Problem In Conservation Biology Research Articles

Phylogenetic diversity statistics for all clades in a phylogeny.

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.

BarcodingGO: A problem-based approach to teach concepts related to environmental-DNA and bioinformatics.

In this paper, we propose and describe a new approach, named BarcodingGO, to teach environmental DNA and bioinformatics concepts to undergraduate or graduate students in molecular biology-related fields. The learning pipeline proposed here aims to solve a simulated environmental monitoring problem, in which a biodiversity survey of a particular region is needed to assess the impact of an environmental disaster. Biological surveys, in the context of environmental DNA studies, are performed by analyzing the DNA released by organisms living in a specific environment. We proposed a scenario in which quick response (QR) codes represented a given environmental DNA, and they were positioned in a scattered pattern across two regions of the classroom (representing pre and post scenarios for a particular environmental disaster). The QR codes redirect to a page that contained a fictional representation of an animal or a plant. Students then survey the region's biodiversity using QR code scanning applications on their cell phones by "capturing" these organisms as an analogy to the Pokémon GO game of the international Pokémon franchise. We believe this method (or even an adaptation of it) can be an essential tool to engage students in molecular biology classes. Moreover, this approach can help to teach how modern genomics and bioinformatics tools can be applied to solve real problems in conservation biology.

Light pollution causes object collisions during local nocturnal manoeuvring flight by adult Manx Shearwaters Puffinus puffinus

Understanding the detrimental effects of anthropogenic light on nocturnally mobile animals is a long-standing problem in conservation biology. Seabirds such as shearwaters and petrels can be especially affected, perhaps because of their propensity to fly close to the surface, making them vulnerable to encountering anthropogenic light sources. We investigated the influence of light pollution on adult Manx Shearwaters Puffinus puffinus at close range in foggy conditions. We recorded collisions with a building at a breeding colony for six consecutive pairs of intervals in which the house lights were left on as normal for 135 seconds, then turned off for 135 seconds. The relationship between lighting condition and collision frequency was highly significant, with a collision rate in the presence of lighting around 25 times that in its absence. Our results show that birds were clearly affected by the lights, by being either directly attracted, or disorientated during flight close to the structure. This could have been due to the light source itself, or an indirect effect of the all-round reflective glow in the fog perhaps interfering with visual or magnetic control inputs on both sides of the bird simultaneously. Our results suggest a mechanism by which the screening of artificial lights close to shearwater breeding areas, at least during foggy nights, could lead to improved welfare and survival at breeding colonies.

Solving multi-objective optimization problems in conservation with the reference point method.

Managing the biodiversity extinction crisis requires wise decision-making processes able to account for the limited resources available. In most decision problems in conservation biology, several conflicting objectives have to be taken into account. Most methods used in conservation either provide suboptimal solutions or use strong assumptions about the decision-maker’s preferences. Our paper reviews some of the existing approaches to solve multi-objective decision problems and presents new multi-objective linear programming formulations of two multi-objective optimization problems in conservation, allowing the use of a reference point approach. Reference point approaches solve multi-objective optimization problems by interactively representing the preferences of the decision-maker with a point in the criteria (objectives) space, called the reference point. We modelled and solved the following two problems in conservation: a dynamic multi-species management problem under uncertainty and a spatial allocation resource management problem. Results show that the reference point method outperforms classic methods while illustrating the use of an interactive methodology for solving combinatorial problems with multiple objectives. The method is general and can be adapted to a wide range of ecological combinatorial problems.

Metapopulation inbreeding dynamics, effective size and subpopulation differentiation—A general analytical approach for diploid organisms

Motivated by problems in conservation biology we study genetic dynamics in structured populations of diploid organisms (monoecious or dioecious). Our analysis provides an analytical framework that unifies substantial parts of previous work in terms of exact identity by descent (IBD) and identity by state (IBS) recursions. We provide exact conditions under which two structured haploid and diploid populations are equivalent, and some sufficient conditions under which a dioecious diploid population can be treated as a monoecious diploid one. The IBD recursions are used for computing local and metapopulation inbreeding and coancestry effective population sizes and for predictions of several types of fixation indices over different time horizons.

