On the biogeography of Centipeda: a species-tree diffusion approach.

Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.

[1]  R. L. Crocker,et al.  Biogeography and Ecology in Australia , 1960, Monographiae Biologicae.

[2]  M. Nei,et al.  THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS , 1975, Evolution; international journal of organic evolution.

[3]  M. Crisp,et al.  A congruent molecular signature of vicariance across multiple plant lineages. , 2007, Molecular phylogenetics and evolution.

[4]  Mark B. Schultz,et al.  Phylogeography of the freshwater crayfish Cherax destructor Clark (Parastacidae) in inland Australia: historical fragmentation and recent range expansion , 2004 .

[5]  J. Hughes,et al.  Mitochondrial DNA and allozymes reveal high dispersal abilities and historical movement across drainage boundaries in two species of freshwater fishes from inland rivers in Queensland, Australia , 2006 .

[6]  Fredrik Ronquist,et al.  Phylogenetic Methods in Biogeography , 2011 .

[7]  C. Yesson,et al.  A phyloclimatic study of Cyclamen , 2006, BMC Evolutionary Biology.

[8]  C. Orme,et al.  Hot, dry and different: Australian lizard richness is unlike that of mammals, amphibians and birds , 2010 .

[9]  M. Westerman,et al.  Systematics and Evolution of the Dasyurid Marsupial Genus Sminthopsis: II. The Murina Species Group , 2006, Journal of Mammalian Evolution.

[10]  J. Panero New combinations and infrafamilial taxa in the Asteraceae , 2005 .

[11]  S. Nylinder,et al.  Species tree phylogeny and character evolution in the genus Centipeda (Asteraceae): evidence from DNA sequences from coding and non-coding loci from the plastid and nuclear genomes. , 2013, Molecular phylogenetics and evolution.

[12]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[13]  P. Hesse,et al.  Late Quaternary climates of the Australian arid zone: a review , 2004 .

[14]  L. Beheregaray,et al.  Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia’s arid zone, the golden perch (Macquaria ambigua) , 2010, Molecular ecology.

[15]  M. Byrne,et al.  Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae) , 2004 .

[16]  P. Alström,et al.  Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). , 2008, Systematic biology.

[17]  Marc A. Suchard,et al.  SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics , 2011, Bioinform..

[18]  J. Keogh,et al.  Phylogeography of Australia’s king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator , 2005, Naturwissenschaften.

[19]  Fredrik Ronquist,et al.  Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography , 1997 .

[20]  Campbell O. Webb,et al.  A LIKELIHOOD FRAMEWORK FOR INFERRING THE EVOLUTION OF GEOGRAPHIC RANGE ON PHYLOGENETIC TREES , 2005, Evolution; international journal of organic evolution.

[21]  A. Drummond,et al.  Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.

[22]  Hayley C. Lanier,et al.  Phylogenetic structure of vertebrate communities across the Australian arid zone , 2013 .

[23]  A. Fried,et al.  Timescales and the role of inheritance in long‐term landscape evolution, northern New England, Australia , 1992 .

[24]  M. Pagel,et al.  Bayesian estimation of ancestral character states on phylogenies. , 2004, Systematic biology.

[25]  T. Sang,et al.  Radiation of the endemic genus Dendroseris (Asteraceae) on the Juan Fernandez Islands: evidence from sequences of the its regions of nuclear ribosomal DNA , 1994 .

[26]  E. Rhodes,et al.  Australian desert dune fields initiated with Pliocene–Pleistocene global climatic shift , 2009 .

[27]  A. Lemmon,et al.  A likelihood framework for estimating phylogeographic history on a continuous landscape. , 2008, Systematic biology.

[28]  N. Walsh A revision of Centipeda (Asteraceae) , 2001, Muelleria: An Australian Journal of Botany.

[29]  D. Schluter,et al.  Evidence for Ecological Speciation and Its Alternative , 2022 .

[30]  Forrest W. Crawford,et al.  Unifying the spatial epidemiology and molecular evolution of emerging epidemics , 2012, Proceedings of the National Academy of Sciences.

[31]  H. Martin The palynology of the Namba Formation in the Wooltana-1 bore, Callabonna Basin (Lake Frome), South Australia, and its relevance to Miocene grasslands in central Australia , 1990 .

[32]  D. Graur,et al.  Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. , 2004, Trends in genetics : TIG.

[33]  T. Sang,et al.  ITS Sequences and the Phylogeny of the Genus Robinsonia (Asteraceae) , 1995 .

