Browsing by Author "Matthews, Thomas J."
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- Assessing taxonomic and functional change in British breeding bird assemblages over timePublication . Wayman, Joseph P.; Sadler, Jonathan P.; Pugh, Thomas A. M.; Martin, Thomas E.; Tobias, Joseph A.; Matthews, Thomas J.AIM: The aim was to identify the primary drivers of compositional change in breeding bird assemblages over a 40-year period. LOCATION: Britain. TIME PERIOD: From 1970 to 2010. MAJOR TAXA STUDIED: Birds. METHODS: Using morphological trait measurements and a dataset of presence-absence data for British breeding birds surveyed in 10 km × 10 km hectads during two time periods, we calculated temporal taxonomic and functional beta diversity for each hectad alongside the change in species richness, mean nearest taxon distance (MNTD) and mean pairwise distance (MPD). We also estimated potential drivers of beta diversity, including climatic and land-use and land-cover (LULC) change variables, elevation and assemblage species richness in 1970 (1970rich). We used random forest regressions to test which variables best explained compositional change in the assemblages. We also assessed spatial taxonomic and functional change by analysing multiple-site beta diversity and pairwise dissimilarities between time periods. RESULTS: Initial (1970) species richness was the most important predictor (highest importance score) across all models, with areas characterized by higher initial richness experiencing less assemblage change overall. The coordinates included to capture spatial autocorrelation in the data were also important predictors of change. Most cli-mate and LULC variables had relatively low explanatory power; elevation and average temperature were the most influential. All metrics increased slightly with increasing elevation, except for species richness change and MPD, which decreased. MAIN CONCLUSIONS: The composition of British breeding bird assemblages changed substantially between 1970 and 2010. Spatial heterogeneity increased, both taxonomically and functionally. We show evidence that hectads with larger assemblages have been buffered from temporal diversity change and that those at higher elevations changed more in composition than those at lower elevations. Overall, coarse-resolution climate and LULC explained only small to moderate amounts of variation, suggesting that stochastic assembly change or finer-scale drivers might be drivers of temporal changes in assemblage composition.
- Assessing tropical forest restoration after fire using birds as indicators : An afrotropical case studyPublication . Rurangwa, Marie Laure; Matthews, Thomas J.; Niyigaba, Protais; Tobias, Joseph A.; Whittaker, Robert J.The necessity to restore rainforest habitats degraded by anthropogenic fires is widely recognized, however, research on restoration approaches has mainly centred on the recovery of forest structural complexity. There is insufficient evidence on the efficacy of restoration methods in the recovery of the faunal diversity and features linked to key ecosystem functions. We assessed the taxonomic diversity and functional trait structure of bird assemblages in undisturbed primary forest and fire-affected habitats undergoing natural regeneration, as well as areas of assisted natural regeneration, in Nyungwe National Park, Rwanda. We compiled bird occurrence data from point-count sampling, and obtained morphological traits for all species in our assemblages using measurements taken from wild birds and museum specimens. We found marked differences in species composition between primary forest habitats and regenerating forest, with similarity increasing over time since perturbation. Taxonomic diversity was higher in primary forest, and similar between the two restoration approaches. Functional diversity was lower in assisted naturally regenerated habitats, although separate analyses within dietary guilds revealed no differences across habitats. Among desired restoration outcomes, tree species diversity was the leading positive driver of avian species diversity, fern coverage exerted negative effects, while canopy cover had a positive but weak influence. Our findings underscore the importance of preventing anthropogenic fires in tropical rainforest since their impacts on ecological processes are not easily reversed, as shown by the lack of improvement in avian diversity metrics under assisted naturally regeneration in relation to natural regeneration. We stress the need to document both floral and faunal recovery in order to aid informed decision-making on restoration methods.
