico‐military statement by Donald Rumsfeld (below) which has, we believe, direct relevance to ecological conservation. Ecological examples of four of the identified categories are provided with discussion of the conservation risks to a species through knowledge or data loss and movement through the categories. We show that so‐called known knowns in terms of global biodiversity are not as accurately known as thought, despite 500 years or more of world‐wide collecting and recording of eukaryotic species. In addition, as fast as new species, living or fossil, are discovered (unknown unknowns), some of which have revolutionised concepts about the biology of particular taxa, meanwhile, sadly other living species are being extirpated, or are assumed to be so (unknown knowns). These often have a high probability of ultimately being rediscovered, especially if small and/or living in remote, under‐sampled regions. Furthermore, we suggest that in some cases it may be possible to predict the existence of known species in new habitats, or the existence of unknown co‐evolved animal species (known unknowns). We discuss how technological advances (e.g. molecular markers and DNA sequencing) are inflating current estimates of biodiversity by identifying the existence of cryptic species. We believe the knowledge‐data matrix provides another tool for conservation practitioners to focus data collection on bridging knowledge gaps for more effective conservation outcomes.     

High levels of genetic differentiation and selfing in the Brazilian cerrado fruit tree Dipteryx alata Vog. (Fabaceae)

Dipteryx alata is a native fruit tree species of the cerrado (Brazilian savanna) that has great economic potential because of its multiple uses. Knowledge of how the genetic variability of this species is organized within and among populations would be useful for genetic conservation and breeding programs. We used nine simple sequence repeat (SSR) primers developed for Dipteryx odorata to evaluate the genetic structure of three populations of D. alata located in central Brazil based on a leaf sample analysis from 101 adults. The outcrossing rate was evaluated using 300 open-pollinated offspring from 25 seed-trees. Pollen dispersal was measured by parentage analysis. We used spatial genetic structure (SGS) to test the minimal distance for harvesting seeds in conservation and breeding programs. Our data indicate that the populations studied had a high degree of genetic diversity and population structure, as suggested by the high level of divergence among populations . The estimated outcrossing rate suggested a mixed mating system, and the intrapopulation fixation index was influenced by SGS. We conclude that seed harvesting for genetic conservation and breeding programs requires a minimum distance between trees of 196 m to avoid collecting seeds from related seed-trees.     

Interaction of climate,demography and genetics: a ten-year study of <Emphasis Type="Italic">Brassica insularis</Emphasis>, a narrow endemic Mediterranean species

Long-term demographic surveys, needed to obtain accurate information on population dynamics and efficiently manage rare species, are still very scarce. Matrix population models are useful tools to identify key demographic transitions and thus help setting up conservation actions. Furthermore, the combination of ecological, demographic and genetic data is likely to improve the identification of the threats acting upon populations and help conservation decisions. In this paper we illustrate the power of this approach on Brassica insularis, a Mediterranean endemic plant species, rare and endangered in Corsica (France). In four populations of this species, a long-term demographic survey (2000–2009), genetic analyses (in 2000 and 2009) and survey of ecological variables (climatic variables, competition and herbivory) were performed. By using both deterministic and stochastic matrix model analyses, we assessed the viability of each population and tested for both spatial and temporal variations in demographic vital rates. Populations exhibited differing demographic behaviours and environmental stochasticity occurred in populations. Significant correlations between climatic variables and vital rates were detected. Stochastic simulations suggested that three out of the four populations studied might present a high risk of extinction on the short-term and should actively be managed, or at least surveyed. It could be, however, that two of these populations are experiencing density-dependent regulation, rather than being declining. Microsatellite diversity was slightly reduced in a single population and similar in the three others, consistently with expectations based on population census size and geographic area, as well as with diversity at the S-locus observed in 2000. The combination of all data led to specific recommendations for managing each population. We discuss the implications for conservation of such a general approach.     

