Museum of Zoology and Department of Biology, University of Michigan
![]() |
Abstract |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Introduction |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
When homoplasious similarity among traits (due to convergence, parallel evolution, or reversals) is abundant relative to homologous similarity, phylogenetic analyses can be misled (Cavender 1978
; Felsenstein 1978
; Hendy and Penny 1989
). Even when sequence evolution is clocklike, tree-building inconsistency can occur due to positional rate heterogeneity and taxon differences in nucleotide/amino acid composition and distribution of variable sites (see Steel, Huson, and Lockhart 2000
), particularly when outgroup taxa are very distantly related to the ingroup taxa. One potential solution for outgroup rooting is to use paralogous genes, with one serving as the phylogenetic root for the other. This can be done when the gene duplication occurs after the divergence between the closest organismal outgroup and the ingroup taxa, but before ingroup diversification. This results in the duplicated forms of the gene being more closely related to one another than either is to the single gene of the outgroup. This innovation was applied first in phylogenetic analyses for the tree of life, where no suitable outgroup organisms exist (Gogarten et al. 1989
; Iwabe et al. 1989
; Doolittle and Brown 1994
), and more recently in analyses of chaetognaths (Telford and Holland 1997
) and angiosperms (Donoghue and Mathews 1998
). A general difficulty with this approach is our limited knowledge of paralogous genes that fit the evolutionary pattern described.
Here, we develop a similar, but different, approach to rooting phylogenetic analyses. Instead of using paralogous genes for reciprocal rooting, we use homologous genes on opposite sex chromosomes. Related genes located on opposite sex chromosomes present a unique and previously unnamed form of homology. We recognize "gametologous" genes as arising via nonrecombination and differentiation of sex chromosomes. Barriers to recombination between entire or portions of opposite sex chromosomes facilitate differentiation for gametologs, in a manner similar to lineage splitting and gene duplication facilitating differentiation for orthologs and paralogs. We use "gamete" as the word root because sex chromosomes are distributed differently in sex-specific gametes.
Recognition of gametologous relationships for characters is warranted in theory, as they fit the criterion of sharing common ancestry which lies at the heart of homology definition (Van Valen 1982
; Roth 1988
; Mindell 1991
; Hillis 1994
), and they arise by an evolutionary process that is different from those underlying the three kinds of homology relationship described previously. Recognition and use of particular gametologs in phylogenetic analyses can be supported by evidence indicating that (1) they are mutually distinguishable and linked to opposite sex chromosomes, (2) they share common, most recent decent from a homologous autosome pair, and (3) they yield phylogenetic hypotheses that are congruent with each other and with hypotheses based on independent data sets. Ideally, gametologs should evolve independently under similar functional constraints, and their age relative to subsequent divergences within gametolog clades should not yield juxtaposition of very long and short branches. Here, we examine rooting with Chromo-helicase-DNA binding gene (CHD) gametologs in birds, and we consider the three criteria of potential support mentioned above. Points 1 and 2 have recently been addressed by others (references below), and our new data and analyses focus on point 3. Brief phylogenetic analyses including CHD-Z and CHD-W have been presented by Fridolfsson et al. (1998)
and Kahn and Quinn (1999)
for one and four bird species, respectively. We seek to extend their analyses with a larger sampling of species providing a more detailed assessment of congruence and to develop and justify the approach more explicitly.
In support of the first criterion, CHD has been shown to exist in two recognizably different forms in most bird species (neognaths; see below). One is found on the Z chromosome and thus is present in both sexes (CHD-Z), and the other is on the W chromosome and present only in females (CHD-W), the heterogametic sex in birds (Woodage et al. 1997
; Fridolfsson et al. 1998
; Griffiths et al. 1998
; Kahn, St. John, and Quinn 1998
; Fridolfsson and Ellegren 1999
). There is no evidence for recombination between these two genes, and no autosomal copies have been detected (Fridolfsson et al. 1998
; Kahn and Quinn 1999
). Traditionally, avian taxonomists have recognized two primary clades for extant birds, Paleognathae (ratites and tinamous) and Neognathae (all others). Distinct CHD-Z and CHD-W genes have been found in all neognaths assessed but not in paleognaths. Although subtle sex chromosome differences exist in at least some paleognaths (Ansari, Takagi, and Sasaki 1988
), the CHD-Z and CHD-W genes (gametologs) cannot be readily distinguished from each other in paleognaths, and we refer to paleognath CHD sequences as CHD-paleognath.
