Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California

Comparative phylogeography has emerged as a means of understanding the spatial patterns of genetic divergence of codistributed species. However, researchers are often frustrated because of the lack of appropriate statistical tests to assess concordancy of multiple phylogeographic trees. We develop a method for testing congruence across multiple species and synthesizing the data into a regional supertree. Nine phylogeographic data sets of species with different life histories and ecologies were statistically compared using maximum agreement subtrees (MAST) and showed a high degree of concordancy. A supertree combining the different phylogeographic trees was then computed using matrix representation with parsimony, and the groups defined by this supertree were tested against climatic data to investigate a potential mechanism driving divergence. Our data suggest that species and genetic lineages in California are shaped by climatic regimes. The supertree method in combination with MAST represents a new approach to test congruence hypotheses and detect common geographic signals in comparative phylogeography.

[1]  Jonathan S. Adams,et al.  Precious heritage : the status of biodiversity in the United States , 2000 .

[2]  Templeton,et al.  Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history , 1998, Molecular ecology.

[3]  J. Atwood,et al.  Genetics, Taxonomy, and Conservation of the Threatened California Gnatcatcher , 2000 .

[4]  R. Mittermeier,et al.  Biodiversity hotspots for conservation priorities , 2000, Nature.

[5]  R. Page.  Maps between trees and cladistic analysis of historical associations among genes , 1994 .

[6]  B. Riddle,et al.  Comparative phylogeography of Baileys' pocket mouse (Chaetodipus baileyi) and the Peromyscus eremicus species group: historical vicariance of the Baja California Peninsular Desert. , 2000, Molecular phylogenetics and evolution.

[7]  A. Purvis,et al.  A phylogenetic supertree of the bats (Mammalia: Chiroptera) , 2002, Biological reviews of the Cambridge Philosophical Society.

[8]  D. Weisrock,et al.  Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces. , 2000, Molecular phylogenetics and evolution.

[9]  THE PHYLOGEOGRAPHY OF AMAZONIA REVISITED: NEW EVIDENCE FROM RIODINID BUTTERFLIES , 2002, Evolution; international journal of organic evolution.

[10]  R. J. Gutiérrez,et al.  PHYLOGEOGRAPHY OF SPOTTED OWL (STRIX OCCIDENTALIS) POPULATIONS BASED ON MITOCHONDRIAL DNA SEQUENCES: GENE FLOW, GENETIC STRUCTURE, AND A NOVEL BIOGEOGRAPHIC PATTERN , 1999, Evolution; international journal of organic evolution.

[11]  J. Rodríguez-Robles,et al.  Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae) , 1999, Molecular ecology.

[12]  O. Bininda-Emonds.  Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life , 2004 .

[13]  D. Swofford.  When are phylogeny estimates from molecular and morphological data incongruent , 1991 .

[14]  D. Wake,et al.  Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West , 2002 .

[15]  R. Martin,et al.  A molecular approach to comparative phylogeography of extant Malagasy lemurs , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Daniel R. Brooks,et al.  How to do BPA, really , 2001 .

[17]  Craig Moritz,et al.  Comparative phylogeography: concepts and applications , 1998 .

[18]  J. Avise.  The history and purview of phylogeography: a personal reflection , 1998 .

[19]  M. Matocq.  Phylogeographical structure and regional history of the dusky‐footed woodrat, Neotoma fuscipes , 2002, Molecular ecology.

[20]  Naomi Nishimura,et al.  Finding Largest Subtrees and Smallest Supertrees , 1998, Algorithmica.

[21]  C. Moritz,et al.  COMPARATIVE PHYLOGEOGRAPHY OF A SIBLING PAIR OF RAINFOREST DROSOPHILA SPECIES (DROSOPHILA SERRATA AND D. BIRCHII) , 1999, Evolution; international journal of organic evolution.

[22]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[23]  R. Page,et al.  Trees within trees: phylogeny and historical associations. , 1998, Trends in ecology & evolution.

[24]  Oliver Eulenstein,et al.  The shape of supertrees to come: tree shape related properties of fourteen supertree methods. , 2005, Systematic biology.

[25]  L. Racheli.  The nightmare of the combination: comments on matrix representation with parsimony and its first application in biogeography , 2004, Cladistics : the international journal of the Willi Hennig Society.

[26]  C. Cicero.  Sibling Species of Titmice in the Parus Inornatus Complex (Aves: Paridae) , 1996 .

[27]  François-Joseph Lapointe,et al.  How good can a consensus get? Assessing the reliability of consensus trees in phylogenetic studies , 2001, Bioconsensus.

[28]  J. Avise.  Phylogeography: The History and Formation of Species , 2000 .

[29]  Taylor H. Ricketts,et al.  Terrestrial ecoregions of North America : a conservation assessment , 1999 .

[30]  O. Bininda-Emonds,et al.  The evolution of supertrees. , 2004, Trends in ecology & evolution.

