Multiple genes and the monophyly of Ischnocera (Insecta: Phthiraptera).

Whereas most traditional classifications identify Ischnocera as a major suborder of lice in the order Phthiraptera, a recent molecular study based on one gene did not recover monophyly of Ischnocera. In this study we test the monophyly of Ischnocera using sequences of portions of three different genes: two nuclear (EF1 alpha and 18S) and one mitochondrial (COI). Analysis of EF1 alpha and COI sequences did not recover monophyly of Ischnocera, but these genes provided little support for ischnoceran paraphyly because homoplasy is high among the divergent taxa included in this study. Analysis of 18S sequences recovered ischnoceran monophyly with strong support. Sequences from these three gene regions showed significant conflict with the partition homogeneity test, but this heterogeneity probably arises from the dramatic differences in substitution rates. In support of this conclusion, Kishino-Hasegawa tests of the EF1 alpha and COI genes did not reject several trees containing ischnoceran monophyly. Combined analysis of all three gene regions supported monophyly of Ischnocera, although not as strongly as analysis of 18S by itself. In sum, although rapidly evolving genes can retain some phylogenetic signal for deep phylogenetic relationships, strong support for such relationships is likely to come from more slowly evolving genes.     

alpha A-crystallin is expressed in non-ocular tissues.

alpha-Crystallin, the predominant structural protein of the ocular lens, has been considered to be composed of two subunits, alpha A-crystallin and alpha B-crystallin. Of these two, alpha B-crystallin has been previously shown to be an extralenticular protein while alpha A-crystallin has been considered to be a lens-specific polypeptide. Using an antiserum directed against an N-terminal peptide of alpha-crystallin, we have detected a 20-kDa protein in various rat tissues including the brain, liver, lung, spleen, skin, and small intestine and in a number of established epithelial and fibroblast cell lines. PCR analysis of poly(A)-enriched RNA and Southern blot analysis indicated the presence of alpha A-crystallin mRNA sequences in different non-lenticular tissues. Among the non-ocular tissues examined, spleen showed the highest levels of alpha A-crystallin protein and mRNA. The identity of alpha A-crystallin sequences in the spleen was established by cloning and sequencing a polymerase chain reaction-amplified region of alpha A-crystallin mRNA. Sequences derived from spleen and eye revealed almost 100% identity at the nucleotide level. Interestingly, alpha A-crystallin and alpha B-crystallin seem to exist in an inverse quantitative relationship in the spleen and the heart, the two non-ocular tissues where they show highest concentrations, respectively. The known conserved evolution of alpha A-crystallin and the definitive demonstration of the non-ocular expression of this polypeptide suggest important non-crystallin functions for this protein.     

Phylogenetic analysis of eleven species of Biomphalaria Preston, 1910 (Gastropoda: Planorbidae) based on comparisons of allozymes

Freshwater snails in the genus Biomphalaria transmit Schistosoma mansoni in Africa, South America and the Caribbean region. Although considerable attention has been given to the identification of species, little is known of evolutionary relationships among the species. A phylogenetic analysis of 25 populations representing 11 species was performed on 25 enzyme loci examined using starch gel electrophoresis. A phylogenetic analysis of the individual populations produced 60 trees of equal length. The 60 trees have a consistency index value of 75.9% and a retention index value of 76.5%. The phylogenetic analysis provided strong support for the monophyly of Biomphalaria with either 14 or 15 synapomorphies uniting all of the species included and separating them from the outgroup, two species of Helisoma. Four nominal species represented by multiple populations formed monophyletic groups. Populations of B. sudanica, B. choanomphala, and B. alexandrina were interspersed. Ten arrangements were obtained for the populations of these three species. A variety of ingroup taxa were used to root the trees, and all provided support for the use of Helisoma species as an outgroup. In all of the trees obtained, the African species together formed a monophyletic group. In none of the trees obtained did the neotropical species form a monophyletic group. A constrained analysis requiring the monophyly of the neotropical species as well as the African species resulted in 90 trees just two steps longer than the shortest trees. Analysis of the species from either hemisphere alone resulted in decreased resolution, as measured by an increase in the number of trees obtained. This finding suggests that further comparisons of species from the two hemispheres will be of considerable value. Finally, two species which are resistant to infection with S. mansoni were included among the eleven studied. Neither of these species formed the sister group to all of the other species included, indicating that susceptibility is the plesiomorphic state, and that resistance is derived. Similarly, in none of the trees obtained did the two resistant species fall out as sister taxa, indicating that resistance arose independently twice.     