![]() |
Materials and Methods |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
PCR and Sequencing Protocol
We obtained PCR products for CHD following standard protocols using primers P2 and P8, described by Griffiths et al. (1998)
. The amplification product included approximately equal parts of a complete intron and portions of its two flanking exons. Single products for homogametic male neognaths and for paleognaths of both sexes were cleaned by column purification using QIAquick columns (QIAgen Inc.) following the supplier's protocol. Two products for heterogametic female neognaths were resolvable in 3% LMP agarose gels, as the amplified fragment spanned an intron that varied in length between CHD-W and CHD-Z (Griffiths et al. 1998
; Miyaki et al. 1998
). The two resulting bands were each excised and cleaned using the gel extraction version of the QIAquick kit. Clean products were sequenced using an ABI377 sequencer. Sequences have been deposited in GenBank under accesion numbers AF288487AF288516 and AF006659AF006662.
Phylogenetic Analyses
Sequences were initially aligned using Clustal X (Thompson et al. 1997
) with the following settings: gap opening = 10; gap extension = 0.05; delay divergent sequences = 40; DNA transition weight = 0.5. The resulting alignment was adjusted by eye to minimize mismatches, and gaps were either treated as missing (in analyses including intron sequences) or excluded (in the analysis of exon sequences only). The alignments are available from us on request. We performed a range of phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML). For MP, we used equal weights for all characters, with gaps treated as missing. For the ML analyses, we chose the Hasegawa-Kishino-Yano (HKY) model accounting for invariable positions and unequal rates of substitution following a gamma distribution based on model performance comparisons using likelihood ratio tests (Huelsenbeck and Rannala 1997
). Alternative tree topologies were compared using the Kishino and Hasegawa (1989)
(KH) test. To estimate support for particular nodes within trees, we performed character bootstrap replicates and jackknife replicates with 50% deletion of sequences and random addition of sequences (Felsenstein 1985
). We also evaluated relationships for all possible species quartets using the ML criterion and 1,000 puzzling steps (Strimmer and von Haeseler 1996
), as implemented in PAUP* (Swofford 1999
).
![]() |
Results and Discussion |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
What is the homology between the crocodilian CHD gene and the avian CHD genes? This depends, of course, on their evolutionary history, which is not well known. If the single CHD gene reported here for three crocodilian taxa and six paleognath birds is descended from a single CHD gene condition in their most recent common ancestor, then the relationship between crocodilian CHD and CHD for paleognath birds would be orthologous. Furthermore, the relationship of these to CHD-Z (or CHD-W) in neognath birds could be called "pro-gametologous." This follows the suggestion by Sharman (in Holland 1999
) to identify the unique homology relationship between a singleton gene and a duplicate of its ortholog in another lineage as "pro-orthologous," substituting "gametologous" for "orthologous" as needed in this case.
Phylogenetic Relationships
Phylogenetic analysis of CHD sequences from 19 species of neognath birds yields distinct, monophyletic groups for CHD-W and CHD-Z sequences (fig. 1a
). Inferred relationships for birds within each of these two primary clades are congruent, with each gametolog showing monophyly of Galloanseres (Galliformes [chicken, pheasants] plus Anseriformes [waterfowl]) and Passeriformes (songbirds) and an early separation of Galloanseres from the other neognaths. Phylogenetic analyses excluding the intron (not shown) yields a tree similar to that in figure 1a
; the distinction between CHD-W and CHD-Z is maintained, as is the monophyly and early branching of Galloanseres in both clades, despite the small number (168 bases total) of characters considered.
|
Many of the phylogenetic relationships depicted in the CHD-Z clade, where our taxon sampling was the most extensive, are congruent with current views of avian phylogeny based, variously, on independent morphological (Cracraft 1988
), nuclear (e.g., Sibley and Ahlquist 1990
; Groth and Barrowclough 1999
; Van Tuinen, Sibley, and Hedges 2000
), and mitochondrial (Mindell et al. 1997, 1999
; Härlid, Janke, and Arnason 1998
; Härlid and Arnason 1999
) data sets. These include monophyly of Galloanseres, Galliformes, Anseriformes, Piciformes (woodpeckers and allies), Passeriformes, Accipitridae (hawks and allies), Picidae (woodpeckers), oscine Passeriformes, and suboscine Passeriformes. Recent analyses of mitochondrial genes indicate a relatively basal position for Passeriformes and a more derived position for paleognaths (Mindell et al. 1997, 1999
; Härlid, Janke, and Arnason 1998
; Härlid and Arnason 1999
); however, recent analyses of nuclear genes support the more traditional view of paleognaths diverging basally and Passeriformes being more derived (Groth and Barrowclough 1999
; Van Tuinen, Sibley, and Hedges 2000
), and it is not surprising that CHD analyses are congruent with those of other nuclear genes. Relatively sparse taxon sampling and distantly related outgroups remain as problems in many of the analyses cited and may underlie the differences found. Mindell et al. (1999
, table 5) did find optimal trees congruent with conventional views (paleognaths diverging basally) based on mitochondrial data when using only 2 reptilian outgroup taxa, rather than 11 outgroup taxa representing reptiles, mammals, and an amphibian, combined with ML analyses accounting for evolutionary rate heterogeneity.