[34]  C. Barton,et al.  Onset of aridity and dune-building in central Australia: sedimentological and magnetostratigraphic evidence from Lake Amadeus , 1991 .

[35]  T. Givnish,et al.  Historical biogeography and the origin of stomatal distributions in Banksia and Dryandra (Proteaceae) based on their cpDNA phylogeny. , 2002, American journal of botany.

[36]  G. A. Leng ON POPULATION. , 1963, Singapore medical journal.

[37]  A. Keast The Australian Environment , 1959 .

[38]  S. Short,et al.  Wetting and drying of Australia over the past 300 ka , 1992 .

[39]  E. De Pauw,et al.  Agrometeorological aspects of agriculture and forestry in the arid zones , 2000 .

[40]  J. McCarter,et al.  The population genetics of the origin and divergence of the Drosophila simulans complex species. , 2000, Genetics.

[41]  M. Orr,et al.  Ecology and speciation. , 1998, Trends in ecology & evolution.

[42]  H. Martin Cenozoic climatic change and the development of the arid vegetation in Australia , 2006 .

[43]  E. Pianka Zoogeography and Speciation of Australian Desert Lizards: An Ecological Perspective , 1972 .

[44]  David C. Tank,et al.  An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: , 2009 .

[45]  Simon J. Greenhill,et al.  Mapping the Origins and Expansion of the Indo-European Language Family , 2012, Science.

[46]  E. Schilling,et al.  Phylogeny and biogeography of Eupatorium (Asteraceae: Eupatorieae) based on nuclear ITS sequence data. , 2000, American journal of botany.

[47]  L. Bromham,et al.  Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. , 2003, Molecular biology and evolution.

[48]  C. Burridge Biogeographic history of geminate cirrhitoids (Perciformes: Cirrhitoidea) with east–west allopatric distributions across southern Australia, based on molecular data , 2000 .

[49]  Alexei J. Drummond,et al.  Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..

[50]  Lindell Bromham,et al.  Population size and molecular evolution on islands , 2005, Proceedings of the Royal Society B: Biological Sciences.

[51]  P. Mather,et al.  Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine , 2007, Molecular ecology.

[52]  Peter J. Bradbury,et al.  The Last Glacial Maximum , 2009, Science.

[53]  Julio A. Rozas Liras,et al.  DnaSP v 5 : a software for comprehensive analysis of DNA polymorphism data , 2009 .

[54]  W. Rice Speciation via habitat specialization: the evolution of reproductive isolation as a correlated character , 1987, Evolutionary Ecology.

[55]  D. Maddison,et al.  Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .

[56]  M. Sanderson,et al.  Age and rate of diversification of the Hawaiian silversword alliance (Compositae). , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[57]  N. Moar,et al.  Aerial dispersal of biological material from Australia to New Zealand , 1978 .

[58]  I. Sanmartín,et al.  New solutions to old problems: widespread taxa, redundant distributions and missing areas in event–based biogeography , 2002 .

[59]  M. Crisp,et al.  Ancient relicts or recent dispersal: how long have cycads been in central Australia? , 2013 .

[60]  K. Bremer,et al.  Asteraceae: Cladistics and Classification , 1994 .

[61]  B. Gemeinholzer,et al.  Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock , 2012, Organisms Diversity & Evolution.

[62]  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.

[63]  M. Adams,et al.  Systematics and Evolution of the Dasyurid Marsupial Genus Sminthopsis: I. The Macroura Species Group , 2004, Journal of Mammalian Evolution.

[64]  J. Burdon,et al.  Genetic structure of Glycine canescens, a perennial relative of soybean , 1990, Theoretical and Applied Genetics.

[65]  R. Fensham,et al.  Water-remoteness for grazing relief in Australian arid-lands , 2008 .

[66]  M. Suchard,et al.  Phylogeography takes a relaxed random walk in continuous space and time. , 2010, Molecular biology and evolution.

[67]  S. Gallagher,et al.  Cenozoic stratigraphic succession in southeastern Australia , 2004 .

[68]  M. Kearney,et al.  Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota , 2008, Molecular ecology.

[69]  G. Nesom Subtribal classification of the Astereae lAsteraceaer , 1994 .

[70]  L. Lancaster Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages , 2010, BMC Evolutionary Biology.

[71]  Alexey S. Kondrashov,et al.  Sympatric speciation: when is it possible? , 1986 .

[72]  M. Pagel The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies , 1999 .

[73]  U. Dieckmann,et al.  On the origin of species by sympatric speciation , 1999, Nature.