The status of dwarf carnivores on Cozumel Island, Mexico

Cozumel Island in the Mexican Caribbean is inhabited by four carnivores, of which two, the Cozumel coati Nasua nelsoni and pygmy raccoon Procyon pygmaeus, are endemic species. The taxonomic status of a third carnivore, a dwarf gray fox Urocyon cinereoargenteus, is undetermined, but may deserve subspecific or species-level recognition. The fourth species, the kinkajou (Potos flavus), may be a recent introduction. We review the status of these carnivores, report our field observations and results of line transect and trapping efforts, discuss current threats to these taxa, and make recommendations for their conservation. A population density of 0.43 ± 0.27 coatis/km², and a total island population size of 150 ± 95 individuals, was estimated from 386 km of line transects in 1994–1995. Intensive trapping efforts (1479 trap-nights) in 2001 at multiple localities were unsuccessful. Pygmy raccoons were observed in the mangrove and coastal wetland areas of the island and in 2001 we captured 11 individuals with the same sampling efforts as for coatis (8.8 raccoons/1000 trap-nights). The gray fox is also apparently very rare on the island. While a few observations of the animals have been made (1984, 1994 and 2001), no animals were seen along transects and none were trapped. The primary threats to the persistence of these taxa include introduced congeners, introduced predators, parasite and disease spill-over from exotic animals, habitat fragmentation, hunting and collection as pets, and hurricanes. We suggest that the Cozumel coati, pygmy raccoon, and the Cozumel population of the gray fox be considered as Critically Endangered according to the IUCN classification system. Current conservation actions focusing on Cozumel carnivores are extremely limited. We recommend eradication of introduced species, maintenance of habitat connectivity, ex situ conservation programs, explicit public policies on land-use and sustainable development, public awareness campaigns, and continuous scientific research and monitoring.     

Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment

Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Here, we develop an open population spatial capture–recapture (SCR) model with sex-specific detection and population dynamics parameters to investigate population trend and sex-specific population dynamics of a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totaling 22 km² within a region of 908 km² and sampled via scat collection. Our model accounts for the patchy distribution of habitat and the uncertainty introduced by collecting data only every third year, while producing sex by patch population trajectories. The estimated population trajectory was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. The decline observed in males was explained by the demography of just two of the eight patches. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.     

Patterns of genetic diversity in the rare Erigeron lemmoni and comparison with its more widespread congener,Erigeron arisolius (Asteraceae)

Analysis of levels and patterns of genetic variation in a rare species is important for determining whether genetic factors associated with small population size, such as genetic drift or inbreeding, may be negatively affecting a species. In this study, we compared estimates of genetic diversity and patterns of population genetic structure in a rare cliff endemic, Erigeron lemmonii, to those of a widespread congener, E. arisolius. Our goals were to assess whether rarity and small population size have negatively affected levels of genetic diversity in E. lemmonii and to identify genetic threats that may limit the ability of E. lemmonii to persist. Levels of observed and expected heterozygosity and allelic richness in E. lemmonii were approximately 60 % of those found in E. arisolius. After correcting for null alleles, inbreeding coefficients in both species of Erigeron were very small, suggesting that both species are highly outcrossing and may demonstrate self-incompatibility. Patterns of genetic structure in both species revealed almost no population substructuring, indicating that widespread gene flow is occurring within each species. Because we found no evidence for inbreeding or a genetic bottleneck in E. lemmonii, it is likely that the species’ lower genetic diversity may be the result of genetic drift. Because E. lemmoni exists in a single population, no other populations exist to bolster population size or genetic diversity in the event of declines; thus, conservation efforts should focus on seed collection from as many individuals as possible to protect against possible future losses of genetic diversity. We also recommend continued monitoring of both population size and genetic diversity in E. lemmonii to ensure the species’ long-term persistence and viability.     

