Choice between phylogram and chronogram can have a dramatic impact on the location of phylogenetic diversity hotspots

[1]  K. Kay,et al.  A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects , 2006, BMC Evolutionary Biology.

[2]  J. Welch,et al.  Correlates of substitution rate variation in mammalian protein-coding sequences , 2008, BMC Evolutionary Biology.

[3]  Anders Larsson,et al.  AliView: a fast and lightweight alignment viewer and editor for large datasets , 2014, Bioinform..

[4]  M. Sanderson.  Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.

[5]  Susanne A. Fritz,et al.  A guide to phylogenetic metrics for conservation, community ecology and macroecology , 2016, Biological reviews of the Cambridge Philosophical Society.

[6]  A. Schmidt‐Lebuhn,et al.  Phylogenetic relationships of the Australasian shrubby everlastings Ozothamnus and Cassinia (Asteraceae: Asteroideae: Gnaphalieae) , 2013, Cladistics : the international journal of the Willi Hennig Society.

[7]  S. Lavergne,et al.  Climatic and topographical correlates of plant palaeo- and neoendemism in a Mediterranean biodiversity hotspot , 2017, Annals of botany.

[8]  T. Davies,et al.  Revisiting the impacts of non-random extinction on the tree-of-life , 2013, Biology Letters.

[9]  Bastian Steudel,et al.  Contrasting biodiversity-ecosystem functioning relationships in phylogenetic and functional diversity. , 2016, The New phytologist.

[10]  Nunzio Knerr,et al.  Phylogenetic diversity and endemism of Australian daisies (Asteraceae) , 2015 .

[11]  Hotspots of diversity of wild Australian soybean relatives and their conservation in situ , 2012, Conservation Genetics.

[12]  Shawn W. Laffan,et al.  Biodiverse, a tool for the spatial analysis of biological and related diversity , 2010 .

[13]  Where the rare species are , 2009, Molecular ecology.

[14]  Rob Knight,et al.  The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework , 2009, International journal of molecular sciences.

[15]  J. Diniz‐Filho,et al.  Understanding global patterns of mammalian functional and phylogenetic diversity , 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[17]  B. Mishler,et al.  Continental‐scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation , 2016 .

[18]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[19]  Mozes P. K. Blom,et al.  Phylogeography, hotspots and conservation priorities: an example from the Top End of Australia , 2016 .

[20]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[21]  R. Lanfear,et al.  Taller plants have lower rates of molecular evolution , 2013, Nature Communications.

[22]  M. Donoghue,et al.  Hemisphere-scale differences in conifer evolutionary dynamics , 2012, Proceedings of the National Academy of Sciences.

[23]  Jian Zhang,et al.  Gains and losses of plant species and phylogenetic diversity for a northern high‐latitude region , 2015 .

[24]  A. Mooers,et al.  Evolutionary Distinctiveness, Threat Status, and Ecological Oddity in Primates , 2010, Conservation biology : the journal of the Society for Conservation Biology.

[25]  Keping Ma,et al.  Identifying hotspots of endemic woody seed plant diversity in China , 2012 .

[26]  Jarrett E. K. Byrnes,et al.  A global synthesis reveals biodiversity loss as a major driver of ecosystem change , 2012, Nature.

[27]  Daniel P Faith,et al.  Phylodiversity to inform conservation policy: An Australian example. , 2015, The Science of the total environment.

[28]  N. Isaac,et al.  Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny , 2007, PloS one.

[29]  J. Joy,et al.  Imperilled phylogenetic endemism of Malagasy lemuriformes , 2013 .

[30]  Helmut Hillebrand,et al.  On the Generality of the Latitudinal Diversity Gradient , 2004, The American Naturalist.

[31]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[32]  W. Jetz,et al.  Phylogenetic endemism in terrestrial mammals , 2015 .

[33]  William A. Freyman,et al.  Spatial phylogenetics of the vascular flora of Chile. , 2017, Molecular phylogenetics and evolution.

[34]  Shawn W. Laffan,et al.  A biogeographical regionalization of Australian Acacia species , 2013 .

[35]  K. Hilu,et al.  Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. , 2013, American journal of botany.

[36]  K. Ma,et al.  Diversity hotspots and conservation gaps for the Chinese endemic seed flora , 2016 .

[37]  B. Mishler,et al.  Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia , 2014, Nature Communications.

[38]  Laura J. Pollock,et al.  Phylogenetic approaches reveal biodiversity threats under climate change , 2016 .

[39]  Campbell O. Webb,et al.  Bioinformatics Applications Note Phylocom: Software for the Analysis of Phylogenetic Community Structure and Trait Evolution , 2022 .

[40]  Priority setting by sites and by species using rarity, richness and phylogenetic diversity: the case of neotropical glassfrogs (Anura: Centrolenidae) , 2014, Biodiversity and Conservation.

[41]  Wilfried Thuiller,et al.  Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. , 2010, Ecology letters.

[42]  D. Greber,et al.  Phylogeny of Australian Gnaphalieae (Asteraceae) Based on Chloroplast and Nuclear Sequences, the trnL Intron, trnL/trnF Intergenic Spacer, matK, and ETS , 2009 .

[43]  E. Biffin,et al.  Identifying Centres of Plant Biodiversity in South Australia , 2016, PloS one.

[44]  Laura J. Pollock,et al.  Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[45]  P. Unmack,et al.  Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups , 2015, Ecology and evolution.

[46]  Richard Grenyer,et al.  Preserving the evolutionary potential of floras in biodiversity hotspots , 2007, Nature.

[47]  R. A. Pyron,et al.  Phylogenetic diversity, habitat loss and conservation in South American pitvipers (Crotalinae: Bothrops and Bothrocophias) , 2014 .

[48]  Stephen A. Smith,et al.  Evolutionary history of the angiosperm flora of China , 2018, Nature.

[49]  Andrew P. Martin,et al.  Body size, metabolic rate, generation time, and the molecular clock. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[50]  S. Trewick,et al.  Fire and slice: palaeogeography for biogeography at New Zealand's North Island/South Island juncture , 2012 .

[51]  A. Vogler,et al.  Endemism and evolutionary history in conflict over Madagascar's freshwater conservation priorities , 2011 .

[52]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[53]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[54]  William A. Freyman,et al.  Spatial phylogenetics of the native California flora , 2017, BMC Biology.

[55]  D. Rosauer,et al.  Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history , 2009, Molecular ecology.

[56]  P. Ehrlich,et al.  Global mammal distributions, biodiversity hotspots, and conservation , 2006, Proceedings of the National Academy of Sciences.

[57]  D. Faith.  Conservation evaluation and phylogenetic diversity , 1992 .

[58]  G. Daily,et al.  Biodiversity loss and its impact on humanity , 2012, Nature.

[59]  Wilfried Thuiller,et al.  Consequences of climate change on the tree of life in Europe , 2011, Nature.

[60]  M. Brändle,et al.  Patterns of freshwater biodiversity in Europe: lessons from the spring snail genus Bythinella , 2011 .

[61]  B. Mishler,et al.  Continental scale patterns and predictors of fern richness and phylogenetic diversity , 2015, Front. Genet..

[62]  James H. Brown,et al.  The rate of DNA evolution: effects of body size and temperature on the molecular clock. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[63]  S. Laffan,et al.  Spatial distribution of species richness and endemism of the genus Acacia in Australia , 2011 .

[64]  H. Schneider,et al.  Ferns diversified in the shadow of angiosperms , 2004, Nature.

[65]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[66]  M. Cadotte,et al.  Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales , 2010 .

[67]  M. McGlone,et al.  Phylogenetic measures of neo- and palaeo-endemism in the indigenous vascular flora of the New Zealand archipelago , 2017, Australian Systematic Botany.

[68]  C. E. González‐Orozco,et al.  Distorted perception of the spatial distribution of plant diversity through uneven collecting efforts: the example of Asteraceae in Australia , 2012 .

[69]  Michael J. Sanderson,et al.  A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy , 1997 .

[70]  C. Graham,et al.  Phylogenetic scale in ecology and evolution , 2016, bioRxiv.

[71]  T. Davies,et al.  Spatial incongruence among hotspots and complementary areas of tree diversity in southern Africa , 2015 .

[72]  C. van den Berg,et al.  Spatial analyses of the phylogenetic diversity of Minaria (Apocynaceae): assessing priority areas for conservation in the Espinhaço Range, Brazil , 2012 .