Opossum carboxylesterases: sequences,phylogeny and evidence for <Emphasis Type="Italic">CES</Emphasis> gene duplication events predating the marsupial-eutherian common ancestor

Background  

Carboxylesterases (CES) perform diverse metabolic roles in mammalian organisms in the detoxification of a broad range of drugs and xenobiotics and may also serve in specific roles in lipid, cholesterol, pheromone and lung surfactant metabolism. Five CES families have been reported in mammals with human CES1 and CES2 the most extensively studied. Here we describe the genetics, expression and phylogeny of CES isozymes in the opossum and report on the sequences and locations of CES1, CES2 and CES6 'like' genes within two gene clusters on chromosome one. We also discuss the likely sequence of gene duplication events generating multiple CES genes during vertebrate evolution.     

Global patterns of Rhododendron diversity: The role of evolutionary time and diversification rates

Aim

Understanding the evolution of the latitudinal diversity gradient (i.e. increase in species diversity towards the tropics) is a prominent issue in ecology and biogeography. Disentangling the relative contributions of environment and evolutionary history in shaping this gradient remains a major challenge because their relative importance has been found to vary across regions and taxa. Here, using the global distributions and a molecular phylogeny of Rhododendron, one of the largest genera of flowering plants, we aim to compare the relative contributions of contemporary environment, evolutionary time and diversification rates in generating extant species diversity patterns.

Location

Global.

Time period

Undefined.

Major taxa studied

Rhododendron.

Methods

We compiled the global distributions of all Rhododendron species, and constructed a dated molecular phylogeny using nine chloroplast genes and seven nuclear regions. By integrating these two datasets, we estimated the temporal trends of Rhododendron diversification, and explored the global patterns of its species diversity, net diversification rates, and species ages. Next, we reconstructed the geographical ancestral area of the clade. Finally, we compared the relative contribution of contemporary environment, time‐for‐speciation, and diversification rates on the species diversity pattern of Rhododendron.

Results

In contrast to the predictions of the time‐for‐speciation hypothesis, we found that although Rhododendron originated at a temperate latitude, its contemporary species diversity is highest in the tropics/subtropics, suggesting an into‐the‐tropics colonization for this genus. We found that the elevated diversification induced by heterogeneous environmental conditions in the tropics/subtropics shapes the global pattern of Rhododendron diversity.

Main conclusions

Our findings support tropical and subtropical mountains as not only biodiversity and endemism hotspots, but also as cradles for the diversification of Rhododendron. Our study emphasizes the need of unifying ecological and evolutionary approaches in order to gain comprehensive understanding of the mechanisms underlying the global patterns of plant diversity.     

A genome-wide survey of changes in protein evolutionary rates across four closely related species of <Emphasis Type="Italic">Saccharomyces</Emphasis> sensu stricto group

Background  

Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolutionary rates of genes involved in such events changed because of changes in functional constraints acting on the genes. However, in the evolution of closely related species, excluding the aforementioned situations, the frequency of changes in protein evolutionary rates is still not clear at the genome-wide level. Here we examine the constancy of protein evolutionary rates in the evolution of four closely related species of the Saccharomyces sensu stricto group (S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus).     

Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

Background  

Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila.     

Unusual conservation of mitochondrial gene order in <Emphasis Type="Italic">Crassostrea</Emphasis>oysters: evidence for recent speciation in Asia

Background  

Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis.     

Reconstruction of ancestral protein sequences and its applications

Background  

Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference.     

Evolutionary constraints on yeast protein size

Background  

Despite a strong evolutionary pressure to reduce genome size, proteins vary in length over a surprisingly wide range also in very compact genomes. Here we investigated the evolutionary forces that act on protein size in the yeast Saccharomyces cerevisiae utilizing a system-wide bioinformatics approach. Data on yeast protein size was compared to global experimental data on protein expression, phenotypic pleiotropy, protein-protein interactions, protein evolutionary rate and biochemical classification.     

Evolutionary relationships of <Emphasis Type="Italic">Fusobacterium nucleatum</Emphasis> based on phylogenetic analysis and comparative genomics

Background  

The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools.     

Structure and expression of two nuclear receptor genes in marsupials: insights into the evolution of the antisense overlap between the α-thyroid hormone receptor and Rev-erbα

Background  

Alternative processing of α-thyroid hormone receptor (TRα, NR1A1) mRNAs gives rise to two functionally antagonistic nuclear receptors: TRα1, the α-type receptor, and TRα2, a non-hormone binding variant that is found only in mammals. TRα2 shares an unusual antisense coding overlap with mRNA for Rev-erbα (NR1D1), another nuclear receptor protein. In this study we examine the structure and expression of these genes in the gray short-tailed opossum, Monodelphis domestica, in comparison with that of eutherian mammals and three other marsupial species, Didelphis virginiana, Potorous tridactylus and Macropus eugenii, in order to understand the evolution and regulatory role of this antisense overlap.     

A DNA and morphology based phylogenetic framework of the ant genus <Emphasis Type="Italic">Lasius</Emphasis> with hypotheses for the evolution of social parasitism and fungiculture

Background  

Ants of the genus Lasius are ecologically important and an important system for evolutionary research. Progress in evolutionary research has been hindered by the lack of a well-founded phylogeny of the subgenera, with three previous attempts disagreeing. Here we employed two mitochondrial genes (cytochrome c oxidase subunit I, 16S ribosomal RNA), comprising 1,265 bp, together with 64 morphological characters, to recover the phylogeny of Lasius by Bayesian and Maximum Parsimony inference after exploration of potential causes of phylogenetic distortion. We use the resulting framework to infer evolutionary pathways for social parasitism and fungiculture.     

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function

Background  

Plants contain numerous Su ( v ar)3-9 h omologues (SUVH) and r elated (SUVR) genes, some of which await functional characterization. Although there have been studies on the evolution of plant Su(var)3-9 SET genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation.     

The minimal kinome of <Emphasis Type="Italic">Giardia lamblia</Emphasis> illuminates early kinase evolution and unique parasite biology

Background  

The major human intestinal pathogen Giardia lamblia is a very early branching eukaryote with a minimal genome of broad evolutionary and biological interest.     

MANET: tracing evolution of protein architecture in metabolic networks

Background  

Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics.     

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Background  

Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.     

Dissecting microregulation of a master regulatory network

Background

All jawed-vertebrates have four T cell receptor (TCR) chains: alpha (TRA), beta (TRB), gamma (TRG) and delta (TRD). Marsupials appear unique by having an additional TCR: mu (TRM). The evolutionary origin of TRM and its relationship to other TCR remain obscure, and is confounded by previous results that support TRM being a hybrid between a TCR and immunoglobulin locus. The availability of the first marsupial genome sequence allows investigation of these evolutionary relationships.

Results

The organization of the conventional TCR loci, encoding the TRA, TRB, TRG and TRD chains, in the opossumMonodelphis domesticaare highly conserved with and of similar complexity to that of eutherians (placental mammals). There is a high degree of conserved synteny in the genomic regions encoding the conventional TCR across mammals and birds. In contrast the chromosomal region containing TRM is not well conserved across mammals. None of the conventional TCR loci contain variable region gene segments with homology to those found in TRM; rather TRM variable genes are most similar to that of immunoglobulin heavy chain genes.

Conclusion

Complete genomic analyses of the opossum TCR loci continue to support an origin of TRM as a hybrid between a TCR and immunoglobulin locus. None of the conventional TCR loci contain evidence that such a recombination event occurred, rather they demonstrate a high degree of stability across distantly related mammals. TRM, therefore, appears to be derived from receptor genes no longer extant in placental mammals. These analyses provide the first genomic scale structural detail of marsupial TCR genes, a lineage of mammals used as models of early development and human disease.     

Historical,temporal, and geographic dynamism of the interaction between Agave and Leptonycteris nectar-feeding bats

Premise

The interaction between ecological and evolutionary processes has been recognized as an important factor shaping the evolutionary history of species. Some authors have proposed different ecological and evolutionary hypotheses concerning the relationships between plants and their pollinators; a special case is the interaction and suspected coevolution among Agave spp. and their main pollinators, the Leptonycteris bats. Agave spp. have, in general, a pollination syndrome compatible with chiropterophily including floral shape and size, nocturnal nectar production, and nectar quality and sugar concentration. Our goal was to analyze the interaction Agave–Leptonycteris and its dynamics during three different climate scenarios.

Methods

We modeled the Agave–Leptonycteris interaction in its spatial and temporal components during the Pleistocene using Ecological Niche Models (ENMs) and three climate scenarios: Current, Last Glacial Maximum (LGM), and Last InterGlacial (LIG). Furthermore, we analyzed the geographic correlation between 96 Agave spp. and two of the Mexican Tequila bats, genus Leptonycteris.

Results

We found that Leptonycteris spp. interact with different Agave spp. over their migratory routes. We propose an interaction refuge in Metztitlán and Tehuacán-Cuicatlán areas, where Agave- Leptonycteris interaction has probably remained active. During the nonmigratory season, both bat species consume nectar of almost the same Agave spp., suggesting the possibility of a diffuse coevolution among Agave and Leptonycteris bats.

Conclusions

We propose that in the areas related to migratory bat movements, each bat species interacts with different Agave spp., whereas in the areas occupied by nonmigrant individuals, both bat species consume nectar of almost the same Agave taxa.

     

Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

Background  

Rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies.