Phylogenetic place of guinea pigs: no support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences

Graur et al.'s (1991) hypothesis that the guinea pig-like rodents have an evolutionary origin within mammals that is separate from that of other rodents (the rodent-polyphyly hypothesis) was reexamined by the maximum-likelihood method for protein phylogeny, as well as by the maximum-parsimony and neighbor-joining methods. The overall evidence does not support Graur et al.'s hypothesis, which radically contradicts the traditional view of rodent monophyly. This work demonstrates that we must be careful in choosing a proper method for phylogenetic inference and that an argument based on a small data set (with respect to the length of the sequence and especially the number of species) may be unstable.      

Exploratory Consensus of Hierarchical Clusterings for Melanoma and Breast Cancer

Finding subtypes of heterogeneous diseases is the biggest challenge in the area of biology. Often, clustering is used to provide a hypothesis for the subtypes of a heterogeneous disease. However, there are usually discrepancies between the clusterings produced by different algorithms. This work introduces a simple method which provides the most consistent clusters across three different clustering algorithms for a melanoma and a breast cancer data set. The method is validated by showing that the Silhouette, Dunne's and Davies-Bouldin's cluster validation indices are better for the proposed algorithm than those obtained by k-means and another consensus clustering algorithm. The hypotheses of the consensus clusters on both the data sets are corroborated by clear genetic markers and 100 percent classification accuracy. In Bittner et al.'s melanoma data set, a previously hypothesized primary cluster is recognized as the largest consensus cluster and a new partition of this cluster into two subclusters is proposed. In van't Veer et al.'s breast cancer data set, previously proposed "basal” and "luminal A” subtypes are clearly recognized as the two predominant clusters. Furthermore, a new hypothesis is provided about the existence of two subgroups within the "basal” subtype in this data set. The clusters of van't Veer's data set is also validated by high classification accuracy obtained in the data set of van de Vijver et al.     

Incongruence of mitochondrial and nuclear gene trees in the Carabid beetles Ohomopterus

We studied the molecular phylogeny of the carabid subgenus Ohomopterus (genus Carabus), using two mitochondrial (mt) DNA regions (16SrRNA and NADH dehydrogenase subunit 5) and three nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an anonymous locus). We revisited the previously reported incongruence between the distribution of mtDNA markers and morphologically defined species (Su et al., 1996; J. Mol. Evol. 43:662-671), which those authors attributed to "type switching", a concerted change in many morphological characters that results in the repeated evolution of a particular morphological type. Our mtDNA gene tree obtained from 44 individuals representing all 15 currently recognized species of Ohomopterus revealed that haplotypes isolated from individuals of a single "species" were frequently separated into distant clades, confirming the previous report. The three nuclear markers generally conformed better-with the morphologically defined species than did the mitochondrial markers. The phylogenetic signal in mtDNA and nuclear DNA data differed strongly, and these two partitions were significantly incongruent with each other according to the incongruence length difference test of Farris et al. (1994; Cladistics 10:315-320), although the three nuclear partitions were not homogeneous either. Our results did not support the type-switching hypothesis that had been proposed to fit the morphological data to the mitochondrial gene tree: The incongruence of the mtDNA tree with other nuclear markers indicates that the mtDNA-based tree does not reflect species history any better than the morphological data do. Incongruence of gene trees in Ohomopterus may have been promoted by the complex processes of geographic isolation and hybridization in the Japanese Archipelago that have led to occasional gene flow and recombination between separated entities. The occurrence of reticulate patterns in this group is intriguing, because species of Ohomopterus exhibit extremely divergent genitalic structures that represent a highly efficient reproductive isolation mechanism.     

"Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis

From an evolutionary perspective, "insectivores" have been one of the most important mammalian groups for over a century. Morphologists have successively pruned flying lemurs, elephant shrews, and tree shrews from Insectivora, but have retained chrysochlorids, tenrecs, erinaceids, soricids, talpids, and solenodontids in crown-group Lipotyphla. With the appearance of large molecular data sets, the monophyly of Lipotyphla has proved untenable. Rather, an emerging consensus is that Lipotyphla is a diphyletic taxon comprised of two monophyletic groups, Afrosoricida and Eulipotyphla. A recent paper by Malia et al. [Mol. Phylogenet. Evol. 24 (2002) 91-101] challenged this view and argued that "While the data [Growth Hormone Receptor] were unable to support the orders Lipotyphla, Eulipotyphla, and Tenrecoidea [= Afrosoricida] this was most likely due to the polyphyly of these groups and not to problems associated with the gene itself such as saturation or highly divergent sequences em leader " (p. 100). We analyzed Malia et al.'s original GHR data set (at both nuclear and protein level), an expanded GHR data set that included 49 additional sequences, and a concatenated data set that included GHR, BRCA1, vWF, and A2AB for a diverse selection of lipotyphlan taxa. Although protein analyses proved inconclusive, all analyses at the DNA level clearly show that the statement of Malia et al. is erroneous. Indeed, likelihood analyses with GHR and with the concatenated data set provide more support for Eulipotyphla and Afrosoricida than for competing hypotheses. These results also highlight the potential pitfalls of single-gene and parsimony-only analyses.     

Molecular phylogeny in mytilids supports the wooden steps to deep-sea vents hypothesis

Molecular data were used to study the diversity of mytilids associated with sunken-woods sampled in the Solomon Islands and discuss the 'wooden steps to deep-sea vent' hypothesis proposed by Distel et al. First, COI data used in a barcoding approach confirm the presence of four distinct species. Analyses of the 18S rDNA and COI dataset then confirmed that these sunken-wood mytilids belonged to a monophyletic group including all species from deep-sea reducing environments. Finally, we analyzed the relationships within this monophyletic group that include the Bathymodiolinae using a COI dataset and a combined analysis of mitochondrial COI and ND4 genes and nuclear rDNA 18S and 28S. Our study supported the 'wooden steps to deep-sea vent' hypothesis: one of the sunken-wood species had a basal position within the Bathymodiolionae, and all described vent and seep mussels included in our analyses were derived taxa within Bathymodiolinae.     

Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima

New methods for parsimony analysis of large data sets are presented. The new methods are sectorial searches, tree-drifting, and tree-fusing. For Chase et al. 's 500-taxon data set these methods (on a 266-MHz Pentium II) find a shortest tree in less than 10 min (i.e., over 15,000 times faster than PAUP and 1000 times faster than PAUP*). Making a complete parsimony analysis requires hitting minimum length several times independently, but not necessarily all "islands" for Chase et al. 's data set, this can be done in 4 to 6 h. The new methods also perform well in other cases analyzed (which range from 170 to 854 taxa).     

Linkage studies in familial Alzheimer disease: Evidence for chromosome 19 linkage

A genetic component in the etiology of Alzheimer disease (AD) has been supported by indirect evidence for several years, with autosomal dominant inheritance with age-dependent penetrance being suggested to explain the familial aggregation of affecteds. St. George Hyslop et al. reported linkage of familial AD (FAD) in four early-onset families (mean age at onset [M] less than 50 years). Subsequent studies have been inconsistent in their results; Goate et al. also reported positive lod scores. However, both Pericak-Vance et al.'s study of a series of mainly late-onset FAD families (M greater than 60 years) and Schellenberg et al.'s study failed to confirm linkage to chromosome 21 (CH21). These various studies suggest the possibility of genetic heterogeneity, with some families linked to CH21 and others unlocalized. Recently, St. George Hyslop et al. extended their analysis to include additional families. The extended analyses supported their earlier finding of linkage to CH21, while showing strong evidence of heterogeneity between early-onset (M less than 65 years) and late-onset (M greater than 60 years) FAD families. Because our families did not show linkage to CH21, we undertook a genomic search for an additional locus for FAD. Because of both the confounding factor of late age at onset of FAD and the lack of clear evidence of Mendelian transmission in some of our families, we employed the affected-pedigree-member (APM) method of linkage analysis as an initial screen for possible linkage. Using this method, we identified two regions suggesting linkage: the proximal long arm of chromosome 19 (CH19) and the CH21 region of FAD linkage reported by St. George Hyslop et al. Application of standard likelihood (LOD score) analysis to these data support the possibility of an FAD gene locate on CH19, particularly in the late-onset FAD families. These data further suggest genetic heterogeneity and delineate this region of CH19 as an area needing additional investigation in FAD.     