- AVONET : morphological, ecological and geographical data for all birdsPublication . Tobias, Joseph A.; Sheard, Catherine; Pigot, Alex L.; Devenish, Adam J. M.; Yang, Jingyi; Sayol, Ferran; Neate‐Clegg, Montague H. C.; Alioravainen, Nico; Weeks, Thomas L.; Barber, Robert A.; Walkden, Patrick A.; Cooper, Jacob C.; Pauwels, Olivier S. G.; Analuddin, Kangkuso; Fjeldså, Jon; Seddon, Nathalie; Sweet, Paul R.; DeClerck, Fabrice A. J.; Naka, Luciano N.; Brawn, Jeffrey D.; Aleixo, Alexandre; MacGregor, Hannah E. A.; Böhning‐Gaese, Katrin; Rahbek, Carsten; Fritz, Susanne A.; Thomas, Gavin H.; Schleuning, Matthias; Jones, Samuel E. I.; Vincent, Claire; Phillips, Anna G.; Marples, Nicola M.; Montaño‐Centellas, Flavia A.; Leandro‐Silva, Victor; Claramunt, Santiago; Darski, Bianca; Freeman, Benjamin G.; Bregman, Tom P.; Cooney, Christopher R.; Hughes, Emma C.; Capp, Elliot J. R.; Varley, Zoë K.; Friedman, Nicholas R.; Korntheuer, Heiko; Corrales‐Vargas, Andrea; Trisos, Christopher H.; Weeks, Brian C.; Hanz, Dagmar M.; Töpfer, Till; Bravo, Gustavo A.; Remeš, Vladimír; Nowak, Larissa; Carneiro, Lincoln S.; Moncada R., Amilkar J.; Matysioková, Beata; Baldassarre, Daniel T.; Martínez‐Salinas, Alejandra; Wolfe, Jared D.; Chapman, Philip M.; Daly, Benjamin G.; Sorensen, Marjorie C.; Neu, Alexander; Ford, Michael A.; Mayhew, Rebekah J.; Fabio Silveira, Luis; Kelly, David J.; Annorbah, Nathaniel N. D.; Pollock, Henry S.; Grabowska‐Zhang, Ada M.; McEntee, Jay P.; Carlos T. Gonzalez, Juan; Meneses, Camila G.; Muñoz, Marcia C.; Powell, Luke L.; Jamie, Gabriel A.; Matthews, Thomas J.; Johnson, Oscar; Brito, Guilherme R. R.; Zyskowski, Kristof; Crates, Ross; Harvey, Michael G.; Jurado Zevallos, Maura; Hosner, Peter A.; Bradfer‐Lawrence, Tom; Maley, James M.; Stiles, F. Gary; Lima, Hevana S.; Provost, Kaiya L.; Chibesa, Moses; Mashao, Mmatjie; Howard, Jeffrey T.; Mlamba, Edson; Chua, Marcus A. H.; Li, Bicheng; Gómez, M. Isabel; García, Natalia C.; Päckert, Martin; Fuchs, Jérôme; Ali, Jarome R.; Derryberry, Elizabeth P.; Carlson, Monica L.; Urriza, Rolly C.; Brzeski, Kristin E.; Prawiradilaga, Dewi M.; Rayner, Matt J.; Miller, Eliot T.; Bowie, Rauri C. K.; Lafontaine, René‐Marie; Scofield, R. Paul; Lou, Yingqiang; Somarathna, Lankani; Lepage, Denis; Illif, Marshall; Neuschulz, Eike Lena; Templin, Mathias; Dehling, D. MatthiasFunctional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.
- AVOTREX: A Global Dataset of Extinct Birds and Their TraitsPublication . Sayol, Ferran; Wayman, Joseph P.; Dufour, Paul; Martin, Thomas E.; Hume, Julian P.; Jørgensen, Maria Wagner; Martínez‐Rubio, Natàlia; Sanglas, Ariadna; Soares, Filipa C.; Cooke, Rob; Mendenhall, Chase D.; Margolis, Jay R.; Illera, Juan Carlos; Lemoine, Rhys; Benavides, Eva; Lapiedra, Oriol; Triantis, Kostas A.; Pigot, Alex L.; Tobias, Joseph A.; Faurby, Søren; Matthews, Thomas J.Motivation Human activities have been reshaping the natural world for tens of thousands of years, leading to the extinction of hundreds of bird species. Past research has provided evidence of extinction selectivity towards certain groups of species, but trait information is lacking for the majority of clades, especially for prehistoric extinctions identified only through subfossil remains. This incomplete knowledge potentially obscures the structure of natural communities, undermining our ability to infer changes in biodiversity across space and time, including trends in functional and phylogenetic diversity. Biases in currently available trait data also limit our ability to identify drivers and processes of extinction. Here we present AVOTREX, an open-access database of species traits for all birds known to have gone extinct in the last 130,000 years. This database provides detailed morphological information for 610 extinct species, along with a pipeline to build phylogenetic trees that include these extinct species. Main Types of Variables Contained For each extinct bird species, we provide information on the taxonomy, geographic location, and period of extinction. We also present data on island endemicity, flight ability, and body mass, as well as standard measurements of external (matching the AVONET database of extant birds) and skeletal morphology from museum specimens where available. To ensure comprehensive morphological data coverage, we estimate all missing morphological measurements using a data imputation technique based on machine learning. Finally, we provide an R package to graft all extinct species onto a global phylogeny of extant species (BirdTree).
- A biogeographical perspective on species abundance distributions : recent advances and opportunities for future researchPublication . Matthews, Thomas J.; Borges, Paulo A. V.; Azevedo, Eduardo B.; Whittaker, Robert J.It has become increasingly recognized that multiple processes can generate similar shapes of species abundance distributions (SADs), with the result that the fit of a given SAD model cannot unambiguously provide evidence in support of a given theory or model. An alternative approach to comparing the fit of different SAD models to data from a single site is to collect abundance data from a variety of sites, and then build models to analyse how different SAD properties (e.g. form, skewness) vary with different predictor variables. Such a biogeographical approach to SAD research is potentially very revealing, yet there has been a general lack of interest in SADs in the biogeographical literature. In this Perspective, we address this issue by highlighting findings of recent analyses of SADs that we consider to be of intrinsic biogeographical interest. We use arthropod data drawn from the Azorean archipelago to further highlight how analyses of SAD form and function may be biogeographically informative. We hope that, by reviewing a number of novel approaches, our article may prove to be a catalyst for a greater interest in analysing SADs in biogeography.
- Biological knowledge shortfalls impede conservation efforts in poorly studied taxa—A case study of LaboulbeniomycetesPublication . Haelewaters, Danny; Matthews, Thomas J.; Wayman, Joseph P.; CAZABONNE, Jonathan; Heyman, Felix; Quandt, C. Alisha; Martin, Thomas EABSTRACT: Most empirical research on biological shortfalls has focused on vertebrate taxa. This is important given many species in poorly studied groups such as invertebrates, plants, and fungi are predicted to possess high conservation risk. Here, we focus on Laboulbeniomycetes: a class of microfungi that are understudied. We examined four shortfalls: Linnean (knowledge gaps in species diversity), Wallacean (knowledge gaps in distributions), Latimerian (knowledge gaps in species persistence), and the newly introduced Scottian (knowledge gaps in species conservation assessments) shortfalls. The Linnean shortfall in Laboulbeniomycetes is hard to predict due to inconsistent spe-cies description rates. Analysis of distribution patterns indicates Laboulbeniomycetes are likely to experience an extremely high Wallacean shortfall, with many species hav-ing highly disjunct known distributions. Latimerian shortfall analysis shows over half (51%) of Laboulbeniomycetes have not been recorded in >50 years, while the group has a collective Scottian shortfall of 100%, given none of the 2454 described species have received an IUCN threat assessment. We suggest continued study of natural his-tory collections, expanded citizen science programmes, and machine- learning iden-tification approaches as important tools for reducing knowledge shortfalls in both Laboulbeniomycetes and poorly studied taxa more generally.
