Catching crabs: a case study in local-scale English conservation

Wells-next-the-Sea and Cromer in Norfolk (England) both rely upon their local crab populations, since crabbing (gillying) is a major part of their tourist industry. Compared to a control site with no crabbing, crabs from Wells harbour and Cromer pier were found to have nearly six times the amount of limb damage. Crabs caught by the general public had more injuries than crabs caught in controlled conditions, suggesting the buckets in which the crabs were kept were to blame. Since there is much evidence that such injuries have negative impacts on the survival and reproductive success of the shore crab, this is taken as evidence of non-lethal injury from humans having a population-level effect on these animals. Questionnaire data demonstrated a public lack of awareness and want for information, which was then used to obtain funding to produce a leaflet campaign informing the public of how to crab responsibly. All data collected is available online at http://dx.doi.org/10.6084/m9.figshare.979288

Animating and exploring phylogenies with fibre plots

Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies

Global Analysis of Population Growth and Decline

Species of plants and animals have populations that are declining at a rapid rate and possibly face extinction. To combat this decline, we must first understand where and why species are declining. We compared known species population growth rates in the COMPADRE (7024 different plant populations) and COMADRE (1927 different animal populations) databases to a variety of possible factors and other databases

Multiple Sequence Alignment While Assessing Saturation Across Sequence Data

Constructing and analyzing phylogenetic trees is central to biological disciplines such as evolutionary and systematic biology. Accurate phylogenetic inference improves the estimation of evolutionary relationships, rates of molecular evolution, and Operational Taxonomic Units (OTUs). Careful alignment of sequence data is critical prior to any phylogenetic reconstruction, and there are many different multiple sequence alignment programs that are currently used (reviewed in Edgar & Batzoglou 2006). However, difficulty persists when using alignments to accurately determine actual genetic divergences. A major, yet under-explored, problem is saturation: the repetition of base substitutions at a single site within a sequence. Saturation causes issues because numerous substitutions in sequences within an alignment can erroneously underestimate divergence. Here, we present an algorithm, Splinter, that identifies and accounts for saturation during DNA sequence alignment

Evolution of Mammalian Migrations for Refuge, Breeding, and Food

Many organisms migrate between distinct habitats, exploiting variable resources while profoundly affecting ecosystem services, disease spread, and human welfare. However, the very characteristics that make migration captivating and significant also make it difficult to study, and we lack a comprehensive understanding of which species migrate and why. Here we show that, among mammals, migration is concentrated within Cetacea and Artiodactyla but also diffusely spread throughout the class (found in 12 of 27 orders). We synthesize the many ecological drivers of round-trip migration into three types of movement—between breeding and foraging sites, between breeding and refuge sites, and continuous tracking of forage/prey—each associated with different traits (body mass, diet, locomotion, and conservation status). Our results provide only partial support for the hypothesis that migration occurs without phylogenetic constraint. Furthermore, our findings suggest that categorizing migration into these three types may aid predictions of migrants’ responses to environmental changes

Preserving Evolutionary History with Improved Confidence

We thank Faith (2019) and Mindell (2019) for their insightful perspectives on our study of the impact of phylogenetic imputation on the assessment of evolutionary distinctiveness (ED; Isaac et al., 2007). As Mindell highlights, the finding that ED scores for species on a phylogeny are remarkably robust despite having species missing from that phylogeny is encouraging; our results suggest that we can be confident in moving forward with prioritization of the species for which we have data. This is important because in some cases, for example, it may take considerable time to obtain samples from the missing species, resulting in further delay before the ED scores for those species already sampled can be used to inform management decisions. We cautioned, however, that the ED scores for those missing species may be imputed imprecisely, and so we gave guidelines for working with imputed species’ ED scores. With this in mind, we offer some additional thoughts resulting from the commentaries of Mindell and Faith

The Effect of Phylogenetic Uncertainty and Imputation on EDGE Scores

Faced with the challenge of saving as much diversity as possible given financial and time constraints, conservation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set such evolutionarily based conservation priorities for a number of taxa, such as mammals, birds, corals, amphibians, and sharks. Each application of EDGE has required some form of correction to account for species whose positions within the tree of life are unknown. Perhaps the most advanced of these corrections is phylogenetic imputation, but to date there has been no systematic assessment of both the sensitivity of EDGE scores to a phylogeny missing species, and the impact of using imputation to correct for species missing from the tree. Here, we perform such an assessment, by simulating phylogenies, removing some species to make the phylogeny incomplete, imputing the position of those species, and measuring (1) how robust ED scores are for the species that are not removed and (2) how accurate the ED scores are for those removed and then imputed. We find that the EDGE ranking for species on a tree is remarkably robust to missing species from that tree, but that phylogenetic imputation for missing species, while unbiased, does not accurately reconstruct species’ evolutionary distinctiveness. On the basis of these results, we provide clear guidance for EDGE scoring in the face of phylogenetic uncertainty

The Interaction of Phylogeny and Community Structure: Linking the Community Composition and Trait Evolution of Clades

Aim Community phylogenetic studies use information about the evolutionary relationships of species to understand the ecological processes of community assembly. A central premise of the field is that the evolution of species maps onto ecological patterns, and phylogeny reveals something more than species traits alone about the ecological mechanisms structuring communities, such as environmental filtering, competition, and facilitation. We argue, therefore, that there is a need for better understanding and modelling of the interaction of phylogeny with species traits and community composition. Innovation We outline a new approach that identifies clades that are ecophylogenetically clustered or overdispersed and assesses whether those clades have different rates of trait evolution. Ecophylogenetic theory would predict that the traits of clustered or overdispersed clades might have evolved differently, in terms of either tempo (fast or slow) or mode (e.g., under constraint or neutrally). We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between the ecological co‐occurrence patterns of a species and its evolutionary history. Main conclusions Using an empirical dataset of mammals from around the world, we identify two clades of rodents whose species tend not to co‐occur in the same local assemblages (are phylogenetically overdispersed) and find independent evidence of slower rates of body mass evolution in these clades. Our approach, which assumes nothing about the mode of species trait evolution but instead seeks to explain it using ecological information, presents a new way to examine ecophylogenetic structure

Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology

Functional traits mediate species’ responses to, and roles within, their environment and are constrained by evolutionary history. While we have a strong understanding of trait evolution for macrotaxa such as birds and mammals, our understanding of invertebrates is comparatively limited. Here, we address this gap in North American beetles with a sample of ground beetles (Carabidae), leveraging a large-scale collection and digitization effort by the National Ecological Observatory Network (NEON). For 154 ground beetle species, we measured seven morphological traits, which we placed into a recently developed effect–response framework that characterizes traits by how they predict species’ effects on their ecosystems or responses to environmental stressors. We then used cytochrome oxidase 1 sequences from the same specimens to generate a phylogeny and tested the evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, ground beetle morphological traits. These results indicate that, for these species, beetle body shape trait evolution is constrained, and phylogenetic inertia is a stronger driver of beetle traits than (recent) environmental responses. Strong correlations among effect and response traits suggest that future environmental drivers are likely to affect both ecological composition and functioning in these beetles