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  • Journal article
    Wearn OR, Rowcliffe JM, Carbone C, Pfeifer M, Bernard H, Ewers RMet al., 2017,

    Mammalian species abundance across a gradient of tropical land-use intensity: A hierarchical multi-species modelling approach

    , Biological Conservation, Vol: 212, Pages: 162-171, ISSN: 1873-2917

    Recent work in the tropics has advanced our understanding of the local impacts of land-use change on species richness. However, we still have a limited ability to make predictions about species abundances, especially in heterogeneous landscapes. Species abundances directly affect the functioning of an ecosystem and its conservation value. We applied a hierarchical model to camera- and live-trapping data from a region in Borneo, and estimated the relative abundance (controlling for imperfect detection) of 57 terrestrial mammal species, as a function of either categorical or continuous metrics of land-use change. We found that mean relative abundance increased (by 28%) from old-growth to logged forest, but declined substantially (by 47%) in oil palm plantations compared to forest. Abundance responses to above-ground live tree biomass (a continuous measure of local logging intensity) were negative overall, whilst they were strongly positive for landscape forest cover. From old-growth to logged forest, small mammals increased in their relative abundance proportionately much more than large mammals (169% compared to 13%). Similarly, omnivores and insectivores increased more than other trophic guilds (carnivores, herbivores and frugivores). From forest to oil palm, species of high conservation concern fared especially poorly (declining by 84%). Invasive species relative abundance consistently increased along the gradient of land-use intensity. Changes in relative abundance across nine functional effects groups based on diet were minimal from old-growth to logged forest, but in oil palm only the vertebrate predation function was maintained. Our results show that, in the absence of hunting, even the most intensively logged forests can conserve the abundance and functional effects of mammals. Recent pledges made by companies to support the protection of High Carbon Stock logged forest could therefore yield substantial conservation benefits. Within oil palm, our results suppo

  • Journal article
    Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, Phillips HR, Alhusseini TI, Bedford FE, Bennett DJ, Booth H, Burton VJ, Chng CW, Choimes A, Correia DL, Day J, Echeverría-Londoño S, Emerson SR, Gao D, Garon M, Harrison ML, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, Pask-Hale GD, Pynegar EL, Robinson AN, Sanchez-Ortiz K, Senior RA, Simmons BI, White HJ, Zhang H, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Albertos B, Alcala EL, Del Mar Alguacil M, Alignier A, Ancrenaz M, Andersen AN, Arbeláez-Cortés E, Armbrecht I, Arroyo-Rodríguez V, Aumann T, Axmacher JC, Azhar B, Azpiroz AB, Baeten L, Bakayoko A, Báldi A, Banks JE, Baral SK, Barlow J, Barratt BI, Barrico L, Bartolommei P, Barton DM, Basset Y, Batáry P, Bates AJ, Baur B, Bayne EM, Beja P, Benedick S, Berg Å, Bernard H, Berry NJ, Bhatt D, Bicknell JE, Bihn JH, Blake RJ, Bobo KS, Bóçon R, Boekhout T, Böhning-Gaese K, Bonham KJ, Borges PA, Borges SH, Boutin C, Bouyer J, Bragagnolo C, Brandt JS, Brearley FQ, Brito I, Bros V, Brunet J, Buczkowski G, Buddle CM, Bugter R, Buscardo E, Buse J, Cabra-García J, Cáceres NC, Cagle NL, Calviño-Cancela M, Cameron SA, Cancello EM, Caparrós R, Cardoso P, Carpenter D, Carrijo TF, Carvalho AL, Cassano CR, Castro H, Castro-Luna AA, Rolando CB, Cerezo A, Chapman KA, Chauvat M, Christensen M, Clarke FM, Cleary DF, Colombo G, Connop SP, Craig MD, Cruz-López L, Cunningham SA, D'Aniello B, D'Cruze N, da Silva PG, Dallimer M, Danquah E, Darvill B, Dauber J, Davis AL, Dawson J, de Sassi C, de Thoisy B, Deheuvels O, Dejean A, Devineau JL, Diekötter T, Dolia JV, Domínguez E, Dominguez-Haydar Y, Dorn S, Draper I, Dreber N, Dumont B, Dures SG, Dynesius M, Edenius L, Eggleton P, Eigenbrod F, Elek Z, Entling MH, Esler KJ, de Lima RF, Faruk A, Farwig N, Fayle TM, Felicioli A, Felton AM, Fensham RJ, Fernandez IC, Ferreira CC, Ficetola GF, Fiera C, Filgueiras BK, Fırıncıoğlu HK, Flaspohler D, Floren A, Fonte SJ, Fournier A, Fowler RE, Franzén M, Fraseret al., 2016,

    The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

    , Ecology and Evolution, Vol: 7, Pages: 145-188, ISSN: 2045-7758

    The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems ( collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

