Multiple Substitutions Affect the Phylogenetic Utility of Cytochrome b and 12S rDNA Data: Examining a Rapid Radiation in Leporid (Lagomorpha) Evolution

Abstract. Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested by paleontological evidence.

[1]  M. Lara,et al.  The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences. , 1996, Molecular phylogenetics and evolution.

[2]  M. Nei,et al.  Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data. , 1991, Molecular biology and evolution.

[3]  M. Novacek.  Morphology, paleontology, and the higher clades of mammals , 1990 .

[4]  K. Halanych.  Lagomorphs misplaced by more characters and fewer taxa. , 1998, Systematic biology.

[5]  D. Hillis.  Inferring complex phylogenies. , 1996, Nature.

[6]  J. A. Chapman,et al.  Evolution of chromosomal variation in cottontails, genus Sylvilagus (Mammalia: Lagomorpha). II. Sylvilagus audubonii, S. idahoensis, S. nuttallii, and S. palustris. , 1984, Cytogenetics and cell genetics.

[7]  A. Wyss,et al.  Primitive fossil rodent from Inner Mongolia and its implications for mammalian phylogeny , 1994, Nature.

[8]  J. Stephens,et al.  Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the pantherine lineage of Felidae. , 1995, Molecular biology and evolution.

[9]  D. Hillis,et al.  Nucleic Acids III. Sequencing , 1990 .

[10]  C. Matthee,et al.  Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences. , 1997, Molecular biology and evolution.

[11]  M. Dawson.  Later Tertiary Leporidae of North America , 1958 .

[12]  D. Klein,et al.  Cytochrome b phylogeny of North American hares and jackrabbits (Lepus, lagomorpha) and the effects of saturation in outgroup taxa. , 1999, Molecular phylogenetics and evolution.

[13]  D M Irwin,et al.  Evolution of the cytochrome b gene of mammals. , 1991, Journal of molecular evolution.

[14]  C. Cunningham,et al.  Can three incongruence tests predict when data should be combined? , 1997, Molecular biology and evolution.

[15]  L. R. Dice.  The phylogeny of the Leporidae, with description of a new genus. , 1929 .

[16]  K. Holsinger,et al.  Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents. , 1995, Molecular biology and evolution.

[17]  T. J. Robinson,et al.  BANDING STUDIES IN THE VOLCANO RABBIT, ROMEROLAGUS DIAZI AND CRAWSHAY'S HARE LEPUS CRAWSHAYI. EVIDENCE OF THE LEPORID ANCESTRAL KARYOTYPE , 1981 .

[18]  A. Meyer,et al.  Shortcomings of the cytochrome b gene as a molecular marker. , 1994, Trends in ecology & evolution.

[19]  C. W. Hibbard.  The Origin of the P3 Pattern of Sylvilagus, Caprolagus, Oryctolagus and Lepus , 1963 .

[20]  V. Flyger,et al.  Proceedings of the World Lagomorph Conference , 1984 .

[21]  S. Easteal,et al.  The pattern of mammalian evolution and the relative rate of molecular evolution. , 1990, Genetics.

[22]  J. Huelsenbeck,et al.  Signal, noise, and reliability in molecular phylogenetic analyses. , 1992, The Journal of heredity.

[23]  A. Graybeal.  The phylogenetic utility of cytochrome b: lessons from bufonid frogs. , 1993, Molecular phylogenetics and evolution.

[24]  K. Halanych.  TESTING HYPOTHESES OF CHAETOGNATH ORIGINS: LONG BRANCHES REVEALED BY 18S RIBOSOMAL DNA , 1996 .

[25]  Laurent Duret,et al.  Phylogenetic position of the order Lagomorpha (rabbits, hares and allies) , 1996, Nature.

[26]  D. Hillis.  Inferring complex phytogenies , 1996, Nature.

[27]  S. Pääbo,et al.  Polymerase chain reaction reveals cloning artefacts , 1988, Nature.

[28]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[29]  M. Ruvolo,et al.  Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions. , 1996, Molecular biology and evolution.

[30]  Daryl E. Wilson,et al.  Mammal Species of the World: A Taxonomic and Geographic Reference , 1993 .

[31]  J. Skinner,et al.  Karyology of the Riverine Rabbit, Bunolagus monticularis, and Its Taxonomic Implications , 1983 .

[32]  O. Ryder,et al.  Different rates of mitochondrial DNA sequence evolution in Kirk's dik-dik (Madoqua kirkii) populations. , 1995, Molecular phylogenetics and evolution.

[33]  J. A. Chapman,et al.  Rabbits, Hares, and Pikas: Status Survey And Conservation Action Plan , 1991 .

[34]  Wayne P. Maddison,et al.  Macclade: Analysis of Phylogeny and Character Evolution/Version 3 , 1992 .

[35]  S. Blair Hedges,et al.  Molecular zoology: Advances, strategies, and protocols , 1997 .

[36]  K. Halanych,et al.  Phylogenetic relationships of cottontails (Sylvilagus, Lagomorpha): congruence of 12S rDNA and cytogenetic data. , 1997, Molecular phylogenetics and evolution.

[37]  A. Meyer,et al.  Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[39]  J. Mounolou,et al.  Direct repeats in the non-coding region of rabbit mitochondrial DNA. Involvement in the generation of intra- and inter-individual heterogeneity. , 1990, European journal of biochemistry.

[40]  L. Krishtalka,et al.  The Origin of Rodents and Lagomorphs , 1987 .

[41]  J. A. Chapman,et al.  Evolution of chromosomal variation in cottontails, genus Sylvilagus (Mammalia: Lagomorpha): S. aquaticus, S. floridanus, and S. transitionalis. , 1983, Cytogenetics and cell genetics.

[42]  M. Allard,et al.  Nucleotide sequence variation in the mitochondrial 12S rRNA gene and the phylogeny of African mole-rats (Rodentia: Bathyergidae). , 1992, Molecular biology and evolution.

[43]  M. Springer,et al.  Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. , 1995, Molecular biology and evolution.

[44]  W. Brown,et al.  EVOLUTION OF ANIMAL MITOCHONDRIAL DNA: RELEVANCE FOR POPULATION BIOLOGY AND SYSTEMATICS , 1987 .

[45]  A. Wilson,et al.  Mitochondrial resolution of a deep branch in the genealogical tree for perching birds , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.