The remaining criterion to be considered in support of using CHD gametologs is that they descend from alternative members of a homologous autosome pair. Our results showing monophyly for CHD-Z and CHD-W sequences and showing those clades to be sister groups do indicate a single common origin for the CHD-Z sequences and for the CHD-W sequences (fig. 1
). This is in agreement with analyses by Fridolfsson et al. (1998)
and Kahn and Quinn (1999)
on smaller sets of taxa.
Others have pointed out that paralogous genes with different functions may evolve under different constraints, yielding differences in rate, nucleotide composition, and distribution of variable sites, and that these can potentially mislead phylogeny reconstruction (Lockhart et al. 1996
; Philippe and Laurent 1998
). The same potential for problems exists in the use of gametologs. Nevertheless, we note that avian CHD-W and CHD-Z gametologs analyzed here appear to share the same function, differing only in intron size (Fridolfsson et al. 1998
; Griffiths et al. 1998
).
Sex Chromosome Evolution in Neognath Birds
Recognition and analyses of gametologs also provides the opportunity to learn about sex chromosome evolution in neognath birds by estimating the time of divergence between the CHD-Z and CHD-W clades. To obtain this estimate, we used an ML approach based on quartets allowing for evolutionary rate heterogeneity (QDate v1.1; Rambaut and Bromham 1998
). A range of sequences and multiple fossil dates are used, rather than reliance on a single calibration rate. We derived the ML model parameters from our optimal tree (fig. 1a
) and implemented 100 replicates of the two-rate model, excluding sequences for which rate heterogeneity was detected. The potential for "male-driven evolution" (see below) yielding faster rates in CHD-Z than in female-specific CHD-W is not a biasing factor in these analyses, as two different rates are accommodated in the calculations. We used fossil-based calibration estimates of 40 MYA for the divergence between Phasianidae and Numididae (Benton 1993
; Kornegay et al. 1993
) and 68 MYA for the divergence between Galliformes and Anseriformes (see Waddell et al. 1999
). Eleven quartets passed the rate homogeneity test and were used to estimate the average divergence between CHD-W and CHD-Z at 123 MYA, with a standard deviation of 6 Myr among the 11 quartets (fig. 2
). This estimate predates an estimate of 55 Myr of age for the primary radiation of extant avian orders based on fossil evidence (e.g., Feduccia 1996
), and is closer to estimates ranging from <90 to >130 Myr based on molecular data (Hedges et al. 1996
; Cooper and Penny 1997
; Kumar and Hedges 1998
; Waddell et al. 1999
). If the estimate of 123 MYA is approximately correct, sex chromosome differentiation began early in the radiation of modern birds.
|
Male-Driven Evolution
Gametologs may also be used to test the notion of male-driven evolution (Shimmin, Chong, and Li 1993
) and potential slower rates of evolution for genes on female-specific sex chromosomes due to fewer bouts of replication per unit time. We made this comparison for the CHD-W and CHD-Z sequences by averaging the branch lengths of the ML tree within the CHD-W and CHD-Z clades in figure 1a
and using a 68-Myr divergence estimate between Galliformes and Anseriformes (Waddell et al. 1999
). We found that CHD-Z sequences were evolving about 20% faster than the female-specific CHD-W sequences. This is also in agreement with findings of Ellegren and Fridolfsson (1997)
and Kahn and Quinn (1999)
. The faster rate reflects a larger number of variable sites in CHD-Z than in CHD-W (50 vs. 34 informative sites, respectively, for the same set of six species).
![]() |
Conclusions |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
The general approach we have outlined could be applied to any set of species sharing a unique origination of sex chromosomes with a subsequent lack of recombination. This situation is apparent in multiple vertebrate taxa (reviewed in Solari 1994
). Although only environmental sex determination is known for crocodilians, male or female heterogamety may have had three or more separate origins within lizards (Sauria), based on the current distribution of those traits in phylogenetically distant taxa (Bull 1980
; Olmo 1986
). Similar disparate appearances of male or female heterogamety suggesting independent origins are found within hidden-neck turtles (cryptodires) and snakes. Male heterogamety, considered homologous in placental mammals and marsupials (but see Toder et al. 1997
), appears to have arisen independently in monotremes. Although understanding of independent origins of sex determination in tetrapods is limited and relatively few gametologous genes have been identified, the general approach we have presented can be applied where such information is available. In turn, estimation of phylogeny for gametologs as we have done for CHDs can provide insights into the evolution of sex determination and the relative timing of its origins.