  • Journal article
    Bladon AJ, Short KM, Mohammed EY, Milner-Gulland EJet al., 2016,

    Payments for ecosystem services in developing world fisheries

    , FISH AND FISHERIES, Vol: 17, Pages: 839-859, ISSN: 1467-2960
  • Journal article
    De Palma A, Purvis A, 2016,

    Predicting bee community responses to land-use changes: effects of geographic and taxonomic biases

    , Scientific Reports, Vol: 6, ISSN: 2045-2322

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

  • Journal article
    Pfeifer M, Kor L, Nilus R, Turner E, Cusack J, Lysenko I, Khoo M, Chey VK, Chung AC, Ewers RMet al., 2016,

    Mapping the structure of Borneo's tropical forests across a degradation gradient

    , Remote Sensing of Environment, Vol: 176, Pages: 84-97, ISSN: 0034-4257

    South East Asia has the highest rate of lowland forest loss of any tropical region, with logging and deforestation for conversion to plantation agriculture being flagged as the most urgent threats. Detecting and mapping logging impacts on forest structure is a primary conservation concern, as these impacts feed through to changes in biodiversity and ecosystem functions. Here, we test whether high-spatial resolution satellite remote sensing can be used to map the responses of aboveground live tree biomass (AGB), canopy leaf area index (LAI) and fractional vegetation cover (FCover) to selective logging and deforestation in Malaysian Borneo. We measured these attributes in permanent vegetation plots in rainforest and oil palm plantations across the degradation landscape of the Stability of Altered Forest Ecosystems project. We found significant mathematical relationships between field-measured structure and satellite-derived spectral and texture information, explaining up to 62% of variation in biophysical structure across forest and oil palm plots. These relationships held at different aggregation levels from plots to forest disturbance types and oil palms allowing us to map aboveground biomass and canopy structure across the degradation landscape. The maps reveal considerable spatial variation in the impacts of previous logging, a pattern that was less clear when considering field data alone. Up-scaled maps revealed a pronounced decline in aboveground live tree biomass with increasing disturbance, impacts which are also clearly visible in the field data even a decade after logging. Field data demonstrate a rapid recovery in forest canopy structure with the canopy recovering to pre-disturbance levels a decade after logging. Yet, up-scaled maps show that both LAI and FCover are still reduced in logged compared to primary forest stands and markedly lower in oil palm stands. While uncertainties remain, these maps can now be utilised to identify conservation win–win

  • Journal article
    Alexander JS, McNamara J, Rowcliffe JM, Oppong J, Milner-Gulland EJet al., 2015,

    The role of bushmeat in a West African agricultural landscape

    , ORYX, Vol: 49, Pages: 643-651, ISSN: 0030-6053
  • Journal article
    Barraclough TG, Humphreys AM, 2015,

    The evolutionary reality of species and higher taxa in plants: a survey of post-modern opinion and evidence

    , NEW PHYTOLOGIST, Vol: 207, Pages: 291-296, ISSN: 0028-646X
  • Journal article
    Milner-Gulland EJ, Sainsbury K, Burgess N, Howe C, Sabuni F, Puis E, Killenga Ret al., 2015,

    Exploring stakeholder perceptions of conservation outcomes from alternative income generating activities in Tanzanian villages adjacent to Eastern Arc mountain forests.

    , Biological Conservation, Vol: 191, Pages: 20-28, ISSN: 0006-3207
  • Journal article
    Milner-Gulland EJ, Wallace A, Bunnefeld N, Jones JPG, Young R, Nicholson Eet al., 2015,

    Quantifying the short-term costs of conservation interventions for fishers at Lake Alaotra, Madagascar

    , PLOS One, Vol: 10, ISSN: 1932-6203

    Artisanal fisheries are a key source of food and income for millions of people, but if poorly managed, fishing can have declining returns as well as impacts on biodiversity. Management interventions such as spatial and temporal closures can improve fishery sustainability and reduce environmental degradation, but may carry substantial short-term costs for fishers. The Lake Alaotra wetland in Madagascar supports a commercially important artisanal fishery and provides habitat for a Critically Endangered primate and other endemic wildlife of conservation importance. Using detailed data from more than 1,600 fisher catches, we used linear mixed effects models to explore and quantify relationships between catch weight, effort, and spatial and temporal restrictions to identify drivers of fisher behaviour and quantify the potential effect of fishing restrictions on catch. We found that restricted area interventions and fishery closures would generate direct short-term costs through reduced catch and income, and these costs vary between groups of fishers using different gear. Our results show that conservation interventions can have uneven impacts on local people with different fishing strategies. This information can be used to formulate management strategies that minimise the adverse impacts of interventions, increase local support and compliance, and therefore maximise conservation effectiveness.