The culture of bird conservation: Australian stakeholder values regarding iconic,flagship and rare birds

Iconic, flagship and rare threatened bird taxa attract disproportionate amounts of public attention, and are often used to enable broader conservation strategies. Yet, little is known about why certain taxa achieve iconic or flagship status. Also unclear is whether the perception of rarity among those acting to conserve threatened birds is sufficient to influence attitudes and behaviour that lead to effective conservation action and, if so, which characteristics of rare birds are important to their conservation. We interviewed 74 threatened bird conservation stakeholders to explore perceptions about iconic, flagship and rare threatened birds and classified their attitudes using a new typology of avifaunal attitudes. There was a relationship between societal interest and conservation effort for threatened species characterised as iconic, flagship and rare. Iconic species tended to arouse interest or emotion in people due to being appealing and readily encountered, thereby attracting conservation interest that can benefit other biodiversity. Flagships tended to have distinguishing physical or cultural characteristics and were used to convey conservation messages about associated biodiversity. Attitudes about rarity mostly related to a taxon’s threatened status and small population size. Rarity was important for threatened bird conservation but not always associated with attitudes and behaviour that lead to effective conservation action. We conclude that conservation action for individual threatened bird taxa is biased and directly influenced by the ways taxa are socially constructed by stakeholders, which is specific to prevailing culture and stakeholder knowledge.     

Predictor species: Improving assessments of rare species occurrence by modeling environmental co‐responses

Designing an effective conservation strategy requires understanding where rare species are located. Because rare species can be difficult to find, ecologists often identify other species called conservation surrogates that can help inform the distribution of rare species. Species distribution models typically rely on environmental data when predicting the occurrence of species, neglecting the effect of species' co‐occurrences and biotic interactions. Here, we present a new approach that uses Bayesian networks to improve predictions by modeling environmental co‐responses among species. For species from a European peat bog community, our approach consistently performs better than single‐species models and better than conventional multi‐species approaches that include the presence of nontarget species as additional independent variables in regression models. Our approach performs particularly well with rare species and when calibration data are limited. Furthermore, we identify a group of “predictor species” that are relatively common, insensitive to the presence of other species, and can be used to improve occurrence predictions of rare species. Predictor species are distinct from other categories of conservation surrogates such as umbrella or indicator species, which motivates focused data collection of predictor species to enhance conservation practices.     

Sheltered from the storm? Population viability analysis of a rare endemic under periodic catastrophe regimes

Rare species are important targets for biodiversity conservation efforts because rarity often equates to small populations and increased endangerment. Rare species are prone to stochastic extinction events and may be particularly susceptible to catastrophes. Therefore, understanding how rare species respond to disturbances is critical for evaluating extinction risk and guiding conservation managers. Population viability analyses (PVAs) are essential for assessing rare species' status yet they seldom consider catastrophic events. Accordingly, we present a PVA of a rare tropical epiphyte, Lepanthes caritensis (Orchidaceae), under simulated disturbance regimes to evaluate its demographics and extinction risk. We aimed to test how demographic models incorporating catastrophes affect population viability estimates. Our goal was to better guide management of these orchids and other rare plants. Results revealed L. caritensis numbers have declined recently, but projected growth rates indicated that most subpopulations should increase in size if undisturbed. Still, projection models show that moderate catastrophes reduce growth rates, increase stochasticity in subpopulation sizes, and elevate extinction risk. Severe catastrophes had a more pronounced effect in simulations; growth rates fell below replacement level, there was greater variation in projected population sizes, and extinction risk was significantly higher. PVAs incorporating periodic catastrophes indicate that rare species may have greater extinction probabilities than standard models suggest. Thus, precautionary conservation measures should be taken in disturbance prone settings and we encourage careful monitoring after environmental catastrophes. Future rare plant PVAs should incorporate catastrophes and aim to determine if rescue and reintroduction efforts are necessary after disturbances to insure long-term population viability.     

Habitat specialization predicts genetic response to fragmentation in tropical birds

Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species‐specific population structure are rare. Here, we used a comparative approach on eight bird species, co‐occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.     

Butterfly diversity and seasonality of Ta Phin mountain area (N. Vietnam,Lao Cai province)

Human pressures on the environment are changing spatially and temporally, with profound implications for the planet’s biodiversity. Butterflies are important indicators for environmental change and are a suitable group to detect areas of high conservation concern and prioritize conservation efforts. To obtain data to support urgently-needed conservation measures, we surveyed the butterfly fauna in a mountainous region of northern Vietnam, using transect counts over 8 months (121 survey days) from June 2014 to April 2015. In total, we recorded >26,000 butterflies belonging to 231 species, including at least two species new to Vietnam, three red-listed and protected species listed by CITES. Most species were rare: we recorded members of 100 species ≤5 times and 52 species just once. Males dominated the sample, accounting for 81% of all observed butterflies and all members of 84 observed species. Species richness and abundance were highest in July, and there were surprisingly large changes in species composition between months. Species richness curves reached saturation, indicating that we detected most species present in the area, except for members of two families (Lycaenidae and Hesperiidae). Our results highlight the importance of thorough studies using standardized methods, capable of detecting most species in an area, over a whole season. There are urgent needs to integrate butterflies into conservation programs and use their potential as indicator species of habitat degradation and land use intensity.     

Genetic diversity assessment of bittersweet (Solanum dulcamara,Solanaceae) germplasm using conserved DNA‐derived polymorphism and intron‐targeting markers

Bittersweet (Solanum dulcamara), a European native weed, is widespread across a variety of habitats and often occurs as a coloniser of open, disturbed, ephemeral environments or wetlands, although it is also found in mountain habitats and on forest edges. As recent studies have shown the potential utility of the species in plant breeding programs, we assembled a collection of bittersweet germplasm from natural populations found in Europe. This collection was analysed with conserved DNA‐derived polymorphism (CDDP) and intron‐targeting (IT) markers to assess genetic diversity found within and among the populations. We found that there is limited genetic variability within the collected S. dulcamara accessions, with a greater proportion of allelic variation distributed among populations and considerably greater population structure at higher regional levels. Although bittersweet is an outcrossing species, its population structure might be affected by its perennial self‐compatible nature, reducing genetic diversity within regional populations and enhancing inbreeding leading to high interpopulation or spatial differentiation. We found that populations have been separated by local selection of alleles, resulting in regional differentiation. This has been accompanied by concurrent loss of genetic diversity within populations, although this process has not affected species‐level genetic diversity. Germplasm collecting strategies should be aimed at preserving overall genetic diversity in bittersweet nightshade by expanding sampling to southern Europe and to smaller regional geographic levels in northern and central Europe.     

Assessing Extinction Risk in Small Metapopulations of Golden‐headed Lion Tamarins (Leontopithecus chrysomelas) in Bahia State,Brazil

Golden‐headed lion tamarins (GHLTs; Leontopithecus chrysomelas) are endangered primates endemic to the Brazilian Atlantic Forest, where loss of forest and its connectivity threaten species survival. Understanding the role of habitat availability and configuration on population declines is critical for guiding proactive conservation for this, and other, endangered species. We conducted population viability analysis to assess vulnerability of ten GHLT metapopulations to habitat loss and small population size. Seven metapopulations had a low risk of extirpation (or local extinction) over the next 100 years assuming no further forest loss, and even small populations could persist with immediate protection. Three metapopulations had a moderate/high risk of extirpation, suggesting extinction debt may be evident in parts of the species’ range. When deforestation was assumed to continue at current rates, extirpation risk significantly increased while abundance and genetic diversity decreased for all metapopulations. Extirpation risk was significantly negatively correlated with the size of the largest patch available to metapopulations, underscoring the importance of large habitat patches for species persistence. Finally, we conducted sensitivity analysis using logistic regression, and our results showed that local extinction risk was sensitive to percentage of females breeding, adult female mortality, and dispersal rate and survival; conservation or research programs that target these aspects of the species’ biology/ecology could have a disproportionately important impact on species survival. We stress that efforts to protect populations and tracts of habitat of sufficient size throughout the species’ distribution will be important in the near‐term to protect the species from continuing decline and extinction.     

广西稀有濒危植物迁地保护评价

从迁地保护的内容、适应性、有效性等方面对桂林植物园迁地保护稀有濒危植物进行评价,结果表明:迁地保护的稀有濒危植物科学性强,96%以上的物种有科学记录,除了银杏等少数几个种属于“保护性收集”外,其它都是“具有保护意义的收集”;75%的种适应或基本适应迁移地的环境,原分布于广西的种明显比分布于广西区外的种适应性更强。按照最小存活种群的标准,该园有73种稀有濒危植物迁地保护有效。