Phylogenetic relationships within the Eurasian cattish family Siluridae (Pisces: Siluriformes), with comments on generic validities and biogeography

A numerical cladistic analysis, based on 23 terminal groups and 63 morphological characters, was done to infer phylogenetic relationships within the Eurasian catfish family Siluridae. Nine hundred and forty-five equally most parsimonious trees (134 steps, consistency index 0.634) were found that differ in their resolutions of four polychotomies. Strict consensus of these trees includes ten internal nodes, does not support monophyly of Silurus, Ompok and Kryptopterus , as usually defined, and offers ambiguous support for monophyly of Wallago. Silurus and Kryptopterus are each composed of two non-sister group clades, and Ompok is composed of at least two such clades. Heuristic searches constrained by monophyly of Silurus, Ompok or Kryptopterus yielded trees five or six steps longer than the shortest trees free of constraints. The strict consensus also infers a basal dichotomy that separates the Siluridae into a temperate Eurasian clade with about 20 nominal species and a subtropical/tropical south and southeast Asian clade with about 75 nominal species. The distributions of these clades overlap in a relatively narrow region of east Asia. A heuristic search for trees 1 step longer than the shortest trees yielded 253890 trees. A strict consensus of these trees also infers a basal dichotomy between the above-mentioned clades. This analysis revealed four additional putative synapomorphies of the Siluridae, pending further resolution of the family's outgroup relationships.     

Phylogeny of Cephalobina (Nematoda): molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications

Nematodes of the suborder Cephalobina include an ecologically and morphologically diverse array of species that range from soil-dwelling microbivores to parasites of vertebrates and invertebrates. Despite a long history of study, certain of these microbivores (Cephaloboidea) present some of the most intractable problems in nematode systematics; the lack of an evolutionary framework for these taxa has prevented the identification of natural groups and inhibited understanding of soil biodiversity and nematode ecology. Phylogenetic analyses of ribosomal (LSU) sequence data from 53 taxa revealed strong support for monophyly of taxa representing the Cephaloboidea, but do not support the monophyly of most genera within this superfamily. Historically these genera have primarily been recognized based on variation in labial morphology, but molecular phylogenies show the same general labial (probolae) morphotype often results from recurrent similarity, a result consistent with the phenotypic plasticity of probolae previously observed for some species in ecological time. Phylogenetic analyses of LSU rDNA also recovered strong support for some other groups of cephalobs, including taxa representing most (but not all) Panagrolaimoidea. In addition to revealing homoplasy of probolae, molecular trees also imply other unexpected patterns of character evolution or polarity, including recurrent similarity of offset spermatheca presence, and representation of complex probolae as the ancestral condition within Cephaloboidea. For Cephalobidae, molecular trees do not support traditional genera as natural groups, but it remains untested if deconstructing probolae morphotypes or other structural features into finer component characters may reveal homologies that help delimit evolutionary lineages.     

Molecular systematics of armadillos (Xenarthra,Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes

The 30 living species of armadillos, anteaters, and sloths (Mammalia: Xenarthra) represent one of the three major clades of placentals. Armadillos (Cingulata: Dasypodidae) are the earliest and most speciose xenarthran lineage with 21 described species. The question of their tricky phylogeny was here studied by adding two mitochondrial genes (NADH dehydrogenase subunit 1 [ND1] and 12S ribosomal RNA [12S rRNA]) to the three protein-coding nuclear genes (alpha2B adrenergic receptor [ADRA2B], breast cancer susceptibility exon 11 [BRCA1], and von Willebrand factor exon 28 [VWF]) yielding a total of 6869 aligned nucleotide sites for thirteen xenarthran species. The two mitochondrial genes were characterized by marked excesses of transitions over transversions-with a strong bias toward CT transitions for the 12S rRNA-and exhibited two- to fivefold faster evolutionary rates than the fastest nuclear gene (ADRA2B). Maximum likelihood and Bayesian phylogenetic analyses supported the monophyly of Dasypodinae, Tolypeutinae, and Euphractinae, with the latter two armadillo subfamilies strongly clustering together. Conflicting branching points between individual genes involved relationships within the subfamilies Tolypeutinae and Euphractinae. Owing to a greater number of informative sites, the overall concatenation favored the mitochondrial topology with the classical grouping of Cabassous and Priodontes within Tolypeutinae, and a close relationship between Euphractus and Chaetophractus within Euphractinae. However, low statistical support values associated with almost equal distributions of apomorphies among alternatives suggested that two parallel events of rapid speciation occurred within these two armadillo subfamilies.     