Application of the Maximal Covering Location Problem to Habitat Reserve Site Selection

The Maximal Covering Location Problem (MCLP) is a classic model from the location science literature which has found wide application. One important application is to a fundamental problem in conservation biology, the Maximum Covering Species Problem (MCSP), which identifies land parcels to protect to maximize the number of species represented in the selected sites. We trace the evolution of the MCSP from the MCLP, review extensions, and offer suggestions for new lines of research related to the MCSP.

‘Strict’, yet ineffective: legal protection of breeding sites and resting places fails with the Siberian flying squirrel

AbstractLack of evaluation of the effectiveness of conservation practices as well as the challenge of converting scientific knowledge into conservation legislation and policy are persistent problems in conservation biology. European Union's Habitats Directive obliges member states to establish and implement a system of strict protection of animal species listed in Annex IV(a). This implies for example, that the deterioration or destruction of breeding sites or resting places of these species is prohibited. Here, we evaluate the effectiveness of the protection procedure aimed at conserving sites occupied by the Siberian flying squirrel Pteromys volans from destruction as a consequence of timber harvesting. We assess the potential effectiveness of the protection procedure by combining survey data with a simulation approach, showing that c. 97% of forests occupied by the species are harvested without authorization, as a result of inadequate information on the occurrence of the species. We assess forest structure around our study sites, visited both at the time of the protection decision and 1–6 years later, and show that clear‐cut areas within 150 m of breeding sites and resting places substantially increase the risk of abandonment. In spite of this, typically only areas of radius 10–30 m are protected from logging. As the territory is abandoned in c. 50% of the cases in spite of protection of breeding sites and resting places, the total effectiveness of this conservation measure is only c. 1.5%. Therefore, the current protection measure is inadequate against the threats that forestry poses for the species in Finland, and the focus should be turned to habitat and population level solutions. We suggest that researchers and decision‐makers should pay more attention to the overall effectiveness of different conservation measures, as this information is crucial for developing effective conservation policies.

Population admixture and high larval viability among urban toads

In terms of evolutionary biology, a population admixture of more than two distinct lineages may lead to strengthened genetic variation through hybridization. However, a population admixture arising from artificial secondary contact poses significant problems in conservation biology. In urban Tokyo, a population admixture has emerged from two lineages of Japanese common toad: native Bufo japonicus formosus and nonnative B. japonicus japonicus, of which the latter was introduced in the early 20th century. To evaluate the degree of genetic disturbance in the admixed population of these two subspecies, we analyzed genotypes of toads distributed within and outside Tokyo by assessing mtDNA and seven microsatellite loci. We found that the introduced B. japonicus japonicus genotype dominates six local populations in the Tokyo admixture zone and was clearly derived from past introgressive hybridization between the two subspecies. These observations were supported by morphological assessments. Furthermore, the average larval survival rate in Tokyo was significantly higher than that outside Tokyo, suggesting that the temporary contribution of introduced toads occurred through introgression. The fitness of toads in urban Tokyo may thus be increasing with the assistance of nonnative individuals.

Regeneração natural de cerrado sob plantio de Eucalyptus camaldulensis Dehn. no norte de Minas Gerais, Brasil

A formação de paisagens homogêneas tornou-se um problema na biologia da conservação, já que essas plantações interferem diretamente na dinâmica das comunidades. Sendo assim, o objetivo deste trabalho foi determinar a composição florística e a estrutura da regeneração natural de cerrado, no sub-bosque de um plantio de Eucalyptus camaldulensis, e verificar se essa regeneração se diferencia, dependendo da distância em relação às bordas do talhão. O estudo foi realizado no município de Montes Claros, MG. Para o levantamento, foram demarcados dois blocos, cada um subdividido em nove parcelas de 10 m x 10 m, utilizando-se, como critério de inclusão, a altura > 0,30 m. Foram registrados 2.413 indivíduos. No bloco 1, foram amostrados 914 indivíduos, pertencentes a 63 espécies e 26 famílias, sendo Eugenia dysenterica, Hymenaea stigonogocarpa, Calliandra sp. e Duguetia furfuracea as espécies mais importantes, segundo o Valor de Importância (VI). No bloco 2, foram registrados 1.499 indivíduos, distribuídos em 71 espécies e 30 famílias, sendo os maiores VIs alcançados por Cupania vernalis, Chamaecrista desvauxii, Pouteria ramiflora . Senna rugosa. A distribuição em classes de altura e de diâmetro mostrou a maioria dos indivíduos nas menores classes, demonstrando que a área ainda reflete um evento de regeneração recente. Entretanto, os resultados deste estudo indicam que existem comunidades distintas no local, estando o bloco 2 em estádio mais avançado de regeneração do que o primeiro. Esse fato foi confirmado pela análise de agrupamento entre as parcelas e as diferenças de diversidade e desenvolvimento estrutural da vegetação de cada bloco.

