Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree—a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes—called the “species tree.” One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the “concordance” with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping—but not identical—sets of labels, is called “supertree.” In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of “containing as a minor” and “containing as a topological minor” in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time \(2^{O(k^2)} \cdot n\), where n is the total size of the input.     

Sustained functional composition of pollinators in restored pastures despite slow functional restoration of plants

Habitat restoration is a key measure to counteract negative impacts on biodiversity from habitat loss and fragmentation. To assess success in restoring not only biodiversity, but also functionality of communities, we should take into account the re‐assembly of species trait composition across taxa. Attaining such functional restoration would depend on the landscape context, vegetation structure, and time since restoration. We assessed how trait composition of plant and pollinator (bee and hoverfly) communities differ between abandoned, restored (formerly abandoned) or continuously grazed (intact) semi‐natural pastures. In restored pastures, we also explored trait composition in relation to landscape context, vegetation structure, and pasture management history. Abandoned pastures differed from intact and restored pastures in trait composition of plant communities, and as expected, had lower abundances of species with traits associated with grazing adaptations. Further, plant trait composition in restored pastures became increasingly similar to that in intact pastures with increasing time since restoration. On the contrary, the trait composition of pollinator communities in both abandoned and restored pastures remained similar to intact pastures. The trait composition for both bees and hoverflies was influenced by flower abundance and, for bees, by connectivity to other intact grasslands in the landscape. The divergent responses across organism groups appeared to be mainly related to the limited dispersal ability and long individual life span in plants, the high mobility of pollinators, and the dependency of semi‐natural habitat for bees. Our results, encompassing restoration effects on trait composition for multiple taxa along a gradient in both time (time since restoration) and space (connectivity), reveal how interacting communities of plants and pollinators are shaped by different trait–environmental relationships. Complete functional restoration of pastures needs for more detailed assessments of both plants dispersal in time and of resources available within pollinator dispersal range.     

Urbanisation and the loss of phylogenetic diversity in birds

Despite the recognised conservation value of phylogenetic diversity, little is known about how it is affected by the urbanisation process. Combining a complete avian phylogeny with surveys along urbanisation gradients from five continents, we show that highly urbanised environments supported on average 450 million fewer years of evolutionary history than the surrounding natural environments. This loss was primarily caused by species loss and could have been higher had not been partially compensated by the addition of urban exploiters and some exotic species. Highly urbanised environments also supported fewer evolutionary distinctive species, implying a disproportionate loss of evolutionary history. Compared with highly urbanised environments, changes in phylogenetic richness and evolutionary distinctiveness were less substantial in moderately urbanised environments. Protecting pristine environments is therefore essential for maintaining phylogenetic diversity, but moderate levels of urbanisation still preserve much of the original diversity.     

Applying complementary species vulnerability assessments to improve conservation strategies in the Galapagos Marine Reserve

Marine biodiversity can be protected by identifying vulnerable species and creating marine protected areas (MPAs) to ensure their survival. A wide variety of methods are employed by environmental managers to determine areas of conservation priority, however which methods should be applied is often a subject of debate for practitioners and scientists. We applied two species vulnerability assessments, the International Union for the Conservation of Nature (IUCN) red list of threatened species and FishBase’s intrinsic vulnerability assessment, to fish communities in three coastal habitats (mangrove, rocky and coral) on the island of San Cristobal, Galapagos. When using the IUCN red list of threatened species, rocky reefs hosted the greatest number of vulnerable species, however when applying the FishBase assessment of intrinsic vulnerability mangroves hosted the greatest abundance of ‘very-highly’ vulnerable species and coral ecosystems hosted the greatest abundance of ‘highly’ vulnerable species. The two methods showed little overlap in determining habitat types that host vulnerable species because they rely on different biological and ecological parameters. Since extensive data is required for IUCN red list assessments, we show that the intrinsic vulnerability assessment from FishBase can be used to complement the IUCN red list especially in data-poor areas. Intrinsic vulnerability assessments are based on less data-intensive methods than the IUCN red list, but nonetheless may bridge information gaps that can arise when using the IUCN red list alone. Vulnerability assessments based on intrinsic factors are not widely applied in marine spatial planning, but their inclusion as a tool for forming conservation strategies can be useful in preventing species loss.     

The influence of trap type on evaluating population structure of the semifossorial and social rodent <Emphasis Type="Italic">Octodon degus</Emphasis>

Trap type may influence captures of individuals in different age-sex categories in small mammal studies, resulting in biased population and demographic information. We deployed 4 live trap types at burrow systems of the rodent, Octodon degus Molina, 1782, in central Chile to determine trap efficacy in capturing individuals of 6 demographic categories. We captured 2672 individuals in 17 709 trap days (15.1% trapping success). Tomahawks were the most efficient trap capturing half of individuals during both years, followed by mesh Sherman traps, large Sherman traps, and medium Sherman traps in 2005. All trap types equally sampled sexes. Large and medium Sherman traps provided similar demographic structure, where half of the individuals captured were pups; Tomahawk traps sampled more adults than pups. Relative captures of pups were similar across different trap types, suggesting that pups are equally sampled by each of the deployed trap types. Relative captures of adults were lower in Sherman traps, suggesting that this age class avoided solid-walled traps. For Octodon degus, the sole use of Tomahawk traps may produce sufficient, unbiased demographic data. Only 4 trap mortalities occurred (0.15%). Researchers may minimize trap mortality without compromising sufficient demographic sampling by trapping during peak animal activity.     

Ceramide levels regulated by carnitine palmitoyltransferase 1C control dendritic spine maturation and cognition

The brain-specific isoform carnitine palmitoyltransferase 1C (CPT1C) has been implicated in the hypothalamic regulation of food intake and energy homeostasis. Nevertheless, its molecular function is not completely understood, and its role in other brain areas is unknown. We demonstrate that CPT1C is expressed in pyramidal neurons of the hippocampus and is located in the endoplasmic reticulum throughout the neuron, even inside dendritic spines. We used molecular, cellular, and behavioral approaches to determine CPT1C function. First, we analyzed the implication of CPT1C in ceramide metabolism. CPT1C overexpression in primary hippocampal cultured neurons increased ceramide levels, whereas in CPT1C-deficient neurons, ceramide levels were diminished. Correspondingly, CPT1C knock-out (KO) mice showed reduced ceramide levels in the hippocampus. At the cellular level, CPT1C deficiency altered dendritic spine morphology by increasing immature filopodia and reducing mature mushroom and stubby spines. Total protrusion density and spine head area in mature spines were unaffected. Treatment of cultured neurons with exogenous ceramide reverted the KO phenotype, as did ectopic overexpression of CPT1C, indicating that CPT1C regulation of spine maturation is mediated by ceramide. To study the repercussions of the KO phenotype on cognition, we performed the hippocampus-dependent Morris water maze test on mice. Results show that CPT1C deficiency strongly impairs spatial learning. All of these results demonstrate that CPT1C regulates the levels of ceramide in the endoplasmic reticulum of hippocampal neurons, and this is a relevant mechanism for the correct maturation of dendritic spines and for proper spatial learning.