- Birds that are more commonly encountered in the wild attract higher public interest onlinePublication . Mittermeier, John C.; Roll, Uri; Matthews, Thomas J.; Correia, Ricardo; Grenyer, RichLarge body size, the defining characteristic of "charismatic megafauna," is often viewed as the most significant correlate of higher public interest in species. However, common, local species (many of which are not large) can also generate public interest. We explored the relative importance of body size versus local occurrence in patterns of online interest in birds using a large sample of digital human-wildlife interactions (367 million Wikipedia pageviews) that included more than 10,000 bird species and a range of cultural and geographic contexts (represented by 25 Wikipedia language editions). We compared interest in Wikipedia, as measured by pageviews, with a bird's body size and its regional observation frequency (using data from ). We found that local species (i.e., those that occur in the wild in the country responsible for the majority of a Wikipedia language edition's pageviews) attract more pageviews than global species. Both body size and observation frequency had a positive correlation with Wikipedia pageviews across languages, but eBird observation frequency explained more of the variance in pageviews on average. In a model that included both observation frequency and body size, observation frequency was a significantly better predictor of pageviews than body size in 24 of 25 languages. Our results demonstrate that the opportunity to encounter birds in the wild is a significant correlate of increased online interest in birds across multiple linguistic and geographic contexts. This relationship provides insight into why some species attract greater interest than others and emphasizes the overlooked potential of common species in conservation marketing.
- Calculating functional diversity metrics using neighbor‐joining treesPublication . Cardoso, Pedro; Guillerme, Thomas; Mammola, Stefano; Matthews, Thomas J.; Rigal, François; Graco‐Roza, Caio; Stahls, Gunilla; Carvalho, José CarlosThe study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers. We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles. We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets. Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space.
- Community dissimilarity of angiosperm trees reveals deep‐time diversification across tropical and temperate forestsPublication . Kusumoto, Buntarou; Kubota, Yasuhiro; Baselga, Andrés; Gómez‐Rodríguez, Carola; Matthews, Thomas J.; Murphy, Daniel J.; Shiono, TakayukiQUESTION: To better understand the influence of deep-time diversification on extant plant communities, we assessed how community dissimilarity increases with spatial and climatic distances at multiple taxonomic ranks (species, genus, family, and order) in angiosperm trees. We tested the prediction that the dissimilarity–distance relationship should change across taxonomic ranks depending on the deep-time diversification in different biogeographical regions reflecting geohistories and geographical settings. LOCATION: Global. METHODS: Using a data set of plot-based surveys across the globe (861 plots), we compiled a community composition matrix comprising 21,455 species, 2,741 genera, 240 families, and 57 orders. We then calculated Sørensen's pairwise dissimilarity (βsor), and its turnover (βsim) and nestedness (βsne) components, among plots within seven biogeographical regions. Finally, we modeled the relationships between the biotic dissimilarities and the spatial/climatic distances at each taxonomic rank, and compared them among regions. RESULTS: βsor and βsim increased with increasing spatial and climatic distance in all biogeographical regions: βsim was dominant in all biogeographical regions in general, while βsne showed relatively high contributions to total dissimilarity in the temperate regions with historically unstable climatic conditions. The βsim-distance curve was more saturated at smaller spatial scales in the tropics than in the temperate regions. In general, the curves became flatter at higher taxonomic ranks (order or family), with the exception of Africa, North America, and Australia, pointing to region-specific geographical constraints. CONCLUSIONS: Compositional dissimilarity was generally shaped through the abrupt turnover of species along spatial/climatic gradients. The relatively high importance of the nestedness component in the temperate regions suggests that historical dispersal filters related to extinction/colonization may play important roles. Region-specific changes in the turnover and nestedness components across taxonomic ranks suggest differential imprints of historical diversification over deep evolutionary time in shaping extant diversity patterns in each biogeographical region.
- Constraints on the distribution of species abundances indicate universal mechanisms of community assemblyPublication . Ulrich, Werner; Matthews, Thomas J.; Kubota, YasuhiroRecently, a 2018 study by Ulrich et al. introduced the Weibull distribution as a flexible approach to model the distribution of species abundances in ecological communities. They pointed to possible limitations in the realized parameter spaces of this distribution as possibly indicating ecological constraints on species abundances. Here, we explore this question in detail using three large global data sets on quantitatively assessed plant, invertebrate, and vertebrate communities. By fitting the Weibull distribution to these communities, we confirm that only a minor amount of the possible ranges in the scale and the shape parameters of the Weibull distribution are realized. Shapes of distributions become more similar across taxa with increasing species richness and average abundances. This finding points to stochastic explanations for species abundance shapes, possibly linked to local colonization and extinction dynamics. We introduce the Weibull survival time parameter as a way to define the proportion of rare species in a community. This proportion increased with increasing species richness.