Biology subjects

Pearse, W. D.

Publications and source records attributed to Pearse, W. D..

30 records · Page 2Linked to original sources

bioRxiv2021

AREAdata: a worldwide climate dataset averaged across spatial units at different scales through time

In an era of increasingly cross-discipline collaborative science, it is imperative to produce data resources which can be quickly and easily utilised by non-specialists. In particular, climate data often require heavy processing before they can be used for analyses. Here we describe AREAdata, a free-to-use online global climate dataset, pre-processed to provide the averages of various climate variables across differing administrative units (e.g., countries, states). These are daily estimates, based on the Copernicus Climate Data Stores ERA-5 data, regularly updated to the near-present and provided as direct downloads from our website (https://pearselab.github.io/areadata/). The daily climate estimates from AREAdata are consistent with other openly available data, but at much finer-grained spatial and temporal scales than available elsewhere. AREAdata complements the existing suite of climate resources by providing these data in a form more readily usable by researchers unfamiliar with GIS data-processing methods, and we anticipate these resources being of particular use to environmental and epidemiological researchers.

ecology↗

bioRxiv2021

Pronounced genetic separation among varieties of the Primula cusickiana species complex, a Great Basin endemic

Distinguishing between unique species and populations with strong genetic structure is a common challenge in population genetics, especially in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the relations between species complex members, and RADseq methods are commonly used to compare closely related species across thousands of genetic loci. Here we use RADseq to clarify the relations between geographically distinct but morphologically similar varieties of the Primula cusickiana species complex, and to contextualize past findings of strong genetic structure among populations within varieties. Our genomic analyses demonstrate pronounced separation between isolated populations of this Great Basin endemic, indicating that the current varietal classification of complex members is inaccurate and emphasizing their conservation importance. We discuss how these results correspond to recent biogeographical models used to describe the distribution of other sky island taxa in western North America. Our findings also fit into a wider trend observed for alpine Primula species complexes, and we consider how heterostylous breeding systems may be contributing to frequent diversification via allopatric speciation in this genus.

evolutionary biology↗

bioRxiv2021

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 macro-taxa 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 one sequences from the same specimens to generate a phylogeny and tested evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, morphological ground beetle 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.

evolutionary biology↗

bioRxiv2021

Fractal triads efficiently sample ecological diversity and processes across spatial scales

The relative influence of ecological assembly processes, such as environmental filtering, competition, and dispersal, vary across spatial scales. Changes in phylogenetic and taxonomic diversity across environments provide insight into these processes, however, it is challenging to assess the effect of spatial scale on these metrics. Here, we outline a nested sampling design that fractally spaces sampling locations to concentrate statistical power across spatial scales in a study area. We test this design in northeast Utah, at a study site with distinct vegetation types (including sagebrush steppe and mixed conifer forest), that vary across environmental gradients. We demonstrate the power of this design to detect changes in community phylogenetic diversity across environmental gradients and assess the spatial scale at which the sampling design captures the most variation in empirical data. We find clear evidence of broad-scale changes in multiple features of phylogenetic and taxonomic diversity across aspect. At finer scales, we find additional variation in phylo-diversity, highlighting the power of our fractal sampling design to efficiently detect patterns across multiple spatial scales. Thus, our fractal sampling design and analysis effectively identify important environmental gradients and spatial scales that drive community phylogenetic structure. We discuss the insights this gives us into the ecological assembly processes that differentiate plant communities found in northeast Utah.

ecology↗

bioRxiv2020

A novel framework for modeling the evolution of cross-scale ecological assembly

Community assembly can be driven by species responses to environmental gradients, and interactions within (e.g., competition) and across (e.g., herbivory) clades. These ecological dynamics are mediated by species traits, which are in turn shaped by past evolution. As such, identifying the drivers of species assembly is made difficult by the differing temporal and spatial scales of ecological and evolutionary dynamics. Two recent advances have emerged to address the cross-scale challenge of modeling species assembly: phylogenetic generalized linear mixed modeling (PGLMM) and earth observation networks (EONs). PGLMM integrates through time by modeling the evolution of trait-based community assembly, while EONs synthesize across space by placing standardized site-level species occurrence data within their regional context. Here we describe a framework for combining these tools to investigate the drivers of species assembly, and so address three outstanding questions: (1) Does evolution adapt or constrain regional-scale environmental responses? (2) Do evolved responses to past competition minimize or enhance present-day competition? (3) Are species cross-clade associations evolutionarily constrained? We provide a conceptual overview of how PGLMM and EONs can be synthesized to answer these questions, and provide exemplar Bayesian PGLMM code. Finally, we describe the capacity of these tools to aid in conservation and natural resource management, including predicting future colonization by rare and invasive species, vulnerable mutualisms, and pest and pathogen outbreaks.

evolutionary biology↗

bioRxiv2020

Cryptic diversity in the model fern genus Ceratopteris (Pteridaceae)

Cryptic species are present throughout the tree of life. They are especially prevalent in ferns, because of processes such hybridization, polyploidy, and reticulate evolution. In addition, the morphological simple body plan of ferns limits phenotypic variation and makes it difficult to detect crypic species in ferns without molecular work. The model fern genus Ceratopteris has long been suspected to harbor cryptic diversity, specifically in the highly polymorphic C. thalictroides. Yet no studies have included samples from throughout the pan-tropical range of Ceratopteris or utilized genomic sequencing, making it difficult to assess the full extent of cryptic variation within this genus. Here, we present the first multilocus phylogeny of the genus using reduced representation genomic sequencing (RADseq) and examine population structure, phylogenetic relationships, and ploidy level variation. We recover similar species relationships found in previous studies, find support for a named cryptic species as genetically distinct, and identify a novel putative species from within C. thalictroides sensu latu in Central and South America.

plant biology↗

bioRxiv2019

The realised velocity of climate change reveals remarkable idiosyncrasy of species’ distributional shifts

To date, our understanding of how species have shifted in response to recent climate warming has been based on a few studies with a limited number of species. Here we present a comprehensive, global overview of species distributional responses to changing climate across a broad variety of taxa (animals, plants, and fungi). We characterise species responses using a metric that describes the realised velocity of climate change: how closely species responses have tracked changing climate through time. In contrast to existing climate velocity metrics that have focused on space, we focus on species and index their responses to a null expectation of change in order to examine drivers of inter-specific variation. Here we show that species are tracking climate on average, but not sufficiently to keep up with the pace of climate change. Further, species responses are highly idiosyncratic, and thus highlight that projections assuming uniform responses may be misleading. This is in stark contrast to species present-day and historical climate niches, which show strong evidence of the imprint of evolutionary history and functional traits. Our analyses are a first step in exploring the vast wealth of empirical data on species historic responses to recent climate change.

ecology↗

bioRxiv2019

Phylogenetic diversity efficiently and accurately prioritizes the conservation of aquatic macroinvertebrate communities

O_LILand degradation is a leading cause of biodiversity loss yet its consequences on freshwater ecosystems are poorly understood, exacerbating difficulties with assessing ecosystem quality and the effectiveness of restoration practices.\nC_LIO_LIMany monitoring programs rely on macroinvertebrates to assess the biotic effects of degradation and/or restoration and management actions on freshwater ecosystems. The ratio of Observed (O) to Expected (E) macroinvertebrate taxa at a given site--O/E--is often used for this purpose, despite the amount of modeling and data required to generate expectations and difficulties quantitatively assessing the degree of degradation at a site.\nC_LIO_LIDespite widespread use in academic biology, phylogenetic diversity is rarely applied in management, regardless of empirical correlations between phylogenetic diversity and management targets such as ecosystem structure and function.\nC_LIO_LIWe use macroinvertebrate data from 1,400 watersheds to evaluate the potential for phylogenetic metrics to inform evaluations of management practices. These data have been collected since 1998, and have been used to determine the effectiveness of conservation management for the maintenance and restoration of riparian and aquatic systems.\nC_LIO_LIPhylogenetic diversity detected degradation as effectively as O/E, despite not having baseline expectation data. Site disturbance, road density, and broader environmental drivers such as mean annual temperature strongly predicted site phylogenetic diversity, providing concrete management objectives to increase site health.\nC_LIO_LISynthesis and applications. Management efforts targeted solely at taxonomic metrics, such as O/E, have been successfully used to manage sites. We show here that phylogenetic diversity metrics can support such efforts by providing additional information about the kind of species at sites. Given the ease with which such approaches can be applied, we call on others to use them to supplement existing prioritization schemes.\nC_LI

ecology↗

bioRxiv2019

Risks to pollinators from different land-use transitions: bee species’ responses to agricultural expansion show strong phylogenetic signal

Bee species worldwide are facing a future of further land-use change and intensification. Populations of closely-related species with similar ecological characteristics are likely to respond similarly to such pressures. Such phylogenetic signal in species responses could undermine the stability of pollination services in agricultural and natural systems. We use abundance data from a global compilation of bee assemblages in different land uses to assess the sensitivity of 573 bee species to agricultural expansion, intensification and urbanization; and combine the results with the Bee Tree of Life to assess phylogenetic signal. In addition, we assess whether variation in species sensitivity to land-use change is better explained by phylogenetic or available functional trait differences. Bee species show strong phylogenetic signal in sensitivity to agricultural land expansion but only a weak signal in sensitivity to agricultural intensification and urbanisation. Sensitivities were usually best explained by a combination of functional and phylogenetic distances. This finding suggests that the commonly-recorded traits, despite being meaningful as functional response traits, do not capture all important determinants of bee species vulnerability or resistance. However, it also suggests that model-based predictions of the sensitivity of poorly known species may be sufficient to help guide conservation efforts.

ecology↗

bioRxiv2018

What we (don’t) know about global plant diversity

RationaleThe era of big biodiversity data has led to rapid, exciting advances in theoretical and applied biological, ecological and conservation sciences. While large genetic, geographic and trait databases are available, these are neither complete nor random samples of the globe. Biases in species absence in these databases create problems, reducing our inferential and predictive power.\n\nMethodsWe performed a comprehensive examination of the taxonomic and spatial sampling in the most complete current databases for plant genes, locations, and traits.\n\nResultsOnly 17.7% of the worlds described land plants feature in all three databases, meaning that more than 82% of plant biodiversity lacks representation in at least one database. Species coverage is highest for location data and lowest for genetic data. Bryophytes and orchids stand out taxonomically and the equatorial region stands out spatially as poorly represented in all databases.\n\nConclusionWe have highlighted a number of clades and regions about which we know little functionally, spatially and genetically, on which we should set research targets. The scientific community should recognize and reward the significant value, both for biodiversity science and conservation, of filling in these gaps in our knowledge of the plant tree of life.

ecology↗

bioRxiv2018

The interaction of phylogeny and community structure: linking clades’ ecological structures and trait evolution

1AimCommunity phylogenetic studies use information about species evolutionary relationships to understand the processes of community ecological assembly. A central premise of the field is that species evolution maps onto ecological patterns, and phylogeny reveals something more than species traits alone. We argue, therefore, that there is a need to better understand and model the interaction of phylogeny with species traits and community composition.\n\nInnovationWe outline a new method that identifies clades with unusual ecological structures, based around partitioning the variation of species site occupancies ({beta}-diversity). Eco-phylogenetic theory would predict that these clades should also demonstrate distinct evolutionary trajectories. We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between species ecological structure and evolutionary history.\n\nMain conclusionsUsing an empirical dataset of mammals from around the world, we identify two clades of rodents that tend not to co-occur (are phylogenetically overdispersed), and then find independent evidence of slower rates of body mass evolution in these clades. We suggest that our approach, which assumes nothing about the mode of species trait evolution but rather seeks to explain it using ecological information, presents a new way to examine eco-phylogenetic structure.

evolutionary biology↗

bioRxiv2018

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 position 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, imputating 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.

zoology↗