Small subunit ribosomal DNA characterization of an unidentified aurantiactinomyxon form and its oligochaete host Tubifex ignotus

In this study, the small subunit (18S) ribosomal DNA gene from an aurantiactinomyxon form of unknown taxonomic position (A1) and from its aquatic oligochaete host (Tubifex ignotus) were characterized. Molecular sequence information on A1 was obtained to allow comparisons of this gene with known sequences from known myxosporean forms, and therefore to investigate possible relationships between this organism and its alternate myxosporean stage. Sequence data for the oligochaete host, together with morphological features, will allow reliable identification of this species in the future. Sequence data derived from the 18S DNA gene and data from other related or non-related organisms were analyzed and used to construct a phylogenetic tree. Phylogenetic studies provided an insight into the taxonomic position of A1. Sequence similarities within the 18S rDNA A1 gene and compared organisms indicated that A1 was most closely related to members of the sub-order Variisporina (Myxidium lieberkuehni [Ml] and Sphaerospora oncorhynchi [So]). Clustering of the 3 organisms in the same branch was well supported by high bootstrap values (81%). A1 showed higher similarities with sequences of Ml (approximately 80%) than with So (approximately 79%). Myxosporean sequence analysis indicated that phylogenetic arrangements do not support traditional classification based on morphological criteria of the spores, but rather support arrangement by tissue location. Marine actinosporeans Triactinomyxon sp. and Tetraspora discoidea were found to be associated with Platysporinid myxosporeans, supporting previous findings. In this study, 18S rDNA sequence data are generated for first time for the aquatic oligochaete T. ignotus. Phylogenetic 18S rDNA gene analyses performed with T. ignotus support and confirm existing morphological and molecular phylogenetic studies. Paraphyly of the Tubificidae family was noticed.     

Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure

We describe a method for comparing nuclear and organelle population differentiation (F(ST)) in seed plants to test the hypothesis that pollen and seed gene flow rates are equal. Wright's infinite island model is used, with arbitrary levels of self-fertilization and biparental organelle inheritance. The comparison can also be applied to gene flow in animals. Since effective population sizes are smaller for organelle genomes than for nuclear genomes and organelles are often uniparentally inherited, organelle F(ST) is expected to be higher at equilibrium than nuclear F(ST) even if pollen and seed gene flow rates are equal. To reject the null hypothesis of equal seed and pollen gene flow rates, nuclear and organelle F(ST)'s must differ significantly from their expected values under this hypothesis. Finite island model simulations indicate that infinite island model expectations are not greatly biased by finite numbers of populations (>/=100 subpopulations). The power to distinguish dissimilar rates of pollen and seed gene flow depends on confidence intervals for fixation index estimates, which shrink as more subpopulations and loci are sampled. Using data from the tropical tree Corythophora alta, we rejected the null hypothesis that seed and pollen gene flow rates are equal but cannot reject the alternative hypothesis that pollen gene flow is 200 times greater than seed gene flow.     

Curiously Modern DNA for a ``250 Million-Year-Old' Bacterium

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. Received: 12 April 2001 / Accepted: 9 June 2001     

灰飞虱体内一种酵母类共生菌的分子鉴定

为明确稻飞虱体内酵母类共生菌（yeast-like symbiont,YLS）的种类,采用超速离心的方法分离纯化灰飞虱Laodelphax striatellus（Fallén）体内YLS,用真菌的通用引物对其18S rDNA、5.8S-ITS rDNA全长序列进行扩增。结果得到一条分子量约为2 340 bp的序列。序列同源性分析表明,该菌与Noda等所报道的类酵母菌的18S rDNA序列差异较大（同源性只有89.6％）,而与季也蒙毕赤酵母Pichia guilliermondii有99.8％的同源性。原位杂交（ISH）和巢氏PCR均证明该菌存在于灰飞虱脂肪体和卵内,但数量较少。因此,灰飞虱体内YLS除了Noda等报道的类酵母菌外,尚存在另外一种季也蒙毕赤酵母菌。     

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.     

Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea)

The systematic relationships of the freshwater shrimp family, Kakaducarididae, were examined using mitochondrial and nuclear DNA sequences. Combined nuclear (18S rDNA, 28S rDNA, Histone) and mitochondrial (16S rDNA) analyses placed the kakaducaridid genera, Kakaducaris and Leptopalaemon, as a strongly supported clade within the Palaemonidae, in a close relationship with the genus Macrobrachium. Monophyly of the Australian Kakaducarididae was strongly supported by the molecular data. Estimated net divergence times between Kakaducaris and Leptopalaemon using mitochondrial 16S rDNA equate to a late Miocene/Pliocene split. Within Leptopalaemon, each locality was distinct for mitochondrial COI haplotypes, suggesting long-term isolation or recent genetic bottlenecks, a lack of contemporary gene flow amongst sites and a small Ne. Mitochondrial groupings within Leptopalaemon were largely congruent with several previously recognised morphotypes. Estimated net divergence times between L. gagadjui and the new Leptopalaemon morphotypes equate to a split in the late Pliocene/early Pleistocene. The hypothesis that the Kakaducarididae is comprised of relict species in specialised ecological niches is not supported by the molecular data, which instead suggest a relatively recent origin for the group in northern Australia, sometime in the late Miocene or Pliocene.     

The anchorosome, a special chromatin granule for the anchorage of the interphase chromosome to the nuclear envelope

Peripheral chromatin granules bound to the nuclear envelope of rat liver nuclei have been further investigated. Judging by the results of Staphylococcal nuclease digestion of nuclei and electron microscopical observations, the peripheral granules have nucleosomal organization. As shown by ultraviolet radiation DNA-protein cross-linkage, the histone-like proteins present in the peripheral chromatin instead of histone H1 (Fais et al., 1982) are in close contact with DNA. The peripheral chromatin contains a DNA firmly bound to the lamina. This DNA, resistant to extraction in high salt, heparin and SDS, is protected against a DNase attack since, as shown by DNA electrophoresis data, high molecular weight molecules (up to 20 kbas) are still present in the lamina residue. However, the high molecular weight DNA disappeared if the nuclear envelope fraction was again DNase-digested after high salt treatment. Altogether, the data of the previous (Fais et al., 1982; Prusov et al., 1980: Prusov et al., 1982) and the present investigations demonstrate that the peripheral chromatin granules are endowed with properties which distinguish them from the bulk chromatin and account for the chromosome bond to the nuclear envelope during interphase. This is why we suggest the term "anchorosome" for the peripheral protein granule attached to the nuclear envelope.     

Genetic activity of the G- and R-band DNA of human mitotic chromosomes

The concept of genetic inactivity of G-band DNA had been reinvestigated using the modified approach of Korenberg et al (1978). Coefficients of correlation and partial correlation between the relative gene density (g'), the relative G-band material richness (kH/C) and the relative chromosome size (s') were calculated. The kH/C was calculated as the ratio of brightness of fluorescence of chromosomes stained by Hoechst 33258 (Hi) and by chromomycin A3(Ci). The kH/C is the characteristics of G-band chromosome richness, because G-bands become bright after Hoechst 33258 staining and R-bands are bright after chromomycin A3 staining, while no significant C-bands in chromosomes which may be stained by these fluorochromes are discovered. For the kH/C determination the flow cytometry data of Langlois et al (1982) were used. The relative size of chromosomes was determined, based on the flow cytometry data of Young et al (1979). According to Korenberg, the "gene density" (g') in a chromosome was calculated as a ratio of the number of genes located in the chromosome before 1984 (Human Gene Mapping 7) to the relative size of this chromosome. Correlation between the "gene density" and the G-band richness was rs = -0.65. Out of 107 genes located in either G- or R-bands (Human Gene Mapping 7), 90 were mapped in the R-band and only 17 were ascribed to the G-band in metaphase chromosomes. The data on gene replication time show that all genes of the general cell activity and a portion of tissue-specific genes replicate during the early S-phase, together with R-band materials. These three independent lines of evidence are consistent with the notion that the R-band DNA is more genetically active than G-band DNA. The nature of "junk" DNA of G-bands is discussed.     

A genetic attack on the defense complex

An increasing number of "non-model" organisms are becoming accessible to genetic analysis in the field, as evolutionary biologists develop dense molecular genetic maps. Peichel et al.'s recent study(1) provides a microsatellite-based map for threespine stickleback fish (Gasterosteus aculeatus), and the first evidence for QTL affecting feeding morphology and defensive armor. This species has undergone rapid and parallel morphological and behavioral evolution, and there is now hope that some of the genes responsible for the divergence may soon be identified.