Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins

Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%) but display strongly different nucleotide composition, divergent CUPrefs and, in humans and in many other vertebrates, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that local synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs sharply differ between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis suggests that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warranting further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. Our results are compatible with a scenario in which a combination of directional mutation–selection processes would have differentially shaped CUPrefs of PTBPs in vertebrates: the observed GC-enrichment of PTBP1 in placental mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated with the evolution of specific CUPrefs.     

An unusual histone H4 gene from Tilapia nilotica exhibiting characteristics of both a replication-dependent histone and a basal-expression histone: evolutionary considerations

The nucleotide sequence of a histone H4 gene from the fish Tilapia nilotica was determined. The deduced amino acid sequence is identical to that of H4 from the trout, Salmo gairdnerii. The 3′ untranslated region of the Tilapia gene exhibits a unique combination of structural features each of which is usually associated with either a replication-dependent histone or a basal-expression histone, but not with both. The direction of nucleotide substitutions in the Tilapia and Salmo lineages was inferred. The Tilapia gene was found to evolve faster and to exhibit a more biased pattern of substitution and codon usage than its Salmo homologue. This combination of features cannot be explained by either mutation or purifying selection. The rapid embryonic development of Tilapia prompts us to suggest that the molecular evolution of the histone H4 gene is driven by fixation of advantageous synonymous mutations.     

Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis

The genome architecture of ciliates, including features such as nuclear dualism and large-scale genome rearrangements, impacts gene and genome evolution in these organisms. To better understand the structure of macronuclear chromosomes in ciliates with extensively processed chromosomes, a sample of complete macronuclear chromosomes was sequenced from three ciliate species: Metopus es (Class [Cl]: Armophorea), Nyctotherus ovalis (Cl: Armophorea), and Chilodonella uncinata (Cl: Phyllopharyngea). By cloning whole macronuclear chromosomes into a plasmid vector, we generated nine clones from each of M. es and C. uncinata, and 37 clones from N. ovalis. Analysis of these macronuclear chromosomes provides insight into the evolution of genome features such as chromosome content, gene structure, and genetic code. Phylogenetic patterns can be found in telomere structure and codon usage, which are both more similar in M. es and N. ovalis than C. uncinata. In addition, we provide evidence of lateral transfer of a bacterial endo-beta-mannanase gene onto a M. es chromosome and report the discovery of a 42-bp conserved sequence motif within N. ovalis untranslated regions.     

Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: Codon usage,map position,and concerted evolution

Summary The nature and extent of DNA sequence divergence between homologous proteincoding genes fromEscherichia coli andSalmonella typhimurium have been examined. The degree of divergence varies greatly among genes at both synonymous (silent) and nonsynonymous sites. Much of the variation in silent substitution rates can be explained by natural selection on synonymous codon usage, varying in intensity with gene expression level. Silent substitution rates also vary significantly with chromosomal location, with genes nearoriC having lower divergence. Certain genes have been examined in more detail. In particular, the duplicate genes encoding elongation factor Tu,tufA andtufB, fromS. typhimurium have been compared to theirE. coli homologues. As expected these very highly expressed genes have high codon usage bias and have diverged very little between the two species. Interestingly, these genes, which are widely spaced on the bacterial chromosome, also appear to be undergoing concerted evolution, i.e., there has been exchange between the loci subsequent to the divergence of the two species.Presented at the NATO Advanced Research Workshop on Genome Organization and Evolution, held in Spetses, Greece, September 1990     

Evolution of the isochore structure in the scale of chromosome: insight from the mutation bias and fixation bias

Following the development of reliable methods for inferring the direction of mutations of the single nucleotide polymorphism (SNP), and the revealing of the human isochore map, it has become possible to investigate the evolution of the isochore structure in a continuous region. In this study, the recent evolution of the isochore structure on human chromosome 18, as inferred from the SNP, was examined. A remarkable mutation bias was found, which was destroying the present isochore structure. However, a fixation bias contributed by the biased gene conversion (BGC) effect and a rising fixation probability of derived alleles with increasing GC content was extending the present isochore structure. Combining the two opposing processes, the old isochore structure was declining and a more homogenous isochore structure with higher GC content was being formed on the chromosome. During this process, both the CpG and genic sites, which were present in the isochore but were paid little attention to before, played an important role. In addition, the recombination was confirmed to promote the GC alleles fixed in the genome because of the BGC effect. For the first time, it was observed that with the occurrence of little recombination, AT alleles had the identical fixation probability with GC alleles in the recombination cold spots.     

