Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

Background  

Several lines of evidence suggest that codon usage in the Drosophila saltans and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages.     

A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone

Background  

Mitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics.     

Contrasting patterns of phylogeographic relationships in sympatric sister species of ironclad beetles (Zopheridae: <Emphasis Type="Italic">Phloeodes</Emphasis> spp.) in California's Transverse Ranges

Background  

Comparative phylogeography of sympatric sibling species provides an opportunity to isolate the effects of geography and demographics on the evolutionary history of two lineages over the same, known time scale. In the current study, we investigated the phylogeographic structure of two zopherid beetle species, Phloeodes diabolicus and P. plicatus, where their ranges overlap in California's Transverse Ranges.     

Staphylococcus aureus biofilm formation at the physiologic glucose concentration depends on the S. aureus lineage

Background  

Since bacteria embedded in biofilms are far more difficult to eradicate than planktonic infections, it would be useful to know whether certain Staphylococcus aureus lineages are especially involved in strong biofilm formation. For this reason, in vitro biofilm formation of 228 clinical S. aureus isolates of distinct clonal lineages was investigated.     

Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River Basin

Aim

To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages.

Location

China, mainly the Yangtze River Basin.

Methods

The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution.

Results

The COI phylogenetic tree delineated the monophyly of 3 major COI clades and 77 distinct COI haplotypes in the Yangtze River Basin. The invasive lineage C/S (FW17) was not identified in our sampling in China, while invasive lineages A/R (FW5 = Hap6), B (FW1 = Hap17) and Rlc (FW4 = Hap43) were identified, abundant and widely distributed in the middle and lower reaches of Yangtze River. Focusing on populations from Yangtze River Basin, both the COI haplotype and nucleotide diversity in the lakes along the Yangtze River increased with longitude, except for the river mouth population. The AMOVA tests showed significant differentiation between the middle and lower reaches of the Yangtze River and among populations. The dbRDA results suggested that the parameter chloride explained most of the spatial COI haplotype distribution variation in the Yangtze River Basin, with the three invasive lineages tolerating broad fluctuations of salinity (chloride levels ranging from 4 to 60 mg/L).

Conclusions

The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range.     

Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications

Background  

Acrodonta consists of Agamidae and Chamaeleonidae that have the characteristic acrodont dentition. These two families and Iguanidae sensu lato are members of infraorder Iguania. Phylogenetic relationships and historical biogeography of iguanian lizards still remain to be elucidated in spite of a number of morphological and molecular studies. This issue was addressed by sequencing complete mitochondrial genomes from 10 species that represent major lineages of acrodont lizards. This study also provided a good opportunity to compare molecular evolutionary modes of mitogenomes among different iguanian lineages.     

Uncovering the mutation-fixation correlation in short lineages

Background  

We recently reported a highly unexpected positive correlation between the fixation probability of nonsynonymous mutations (estimated by ω) and neutral mutation rate (estimated by K _s) in mammalian lineages. However, this positive correlation was observed for lineages with relatively long divergence time such as the human-mouse lineage, and was not found for very short lineages such as the human-chimpanzee lineage. It was previously unclear how to interpret this discrepancy. It may indicate that the positive correlation between ω and K _s in long lineages is a false finding. Alternatively, it may reflect a biologically meaningful difference between various lineages. Finally, the lack of positive correlation in short lineages may be the result of methodological artifacts.     

Molecular evolution of the cytochrome c oxidase subunit <Emphasis Type="Italic">5</Emphasis> A gene in primates

Background  

Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains.     

Longitudinal survey of <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method

Background  

Staphylococcus aureus infection in patients with cystic fibrosis (CF) is frequent and may be due to colonization by a few pathogenic lineages. Systematic genotyping of all isolates, methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) is necessary to identify such lineages and follow their evolution in patients. Multiple-locus variable-number tandem repeat analysis (MLVA/VNTR) was used to survey S. aureus clinical isolates in a French paediatric CF centre.     

