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At least 217 records · Page 12Linked to original sources
PubMed2002

Repeated losses of TTAGG telomere repeats in evolution of beetles (Coleoptera).

We studied the occurrence of (TTAGG)n telomere repeats in 12 species of beetles, representing main lineages of the Coleoptera phylogenetic tree, by Southern hybridization and fluorescence in situ hybridization (FISH). In contrast to other insect orders, beetles were heterogeneous with respect to the occurrence of TTAGG repeats. In addition, the presence or absence of (TTAGG)n motif was irrespective of phylogenetic relationships. In the suborder Polyphaga, six species displayed positive hybridization signals. These were Silpha obscura, Agrilus viridis, Ampedus sanguineus, Stegobium paniceum, Oryzaephilus surinamensis, and Leptinotarsa decemlineata. Whereas negative signals were obtained in three polyphagan species, Geotrupes stercorarius, Thanasimusformicarius, and Sitophilus granarius. In the suborder Adephaga, the TTAGG sequence was present in one species, Graphoderus cinereus, and absent in two species, Orectochilus villosus and Pterostichus oblongopunctatus. We concluded that the telomerase-dependent (TTAGG)n motif had been repeatedly lost in different phylogenetic branches of Coleoptera and probably replaced with another mechanism of telomere elongation. This had to happen at least 5-6 times. The results suggest a predisposition or a backup mechanism of telomere maintenance in the genome of beetles that enabled them to make frequent evolutionary changes in the telomere composition.

Animals↗
PubMed1999

Absolute measures of the completeness of the fossil record.

Measuring the completeness of the fossil record is essential to understanding evolution over long timescales, particularly when comparing evolutionary patterns among biological groups with different preservational properties. Completeness measures have been presented for various groups based on gaps in the stratigraphic ranges of fossil taxa and on hypothetical lineages implied by estimated evolutionary trees. Here we present and compare quantitative, widely applicable absolute measures of completeness at two taxonomic levels for a broader sample of higher taxa of marine animals than has previously been available. We provide an estimate of the probability of genus preservation per stratigraphic interval, and determine the proportion of living families with some fossil record. The two completeness measures use very different data and calculations. The probability of genus preservation depends almost entirely on the Palaeozoic and Mesozoic records, whereas the proportion of living families with a fossil record is influenced largely by Cenozoic data. These measurements are nonetheless highly correlated, with outliers quite explicable, and we find that completeness is rather high for many animal groups.

Animals↗
PubMed2005

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.

In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.

Africa↗
PubMed2000

Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny.

Plant phylogenetic estimates are most likely to be reliable when congruent evidence is obtained independently from the mitochondrial, plastid, and nuclear genomes with all methods of analysis. Here, results are presented from separate and combined genomic analyses of new and previously published data, including six and nine genes (8, 911 bp and 12,010 bp, respectively) for different subsets of taxa that suggest Amborella + Nymphaeales (water lilies) are the first-branching angiosperm lineage. Before and after tree-independent noise reduction, most individual genomic compartments and methods of analysis estimated the Amborella + Nymphaeales basal topology with high support. Previous phylogenetic estimates placing Amborella alone as the first extant angiosperm branch may have been misled because of a series of specific problems with paralogy, suboptimal outgroups, long-branch taxa, and method dependence. Ancestral character state reconstructions differ between the two topologies and affect inferences about the features of early angiosperms.

Cycadopsida↗
PubMed2006

Telonemia, a new protist phylum with affinity to chromist lineages.

Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup.

Cryptophyta↗
PubMed1991

Nucleotide sequence of the genes encoding the matrix protein of two wild-type measles virus strains.

The nucleotide sequences of the matrix protein (M) genes of two wild-type measles virus (MV) isolates (JM and CM) have been determined and shown to differ in 56 positions; 31 of these differences are located in the non-coding region and 25 in the coding region of the gene. Most (80%) of the mutations in the coding region are changes to the third base of a codon. A maximum parsimony analysis of the available M gene nucleotide sequences allowed the construction of a tree with at least three lineages or subtypes. One wild-type strain (JM) was very similar to a subacute sclerosing panencephalitis virus strain (case B); the second wild-type strain, CM, showed nucleotide sequence similarity with MV from a case of measles inclusion body encephalitis. Both wild-type virus sequences are distinct from those so far determined for vaccine strains.

Animals↗
PubMed2001

Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia.

The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process.

Adult↗
PubMed2006

Thermostable RNase P RNAs lacking P18 identified in the Aquificales.

