Publications
98 results found
Tucker CM, Davies TJ, Cadotte MW, et al., 2018, On the relationship between phylogenetic diversity and trait diversity, Ecology, Vol: 99, Pages: 1473-1479
Pearse WD, Chamberlain SA, 2018, Suppdata: Downloading Supplementary Data from Published Manuscripts, The Journal of Open Source Software, Vol: 3, Pages: 721-721
Pearse WD, Barbosa AM, Fritz SA, et al., 2018, Building up biogeography: Pattern to process, Journal of Biogeography
Zanne AE, Pearse WD, Cornwell WK, et al., 2018, Functional biogeography of angiosperms: life at the extremes, New Phytologist, Vol: 218, Pages: 1697-1709
Pearse WD, Cavender-Bares J, Hobbie SE, et al., 2018, Homogenization of plant diversity, composition, and structure in North American urban yards, Ecosphere, Vol: 9, Pages: e02105-e02105
Pearse WD, Morales-Castilla I, James LS, et al., 2018, Global macroevolution and macroecology of passerine song, Evolution, Vol: 72, Pages: 944-960
Fountain-Jones NM, Pearse WD, Escobar LE, et al., 2018, Towards an eco-phylogenetic framework for infectious disease ecology, Biological Reviews, Vol: 93, Pages: 950-970
Isaac NJB, Pearse WD, 2018, The use of EDGE (Evolutionary Distinct Globally Endangered) and EDGE-like metrics to evaluate taxa for conservation, Phylogenetic diversity, Publisher: Springer, Cham, Pages: 27-39
Pearse WD, Morales-Castilla I, James LS, et al., 2018, Complexity is complicated and so too is comparing complexity metrics-A response to Mikula et al.(2018), Evolution, Vol: 72, Pages: 2836-2838
Pearse WD, Davis CC, Inouye DW, et al., 2017, A statistical estimator for determining the limits of contemporary and historic phenology, Nature Ecology & Evolution, Vol: 1, Pages: 1876-1882, ISSN: 2397-334X
Brooks SJ, Self A, Powney GD, et al., 2017, The influence of life history traits on the phenological response of British butterflies to climate variability since the late-19th century, Ecography, Vol: 40, Pages: 1152-1165
Gnanadesikan GE, Pearse WD, Shaw AK, 2017, Evolution of mammalian migrations for refuge, breeding, and food, Ecology and evolution, Vol: 7, Pages: 5891-5900
Pearse WD, 2017, Animating and exploring phylogenies with fibre plots, F1000 Research, Vol: 5, Pages: 2790-2790
Rubio de Casas R, Willis CG, Pearse WD, et al., 2017, Global biogeography of seed dormancy is determined by seasonality and seed size: a case study in the legumes, New Phytologist, Vol: 214, Pages: 1527-1536
Morales-Castilla I, Davies TJ, Pearse WD, et al., 2017, Combining phylogeny and co-occurrence to improve single species distribution models, Global Ecology and Biogeography, Vol: 26, Pages: 740-752
Pearse WD, 2016, Animating and exploring phylogenies with fibre plots, F1000Research, Vol: 5, Pages: 2790-2790
<ns4:p>Despite the progress that has been made in the visualisation of information since Haeckel's time, phylogenetic visualisation has moved forward remarkably little. 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. As an animation, I suggest it is a powerful method to help interpret large phylogenetic hypotheses, although snapshots of it can also be displayed. As we enter the Anthropocene, I argue there has never been a greater need to know humanity's true place in the world, as depicted in the tree of life.</ns4:p>
Pearse WD, 2016, Animating and exploring phylogenies with fibre plots., F1000Res, Vol: 5, ISSN: 2046-1402
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.
Nelson EJ, Helmus MR, Cavender-Bares J, et al., 2016, Commercial plant production and consumption still follow the latitudinal gradient in species diversity despite economic globalization, PloS one, Vol: 11, Pages: e0163002-e0163002
Hall SJ, Learned J, Ruddell B, et al., 2016, Convergence of microclimate in residential landscapes across diverse cities in the United States, Landscape ecology, Vol: 31, Pages: 101-117
Barak RS, Hipp AL, Cavender-Bares J, et al., 2016, Taking the long view: integrating recorded, archeological, paleoecological, and evolutionary data into ecological restoration, International Journal of Plant Sciences, Vol: 177, Pages: 90-102
Banks-Leite C, Pardini R, Tambosi LR, et al., 2015, Response to Comment on “Using ecological thresholds to evaluate the costs and benefits of set-asides in a biodiversity hotspot”, Science, Vol: 347, Pages: 731-731
Pearse WD, Chase MW, Crawley MJ, et al., 2015, Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline., PloS one, Vol: 10, Pages: e0126524-e0126524
Pearse WD, Cadotte MW, Cavender-Bares J, et al., 2015, Pez: Phylogenetics for the environmental sciences, Bioinformatics, Vol: 31, Pages: 2888-2890
Banks-Leite C, Pardini R, Tambosi LR, et al., 2014, Using ecological thresholds to evaluate the costs and benefits of set-asides in a biodiversity hotspot, Science, Vol: 345, Pages: 1041-1045, ISSN: 1095-9203
Ecological set-asides are a promising strategy for conserving biodiversity in human-modified landscapes; however, landowner participation is often precluded by financial constraints. We assessed the ecological benefits and economic costs of paying landowners to set aside private land for restoration. Benefits were calculated from data on nearly 25,000 captures of Brazilian Atlantic Forest vertebrates, and economic costs were estimated for several restoration scenarios and values of payment for ecosystem services. We show that an annual investment equivalent to 6.5% of what Brazil spends on agricultural subsidies would revert species composition and ecological functions across farmlands to levels found inside protected areas, thereby benefiting local people. Hence, efforts to secure the future of this and other biodiversity hotspots may be cost-effective.
Pearse WD, Purvis A, Roy DB, et al., 2014, Modelling ecological communities as if they were DNA, arXiv preprint arXiv:1403.7668
Pearse WD, Purvis A, Cavender-Bares J, et al., 2014, Metrics and models of community phylogenetics, Modern phylogenetic comparative methods and their application in evolutionary biology, Publisher: Springer, Berlin, Heidelberg, Pages: 451-464
Pearse WD, Green HK, Aldridge D, 2014, Catching crabs: a case study in local-scale English conservation, arXiv preprint arXiv:1404.0290
Banks-Leite C, Pardini R, Tambosi LR, et al., 2014, Conserving Brazil’s Atlantic forests–response., Science (New York, NY), Vol: 346, Pages: 1193-1193
Robert M Ewers DCR, 2013, Using landscape history to predict biodiversity patterns in fragmented landscapes, Ecology Letters, Vol: 16, Pages: 1221-1233, ISSN: 1461-023X
Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape ‘terrageny’, which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscapes.
Díaz S, Purvis A, Cornelissen JHC, et al., 2013, Functional traits, the phylogeny of function, and ecosystem service vulnerability, Ecology and Evolution, Vol: 3, Pages: 2958-2975, ISSN: 2045-7758
People depend on benefits provided by ecological systems. Understanding how these ecosystem services – and the ecosystem properties underpinning them – respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species’ effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms – which both depend on combinations of functional traits – correlate across species and how they are arranged on the species’ phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.
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