![]() |
Acknowledgements |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Footnotes |
---|
1 Present address: Department of Biology, University of Konstanz, Konstanz, Germany.
1 Keywords: gametolog
homology
phylogeny rooting
avian phylogeny
sex chromosome evolution
Chromo-helicase-DNA binding gene
2 Address for correspondence and reprints: Jaime García-Moreno, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany. E-mail: jaime.garcia-moreno;cauni-konstanz.de.
![]() |
literature cited |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Ansari, H. A., N. Takagi, and M. Sasaki. 1988. Morphological differentiation of sex chromosomes in three species of ratite birds. Cytogenet. Cell Genet. 47:185188[ISI]
Benton, M. J., ed. 1993. The fossil record 2. Chapman and Hall, London
Bull, J. J. 1980. Sex determination in reptiles. Q. Rev. Biol. 55:320[ISI]
Cavender, J. A. 1978. Taxonomy with confidence. Math. Biosci. 40:271280[ISI]
Cooper, A., and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275:11091113
Cracraft, J. 1988. The major clades of birds. Pp. 333355 in M. J. Benton, ed. The phylogeny and classification of the tetrapods. Systematics Association Special Vol. 35A, Clarendon Press, Oxford, England
Donoghue, M. S., and S. Mathews. 1998. Duplicate genes and the root of angiosperms, with an example using phytochrome sequences. Mol. Phylogenet. Evol. 9:489500[ISI][Medline]
Doolittle, W. F., and J. R. Brown. 1994. Tempo, mode, the progenote and the universal root. Proc. Natl. Acad. Sci. USA 91:67216728
Ellegren, H. 2000. Evolution of the avian sex chromosomes and their role in sex determination. TREE 15:188192
Ellegren, H., and A. K. Fridolfsson. 1997. Male-driven evolution of DNA sequences in birds. Nat. Genet. 17:182184[ISI][Medline]
Feducia, A. 1996. The origin and evolution of birds. Yale University Press, New Haven, Conn
Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401410[ISI]
. 1985. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39:783791
Fridolfsson, A. K., H. Cheng, N. G. Copeland, N. A. Jenkins, H. C. Liu, T. Raudsepp, T. Woodage, B. Choehary, H. Halverson, and H. Ellegren. 1998. Evolution of the avian sex chromosomes from an ancestral pair of autosomes. Proc. Natl. Acad. Sci. USA 95:81478152
Fridolfsson, A. K., and H. Ellegren. 1999. A simple and universal method for molecular sexing of non-ratite birds. J. Avian Biol. 30:116121[ISI]
Gogarten, J. P., H. Kilbak, P. Dittrich, L. Taiz, E. J. Bowman, B. J. Bowman, M. F. Manolson, R. J. Poole, T. Date, and T. Oshima. 1989. Evolution of vacuolar H-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA 86:66616665
Griffiths, R., M. C. Double, K. Orr, and R. J. G. Dawson. 1998. A DNA test to sex most birds. Mol. Ecol. 7:10711075[ISI][Medline]
Groth, J. G., and G. F. Barrowclough. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12:115123[ISI][Medline]
Härlid, A., and U. Arnason. 1999. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters. Proc. R. Soc. Lond. Biol. Sci. B 266:305309
Härlid, A., A. Janke, and U. Arnason. 1998. The complete mitochondrial genome of Rhea americana and early avian divergences. J. Mol. Evol. 46:669679[ISI][Medline]
Hedges, S. B., P. H. Parker, C. G. Sibley, and S. Kumar. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226229
Hendy, M. D., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297309[ISI]
Hillis, D. M. 1994. Homology in molecular biology. Pp. 339368 in B. K. Hall, ed. Homology: the hierarchical basis of comparative biology. Academic Press, San Diego
Holland, P. W. H. 1999. The effect of gene duplication on homology. Pp. 226236 in G. R. Bock and G. Cardew, eds. Homology. John Wiley and Sons, New York
Huelsenbeck, J. P., and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227232
Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 84:93559359
Kahn, N. W., and T. W. Quinn. 1999. Male-driven evolution among Eoaves? A test of the replicative division hypothesis in a heterogametic female (ZW) system. J. Mol. Evol. 49:750759[ISI][Medline]