The RNase P RNA (rnpB) and protein (rnpA) genes were identified in the two Aquificales Sulfurihydrogenibium azorense and Persephonella marina. In contrast, neither of the two genes has been found in the sequenced genome of their close relative, Aquifex aeolicus. As in most bacteria, the rnpA genes of S. azorense and P. marina are preceded by the rpmH gene coding for ribosomal protein L34. This genetic region, including several genes up- and downstream of rpmH, is uniquely conserved among all three Aquificales strains, except that rnpA is missing in A. aeolicus. The RNase P RNAs (P RNAs) of S. azorense and P. marina are active catalysts that can be activated by heterologous bacterial P proteins at low salt. Although the two P RNAs lack helix P18 and thus one of the three major interdomain tertiary contacts, they are more thermostable than Escherichia coli P RNA and require higher temperatures for proper folding. Related to their thermostability, both RNAs include a subset of structural idiosyncrasies in their S domains, which were recently demonstrated to determine the folding properties of the thermostable S domain of Thermus thermophilus P RNA. Unlike 16S rRNA phylogeny that has placed the Aquificales as the deepest lineage of the bacterial phylogenetic tree, RNase P RNA-based phylogeny groups S. azorense and P. marina with the green sulfur, cyanobacterial, and delta/epsilon proteobacterial branches.

Bacteria↗
PubMed2001

Phylogenetic and biogeographical relationships among some holarctic frog lung flukes (Digenea: Haematoloechidae).

A phylogenetic study of 8 North American and European species of frog lung flukes belonging to Haematoloechus was conducted using approximately 850 to 1,000 bases of the intemal transcribed spacer region (ITS 1 + 5.8S + ITS 2) and 1,250 bases of the large subunit (LSU) of the nuclear ribosomal DNA. Adequate phylogenetic resolution could not be obtained from 5.8S or ITS 2 data. Analysis of ITS 1 data produced 2 equally parsimonious trees that differed only in the position of Haematoloechus breviplexus relative to H. medioplexus and H. varioplexus. Single, identical trees were produced by analysis of both LSU sequence data and a data set comprised of all ITS and LSU data. All trees demonstrated 3 distinct evolutionary lineages within the Holarctic Haematoloechus examined. The results confirmed the taxonomic validity of H. abbreviatus and demonstrated that the presence or absence of extracecal uterine loops is not a character meaningful to the recognition of evolutionary lineages or differentiation of genera. Examination of ITS sequence data revealed almost no intraspecific variation within 5 species of Haematoloechus and demonstrated an approximately 150-base indel common to the North American H. longiplexus and the European H. asper. Two of 3 clades revealed by the phylogenetic analyses are comprised of both European and North American species, indicating that lineages of Haematoloechus arose before the breakup of Laurasia and radiated after Eurasia and North America split. Within each of 3 evolutionary lineages, members share similar patterns of arthropod host specificity distinct from patterns found in the other lineages. This suggests that second intermediate host specificity may be a trait that has been conserved through evolutionary time.

Animals↗
PubMed2001

Molecular and morphological phylogenetic analysis of an insular radiation in Pacific black flies (Simulium).

Ecological adaptation within islands may have figured prominently in the insular radiation of black flies (subgenus Inseliellum) in the Society Islands, French Polynesia. To aid in understanding the sequence of ecological shifts in this group, we have constructed a phylogeny by using morphology, the cytochrome oxidase I (COI) gene, and the small ribosomal subunit (12S) gene. The strong influence of COI on the combined analysis tree was evident from its contribution to the partitioned Bremer support (62%). The net effect of including 12S was to reduce overall tree support. Different character sets resolved different portions of the combined analysis tree, with COI resolving recent lineages, 12S resolving basal relationships, and morphology supporting the monophyly of taxa having smaller larval feeding fans (oviceps group). The Partition Homogeneity and Kashino-Hasegawa tests indicated significant incongruence between morphological and mitochondrial data. The Templeton test revealed that morphology and the combined (COI + 12S) mitochondrial data were incongruent. This conflict stems primarily from disagreement over the monophyly of taxa having much smaller larval feeding fans. Either convergence in a subset of morphological characters, low phylogenetic signal among mitochondrial sequences, or lineage-sorting causing the mitochondrial data to track an incorrect evolutionary history may be responsible for these results.

Animals↗
PubMed2003

Chloroplast DNA phylogeography reveals colonization history of a Neotropical tree, Cedrela odorata L., in Mesoamerica.