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

Accurate delimitation of species is a critical first step in protecting biodiversity. Detection of distinct species is especially important for groups of organisms that inhabit sensitive environments subject to recent degradation, such as creeks, springs, and rivers in arid or semi-desert regions. The genus Dionda currently includes six recognized and described species of minnows that live in clear springs and spring-fed creeks of Texas, New Mexico (USA), and northern Mexico, but the boundaries, delimitation, and characterization of species in this genus have not been examined rigorously. The habitats of some of the species in this genus are rapidly deteriorating, and many local populations of Dionda have been extirpated. Considering the increasing concerns over degradation of their habitat, and pending a more detailed morphological revision of the genus, we undertook a molecular survey based on four DNA regions to examine variation over the range of the genus, test species boundaries, and infer phylogenetic relationships within Dionda. Based on analyses of two mitochondrial (cytb and D-loop) and two nuclear (Rag1 and S7) DNA regions from specimens collected throughout the range of Dionda, we identified 12 distinct species in the genus. Formerly synonymized names are available for two of these species, and four other species remain undescribed. We also redefine the known range of six species. The limited distribution of several of the species, coupled with widespread habitat degradation, suggests that many of the species in this genus should be targets for conservation and recovery efforts.     

Systematics of Maxomys Sody, 1936. (Rodentia: Muridae: Murinae): DNA/DNA hybridization studies of some Borneo-Javan species and allied Sundaic and Australo-Papuan genera

We compared five species of the murine genus Maxomys and representatives of nine other murid genera in a complete 15 × 15 DNA-hybridization matrix. FITCH trees were calculated for the entire suite of taxa and for subsets including only the five Maxomys and these together with the four nearest outgroups. All trees were validated by 'bootstrapping' and by jackknifing, performing both single- and multiple-deletions of taxa. The full 15 times 15 data set indicated a sister-group relationship between Maxomys and two pairs of genera ( Sundamys-Rattus sensu stricto and Mviventer-Leopoldamys ) that are more closely related to each other than to Maxomys; addition of data on Bandicota and Berylmys from another recent DNA-hybridization study confirmed that these genera are successive sister-taxa to the Sundamys-Rattus pair. Mus-Myomys and Uromys-Melomys were each distinct lineages from the above grouping of Rattus sensu lata species, and from the putative outgroup sigmodontine Peromyscus, but the interrelations of the three murine clades were unresolved. Within Maxomys, M. surifer and M. bartelsii are a related pair, and M. ochraceiventer probably forms an unresolved trio with M. rajah and M. whiteheadi. Calibration of a tree generated from saturation-corrected distances against a likely divergence-date of 12.2 Mybp for the separation of Mus and Rattus confirms a high rate of single-copy DNA change in murids (2.1%/Myr); and suggests that Sigmodontinae and Murinae diverged at around 15.3 Mybp, that Maxomys and the group of six other Rattus sensu lato separated approximately 7.6 Myr ago, and that Maxomys began to diversify 4.8 Myr ago.     

Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation

The G domain and domain II in the crystal structure of Thermus thermophilus elongation factor G (EF-G) were compared with the homologous domains in Thermus aquaticus elongation factor Tu (EF-Tu). Sequence alignment derived from the structural superposition was used to define conserved sequence elements in domain II. These elements and previously known conserved sequence elements in the G domain were used to guide the alignment of the sequences of Sulfolobus acidocaldarius elongation factor 2, human elongation factor 2, and Escherichia coli initiation factor 2 and release factor 3 to the aligned sequences of EF-G and EF-Tu. This alignment, which deviates from previously published alignments, has evolutionary implications and leads to alternative interpretations of biochemical data concerning the interaction of elongation factors with the -sarcin/ricin region of the ribosome. A single conserved sequence motif in domain II was identified and used to further characterize the GTPase subfamily of translation factors and related proteins. It was shown that the motif is found in most if not all the members of the family. Apparently, the common characteristic of these GTPases is an extensive consensus structural unit that possibly accounts for a similar interaction with the ribosome and is composed of two domains homologous to the G domain and domain II in EF-Tu and EF-G.     

Evolution of hydraulic traits in closely related species pairs from Mediterranean and nonMediterranean environments of North America

Chaparral shrubs in California experience cool, wet winters and hot, dry summers characteristic of mediterranean-type climates; by contrast, morphologically similar close relatives in central Mexico experience summer rainfall. A comparison of closely related species pairs was conducted to examine whether evolutionary divergences in plant hydraulic conductivity were associated with contrasting seasonality of precipitation. Six species pairs in Santa Barbara, California and Tehuacan, Mexico were chosen to test for repeated directional divergences across the habitat contrast. Additionally, evolutionary correlations were examined using phylogenetically independent contrasts (PICs) among a suite of hydraulic traits, including stem- and leaf-specific conductivity, resistance to embolism, wood density, inverse Huber value, and minimum seasonal water potential. Leaf-specific conductivity was generally higher in California, but for most hydraulic traits the species pairs exhibited varied evolutionary trajectories across the climate contrast. A significant correlation was found between divergences in xylem resistance to embolism and minimum seasonal water potential, but no evolutionary trade-off was found between resistance and stem conductivity. Higher leaf-specific conductivity may be adaptive in California, where soil and atmospheric droughts coincide during summer months. This response is consistent with a hydraulic strategy of high leaf water supply under high evaporative demand to prevent excessive drops in water potential.     

Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumb-aginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL-trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon, Dictyolimon and the remaining species of Limoniastrum . In all analyses, the five remaining species of Limoniastrum (excluding Limoniatrum ifniense ) formed a clade with two groups of species: L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L.feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniatrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.     

Systematic review of Atractus schach (Serpentes: Dipsadidae) species complex from the Guiana Shield with description of three new species

The Guiana Shield harbours one of the best preserved and largest extents of tropical forest on Earth and an immense biodiversity. The herpetofauna of this region remains poorly known. The species-rich snake genus Atractus contains ～140 species, many with complicated taxonomic histories, including A. schach. Examination of specimens in museums and newly collected material from French Guiana has allowed the illustration of hemipenial morphology for the first time and an expanded diagnosis. Concatenated molecular phylogenetic (mitochondrial and nuclear genes) and phenotypic (morphometrics, external and hemipenial morphology) analyses confirm non-monophyly of the A. flammigerus group and indicate that A. schach is a species complex with three new species described here. The geographic distribution of A. schach sensu stricto is restricted to Guiana, Surinam, and French Guiana north of Tumucumaque massif. Populations tentatively assigned to A. schach from the east from French Guiana in the Roura lowlands to Almeirim, and from central Amazonia between the Negro and Trombetas rivers in Brazil are also recognized as new species. Our results suggest that populations from south of the Amazon River are not conspecific with those from the Guiana Shield.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A7AE40BC-4716-4302-B3BE-1F43600B0A72     

Phylogenetic relationships and rates of evolution in primates: Allozymic data from catarrhine and platyrrhine species

The genetic electrophoretic variation at up to 43 protein loci was studied in four hominoid, three cercopithecoid, and three ceboid species. Phylogenetic reconstructions based on genetic distances show that the two chimpanzee species are closest to humans, while the gorilla diverged earlier than the split between humans and the chimpanzee. Within the cercopithecoids the green monkey apparently diverged earlier than the macaques, and within the ceboids, the owl monkey is only distantly related to the capuchin and squirrel monkeys. The hypothesis that rates of evolution at the level of protein electrophoretic variation are equal both among the groups, as well as within each group, could not be rejected.     

A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering

R.MvaI is a Type II restriction enzyme (REase), which specifically recognizes the pentanucleotide DNA sequence 5'-CCWGG-3' (W indicates A or T). It belongs to a family of enzymes, which recognize related sequences, including 5'-CCSGG-3' (S indicates G or C) in the case of R.BcnI, or 5'-CCNGG-3' (where N indicates any nucleoside) in the case of R.ScrFI. REases from this family hydrolyze the phosphodiester bond in the DNA between the 2nd and 3rd base in both strands, thereby generating a double strand break with 5'-protruding single nucleotides. So far, no crystal structures of REases with similar cleavage patterns have been solved. Characterization of sequence-structure-function relationships in this family would facilitate understanding of evolution of sequence specificity among REases and could aid in engineering of enzymes with new specificities. However, sequences of R.MvaI or its homologs show no significant similarity to any proteins with known structures, thus precluding straightforward comparative modeling. We used a fold recognition approach to identify a remote relationship between R.MvaI and the structure of DNA repair enzyme MutH, which belongs to the PD-(D/E)XK superfamily together with many other REases. We constructed a homology model of R.MvaI and used it to predict functionally important amino acid residues and the mode of interaction with the DNA. In particular, we predict that only one active site of R.MvaI interacts with the DNA target at a time, and the cleavage of both strands (5'-CCAGG-3' and 5'-CCTGG-3') is achieved by two independent catalytic events. The model is in good agreement with the available experimental data and will serve as a template for further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes.     

Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle

There is strong community-wide interest in applying molecular techniques to fungal species delimitation and identification, but selection of a standardized region or regions of the genome has not been finalized. A single marker, the ribosomal DNA internal transcribed spacer region, has frequently been suggested as the standard for fungi. We used a group of closely related blue stain fungi associated with the mountain pine beetle (Dendroctonus ponderosae Hopkins) to examine the success of such single-locus species identification, comparing the internal transcribed spacer with four other nuclear markers. We demonstrate that single loci varied in their utility for identifying the six fungal species examined, while use of multiple loci was consistently successful. In a literature survey of 21 similar studies, individual loci were also highly variable in their ability to provide consistent species identifications and were less successful than multilocus diagnostics. Accurate species identification is the essence of any molecular diagnostic system, and this consideration should be central to locus selection. Moreover, our study and the literature survey demonstrate the value of using closely related species as the proving ground for developing a molecular identification system. We advocate use of a multilocus barcode approach that is similar to the practice employed by the plant barcode community, rather than reliance on a single locus.     

DNA barcoding of xeniid soft corals (Octocorallia: Alcyonacea: Xeniidae) from Indonesia: species richness and phylogenetic relationships

We conducted the first ever survey of xeniid octocorals in the Indonesian Archipelago, centre of the highly biodiverse Coral Triangle region of the Indo-Pacific. Among 48 xeniid specimens collected from Lembeh Strait, North Sulawesi, we identified 26 morphospecies belonging to six genera based on assessment of the morphological characters traditionally used for xeniid taxonomy. Multilocus DNA barcodes obtained from 23 morphospecies clustered into 21 molecular operational taxonomic units (MOTUs) separated by average genetic distance values >0.3%. The overall concordance between morphospecies and MOTUs was 91%; just one pair and one trio of morphospecies were not distinguished by the DNA barcodes. A molecular phylogenetic reconstruction of family Xeniidae based on four loci (COI, mtMutS, ND2, 28S rDNA) supported the distinction of Anthelia and Cespitularia+Efflatounaria from all other xeniid genera. Although the remaining genera for which molecular data were available (Asterospicularia, Heteroxenia, Ovabunda, Sansibia, Sarcothelia, Sympodium, Xenia) belonged to a single, well-supported clade, the phylogenetic relationships among them were poorly resolved. Species of Xenia were distributed among three different sub-clades within which they were paraphyletic with Ovabunda (clade X1), Heteroxenia (clade X2) and Sansibia plus Sarcothelia (clade X3). No morphological characters have yet been identified that differentiate these three phylogenetically distinct clades of Xenia. Use of molecular barcodes to discriminate species will facilitate future ecological studies of Xeniidae, a group that has been shown to opportunistically monopolize disturbed reef habitat.     

Expression patterns and organization of the hsp70 genes correlate with thermotolerance in two congener endemic amphipod species (Eulimnogammarus cyaneus and E. verrucosus) from Lake Baikal

We studied various aspects of heat‐shock response with special emphasis on the expression of heat‐shock protein 70 (hsp70) genes at various levels in two congener species of littoral endemic amphipods (Eulimnogammarus cyaneus and E. verrucosus) from Lake Baikal which show striking differences in their vertical distribution and thermal tolerance. Although both the species studied demonstrate high constitutive levels of Hsp70, the thermotolerant E. cyaneus exhibited a 5‐fold higher basal level of Hsp70 proteins under normal physiological conditions (7 °C) and significantly lower induction of Hsp70 after temperature elevation compared with the more thermosensitive E. verrucosus. We isolated the hsp70 genes from both species and analysed their sequences. Two isoforms of the cytosolic Hsp70/Hsc70 proteins were detected in both species under normal physiological conditions and encoded by two distinct hsp/hsc70 family members. While both Hsp70 isoforms were synthesized without heat shock, only one of them was induced by temperature elevation. The observed differences in the Hsp70 expression patterns, including the dynamics of Hsp70 synthesis and threshold of induction, suggest that the increased thermotolerance in E. cyaneus (compared with E. verrucosus) is associated with a complex structural and functional rearrangement of the hsp70 gene family and favoured the involvement of Hsp70 in adaptation to fluctuating thermal conditions. This study provides insights into the molecular mechanisms underlying the thermal adaptation of Baikal amphipods and represents the first report describing the structure and function of the hsp70 genes of endemic Baikal species dwelling in thermally contrasting habitats.     

DNA content in species of Vernonia and Vernonanthura from South America: An approach to systematics and evolution of the Vernonieae (Asteraceae)

There are relatively few studies of DNA content in the Vernonieae (Asteraceae) tribe. The first studies were realized in the Lessingianthus genus and determined the DNA content of 25 species. After DNA content, ploidy level and the total karyotype were compared in 6 Chrysolaena species. The aim of this study was to present, for the first time, the DNA content values of Vernonanthura and Vernonia and to thereby expand knowledge of the Vernonieae tribe. A total of 19 natural populations belonging to the genera Vernonanthura and Vernonia were studied for the first time. The results were compared with other Vernonieae genera and with other Asteraceae tribes. Our results found that Vernonieae have the smallest range of 1C value variation in Asteraceae. Furthermore, there were differences in the DNA content of Vernonia and Vernonanthura. These results show that low DNA content and herbaceous habit in Vernonia are characters derived from the higher DNA content and woody habit present in Vernonanthura. These results could indicate a hybrid origin of one species and allow the determination of both the ploidy and chromosome number of other taxa. The results observed in Vernonanthura species showed a highly significant correlation between 1C-value and latitude.     

Gonochorism vs. hermaphroditism: relationship between life history and fitness in three species of Ophryotrocha (Polychaeta: Dorvilleidae) with different forms of sexuality

1. The relationships between life history, fitness and sexuality, together with their ecological and evolutionary significance, has been analysed comparing the main life-history traits and demography in three closely related species belonging to the genus Ophryotrocha. The species are: the gonochoristic O. labronica, the simultaneous hermaphrodite O. diadema and the protandrous hermaphrodite O. puerilis. 2. Survivorship and reproductive data were collected weekly and were used to construct life tables and population projection matrices for each species and compare life-history characteristics. Elasticity, life-table response and decomposition analyses were performed to examine the relative contribution of fecundity and survivorship to differences in lamda between species. 3. The gonochoristic and hermaphroditic species differ in all the main life-history parameters and also in demographic characteristics. In particular the value of lamda, used commonly to express fitness, is markedly higher in the gonochoristic species while in terms of fitness simultaneous and sequential hermaphroditism are very similar. In the genus Ophryotrocha gonochorism currently represents the most widespread condition, being characteristic of the majority of the known species in the genus. 4. Given the demographic advantage ensured by gonochorism, it remains be understood why some species have retained simultaneous hermaphroditism and one has evolved a sequential type hermaphroditism; the most probable hypothesis is correlated with the density of the species in natural habitats.