  • Journal article
    Milner-Gulland EJ, mcnamara J, rowcliffe M, cowlishaw G, kusimi Jet al., 2015,

    Long-term spatio-temporal changes in a West African bushmeat trade system

    , Conservation Biology, Vol: 29, Pages: 1446-1457, ISSN: 0888-8892

    Landscapes in many developing countries consist of a heterogeneous matrix of mixed agriculture and forest. Many of the generalist species in this matrix are increasingly traded in the bushmeat markets of West and Central Africa. However, to date there has been little quantification of how the spatial configuration of the landscape influences the urban bushmeat trade over time. As anthropogenic landscapes become the face of rural West Africa, understanding the dynamics of these systems has important implications for conservation and landscape management. The bushmeat production of an area is likely to be defined by landscape characteristics such as habitat disturbance, hunting pressure, level of protection, and distance to market. We explored (SSG, tense) the role of these four characteristics in the spatio-temporal dynamics of the commercial bushmeat trade around the city of Kumasi, Ghana, over 27 years (1978 to 2004). We used geographic information system methods to generate maps delineating the spatial characteristics of the landscapes. These data were combined with spatially explicit market data collected in the main fresh bushmeat market in Kumasi to explore the relationship between trade volume (measured in terms of number of carcasses) and landscape characteristics. Over time, rodents, specifically cane rats (Thryonomys swinderianus), became more abundant in the trade relative to ungulates and the catchment area of the bushmeat market expanded. Areas of intermediate disturbance supplied more bushmeat, but protected areas had no effect. Heavily hunted areas showed significant declines in bushmeat supply over time. Our results highlight the role that low intensity, heterogeneous agricultural landscapes can play in providing ecosystem services, such as bushmeat, and therefore the importance of incorporating bushmeat into ecosystem service mapping exercises. Our results also indicate that even where high bushmeat production is possible, current harvest levels may

  • Journal article
    Hui T-YJ, Burt A, 2015,

    Estimating effective population size from temporally spaced samples with a novel, efficient maximum-likelihood algorithm

    , Genetics, Vol: 200, Pages: 285-293, ISSN: 1943-2631

    The effective population size Embedded Image is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating Embedded Image have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator Embedded Image for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying Embedded Image is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator Embedded Image, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of Embedded Image to several million, hence allowing the estimation of larger Embedded Image. Finally, we demonstrate how this algorithm can cope with nonconstant Embedded Image scenarios and be used as a likelihood-ratio test to test for the equality of Embedded Image throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.

  • Journal article
    Fiegna F, Moreno-Letelier A, Bell T, Barraclough TGet al., 2015,

    Evolution of species interactions determines microbial community productivity in new environments

    , ISME JOURNAL, Vol: 9, Pages: 1235-1245, ISSN: 1751-7362
  • Journal article
    Woodhouse E, Mills MA, McGowan PJK, Milner-Gulland EJet al., 2015,

    Religious Relationships with the Environment in a Tibetan Rural Community: Interactions and Contrasts with Popular Notions of Indigenous Environmentalism

    , HUMAN ECOLOGY, Vol: 43, Pages: 295-307, ISSN: 0300-7839
  • Journal article
    Maxwell SL, Milner-Gulland EJ, Jones JPG, Knight AT, Bunnefeld N, Nuno A, Bal P, Earle S, Watson JEM, Rhodes JRet al., 2015,

    Being smart about SMART environmental targets

    , SCIENCE, Vol: 347, Pages: 1075-1076, ISSN: 0036-8075
  • Journal article
    Samani P, Low-Decarie E, McKelvey K, Bell T, Burt A, Koufopanou V, Landry CR, Bell Get al., 2015,

    Metabolic variation in natural populations of wild yeast

    , ECOLOGY AND EVOLUTION, Vol: 5, Pages: 722-732, ISSN: 2045-7758
  • Journal article
    Tidd AN, Vermard Y, Marchal P, Pinnegar J, Blanchard JL, Milner-Gulland EJet al., 2015,

    Fishing for Space: Fine-Scale Multi-Sector Maritime Activities Influence Fisher Location Choice

    , PLOS ONE, Vol: 10, ISSN: 1932-6203
  • Journal article
    Fujisawa T, Vogler AP, Barraclough TG, 2015,

    Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

  • Journal article
    Igea J, Bogarin D, Papadopulos AST, Savolainen Vet al., 2015,

    A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation

    , Evolution, Vol: 69, Pages: 482-491, ISSN: 0014-3820

    Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy-based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.