Phenotypic Effects of Cattle Mitochondrial DNA in American Bison

Hybridization between endangered species and more common species is a significant problem in conservation biology because it may result in extinction or loss of adaptation. The historical reduction in abundance and geographic distribution of the American plains bison (Bison bison bison) and their recovery over the last 125 years is well documented. However, introgression from domestic cattle (Bos taurus) into the few remaining bison populations that existed in the late 1800s has now been identified in many modern bison herds. We examined the phenotypic effect of this ancestry by comparing weight and height of bison with cattle or bison mitochondrial DNA (mtDNA) from Santa Catalina Island, California (U.S.A.), a nutritionally stressful environment for bison, and of a group of age-matched feedlot bison males in Montana, a nutritionally rich environment. The environmental and nutritional differences between these 2 bison populations were very different and demonstrated the phenotypic effect of domestic cattle mtDNA in bison over a broad range of conditions. For example, the average weight of feedlot males that were 2 years of age was 2.54 times greater than that of males from Santa Catalina Island. In both environments, bison with cattle mtDNA had lower weight compared with bison with bison mtDNA, and on Santa Catalina Island, the height of bison with cattle mtDNA was lower than the height of bison with bison mtDNA. These data support the hypothesis that body size is smaller and height is lower in bison with domestic cattle mtDNA and that genomic integrity is important for the conservation of the American plains bison.

Use of Cross-Taxon Congruence for Hotspot Identification at a Regional Scale

One of the most debated problems in conservation biology is the use of indicator (surrogate) taxa to predict spatial patterns in other taxa. Cross-taxon congruence in species richness patterns is of paramount importance at regional scales to disclose areas of high conservation value that are significant in a broader biogeographical context but yet placed in the finer, more practical, political context of decision making. We analysed spatial patterns of diversity in six arthropod taxa from the Turkish fauna as a regional case study relevant to global conservation of the Mediterranean basin. Although we found high congruence in cross-taxon comparisons of species richness (0.241<r<0.645), hotspots of different groups show limited overlap, generally less than 50 per cent. The ability of a given taxon to capture diversity of other taxa was usually modest (on average, 50 percent of diversity of non-target taxa), limiting the use of hotspots for effective conservation of non-target groups. Nevertheless, our study demonstrates that a given group may partially stand in for another with similar ecological needs and biogeographical histories. We therefore advocate the use of multiple sets of taxa, chosen so as to be representative of animals with different ecological needs and biogeographical histories.

Choosing ecosystem service investments that are robust to uncertainty across multiple parameters

Info-gap decision theory facilitates decision making for problems in which uncertainty is large and probability distributions of uncertain variables are unknown. The info-gap framework allows the decision maker to maximize robustness to failure in the presence of uncertainty, where uncertainty is in the parameters of the model and failure is defined as the model output falling below some minimally acceptable performance threshold. Info-gap theory has found particular application to problems in conservation biology and ecological economics. In this study, we applied info-gap theory to an ecosystem services tradeoff case study in which a decision maker aiming to maximize ecosystem service investment returns must choose between two alternative land uses: native vegetation conservation or the establishment of an exotic timber plantation. The uncertain variables are the carbon price and the water price. With a "no-information" uncertainty model that assumes equal relative uncertainty across both variables, info-gap theory identifies a minimally acceptable reward threshold above which conservation is preferred, but below which plantation establishment is preferred. However, with an uncertainty model that allows the carbon price to be substantially more uncertain than the water price, conservation of native vegetation becomes an economically more robust investment option than establishing alien pine plantations. We explored the sensitivity of the results to the use of alternative uncertainty models, including asymmetric uncertainty in individual variables. We emphasize the general finding that the results of info-gap analyses can be sensitive to the choice of uncertainty model and that, therefore, future applications to ecological problems should be careful to incorporate all available qualitative and quantitative information relating to uncertainties or should at least justify the no-information uncertainty model.