Spanish Cedar (Cedrela odorata L.) is a globally important timber species which has been severely exploited in Mesoamerica for over 200 years. Using polymerase chain reaction-restriction fragment length polymorphisms, its chloroplast (cp) DNA phylogeography was studied in Mesoamerica with samples from 29 populations in six countries. Five haplotypes were characterized, phylogenetically grouped into three lineages (Northern, Central and Southern). Spatial analysis of ordered genetic distance confirmed deviation from a pattern of isolation by distance. The geographically proximate Northern and Central cpDNA lineages were genetically the most differentiated, with the Southern lineage appearing between them on a minimum spanning tree. However, populations possessing Southern lineage haplotypes occupy distinct moist habitats, in contrast to populations possessing Northern and Central lineage haplotypes which occupy drier and more seasonal habitats. Given the known colonization of the proto-Mesoamerican peninsula by South American flora and fauna prior to the formation of the Isthmus of Panama, it seems most likely that the observed population structure in C. odorata results from repeated colonization of Mesoamerica from South American source populations. Such a model would imply an ancient, pre-Isthmian colonization of a dry-adapted type (possessing the Northern lineage or a prototype thereof), with a secondary colonization via the land bridge. Following this, a more recent (possibly post-Pleistocene) expansion of moist-adapted types possessing the Southern lineage from the south fits the known vegetation history of the region.

Cedrela↗
PubMed2002

Molecular phylogeny of Japanese Leporidae, the Amami rabbit Pentalagus furnessi, the Japanese hare Lepus brachyurus, and the mountain hare Lepus timidus, inferred from mitochondrial DNA sequences.

We determined mitochondrial 12S ribosomal RNA (rRNA) and cytochrome b (cyt b) gene sequences in three leporid species of Japan, the Amami rabbit Pentalagus furnessi from the Ryukyu Islands, the Japanese hare Lepus brachyurus from Honshu, and a Japanese form of the mountain hare Lepus timidus ainu from Hokkaido. We compared the sequences with those of other taxa of leporids available in databases. Phylogenetic trees of the 12S rRNA gene sequences indicated that the lineage of P. furnessi diversified during the generic radiation of the leporids at an ancient time, which was estimated to have been the middle Miocene. Cyt-b gene trees revealed that the lineage of L. brachyurus branched off at an early stage in the speciation of Lepus, probably at the beginning of the Pliocene. The cyt b sequences of L. t. ainu were somewhat distinct from those of continental conspecific populations; this lineage divergence is likely to have occurred during the middle or late Pleistocene. The results show that the three regions of the Japanese archipelago, Ryukyu, Honshu-Shikoku-Kyushu, and Hokkaido, now preserve their own leporid taxa, each with a different extent of genetic endemicity. It is possible that the zoogeographic traits of the Japanese leporids are a consequence of the evolutionary dynamics of leporids in East Asia, in that the radiation centers of leporids are likely to have shifted from tropical, through temperate, to arctic zones.

Animals↗
PubMed2004

The role of immigrants in the assembly of the South American rainforest tree flora.

The Amazon lowland rainforest flora is conventionally viewed as comprising lineages that evolved in biogeographic isolation after the split of west Gondwana (ca. 100 Myr ago). Recent molecular phylogenies, however, identify immigrant lineages that arrived in South America during its period of oceanic isolation (ca. 100-3 Myr ago). Long-distance sweepstakes dispersal across oceans played an important and possibly predominant role. Stepping-stone migration from Africa and North America through hypothesized Late Cretaceous and Tertiary island chains may have facilitated immigration. An analysis of inventory plot data suggests that immigrant lineages comprise ca. 20% of both the species and individuals of an Amazon tree community in Ecuador. This is more than an order of magnitude higher than previous estimates. We also present data on the community-level similarity between South American and palaeotropical rainforests, and suggest that most taxonomic similarity derives from trans-oceanic dispersal, rather than a shared Gondwanan history.

Biological Evolution↗
PubMed2001

Evolution of myrmecophytism in western Malesian Macaranga (Euphorbiaceae).

Plants inhabited by ants (myrmecophytes) have evolved in a diversity of tropical plant lineages. Macaranga includes approximately 300 paleotropical tree species; in western Malesia there are 26 myrmecophytic species that vary in morphological specializations for ant association. The origin and diversification of myrmecophytism in Macaranga was investigated using phylogenetic analyses of morphological and nuclear ITS DNA characters and studies of character evolution. Despite low ITS variation, the combined analysis resulted in a well-supported hypothesis of relationships. Mapping myrmecophytism on all most parsimonious trees resulting from the combined analysis indicated that the trait evolved independently between two and four times and was lost between one and three times (five changes). This hypothesis was robust when tested against trees constrained to have three or fewer evolutionary transformations, although increased taxon sampling for the ITS analysis is required to confirm this. Mapping morphological traits on the phylogeny indicated that myrmecophytism was not homologous among lineages; each independent origin involved a suite of different specializations for ant-plant association. There was no evidence that myrmecophytic traits underwent sequential change through evolution; self-hollowing domatia evolved independently from ant-excavated domatia, and different food-body production types evolved in different lineages. The multiple origins of myrmecophytism in Macaranga were restricted to one small, exclusively western Malesian lineage of an otherwise large and nonmyrmecophytic genus. Although the evolution of aggregated food-body production and the formation of domatia coincided with the evolution of myrmecophytism in all cases, several morphological, ecological, and biogeographic factors appear to have facilitated and constrained this radiation of ant-plants.

