Computing evolutionary distinctiveness indices in large scale analysis

We present optimal linear time algorithms for computing the Shapley values and 'heightened evolutionary distinctiveness' (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency of these new algorithms by applying them to a set of 10,000 reasonable 5139-species mammal trees. This is the first time these indices have been computed on such a large taxon and we contrast our finding with an ad-hoc index for mammals, fair proportion (FP), used by the Zoological Society of London's EDGE programme. Our empirical results follow expectations. In particular, the Shapley values are very strongly correlated with the FP scores, but provide a higher weight to the few monotremes that comprise the sister to all other mammals. We also find that the HED score, which measures a species' unique contribution to future subsets as function of the probability that close relatives will go extinct, is very sensitive to the estimated probabilities. When they are low, HED scores are less than FP scores, and approach the simple measure of a species' age. Deviations (like the Solendon genus of the West Indies) occur when sister species are both at high risk of extinction and their clade roots deep in the tree. Conversely, when endangered species have higher probabilities of being lost, HED scores can be greater than FP scores and species like the African elephant Loxondonta africana, the two solendons and the thumbless bat Furipterus horrens can move up the rankings. We suggest that conservation attention be applied to such species that carry genetic responsibility for imperiled close relatives. We also briefly discuss extensions of Shapley values and HED scores that are possible with the algorithms presented here

Prioritizing Populations for Conservation Using Phylogenetic Networks

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations

DM-PhyClus: A Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Background. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus, that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement. Results. Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis. Conclusions. DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies

Quantifying the relative importance of climate and habitat on structuring the species and taxonomic diversity of aquatic plants in a biodiversity hotspot of tropical Asia

It has not been well known how climate and habitat variables will influence the distribution of plant species to some extents at mesoscales. In this report, by using the distribution of aquatic plants in Western Ghats, a biodiversity hotspot in tropical Asian region, I quantify the relative importance of climate and habitat variables on structuring spatially species richness and taxonomic diversity patterns using structural equation modeling. All the sampling qudrats in the region used for the study has a spatial resolution of 0.5 latitude × 0.5 longitude. The results showed that species richness is high in both northern and southern part of the region, while low in the middle part. In contrast, taxonomic distinctiveness is relatively homogeneous over all the sampling quadrats in the region. Structural equation modeling suggested that taxonomic distinctiveness patterns of aquatic plants in the region follow temperature (partial regression coefficient=0.31, p<0.05) and elevational (partial regression coefficient=0.31, p<0.05) gradients, while richness patterns cannot be explained by any of the currently used variables. In conclusion, environmental variables that are related to taxonomic distinctiveness would not be related to richness, given the fact that these two quantities are orthogonal more or less. Both climate and habitat are equally influential on taxonomic distinctiveness patterns for aquatic plants in Western Ghats of India

How are Natura 2000 protected areas covering different components of avian diversity in Spain?

We are grateful to all ornithologists involved in fieldwork, data collection, and data entry. We would like to thank SEO/Birdlife for kindly allowing us to use their Spanish Atlas of Breeding Birds (Martí & del Moral 2003) and particularly J.C. del Moral, B. Molina, and V. Escandell for their help and patience. Finally, we thank anonymous reviewers for their careful reading of our manuscript and their useful suggestions, which helped us improve the text’s final version.Protected areas are a relevant conservation tool at our disposal, especially for developing management strategies of natural habitats. However, explicit tests at large spatial scales about its effectivity protecting different components of biodiversity are still rare. This study explored the spatial matching between the distribution of three components of avian diversity (taxonomic, functional, and phylogenetic metrics) and the network of Natura 2000 protected areas in Spain, the EU country with the most extensive terrestrial coverage. Overall, the spatial distribution of taxonomic, functional, and phylogenetic diversity was slightly spatially congruent, matching with protected areas. However, each avian diversity metric showed differences in the arrangement of spatial clusters, also regarding the environment type. Species richness was higher in forests while it was lower in orchards, mixed environments, and arable lands. Functional dispersion was higher in forest and arable lands, while it was lower in wetlands. In contrast, the highest phylogenetic diversity was associated with wetlands and water bodies, with shrublands showing the lowest levels for this metric. All three avian diversity metrics were overall higher within than outside the Natura 2000 network. The species richness was higher in areas simultaneously protected by the Habitat and Birds Directives. Functional dispersion was higher in protected areas designed under the Birds Directive. Finally, the evolutionary uniqueness was well represented in all protected areas, although areas designed under Birds Directive showed the higher values for this metric. The presence of spatial mismatch among avian diversity components suggests the importance of considering taxonomic, functional, and evolutionary metrics simultaneously for a better spatial prioritisation in conservation planning