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.     

An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes

Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. To examine the utility of EF-1 alpha as a phylogenetic marker for eukaryotes, we studied three properties of EF-1 alpha trees: congruency with other phyogenetic markers, the impact of species sampling, and the degree of substitutional saturation occurring between taxa. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent. However, the topology of the intermediate portion of the EF-1 alpha tree, occupied by most of the protist lineages, differs for different phylogenetic methods, and bootstrap values for branches are low. Most problematic in this region is the failure of all phylogenetic methods to resolve the monophyly of two higher-order protistan taxa, the Ciliophora and the Alveolata. JACKMONO analyses indicated that the impact of species sampling on bootstrap support for most internal nodes of the eukaryotic EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus inferred numbers of substitutions indicates that multiple overlapping substitutions have occurred, especially on the branch separating the Eukaryota from the Archaebacteria, suggesting that the rooting of the eukaryotic tree on the diplomonad lineage should be treated with caution. Overall, these results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. This lack of resolution may result from the combined effects of poor taxonomic sampling, relatively few informative positions, large numbers of overlapping substitutions that obscure phylogenetic signal, and lineage-specific rate increases in the EF-1 alpha data set. It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution.     

Phylogenetic relationships of sponges with placochelae or related spicules (Poecilosclerida, Guitarridae) with a systematic revision

All the currently known sponge species bearing placochelae or placochelae-like spicules (i.e. belonging to the genera Guitarra, Coelodischela, Tetrapocillon, Euchelipluma , and Hoplakithara ) have been reviewed and their relationships delineated by cladistic analysis. A matrix of 18 taxa and 14 characters is included. The species Isodictya palmata and Esperiopsis fucorum were used as an outgroup, because they shared either monactines or diactines and smooth palmate isochelae with different members of the ingroup. Cladistic analysis using PAUP produced two equally parsimonious trees of 33 steps (CI = 0.758). Strict, Semistrict and Majority Rule consensus trees displayed the same topology. The phylogeny of the trees was not totally resolved. The bootstrap 50% majority-rule consensus tree supported, to a greater or lesser extent, the previously detected monophyletic groups. A common linkage for the ingroup was found in 72% of instances. The genus Euchelipluma appeared as monophyletic in 75% of instances while the group which included the genus Guitarra did so in 66%. The monophyly of the species with sigmoid microscleres and without spiny isochelae (G. isabellae/sigmatifera/antarctica/dendyi and C. diatomorpha/massa ) received 56% support as did the group of species with spiny isochelae, whereas monophyly of the group laplani/ bipocillifera received 64% support and the genus Tetrapocillon 56%. According to our cladistic analysis, all the species bearing placochelae or derived forms should be allocated to Guitarridae. Within this family, the genus Euchelipluma appeared as monophyletic while Guitarra was paraphyletic. The single species of the genus Hoplakithara clearly belongs to the Guitarra ( sigmatifera ) group and thus becomes synonymous with Guitarra. G. solorzanoi is considered here a synonymy of G. laplani. A diagnosis for the 10 valid species of Guitarra known to date as well as for the two species of Coelodischela and the two of Euchelipluma is given.     

基于16S rDNA序列探讨中国剑角蝗科的单系性及其六属的系统发育关系

在中国学者夏凯龄的分类系统中,剑角蝗科Acrididae一直被看作是单系群,包含6个亚科。但是,近年来的研究对其单系性争议较大。为探讨其单系性和剑角蝗属等6属的系统发育关系,我们测定了剑角蝗科14种蝗虫的16S rRNA基因部分序列,并从GenBank中下载了1种蝗虫的同源序列。以蚱科的2个种作外群,用NJ、MP及ML法重建系统发生树。由三棵分子系统树中得出的系统发生关系与中国的分类系统差别较大,都不支持剑角蝗科是单系群,但与国外Kevan的系统相一致,提示我们国内的分类系统亟待修改和完善。长腹蝗亚科与斑腿蝗科的亲缘关系要近于与剑角蝗科的其他种类的关系。另外,尽管所测的红足剑角蝗和上海剑角蝗的16S rDNA的片段序列完全相同,我们仍不能断定二者是同一个物种[动物学报52 (2) : 302 -308 , 2006]。     

Expression and aggregation of recombinant alpha A-crystallin and its two domains.