Animals↗
PubMed2006

Molecular evolution of the AP2 subfamily.

The AP2 (APETALA2)/EREBP (Ethylene Responsive Element Binding Protein) multigene family includes developmentally and physiologically important transcription factors. AP2/EREBP genes are divided into two subfamilies: AP2 genes with two AP2 domains and EREBP genes with a single AP2/ERF (Ethylene Responsive Element Binding Factor) domain. Based on previous phylogenetic analyses, AP2 genes can be divided into two clades, AP2 and ANT groups. To clarify the molecular evolution of the AP2 subfamily, we isolated and sequenced genes with two AP2 domains from three gymnosperms, Cycas revoluta, Ginkgo biloba, and Gnetum parvifolium,as well as from the moss Physcomitrella patens. Expressions of AP2-like genes, including AP2, in Arabidopsis thaliana are regulated by the microRNA miR172. We found that the target site of miR172 is significantly conserved in gymnosperm AP2 homologs, suggesting that regulatory mechanisms of gene expression using microRNA have been conserved over the three hundred million years since the divergence of gymnosperm and flowering plant lineages. We inferred a phylogenetic relationship of these genes with the green alga Chlamydomonas reinhardtii and seed-plant genes available in public DNA databases. The phylogenetic tree showed that the AP2 subfamily diverged into the AP2 and ANT groups before the last common ancestor of land plants and after C. reinhardtii diverged from the land-plant lineage. The tree also indicated that each AP2 and ANT group further diverged into several clades through gene duplications prior to the divergence of gymnosperms and angiosperms.

Animals↗
PubMed1991

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts.

A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences. The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species. Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees. In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences. The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.

Archaea↗
PubMed2004

Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data.

A phylogeny of Iberian Aphodiini dung beetles was reconstructed based on morphological and molecular data. The data set included a total of 84 variable characters from wing venation, mouthparts, genitalia, and external morphology, as well as mitochondrial partial cytochrome c oxidase I (COI), complete tRNA-Leu (UUR), and partial cytochrome c oxidase II (COII) gene nucleotide sequences (1210 positions). Phylogenetic trees based on molecular data were relatively more resolved than those based on morphological characters. The Bayesian analysis of combined molecular and morphological data provided resolution not achieved by each data set separately. Ammoecius and Aphodius are the first lineages that branch off from the tree, followed by Acrossus, Nimbus, and Heptaulacus. The remaining studied taxa are recovered in a more derived clade that lacks internal resolution. Reconstructed trees based on molecular data showed relatively short internal nodes that were weakly supported. Such pattern may reflect a rapid radiation at the origin of the tribe Aphodiini, but also saturation of mutational changes. Several tests were conducted to discern between both competing hypotheses, as well as to assess the effect of incomplete taxon sampling.

Animals↗
PubMed2002

Sequence polymorphism of dotA and mip alleles mediating invasion and intracellular replication of Legionella pneumophila.

Legionella pneumophila inhabit a variety of natural and man-made aquatic environments, where they live primarily as intracellular parasites of protozoans. Given the proper exposure, however, they can cause opportunistic pneumonic infections in humans. The products of two L. pneumophila genes, dotA and mip, are part of the mechanism mediating the initial invasion of eukaryotic cells, and subsequent intracellular survival and multiplication. In this study, DNA polymorphism of the dotA and mip genes was assessed for 17 clinical and environmental isolates by nucleotide sequencing to determine the level of sequence variation, rates of molecular evolution, and history of gene divergence. The mip gene is highly conserved, whereas dotA is extremely variable, with an average level of nucleotide diversity four times greater than that of mip. Gene trees for each locus support a division of the L. pneumophila isolates into two clonal lineages. There are several disagreements between the gene trees suggesting that although L. pneumophila has a clonal population structure, genetic exchange has contributed to genotypic variation among strains in nature.

Alleles↗