Global priorities for conservation across multiple dimensions of mammalian diversity

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts

Global patterns in functional rarity of marine fish

Funding: I.T.S. thanks CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Coordination for the Improvement of Higher Education Personnel), process number: #88881.129579/2016–01 (Finance Code 001) for a PhD scholarship. A.E.M. thanks the Leverhulme Trust (RPG-2019–402) for support.Rare species, which represent a large fraction of the taxa in ecological assemblages, account for much of the biological diversity on Earth. These species make substantial contributions to ecosystem functioning, and are targets of conservation policy. Here we adopt an integrated approach, combining information on the rarity of species trait combinations, and their spatial restrictedness, to quantify the biogeography of rare fish (a taxon with almost 13,000 species) in the world’s oceans. We find concentrations of rarity, in excess of what is predicted by a null expectation, near the coasts and at higher latitudes. We also observe mismatches between these rarity hotspots and marine protected areas. This pattern is repeated for both major groupings of fish, the Actinopterygii (bony fish) and Elasmobranchii (sharks, skates and rays). These results uncover global patterns of rarity that were not apparent from earlier work, and highlight the importance of using metrics that incorporate information on functional traits in the conservation and management of global marine fishes.Publisher PDFPeer reviewe

Habitats hold an evolutionary signal of past climatic refugia

Climatic refugia have often been associated with hotspots of richness and endemism, and identified on the basis of molecular or paleobotanical information. Here, we apply a phylogenetic analysis to 18,000 plant communities distributed across the Pyrenees, a south European mountain range, to identify climatic refugia from imprints of relictuality inferred from species' evolutionary distinctiveness (ED). We produced a genus-level phylogenetic tree to calculate the standardized mean ED value of plant communities (cED). Then, we explored which habitats concentrate the plant communities with the highest cED and the interrelated effect of past (long-term climatic stability) and present (topographic and spatial position) factors. Results show strong differences of cED among habitats: forests ranked first, followed by some open habitats like high altitude wetlands. Climate stability and roughness positively influenced cED. A weak negative association resulted between the two diversity measurements (richness and endemism rate) and also with cED. We propose that forests acted as 'mobile refugia' during the glacial-interglacial periods, supported by paleoenvironmental reconstructions revealing continuous presence at regional scale of key broadleaved trees at that time. Azonal habitats like the endemic-poor humid communities at high elevation would have also played an important role as more permanent microrefugia. Our approach identifies a variety of habitats and plant assemblages that have successfully withstood past climate change in different ways, and therefore would hold an important evolutionary potential to cope with current climate change. Given their potential role in preserving biodiversity, they should be integrated in future conservation agendas

Towards product platform introduction: optimising commonality of components

Companies that design and manufacture products for a wide range of related applications need to offer the right product for each use. A platform design strategy allows designing the product range based on product platforms, where some of the components and systems are common across the range whereas other components are individual for each product variant. This paper presents the problems that a company faces when trying to introduce a platform strategy and outlines a method to find suitable components to be made common. The method is shown with a simple case. The approach uses fuzzy logic to obtain a suitable criterion to assess the overall value of the product line and a genetic algorithm for finding the set of components to be made commo