The 20 kDa alpha A and alpha B subunits of alpha-crystallin from mammalian eye lenses form large aggregates with an average molecular weight of 800,000. To get insight into the interactions responsible for aggregate formation, we expressed in Escherichia coli the putative N- and C-terminal domains of alpha A-crystallin, as well as the intact alpha A-crystallin chain. The proteins are expressed in a stable form and in relatively high amounts (20-60% of total protein). Recombinant alpha A-crystallin and the C-terminal domain are expressed in a water-soluble form. Recombinant alpha A-crystallin forms aggregates comparable with alpha-crystallin aggregates from calf lenses, whereas the C-terminal domain forms dimers or tetramers. The N-terminal domain is expressed in an initially water-insoluble form. After solubilization, denaturation and reaggregation the N-terminal domain exists in a high molecular weight multimeric form. These observations suggest that the interactions leading to aggregation of alpha A-crystallin subunits are mainly located in the N-terminal half of the chain.     

Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA

The controversy over generic delimitation between Maianthemum and Smilacina has been unresolved for almost two centuries. Distributions of the two genera in the Northern Hemisphere also provide an excellent opportunity to further understand the disjunct distribution patterns of the North Temperate Flora. To test the generic delimitation and to investigate biogeographic patterns, we sequenced the partial 3′ matK gene and trnK 3′ intron of chloroplast DNA for 38 accessions, representing three species of Maianthemum, seven species of Smilacina, and four outgroup taxa. Maximum parsimony and neighbor-joining trees showed reciprocal monophyly of the two genera with very weak bootstrap support for each genus. Within each genus, relationships among species were poorly resolved. Despite its low resolution, this study shows that eastern Asian species of Smilacina and Maianthemum are generally more closely related to eastern North American taxa than to western ones. More detailed sampling of Smilacina from different geographic regions, especially from the two centers of diversity (southeastern Asia and Mexico/Central America), and additional sequences from cpDNA, as well as from nuclear DNA, are needed to test the reciprocal monophyly of the two genera and also to understand current distributions of disjunct taxa.     

Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi)

A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.     

Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences

Myriapods play a pivotal position in the arthropod phylogenetic tree. The monophyly of Myriapoda and its internal relationships have been difficult to resolve. This study combined nearly complete 28S and 18S ribosomal RNA gene sequences (3,826 nt in total) to estimate the phylogenetic position of Myriapoda and phylogenetic relationships among four myriapod classes. Our data set consists of six new myriapod sequences and homologous sequences for 18 additional species available in GenBank. Among the six new myriapod sequences, those of the one pauropod and two symphylans are very important additions because they were such difficult taxa to classify in past molecular-phylogenetic studies. Phylogenetic trees were constructed with maximum parsimony, maximum likelihood, and Bayesian analyses. All methods yielded moderate to strong support for the monophyly of Myriapoda. Symphyla grouped strongly with Pauropoda under all analytical conditions. The KH test rejected the traditional view of Dignatha and Progoneata, and the topology obtained here, though not significantly supported, was Diplopoda versus ((Symphyla + Pauropoda) + Chilopoda).     

Comparison of d-aspartic acid contents in alpha A-crystallin from normal and age-matched cataractous human lenses

We have previously shown that biologically uncommon d-beta-aspartic acids (Asp) were localized with very high contents at Asp-151 and Asp-58 of alpha A-crystallin from aged human lenses. The amounts increased with age, and we have proposed the mechanism of this reaction. In the present study, in order to elucidate the possible relationship between the formation of d-beta-aspartic acids in alpha A-crystallin and cataract formation, we measured the d/l ratio of beta-Asp-151 of alpha A-crystallin from both cataractous and age-matched normal human lenses. alpha A-crystallin from total proteins of cataractous and age-matched normal lenses was prepared, followed by tryptic digestion and quantification of d/l ratios for tryptic fragments containing the alpha- and beta-aspartate forms of Asp-151 residues. The results demonstrate that the d/l ratio of beta-Asp-151 of alpha A-crystallin from normal lenses is not statistically significant from that of alpha A-crystallin from cataractous lenses, suggesting that formation of this biologically uncommon amino acid may not play a role in human cataractogenesis.     

Systematics and origin of moths in the subfamily Arctiinae (Lepidoptera,Erebidae) in the Neotropical region

The availability of standard protocols to obtain DNA sequences has allowed the inference of phylogenetic Hypotheses for many taxa, including moths. We here have inferred a phylogeny using maximum‐Likelihood and Bayesian approaches for a species‐rich group of moths (Erebidae, Arctiinae), with strong emphasis on Neotropical genera collected in different field campaigns in the Atlantic Forest of Brazil, eastern Amazon and southern Ecuador. A total of 277 species belonging to 246 genera were included in the analysis. Our main objectives were to shed light on the relationships between suprageneric groups, especially subtribes, and hypothesize colonization events in and out of the Neotropics. The monophyly of Arctiinae and its four tribes (Lithosiini, Amerilini, Syntomini and Arctiini) was recovered in the ML and Bayesian trees. Three Lithosiini subtribes previously found and two additional species groups were recovered monophyletic in both phylogenetic estimation methods. In Arctiini, the monophyly of Spilosomina and Arctiina was highly supported in the ML and Bayesian trees, but the monophyly of Ctenuchina and Echromiina was weakly supported in the ML tree and absent in the Bayesian tree; the remaining subtribes were paraphyletic and, in the case of Phageopterina, formed several species groups. The mapping of species occurrence in our ML tree suggests that Arctiinae have an Old World origin and that the Neotropical region was colonized at least six times independently. Our analysis also suggests that a number of species that occur in Neotropical and other zoogeographic regions may have originated in the Neotropics, although further taxon sampling is required to support this hypothesis. To our knowledge, this is the first time that a highly speciose group of tropical moths is well covered in a phylogeny, and it seems plausible that the results reported here may be extendable to other species‐rich tropical undersampled moth taxa.     

Enhanced stability of alpha B-crystallin in the presence of small heat shock protein Hsp27

Lens alpha-crystallin, alpha A- and alpha B-crystallin, and Hsp27 are members of the small heat shock protein family. Both alpha A- and alpha B-crystallin are expressed in the lens and serve as structural proteins and as chaperones, but alpha B-crystallin is also expressed in nonlenticular organs where Hsp27, rather than alpha A-crystallin, is expressed along with alpha B-crystallin. It is not known what additional function Hsp27 has besides as a heat shock protein, but it may serve, as alpha A-crystallin does in the lens, to stabilize alpha B-crystallin. In this study, we investigate aspects on conformation and thermal stability for the mixture of Hsp27 and alpha B-crystallin. Size exclusion chromatography, circular dichroism (CD), and light scattering measurements indicated that Hsp27 prevented alpha B-crystallin from heat-induced structural changes and high molecular weight (HMW) aggregation. The results indicate that Hsp27 indeed promotes stability of alpha B-crystallin.     

Phylogenetic relationships in the genus mus,based on paternally,maternally, and biparentally inherited characters

Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses. Although each of the six genes yielded a unique phylogeny, several clades were supported by four or more gene trees. Nodes that conflicted between trees were generally characterized by weak support for one or both of the alternative topologies, thus providing no compelling evidence that any individual gene, or part of the genome, was misleading with respect to the evolutionary history of these mice. Analysis of the combined data resulted in a fully resolved tree that strongly supports monophyly of the genus Mus, monophyly of the subgenus Mus, division of the subgenus Mus into Palearctic (M. musculus, M. macedonicus, M. spicilegus, and M. spretus) and Asian (M. cervicolor, M. cookii, and M. caroli) clades, monophyly of the house mice (M. m. musculus, "M. m. molossinus," M. m. castaneus, and M. m. domesticus), and a sister-group relationship between M. macedonicus and M. spicilegus. Other clades that were strongly supported by one or more gene partitions were not strongly supported by the combined data. This appears to reflect a localized homoplasy in one partition obscuring the phylogenetic signal from another, rather than differences in gene or genome histories.