Does accounting for imperfect detection improve species distribution models?

Models of species distributions are increasingly being used to address a variety of problems in conservation biology. In many applications, perfect or constant detectability of species, given presence, is assumed. While this problem has been acknowledged and addressed through the development of occupancy models, we still know little regarding whether addressing the potential for imperfect detection improves the predictive performance of species distribution models in nature. Here, we contrast logistic regression models of species occurrence that do not correct for detectability to hierarchical occupancy models that explicitly estimate and adjust for detectability, and maximum entropy models that attempt to circumvent the detectability problem by using data from known presence locations only. We use a large-scale, long-term monitoring database across western Montana and northern Idaho to contrast these models for nine landbird species that cover a broad spectrum in detectability. Overall, occupancy models were similar to or better than other approaches in terms of predictive accuracy, as measured by the Area Under the ROC Curve (AUC) and Kappa, with maximum entropy tending to provide the lowest predictive accuracy. Models varied in the types of errors associated with predictions, such that some model approaches may be preferred over others in certain situations. As expected, predictive performance varied across a gradient in species detectability, with logistic regression providing lower relative performance for less detectable species and Maxent providing lower performance for highly detectable species. We conclude by discussing the advantages and limitations to each approach for developing large-scale species distribution models.

Possible shift in macaque trophic level following a century of biodiversity loss in Singapore

Biodiversity loss in tropical forests is a major problem in conservation biology, and nowhere is this more dire than in Southeast Asia. Deforestation and the associated loss of species may trigger shifts in habitat and feeding preferences of persisting species. In this study, I compared the habitat use and diet of long-tailed macaque (Macaca fascicularis) populations in Singapore from two time periods: museum specimens originally collected between 1893 and 1944, and living macaques sampled in 2009. I collected hair and used stable carbon and nitrogen isotope analysis to identify temporal changes in dietary source and trophic position, respectively. δ(13)C ratios were virtually identical, suggesting that macaques foraged in similar habitats during both time periods. However, δ(15)N ratios decreased considerably over time, suggesting that macaques today feed at a lower trophic level than previously. This decline in trophic level may be because of the disappearance or decline of other species that compete with macaques for fruit. This study highlights the effect of biodiversity loss on persisting species in degraded habitats of Southeast Asia, and improves our understanding of how species will adapt to further human-driven changes in tropical forest habitats.

Biodiversity is not (and never has been) a bed of roses!

Over the last decades, the critical study of fossil diversity has led to significant advances in the knowledge of global macroevolutionary patterns of biodiversity. The deep-time history of life on Earth results from background originations and extinctions defining a steady-state, nonstationary equilibrium occasionally perturbed by biotic crises and “explosive” diversifications. More recently, a macroecological approach to the large-scale distribution of extant biodiversity offered new, stimulating perspectives on old theoretical questions and current practical problems in conservation biology. However, time and space are practically distinct, but functionally related dimensions of ecological systems. This calls for a spatially-integrated study of biodiversity dynamics at an evolutionary timescale. Indeed, the biosphere is a complex adaptive system whose study cannot be arbitrarily reduced to any single spatial- and/or temporal-scale level of resolution without a loss of content. From such an integrated perspective, a simple fact emerges: in a physically heterogeneous and ever-changing world, spatiotemporal variations in biodiversity are the rule– not the exception.

On some multiobjective optimization problems arising in biology

In this paper, we discuss modelling and solving some multiobjective optimization problems arising in biology. A class of comparison problems for string selection in molecular biology and a relocation problem in conservation biology are modelled as multiobjective optimization programmes. Some discussions about applications, solvability and different variants of the obtained models are given, as well. A crucial part of the study is based upon the Pareto optimization which refers to the Pareto solutions of multiobjective optimization problems. For such solution, improvement of some objective function can only be obtained at the expense of the deterioration of at least one other objective function.

