Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
Aim: After environmental disasters, species with large population losses may need urgent protection to prevent extinction and support recovery. Following the 2019-2020 Australian megafires, we estimated population losses and recovery in fire-affected fauna, to inform conservation status assessments and management. Location: Temperate and subtropical Australia. Time period 2019-2030 and beyond. Major taxa: Australian terrestrial and freshwater vertebrates; one invertebrate group. Methods: From > 1,050 fire-affected taxa, we selected 173 whose distributions substantially overlapped the fire extent. We estimated the proportion of each taxon's distribution affected by fires, using fire severity and aquatic impact mapping, and new distribution mapping. Using expert elicitation informed by evidence of responses to previous wildfires, we estimated local population responses to fires of varying severity. We combined the spatial and elicitation data to estimate overall population loss and recovery trajectories, and thus indicate potential eligibility for listing as threatened, or uplisting, under Australian legislation. Results: We estimate that the 2019-2020 Australian megafires caused, or contributed to, population declines that make 70-82 taxa eligible for listing as threatened; and another 21-27 taxa eligible for uplisting. If so-listed, this represents a 22-26% increase in Australian statutory lists of threatened terrestrial and freshwater vertebrates and spiny crayfish, and uplisting for 8-10% of threatened taxa. Such changes would cause an abrupt worsening of underlying trajectories in vertebrates, as measured by Red List Indices. We predict that 54-88% of 173 assessed taxa will not recover to pre-fire population size within 10 years/three generations. Main conclusions We suggest the 2019-2020 Australian megafires have worsened the conservation prospects for many species. Of the 91 taxa recommended for listing/uplisting consideration, 84 are now under formal review through national processes. Improving ...
In: Gallagher , R V , Falster , D S , Maitner , B S , Salguero-Gómez , R , Vandvik , V , Pearse , W D , Schneider , F D , Kattge , J , Poelen , J H , Madin , J S , Ankenbrand , M J , Penone , C , Feng , X , Adams , V M , Alroy , J , Andrew , S C , Balk , M A , Bland , L M , Boyle , B L , Bravo-Avila , C H , Brennan , I , Carthey , A J R , Catullo , R , Cavazos , B R , Conde , D A , Chown , S L , Fadrique , B , Gibb , H , Halbritter , A H , Hammock , J , Hogan , J A , Holewa , H , Hope , M , Iversen , C M , Jochum , M , Kearney , M , Keller , A , Mabee , P , Manning , P , McCormack , L , Michaletz , S T , Park , D S , Perez , T M , Pineda-Munoz , S , Ray , C A , Rossetto , M , Sauquet , H , Sparrow , B , Spasojevic , M J , Telford , R J , Tobias , J A , Violle , C , Walls , R , Weiss , K C B , Westoby , M , Wright , I J & Enquist , B J 2020 , ' Open Science principles for accelerating trait-based science across the Tree of Life ' , Nature Ecology & Evolution , vol. 4 , pp. 294–303 . https://doi.org/10.1038/s41559-020-1109-6
Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.
Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.
In: Gallagher , R V , Falster , D S , Maitner , B S , Salguero-Gómez , R , Vandvik , V , Pearse , W D , Schneider , F D , Kattge , J , Poelen , J H , Madin , J S , Ankenbrand , M J , Penone , C , Feng , X , Adams , V M , Alroy , J , Andrew , S C , Balk , M A , Bland , L M , Boyle , B L , Bravo-Avila , C H , Brennan , I , Carthey , A J R , Catullo , R , Cavazos , B R , Conde , D A , Chown , S L , Fadrique , B , Gibb , H , Halbritter , A H , Hammock , J , Hogan , J A , Holewa , H , Hope , M , Iversen , C M , Jochum , M , Kearney , M , Keller , A , Mabee , P , Manning , P , McCormack , L , Michaletz , S T , Park , D S , Perez , T M , Pineda-Munoz , S , Ray , C A , Rossetto , M , Sauquet , H , Sparrow , B , Spasojevic , M J , Telford , R J , Tobias , J A , Violle , C , Walls , R , Weiss , K C B , Westoby , M , Wright , I J & Enquist , B J 2020 , ' Open Science principles for accelerating trait-based science across the Tree of Life ' , Nature Ecology and Evolution , vol. 4 , no. 3 , pp. 294-303 . https://doi.org/10.1038/s41559-020-1109-6
Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.