Kahn, N. W., J. St. John, and T. W. Quinn. 1998. Chromosome-specific intron size differences in the avian CHD gene provide and efficient method for sex identification in birds. Auk 115:10741078
Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170179[ISI][Medline]
Kornegay, J. R., T. D. Kocher, L. A. Williams, and A. C. Wilson. 1993. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. J. Mol. Evol. 37:367379[ISI][Medline]
Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature 392:917920
Lockhart, P. J., A. W. Larkum, M. Steel, P. J. Waddell, and D. Penny. 1996. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:19301934
Mindell, D. P. 1991. DNA sequence alignments and the role of homology. Pp. 7389 in M. M. Miyamoto and J. Cracraft, eds. Phylogenetic analysis of DNA sequences. Oxford University Press, New York
Mindell, D. P., M. D. Sorenson, D. E. Dimcheff, M. Hasegawa, J. C. Ast, and T. Yuri. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138152[ISI][Medline]
Mindell, D. P., M. D. Sorenson, C. J. Huddleston, H. C. Miranda Jr., A. Knight, S. J. Sawchuck, and T. Yuri. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. Pp. 213247 in D. P. Mindell, ed. Avian molecular evolution and systematics. Academic Press, San Diego
Miyaki, C. Y., R. Griffiths, K. Orr, L. A. Nahum, S. L. Pereira, and A. Wajntal. 1998. Sex identification of parrots, toucans, and curassows by PCR: perspectives for wild and captive population studies. Zoo Biol. 17:415423[ISI]
Ogawa, A., K. Murata, and S. Mizuno. 1998. The location of Z- and W-linked marker genes and sequence on the homomorphic sex chromosomes of the ostrich and the emu. Proc. Natl. Acad. Sci. USA 95:44154418
Ohno, S. 1967. Sex chromosomes and sex-linked genes. In A. Labhart, T. Mann, and L. T. Samuels, eds. Monographs on endocrinology. Vol. 1. Springer-Verlag, Berlin
Olmo, E. 1986. Reptilia. Pp. 1100 in J. Bernard, ed. Animal cytogenetics, Vol. 4. Chordata 3. Gebrüder Borntraeger, Berlin
Philippe, H., and J. Laurent. 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8:616623[ISI][Medline]
Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:442448[Abstract]
Roth, V. L. 1988. The biological basis of homology. Pp. 126 in C. J. Humphries, ed. Ontogeny and systematics. Columbia University Press, New York
Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N.Y
Shimmin, L. C., B. H.-J. Chong, and W.-H. Li. 1993. Male driven evolution of DNA sequences. Nature 362:745747
Sibley, C. G., and J. Ahlquist. 1990. Phylogeny and classification of birds. Yale University Press, New Haven, Conn
Solari, A. J. 1994. Sex chromosomes and sex determination vertebrates. CRC Press, Boca Raton, Fla
Steel, M., D. Huson, and P. J. Lockhart. 2000. Invariable sites models and their use in phylogeny reconstruction. Syst. Biol. 49:225232[ISI][Medline]
Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964969
Swofford, D. L. 1999. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer, Sunderland, Mass
Telford, M. J., and P. W. H. Holland. 1997. Evolution of 28S ribosomal DNA in chaetognaths: duplicate genes and molecular phylogeny. J. Mol. Evol. 44:135144[ISI][Medline]
Thompson, J. D., T. J. Gibson, F. Plewniak, J. Jeanmougin, and D. G. Higgins. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:48764882
Toder, R., J. Wienberg, L. Voullaire, P. C. M. O'Brien, P. Maccarone, and J. A. Marshall Graves. 1997. Shared DNA sequences between the X and Y chromosomes in the tammar wallabyevidence for independent additions to eutherian and marsupial sex chromosomes. Chromosoma 106:9498
Van Tuinen, M., C. G. Sibley, and S. B. Hedges. 2000. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Mol. Biol. Evol. 17:451457
Van Valen, L. M. 1982. Homology and causes. J. Morphol. 173:305312[ISI][Medline]
Waddell, P. J., Y. Cao, M. Hasegawa, and D. P. Mindell. 1999. Assessing the Cretaceous superordinal divergence times within birds and placental mammals using whole mitochondrial protein sequences and an extended statistical framework. Syst. Biol. 48:119137[ISI][Medline]
Woodage, T., M. A. Basrai, A. D. Baxevanis, P. Hieter, and F. S. Collins. 1997. Characterization of the CHD family of proteins. Proc. Natl. Acad. Sci. USA 94:1147211477