  • Journal article
    Gossa C, Fisher M, Milner-Gulland EJ, 2015,

    The research-implementation gap: howpractitioners and researchers from developing countries perceive the role of peer-reviewed literature in conservation science

    , ORYX, Vol: 49, Pages: 80-87, ISSN: 0030-6053
  • Journal article
    Johnson LR, Ben-Horin T, Lafferty KD, McNally A, Mordecai E, Paaijmans KP, Pawar S, Ryan SJet al., 2015,

    Understanding uncertainty in temperature effects on vector-borne disease: a Bayesian approach

    , ECOLOGY, Vol: 96, Pages: 203-213, ISSN: 0012-9658
  • Journal article
    Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arca B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VLM, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DST, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MKN, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon NF, Sharakhova MV, Shea T, Simao FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GWC, Tojo M, Topalis P, Tubio JMC, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu Y-C, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MAT, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJet al., 2015,

    Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

    , Science, Vol: 347
  • Journal article
    Gill RJ, Raine NE, 2014,

    Chronic impairment of bumblebee natural foraging behaviour induced by sublethal pesticide exposure

    , FUNCTIONAL ECOLOGY, Vol: 28, Pages: 1459-1471, ISSN: 0269-8463
  • Journal article
    Batsaikhan N, Buuveibaatar B, Chimed B, Enkhtuya O, Galbrakh D, Ganbaatar O, Lkhagvasuren B, Nandintsetseg D, Berger J, Calabrese JM, Edwards AE, Fagan WF, Fuller TK, Heiner M, Ito TY, Kaczensky P, Leimgruber P, Lushchekina A, Milner-Gulland EJ, Mueller T, Murray MG, Olson KA, Reading R, Schaller GB, Stubbe A, Stubbe M, Walzer C, Von Wehrden H, Whitten Tet al., 2014,

    Conserving the World's Finest Grassland Amidst Ambitious National Development

    , CONSERVATION BIOLOGY, Vol: 28, Pages: 1736-1739, ISSN: 0888-8892
  • Journal article
    Clements T, Suon S, Wilkie DS, Milner-Gulland EJet al., 2014,

    Impacts of Protected Areas on Local Livelihoods in Cambodia

    , WORLD DEVELOPMENT, Vol: 64, Pages: S125-S134, ISSN: 0305-750X
  • Journal article
    Ahmed SE, Lees AC, Moura NG, Gardner TA, Barlow J, Ferreira J, Ewers RMet al., 2014,

    Road networks predict human influence on Amazonian bird communities

  • Journal article
    Carrasco LR, Larrosa C, Milner-Gulland EJ, Edwards DPet al., 2014,

    Tropical crops: cautious optimism Response

    , SCIENCE, Vol: 346, Pages: 928-928, ISSN: 0036-8075
  • Journal article
    Milner-Gulland EJ, Baillie J, Washington H, Waterman Cet al., 2014,

    A framework for evaluating the effectiveness of conservation attention at the species level

    , Oryx, ISSN: 1365-3008

    It is essential to understand whether conservation interventions are having the desired effect, particularly in light of increasing pressures on biodiversity and because of requirements by donors that project success be demonstrated. Whilst most evaluations look at effectiveness at a project or organizational level, local efforts need to be connected to an understanding of the effectiveness of conservation directed at a species as a whole, particularly as most metrics of conservation success are at the level of species. We present a framework for measuring the effectiveness of conservation attention at a species level over time, based on scoring eight factors essential for species conservation (engaging stakeholders, management programme, education and awareness, funding and resource mobilization, addressing threats, communication, capacity building and status knowledge), across input, output and outcome stages, in relation to the proportion of the species’ range where each factor attains its highest score. The framework was tested using expert elicitation for 35 mammal and amphibian species on the Zoological Society of London's list of Evolutionarily Distinct and Globally Endangered species. Broad patterns in the index produced by the framework could suggest potential mechanisms underlying change in species status. Assigning an uncertainty score to information demonstrates not only where gaps in knowledge exist, but discrepancies in knowledge between experts. This framework could be a useful tool to link local and global scales of impact on species conservation, and could provide a simple and visually appealing way of tracking conservation over time.

  • Journal article
    Tessarolo G, Rangel TF, Araujo MB, Hortal Jet al., 2014,

    Uncertainty associated with survey design in Species Distribution Models

    , DIVERSITY AND DISTRIBUTIONS, Vol: 20, Pages: 1258-1269, ISSN: 1366-9516
  • Journal article
    Lim J, Crawley MJ, De Vere N, Rich T, Savolainen Vet al., 2014,

    A phylogenetic analysis of the British flora sheds light on the evolutionary and ecological factors driving plant invasions

    , ECOLOGY AND EVOLUTION, Vol: 4, Pages: 4258-4269, ISSN: 2045-7758
  • Journal article
    Tang CQ, Humphreys AM, Fontaneto D, Barraclough TGet al., 2014,

    Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

    , Methods in Ecology and Evolution, Vol: 5, Pages: 1086-1094, ISSN: 2041-210X

    1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such asDNAbarcodes. 2. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothingmethods.We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYCapproaches with BEAST trees for obtaining species hypotheses.

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