[31]  J. Cracraft,et al.  PATTERNS AND PROCESSES OF DIVERSIFICATION: SPECIATION AND HISTORICAL CONGRUENCE IN SOME NEOTROPICAL BIRDS , 1988, Evolution; international journal of organic evolution.

[32]  J. L. Gittleman,et al.  The (Super)Tree of Life: Procedures, Problems, and Prospects , 2002 .

[33]  S. Edwards,et al.  GENE DIVERGENCE , POPULATION DIVERGENCE , AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES , 2001 .

[34]  J. Neigel,et al.  Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics , 1987 .

[35]  David M. Stoms,et al.  Extinction rates under nonrandom patterns of habitat loss , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Veller,et al.  Cladistic and phylogenetic biogeography: the art and the science of discovery , 2003 .

[37]  R. Zink.  Methods in Comparative Phylogeography, and Their Application to Studying Evolution in the North American Aridlands1 , 2002, Integrative and comparative biology.

[38]  A. Ditchfield.  The comparative phylogeography of Neotropical mammals: patterns of intraspecific mitochondrial DNA variation among bats contrasted to nonvolant small mammals , 2000, Molecular ecology.

[39]  C. Chamberlain,et al.  Reconstructing the paleotopography of mountain belts from the isotopic composition of authigenic minerals , 2000 .

[40]  P. Welzen,et al.  Historical biogeography of Southeast Asia and the West Pacific, or the generality of unrooted area networks as historical biogeographic hypotheses , 2003 .

[41]  M. Kennedy,et al.  SEABIRD SUPERTREES: COMBINING PARTIAL ESTIMATES OF PROCELLARIIFORM PHYLOGENY , 2002 .

[42]  K. Zamudio,et al.  HISTORICAL ISOLATION, RANGE EXPANSION, AND SECONDARY CONTACT OF TWO HIGHLY DIVERGENT MITOCHONDRIAL LINEAGES IN SPOTTED SALAMANDERS (AMBYSTOMA MACULATUM) , 2003, Evolution; international journal of organic evolution.

[43]  A. Dobson,et al.  Geographic Distribution of Endangered Species in the United States , 1997, Science.

[44]  B. Crespi,et al.  The evolution of geographic parthenogenesis in Timema walking‐sticks , 2002, Molecular ecology.

[45]  R. Wayne,et al.  Tripartite genetic subdivisions in the ornate shrew (Sorex ornatus) , 2001, Molecular ecology.

[46]  A. Dobson,et al.  SYNOPTIC TINKERING: INTEGRATING STRATEGIES FOR LARGE-SCALE CONSERVATION , 2001 .

[47]  J. Doyle,et al.  Comparative phylogeography of Amphicarpaea legumes and their root‐nodule symbionts in Japan and North America , 2004 .

[48]  J. L. Gittleman,et al.  Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia) , 1999, Biological reviews of the Cambridge Philosophical Society.

[49]  R. Calsbeek,et al.  Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province , 2003, Molecular ecology.

[50]  P. Taberlet,et al.  Comparative phylogeography and postglacial colonization routes in Europe , 1998, Molecular ecology.

[51]  R. Zink,et al.  COMPARATIVE PHYLOGEOGRAPHY OF SOME ARIDLAND BIRD SPECIES , 2001 .

[52]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[53]  Daniel R. Brooks,et al.  HISTORICAL ECOLOGY: A NEW APPROACH TO STUDYING THE EVOLUTION OF ECOLOGICAL ASSOCIATIONS , 1985 .

[54]  J. Sullivan,et al.  Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations , 2000, The American Naturalist.

[55]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[56]  Joseph L. Thorley,et al.  RadCon: phylogenetic tree comparison and consensus , 2000, Bioinform..

[57]  B. G. Baldwin,et al.  Higher-Level Relationships and Major Lineages of Lessingia (Compositae, Astereae) Based on Nuclear rDNA Internal and External Transcribed Spacer (ITS and ETS) Sequences , 2001 .

[58]  H. Robison,et al.  LIFE‐HISTORY VARIATION AND COMPARATIVE PHYLOGEOGRAPHY OF DARTERS (PISCES: PERCIDAE) FROM THE NORTH AMERICAN CENTRAL HIGHLANDS , 1996, Evolution; international journal of organic evolution.

[59]  A. D. Gordon,et al.  Obtaining common pruned trees , 1985 .

[60]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[61]  James C. Hickman,et al.  The Jepson Manual: Higher Plants of California , 1993 .

[62]  Andy Purvis,et al.  Phylogenetic supertrees: Assembling the trees of life. , 1998, Trends in ecology & evolution.

[63]  François-Joseph Lapointe,et al.  Matrix representations with parsimony or with distances: two sides of the same coin? , 2003, Systematic biology.

[64]  T. Brooks,et al.  Hotspots Revisited: Earth's Biologically Richest and Most Endangered Terrestrial Ecoregions , 2000 .

[65]  Michael M. Miyamoto,et al.  Molecular and Morphological Supertrees for Eutherian (Placental) Mammals , 2001, Science.