Biodiversity conservation planning tools: Present status and challenges for the future

Species extinctions and the deterioration of other biodiversity features worldwide have led to the adoption of systematic conservation planning in many regions of the world. As a consequence, various software tools for conservation planning have been developed over the past twenty years. These, tools implement algorithms designed to identify conservation area networks for the representation and persistence of biodiversity features. Budgetary, ethical, and other sociopolitical constraints dictate that the prioritized sites represent biodiversity with minimum impact on human interests. Planning tools are typically also used to satisfy these criteria. This chapter reviews both the concepts and technical choices that underlie the development of these tools. Conservation planning problems can be formulated as optimization problems, and we evaluate the suitability of different algorithms for their solution. Finally, we also review some key issues associated with the use of these tools, such as computational efficiency, the effectiveness of taxa and abiotic parameters at choosing surrogates for biodiversity, the process of setting explicit targets of representation for biodiversity surrogates, and

Assessing the Conservation Status and Threats to Priority Plants: a threat assessment approach and case study in South-East Queensland, Australia

bstract: During the Regional Forest Agreement (RFA) process in south-east Queensland, the conservation status of, and threats to, priority vascular plant taxa in the region was assessed. Characteristics of biology, demography and distribution were used to assess the species' intrinsic risk of extinction. In contrast, the threats to the taxa (their extrinsic risk of extinction) were assessed using a decision-support protocol for setting conservation targets for taxa lacking population viability analyses and habitat modelling data. Disturbance processes known or suspected to be adversely affecting the taxa were evaluated for their intensity, extent and time-scale. Expert opinion was used to provide much of the data and to assess the recommended protection areas. Five categories of intrinsic risk of extinction were recognised for the 105 priority taxa: critically endangered (43 taxa); endangered (29); vulnerable (21); rare (10); and presumed extinct (2). Only 6 of the 103 extant taxa were found to be adequately reserved and the majority were considered inadequately protected to survive the current regimes of threatening processes affecting them. Data were insufficient to calculate a protection target for one extant taxon. Over half of the taxa require all populations to be conserved as well as active management to alleviate threatening processes. The most common threats to particular taxa were competition from weeds or native species, inappropriate fire regimes, agricultural clearing, forestry, grazing by native or feral species, drought, urban development, illegal collection of plants, and altered hydrology. Apart from drought and competition from native species, these disturbances are largely influenced or initiated by human actions. Therefore, as well as increased protection of most of the taxa, active management interventions are necessary to reduce the effects of threatening processes and to enable the persistence of the taxa.

Risk from cattle trampling to nests of an endangered passerine evaluated using artificial nest experiments and simulations

Grasslands are often grazed by cattle and many grassland birds nest on the ground, potentially exposing nests to trampling. We tested for trampling risk introduced by cattle to nests of endangered Florida Grasshopper Sparrows (Ammodramus savannarum floridanus) using experimentally paired grids of artificial nests (i.e., clay targets) similar in size to nests of Florida Grasshopper Sparrows and counted the number of clay targets that were broken in paired grazed and ungrazed enclosures. Clay targets in grazed grids were trampled 3.9% more often than their respective ungrazed grids, and measurements of cattle presence or density were correlated with the number of broken clay targets, suggesting that excluding cattle during breeding is an important management recommendation for the Florida Grasshopper Sparrow. Trampling rates within grazed enclosures were spatially homogeneous with respect to cattle infrastructure such as supplemental feeding troughs and fences, and forests and stocking density were poor predictors of trampling rates when excluding ungrazed grids. We used population viability analysis to compare quasi-extinction rates, intrinsic growth rates, and median abundance in grazed and ungrazed Florida Grasshopper Sparrow aggregations to further understand the biological significance of management aimed at reducing trampling rates during the breeding season. Simulations indicated that trampling from grazing increased quasi-extinction rates by 41% while reducing intrinsic growth rates by 0.048, and reducing median abundance by an average of 214 singing males after 50 years. Management should avoid grazing enclosures occupied by Florida Grasshopper Sparrows during the nesting season to minimize trampling rates. Our methods that combine trampling experiments with population viability analysis provide a framework for testing effects from trampling on other grassland ground-nesting birds, and can directly inform conservation and management of the Florida Grasshopper Sparrow.

Reproductive state of hunted female mammals during 2000-2015 in Nueva Esperanza, Peruvian Andes

The annual birthrate of female offspring and the intrinsic rate of natural increase (rmax) of populations are key reproductive parameters in models for assessing hunting sustainability or population viability of species. We calculated wild birthrate (pregnancy rate) for ten mammal species, using 180 months (from 2000 to 2015) of reproductive data from 950 hunted female animals collected with the participation of local hunters in the Peruvian Amazon. The methodology assured that no animals were killed outside the hunter's normal activities. The data included shows the reproductive state (pregnant or non-pregnant) of all collected individuals (n=1090), related to the date of collection. Hunters registered required data from genital organs from 950 (87.2%) hunted females, and 140 (12.8%) collected tracts lacked the collection date due to lost or non-legible individual sample codification.

Avian Cholera emergence in Arctic-nesting northern Common Eiders: using community-based, participatory surveillance to delineate disease outbreak patterns and predict transmission risk

Emerging infectious diseases are a growing concern in wildlife conservation. Documenting outbreak patterns and determining the ecological drivers of transmission risk are fundamental to predicting disease spread and assessing potential impacts on population viability. However, evaluating disease in wildlife populations requires expansive surveillance networks that often do not exist in remote and developing areas. Here, we describe the results of a community-based research initiative conducted in collaboration with indigenous harvesters, the Inuit, in response to a new series of Avian Cholera outbreaks affecting Common Eiders (Somateria mollissima) and other comingling species in the Canadian Arctic. Avian Cholera is a virulent disease of birds caused by the bacterium Pasteurella multocida. Common Eiders are a valuable subsistence resource for Inuit, who hunt the birds for meat and visit breeding colonies during the summer to collect eggs and feather down for use in clothing and blankets. We compiled the observations of harvesters about the growing epidemic and with their assistance undertook field investigation of 131 colonies distributed over >1200 km of coastline in the affected region. Thirteen locations were identified where Avian Cholera outbreaks have occurred since 2004. Mortality rates ranged from 1% to 43% of the local breeding population at these locations. Using a species-habitat model (Maxent), we determined that the distribution of outbreak events has not been random within the study area and that colony size, vegetation cover, and a measure of host crowding in shared wetlands were significantly correlated to outbreak risk. In addition, outbreak locations have been spatially structured with respect to hypothesized introduction foci and clustered along the migration corridor linking Arctic breeding areas with wintering areas in Atlantic Canada. At present, Avian Cholera remains a localized threat to Common Eider populations in the Arctic; however expanded, community-based surveillance will be required to track disease spread.

Richards growth model and viability indicators for populations subject to interventions

In this work we study the problem of modeling identification of a population employing a discrete dynamic model based on the Richards growth model. The population is subjected to interventions due to consumption, such as hunting or farming animals. The model identification allows us to estimate the probability or the average time for a population number to reach a certain level. The parameter inference for these models are obtained with the use of the likelihood profile technique as developed in this paper. The identification method here developed can be applied to evaluate the productivity of animal husbandry or to evaluate the risk of extinction of autochthon populations. It is applied to data of the Brazilian beef cattle herd population, and the the population number to reach a certain goal level is investigated.

On the use of correlated beta random variables with animal population modelling

We give reasons why demographic parameters such as survival and reproduction rates are often modelled well in stochastic population simulation using beta distributions. In practice, it is frequently expected that these parameters will be correlated, for example with survival rates for all age classes tending to be high or low in the same year. We therefore discuss a method for producing correlated beta random variables by transforming correlated normal random variables, and show how it can be applied in practice by means of a simple example. We also note how the same approach can be used to produce correlated uniform triangular, and exponential random variables. (C) 2008 Elsevier B.V. All rights reserved.

Mark-recapture may reveal more about ecology than about population trends: Demography of a threatened ghost bat (Macroderma gigas) population

Since European settlement in Australia, the geographical range of ghost bats (Macroderma gigas) has contracted northwards. Ghost bats are thought to occur in disjunct populations with little interpopulation migration, raising concerns over the current status and future viability of the southernmost colony, which has also been threatened by mining activity. To address these concerns, demographic parameters of the southernmost colony were estimated from a mark-recapture study conducted during 1975-1981. Female bats gave birth to a single young in late spring, but only 40% (22-70%, 95% CI) of females bred in their second year, increasing to 93% (87-97%, 95% CI) for females greater than or equal to 2 years old. Sixty-five percent of juveniles caught were female. Annual adult survival ranged between 0.57-0.77 for females and 0.43-0.66 for males, and was lowest over winter-spring and greatest in autumn-winter. Juvenile survival for the first year ranged between 0.35-0.46 for females and 0.29-0.42 for males. Adult survival varied among seasons, was negatively associated with rainfall, but was not associated with temperature beyond being lower in late winter. Poor survival may result from the inferior daytime roosts that bats must use if water seepage forces them to leave their normal roosts. Although these age-specific rates of fecundity and survival suggested a declining population, mark-recapture estimates of the population trend indicated stability over the study period. Counts at daytime roosts also suggested a population decline, but were considered unreliable because of an increasing tendency of bats to avoid detection. It is therefore likely that some assumptions in estimating survival were violated. These results provide a caution against the uncritical use of population projections derived from mark-recapture estimates of demographic parameters, and the use of untested indices as the basis for conservation decisions.

A Triatoma maculata (Hemiptera, Reduviidae, Triatominae) population from Roraima, Amazon region, Brazil, has some bionomic characteristics of a potential Chagas disease vector

Even though Chagas disease is rare in the Brazilian Amazon, the conditions for the establishment of domiciliated cycles prevail in many areas where triatomines are of frequent occurrence. In Roraima, a previous serological and entomological survey in three agricultural settlements showed the existence of all transmission cycle elements, i.e., individuals infected by Trypanosoma cruzi, triatomine species previously found harboring T. cruzi in the broader Amazon region of neighboring countries and, domicile/ peridomicile conditions favorable to triatomine colonization. Triatoma maculata was the most frequent species, found in chicken houses in the peridomicile and sporadically within residences. Aiming to investigate the possibility of T. maculata to possess the potentiality to transmit T. cruzi in the area, bionomic characteristics were studied under laboratory conditions. These were feeding frequency, time for defecation after a blood meal, time elapsed in voluntary fasting pre- and pos-ecdysis, moulting time periods, pre-oviposition and oviposition periods and index of oviposition, incubation period, egg viability, longevity and mortality rate. Results show that the Passarão population of T. maculata should be considered a potential vector of T. cruzi since it shows a capacity to infest artificial ecotopes in the peridomicile, to carry out large number of meals during the nymphal cycle, to have a relatively short developmental cycle capable of producing 2.9 generations/year, to blood source eclecticism, to defecate immediately after the blood meal while still on the host and to the fact that has been previously found naturally infected by T.cruzi.

Fitness components of a recently-established population of Zaprionus indianus (Diptera, Drosophilidae) in Brazil

This study aimed to evaluate fitness components of Zaprionus indianus Gupta, 1970, a species recently introduced in Brazil and currently in process of colonization. Longevity, productivity, developmental speed and viability of flies sampled from a population from Mirassol (state of São Paulo, Brazil) were evaluated. Longevity was higher than that of some Indian populations and productivity was similar or higher than in other Drosophilidae. Time of development, one of the main fitness components for competition, was very similar to the values scored in Drosophila sturtevanti Duda, 1927, a species that occurs in high frequencies in the same area as Z. indianus. These data might contribute further for understanding the colonization success of this newcomer species in South America.

Density estimates and conservation of Leopardus pardalis southernmost population of the Atlantic Forest

ABSTRACT Using camera traps and capture/recapture analyses we recorded the presence and abundance of cat species at Turvo State Park, in southern Brazil. Ocelot [Leopardus pardalis (Linnaeus, 1758)] population density was estimated for two areas of the park, with differing management profiles. Density estimates varied from 0.14 to 0.26 indiv. km2. Another five cat species were recorded at very low frequencies, precluding more accurate analyses. We estimate 24 to 45 ocelots occur in the reserve, which is probably too small for long-term maintenance of the population, if isolated. However, if habitat integrity and connectivity between the Park and the Green Corridor of Misiones is maintained, an estimated ocelot population of 1,680 individuals should have long-term viability.

Effects of different mating scenarios on embryo viability in brown trout.

Mating with attractive or dominant males is often predicted to offer indirect genetic benefits to females, but it is still largely unclear how important such non-random mating can be with regard to embryo viability. We sampled a natural population of adult migratory brown trout (Salmo trutta), bred them in vitro in a half-sib breeding design to separate genetic from maternal environmental effects, raised 2098 embryos singly until hatching, and exposed them experimentally to different levels of pathogen stress at a late embryonic stage. We found that the embryos' tolerance to the induced pathogen stress was linked to the major histocompatibility complex (MHC) of their parents, i.e. certain MHC genotypes appeared to provide better protection against infection than others. We also found significant additive genetic variance for stress tolerance. Melanin-based dark skin patterns revealed males with 'good genes', i.e. embryos fathered by dark coloured males had a high tolerance to infection. Mating with large and dominant males would, however, not improve embryo viability when compared to random mating. We used simulations to provide estimates of how mate choice based on MHC or melanin-based skin patterns would influence embryos' tolerance to the experimentally induced pathogen stress.

Evolution of life history traits in a natural population of the shrew Crocidura russula

Abstract Life history traits encompass all the decisions concerning fitness an individual is faced with during his life. The study of these traits is crucial to understand the factors shaping the biology of living organisms. Up until now, most of the information on the evolution of life history traits comes from laboratory studies. While these studies are interesting to test the effect of specific parameters, their conclusions are difficult to extrapolate to natural populations. Investigating the evolution of life history traits in natural populations is of great interest. This may be tricky because it requires information on reproduction, survival and morphology of individuals. Mark-recapture methods allow most of this information to be obtained. However, when direct observations of a species are not possible due to its ecology, indirect methods must be used to infer lifetime reproductive success. In this case, molecular markers are particularly helpful in assessing the genetic relationships between individuals and allow the construction of a pedigree. This thesis focuses on a natural population of a small insectivorous mammal, the greater white-toothed shrew, Crocidura russula. Because of its hidden lifestyle, the two complementary techniques mentioned above were combined to gather information on this population. The data were used to explore diverse aspects of evolutionary biology. We demonstrated that the high genetic variance displayed by the species was not maintained by its mating system because this shrew was less monogamous than previously thought. The large genetic diversity was most likely promoted by gene flow from the neighborhood. Dispersal was thus a central topic in this thesis. We showed that dispersal was not driven by inbreeding avoidance. In addition, we did not find any inbreeding depression in the population. Dispersal was promoted by a high number of vacant territories in the population for both sexes, meaning that territory acquisition played an important role in driving dispersal. Moreover, dispersal propensity was shown to have a genetic basis and, once achieved, to have no effect on individual fitness. Body mass was found to be a life history trait strongly influenced by sexual and viability selection in both sexes. Larger individuals had higher access to reproduction through territory acquisition and defense than lighter ones. By contrast, intermediate size individuals were favored by viability selection presumably because of ecological constraints and metabolic costs. Finally, we demonstrated that the majority of the life history traits in our shrew population has the potential to evolve because they maintained substantial amounts of additive genetic variance. Nonetheless, life history traits had no significant heritability due to their high level of nonadditive or environmental variance. Résumé Les traits d'histoire de vie comprennent toutes les décisions auxquelles un individu est confronté au cours de sa vie et qui concernent sa valeur adaptative. L'étude de ces traits est cruciale pour comprendre les facteurs qui façonnent la biologie des êtres vivants. Jusqu'à ce jour, la majorité des informations sur l'évolution des traits d'histoire de vie provient d'études réalisées en laboratoire. Alors que ces études sont intéressantes pour tester l'effet de paramètres spécifiques, leurs conclusions sont difficilement extrapolables aux populations naturelles. Il est particulièrement intéressant d'étudier l'évolution des traits d'histoire de vie dans des populations naturelles. Toutefois, ces études peuvent se révéler difficiles parce qu'elles requièrent des informations sur la reproduction, la survie et la morphologie des individus. Des méthodes de marquage-recapture permettent d'obtenir ces informations. Cependant, lorsque l'écologie de l'espèce rend les obervations directes impossibles, des méthodes indirectes doivent être utilisées pour obtenir le succès reproducteur des individus. Dans ce cas, les marqueurs moléculaires sont particulièrement utiles pour évaluer les relations génétiques entre individus et permettre la construction d'un pedigree. Cette thèse porte sur une population naturelle d'un petit mammifère insectivore, la musaraigne musette, Crocidura russula. Parce que cette espèce présente un mode de vie souterrain, les deux techniques complémentaires mentionnées ci-dessus ont été combinées pour acquérir les informations nécessaires. Les données ont été utilisées pour explorer divers aspects de biologie evolutive. Nous avons montré que la grande quantité de variance génétique trouvée chez cette espèce n'est pas maintenue par son système d'appariement. Celle-ci s'est en effet avérée être moins monogame que ce qui était admis jusqu'ici. Sa grande diversité génétique est plutôt entretenue par le flux de gènes provenant du voisinage. La dispersion a donc été un sujet phare dans cette thèse. Nous avons montré qu'elle n'est pas provoquée par un évitement de la consanguinité et nous n'avons pas trouvé de dépression de consanguité dans notre population. L'acquisition d'un territoire joue par contre un rôle important dans la dispersion. En outre, la dispersion possède une base génétique chez cette espèce. De plus, une fois qu'ils ont dispersé, les individus n'ont pas une valeur adaptative differente d'individus philopatriques. Le poids s'est avéré être un trait d'histoire de vie fortement influencé par la sélection sexuelle et de viabilité chez les deux sexes. Les gros individus ont accès à la reproduction parce qu'ils acquièrent et défendent un territoire plus facilement que les plus légers. Au contraire, les individus de taille intermédiaire sont favorisés par la sélection de viabilité, certainement à cause de contraintes écologiques et de coûts métaboliques. Finalement, nous avons montré que la majorité des traits d'histoire de vie dans notre population a le potentiel d'évoluer parce qu'elle maintient des quantités considérables de variance génétique additive. Néanmoins, l'héritabilité de ces traits d'histoire de vie n'est pas significative à cause de la grande quantité de variance non-additive ou environmentale associée à ces traits.