Genetic and Morphological Variation Between Populations of the Pascagoula Map Turtle (Graptemys gibbonsi) in the Pearl and Pascagoula Rivers with Description of a New Species

Abstract Cryptic or undescribed species pose a major problem in conservation biology. Managing multiple unresolved taxa collectively as a single entity could precipitate the loss of unrecognized genetic variation and unique populations and, possibly, lead to extinction of undiscovered or unrecognized taxa. In contrast to other species in its clade, the Pascagoula map turtle (Graptemys gibbonsi), as currently recognized, is not confined to a single major river system (or a cluster formed by a major river and adjacent minor drainages) but occurs in two major river systems, the Pearl and Pascagoula Rivers. We analyzed G. gibbonsi samples from both rivers for the first time in a morphological and molecular assessment of the taxonomic status of this poorly studied species. We compared the extent of genetic differentiation (mitochondrial DNA; mtDNA) between G. gibbonsi populations with members within the pulchra clade and between Graptemys oculifera and Graptemys flavimaculata. We found significant carapace pat...

Translocating lions into an inbred lion population in the Hluhluwe‐iMfolozi Park, South Africa

AbstractA fundamental problem in conservation biology is the risk of inbreeding in fragmented and declining populations. In the Hluhluwe‐iMfolozi Park (HiP), a small, enclosed reserve in South Africa, a large lion Panthera leo population arose from a founder group of five individuals in the 1960s. The HiP lion population went through a persistent decline and showed indications of inbreeding depression. To restore the genetic variation of the inbred HiP lion population, new lions were translocated into the existing population. Translocated females formed stable associations and established enduring pride areas with other translocated lionesses, but did not bond into native female prides. The translocated male coalition was more successful in gaining and maintaining residence in a pride than the translocated lone male that split off on his own from the male coalition. Litter size and cub survival was about twice as high for pairings involving at least one translocated parent than for pairings of two native lions. It is therefore possible to infuse new genes rapidly and successfully into a small, isolated lion population. Such translocations may become an important adaptive management tool as lion populations become increasingly fragmented.

Maximum Entropy Density Estimation with Generalized Regularization and an Application to Species Distribution Modeling

We present a unified and complete account of maximum entropy density estimation subject to constraints represented by convex potential functions or, alternatively, by convex regularization. We provide fully general performance guarantees and an algorithm with a complete convergence proof. As special cases, we easily derive performance guarantees for many known regularization types, including l1, l2, l22, and l2 + l22 style regularization. We propose an algorithm solving a large and general subclass of generalized maximum entropy problems, including all discussed in the paper, and prove its convergence. Our approach generalizes and unifies techniques based on information geometry and Bregman divergences as well as those based more directly on compactness. Our work is motivated by a novel application of maximum entropy to species distribution modeling, an important problem in conservation biology and ecology. In a set of experiments on real-world data, we demonstrate the utility of maximum entropy in this setting. We explore effects of different feature types, sample sizes, and regularization levels on the performance of maxent, and discuss interpretability of the resulting models.

Common species determine richness patterns in biodiversity indicator taxa

Identification of spatial patterns of species diversity is a central problem in conservation biology, with the patterns having implications for the design of biodiversity monitoring programs. Nonetheless, there are few field data with which to examine whether variation in species richness represents consistent correlations among taxa in the richness of rare or common species, or the relative importance of common and rare species in establishing trends in species richness within taxa. We used field data on three higher taxa (birds, butterflies, vascular plants) to examine the correlation of species richness among taxa and the contribution of rare and common species to these correlations. We used graphical analysis to compare the contributions to spatial variation in species richness by widely-distributed (‘common’) and sparsely-distributed (‘rare’) species. The data came from the Swiss Biodiversity Monitoring Program, which is national in scope and based on a randomly located, regular sampling grid of 1 km 2 cells, a scale relevant to real-world monitoring and management. We found that the correlation of species richness between groups of rare and common species varies among higher taxa, with butterflies exhibiting the highest levels of correlation. Species richness of common species is consistently positively correlated among these three taxa, but in no case exceeded 0.69. Spatial patterns of species richness are determined mainly by common species, in agreement with coarse resolution studies, but the contribution of rare species to variation in species richness varies within the study area in accordance with elevation. Our analyses suggest that spatial patterns in species richness can be described by sampling widely distributed species alone. Butterflies differ from the other two taxa in that the richness of red-listed species and other rare species is correlated with overall butterfly species richness. Monitoring of butterfly species richness may provide information on rare butterflies and on species richness of other taxa as well.