Phylogeography of the common vampire bat (Desmodus rotundus): Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

Background  

The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA) marker and two nuclear markers (RAG2 and DRB) to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat.     

Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

Background  

The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization.     

Allopolyploid speciation and ongoing backcrossing between diploid progenitor and tetraploid progeny lineages in the <Emphasis Type="Italic">Achillea millefolium</Emphasis>species complex: analyses of single-copy nuclear genes and genomic AFLP

Background  

In the flowering plants, many polyploid species complexes display evolutionary radiation. This could be facilitated by gene flow between otherwise separate evolutionary lineages in contact zones. Achillea collina is a widespread tetraploid species within the Achillea millefolium polyploid complex (Asteraceae-Anthemideae). It is morphologically intermediate between the relic diploids, A. setacea-2x in xeric and A. asplenifolia-2x in humid habitats, and often grows in close contact with either of them. By analyzing DNA sequences of two single-copy nuclear genes and the genomic AFLP data, we assess the allopolyploid origin of A. collina-4x from ancestors corresponding to A. setacea-2x and A. asplenifolia-2x, and the ongoing backcross introgression between these diploid progenitor and tetraploid progeny lineages.     

Are mimics monophyletic? The necessity of phylogenetic hypothesis tests in character evolution

Background  

The processes governing the origin and maintenance of mimetic phenotypes can only be understood in a phylogenetic framework. Phylogenetic estimates of evolutionary relationships can provide a context for analyses of character evolution; however, when phylogenetic estimates conflict, rigorous analyses of alternative evolutionary histories are necessary to determine the likelihood of a specific history giving rise to the observed pattern of diversity. The polyphenic butterfly Limenitis arthemis provides a case in point. This species is comprised of three lineages, two of which are mimetic and one of which is non-mimetic. Conflicting estimates of the relationships among these three lineages requires direct evaluation of the alternative hypotheses of mimicry evolution.     

Extra-embryonic endoderm cells derived from ES cells induced by GATA Factors acquire the character of XEN cells

Background  

Three types of cell lines have been established from mouse blastocysts: embryonic stem (ES) cells, trophoblast stem (TS) cells, and extra-embryonic endoderm (XEN) cells, which have the potential to differentiate into their respective cognate lineages. ES cells can differentiate in vitro not only into somatic cell lineages but into extra-embryonic lineages, including trophectoderm and extra-embryonic endoderm (ExEn) as well. TS cells can be established from ES cells by the artificial repression of Oct3/4 or the upregulation of Cdx2 in the presence of FGF4 on feeder cells. The relationship between these embryo-derived XEN cells and ES cell-derived ExEn cell lines remains unclear, although we have previously reported that overexpression of Gata4 or Gata6 induces differentiation of mouse ES cells into extra-embryonic endoderm in vitro.     

The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured

Background  

Loss of photosynthesis has occurred independently in several plant and algal lineages, and represents a major metabolic shift with potential consequences for the content and structure of plastid genomes. To investigate such changes, we sequenced the complete plastid genome of the parasitic, non-photosynthetic green alga, Helicosporidium.     

Functional conservation of the Drosophila hybrid incompatibility gene Lhr

Background  

Hybrid incompatibilities such as sterility and lethality are commonly modeled as being caused by interactions between two genes, each of which has diverged separately in one of the hybridizing lineages. The gene Lethal hybrid rescue (Lhr) encodes a rapidly evolving heterochromatin protein that causes lethality of hybrid males in crosses between Drosophila melanogaster females and D. simulans males. Previous genetic analyses showed that hybrid lethality is caused by D. simulans Lhr but not by D. melanogaster Lhr, confirming a critical prediction of asymmetry in the evolution of a hybrid incompatibility gene.     

Major genomic mitochondrial lineages delineate early human expansions

Background  

The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation.     

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

Background  

Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots.