Adaptive molecular evolution of HINTW,a female-specific gene in birds

It is well established that many genes on the male-specific Y chromosome of organisms such as mammals are involved in male reproduction and may evolve rapidly because of positive selection on male reproductive traits. In contrast, very little is known about the function and evolution of W-linked genes restricted to the female genome of organisms with female heterogamety. For birds (males ZZ, females ZW), only one W-linked gene (HINTW) is sufficiently different from its Z-linked homolog to indicate a female-specific function. Here, we report that HINTW shows evidence of adaptive molecular evolution, implying strong positive selection for new functional properties in female birds. Moreover, because HINTW is expressed in the gonads of female birds just before sexual differentiation and is thus a candidate for sex determination, it suggests adaptive evolution related to female development. This provides the first example of Darwinian evolution of a gene restricted to the female genome of any organism. Given that HINTW exists in multiple copies on W, similar to some testis-specific genes amplified on mammalian Y, avian HINTW may thus potentially represent a female parallel to the organization and evolution of Y chromosome genes involved in male reproduction and development.     

Gene conversion and GC-content evolution in mammalian Hsp70

To investigate the mechanisms regulating the nucleotide usage in mammalian genes, we analyzed the sequences of three physically linked Hsp70 paralogs in human and mouse. We report that the sequences of HSPA1A and HSPA1B genes are almost identical, whereas the HSPA1L gene contains some regions very similar to HSPA1A/B and some regions with much higher divergence. Phylogenetic analysis reveals that gene conversion has homogenized the entire coding regions of HSPA1A/B and several fragments of HSPA1L. The regions undergoing conversion are all very GC rich, contrarily to the regions not subject to conversion. The pattern of nucleotide substitution in mammalian orthologs suggests that the mechanism increasing the GC content is still functioning. To test the possibility that the high GC content facilitates the expression of Hsp70 during heat-shock, we performed in vitro translation experiments. We failed to detect any effect of GC content on the translation efficiency at high temperatures. Taken together, our data strongly support the biased gene conversion hypothesis of GC-content evolution.     

Male-biased mutation, sex linkage, and the rate of adaptive evolution

An interaction between sex-linked inheritance and sex-biased mutation rates may affect the rate of adaptive evolution. Males have much higher mutation rates than females in several vertebrate and plant taxa. When evolutionary rates are limited by the supply of favorable new mutations, then genes will evolve faster when located on sex chromosomes that spend more time in males. For mutations with additive effects, Y-linked genes evolve fastest, followed by Z-linked genes, autosomal genes, X-linked genes, and finally W-linked and cytoplasmic genes. This ordering can change when mutations show dominance. The predicted differences in substitution rates may be detectable at the molecular level. Male-biased mutation could cause adaptive changes to accumulate more readily on certain kinds of chromosomes and favor animals with Z-W sex determination to have rapidly evolving male sexual displays.     

Cytogenetic mapping of the W chromosome in the genus Leporinus (Teleostei, Anostomidae) using a highly repetitive DNA sequence

The distribution of the Leporinus elongatus LeSpeI repetitive sequence in other Leporinus species was studied in an attempt to elucidate the evolutionary history of sex chromosomes in this genus using chromosome fluorescence in situ hybridization. The presence of fluorescent signals only in species that have differentiated sex chromosomes suggests that this sequence is related to the differentiation of sex chromosomes in this genus. Thus, these data will contribute to a better understanding of chromosome evolution, especially for sex chromosomes, in the Leporinus genus.     

Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana

The high number of duplicated genes in plant genomes provides a potential template for gene conversion and unequal crossing-over. Within a gene family these two processes can render all members homogeneous or generate diversity by reassorting variants among paralogs. The latter is especially feasible in families where gene diversity confers a selective advantage and thus conversion events are likely to be retained. Consequently, the most complete record of gene conversion is expected to be most evident in gene families commonly subjected to positive selection. Here, we describe the extent and characteristics of gene conversion and unequal crossing-over in the coding and noncoding regions of nucleotide-binding site leucine-rich repeat (NBS-LRR), receptor-like kinases (RLK), and receptor-like proteins (RLP) in the plant Arabidopsis thaliana. Members of these three gene families are associated with disease resistance and their pathogen-recognition domain is a documented target of positive selection. Our bioinformatic approach to study the major family features that may influence gene conversion revealed that in these families there is a significant association between the occurrence of gene conversion and high levels of sequence similarity, close physical clustering, gene orientation, and recombination rate. We discuss these results in the context of the overlap between gene conversion and positive selection during the evolutionary expansion of the NBS-LRR, RLK, and RLP gene families.     

Within- and between-individual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion

Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For each individual, the level of intra-individual variation was estimated from a sample of 20 ITS1 copies. The level of differentiation in haplotype frequency among individuals was then estimated by maximum likelihood using models based on the Dirichlet distribution. This confirmed the existence of significant levels of variation among individuals within each population studied. The most likely turnover mechanism that could generate this pattern of variation is gene conversion, operating at the intrachromosomal level. Furthermore, the discovery of linkage disequilibrium among the ITS1 haplotypes of C. parallelus suggests that intrachromosomal gene conversion occurs more frequently than interchromosomal recombination. Subspecies of C. parallelus showed significantly different haplotype distributions following about 0.5 Myr of divergence. With respect to the process of concerted evolution, we show that homogenization of repeats is slow relative to speciation, and the standing variation among individuals is sufficient for selection to operate.     

Evolution of the Spindlin Gene in Birds: Independent Cessation of the Recombination of Sex Chromosomes at the Spindlin Locus in Neognathous Birds and Tinamous, a Palaeognathous Avian Family

Tinamous (Aves, Palaeognathae, Tinamiformes) are primitive birds, generally considered to be the sister group to the ratites. Tinamous possess a W sex-chromosome, intermediate in heterochromatization between the largely euchromatic W chromosome of the ratites and the highly condensed W chromosome of the neognathous birds. Of the four genes which are known to have diverged copies on the neognathous avian W and Z chromosome (ATP5A1, CHD1, PKC and SPIN) only the spindlin gene has W- and Z-chromosomal forms in the tinamiformes. This paper describes experiments which show that the sequences of these forms are more similar to each other and to the homologous undifferentiated spindlin gene sequences in the ratite genome than to the W or Z forms of the spindlin gene in other, neognathous species. This suggests that cessation of recombination at the spindlin locus of the ancestral W and Z chromosomes of the paleognathous tinamiformes and the neognathous avian species were independent events.     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

The evolution of the vertebrate beta-globin gene promoter

Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed "promoter shuffling") that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous beta-globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the beta-globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human beta-like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the beta-globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base-pair substitutions, it is clear that some redefinition of the term "promoter shuffling" is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the beta-globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate beta-globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression.     

Transfer of a parasitic sex factor to the nuclear genome of the host: A hypothesis on the evolution of sex-determining mechanisms in the terrestrial Isopod Armadillidium vulgare Latr.

In A. vulgare sex is usually determined either by a cytoplasmic feminizing factor (F symbiotic bacteria) or by another feminizing factor (f) which behaves like a mobile element of DNA and which seems to correspond to a fragment of bacterial DNA. By inhibiting the expression of male genes carried by the Z heterochromosome, these feminizing factors induce differentiation of neo-females [ZZ(+F) or ZZ(+f)]. Such a mechanism leads to the production of progenies whose sex ratio is highly female biased. In some populations in which F and/or f factors are present, genetic females (WZ) have disappeared and all individuals (males and females) are genetic males. However in other populations, cohabitation of ZZ(+f) neo-females and females in all points similar to genetic females is observed. Such a situation may be unstable and is not likely to be explainable only by migrations of individuals from distinct populations. Owing to certain types of crosses, in particular those which involve an artificial neo-male ( = female reversed into a functional male by an implant of androgenic gland) we show here that the f factor can be transmitted as a Mendelian gene. In these progenies Z_fZ females may appear: like WZ females, they breed broods whose sex ratio is unbiased. The hypothesis that the “F bacteria—A. vulgare” symbiosis may have led, after a complex co-evolutive process (F bacteria → f mobile element → insertion of f on Z heterochromosome), to the creation (from a male genotype) of a female genotype, is put forward. The consequences of such a phenomenon on the composition and the evolution of A. vulgare populations are examined.     

Insight into the molecular evolution of non-specific lipid transfer proteins via comparative analysis between rice and sorghum

Phylogenetic analysis was conducted on 9 kDa non-specific lipid transfer protein (nsLTP) genes from nine plant species. Each of the five classified types in angiosperms exhibited eight conserved cysteine patterns. The most abundant nsLTP genes fell into the type I category, which was particularly enriched in a grass-specific lineage of clade I.1. Six pairs of tandem copies of nsLTP genes on the distal region of rice chromosomes 11 and 12 were well-preserved under concerted evolution, which was not observed in sorghum. The transgenic promoter-reporter assay revealed that both rice and sorghum nsLTP genes of type I displayed a relatively conserved expression feature in the epidermis of growing tissue, supporting its functional roles in cutin synthesis or defence against phytopathogens. For type I, the frequent expression in the stigma and seed are indicative of functional involvement in pistil-pollen interactions and seed development. By way of contrast, several type V genes were observed, mainly in the vascular bundle of the rosette as well as the young shoots, which might be related with vascular tissue differentiation or defence signalling. Compared with sorghum, the highly redundant tissue-specific expression pattern among members of rice nsLTP genes in clade I.1 suggests that concerted evolution via gene conversion favours the preservation of crucial expression motifs via the homogenization of proximal promoter sequences under high selection constraints. However, extensive regulatory subfunctionalization might also have occurred under relative low selection constraints, resulting in functional divergence at the expression level.     

PCP gene family in Symbiodinium from Hippopus hippopus: low levels of concerted evolution,isoform diversity,and spectral tuning of chromophores

Photosynthetic dinoflagellates have evolved unique water-soluble light harvesting complexes known as peridinin-chlorophyll a-binding proteins (PCPs). Most species of dinoflagellates express either 14 to 17 kDa or 32 to 35 kDa mature PCP apoproteins and do so in stable combinations of isoforms that differ in isoelectric point (pI). The source (posttranslational modification, protein degradation, or genetic) and functional significance of PCP isoform variation have remained unclear. PCPs are encoded by multigene families. However, previous reports conflict over the diversity of PCP genes within gene arrays. We present the first genomic characterization of the PCP gene family from a symbiotic dinoflagellate. Symbiodinium from the Pacific bivalve Hippopus hippopus (203) contains genes for 33 kDa PCP apoproteins that are organized in tandem arrays like those of free-living dinoflagellates Amphidinium carterae, Lingulodinium (Gonyaulax) polyedra, and Heterocapsa pygmaea. The Symbiodinium 203 PCP cassette consists of 1,098-bp coding regions separated by approximately 900-bp spacers. The spacers contain a conserved upstream sequence similar to the promoter in L. polyedra. Surprisingly, sequences of cloned coding regions are not identical, and can differ at up to 2.2% of the nucleotide sites. Sequence variation is found at both silent and nonsilent sites, and analysis of cDNA clones indicate that the variation is present in the mRNA pool. We propose that this variation represents nucleotide diversity among PCP gene copies that are evolving under low-level concerted evolution. Interestingly, the predicted proteins have pIs that are within the range of those published for other species of Symbiodinium. Thus, posttranslational modifications are not necessary to explain the multiple PCP isoforms. We have also identified several polymorphic sites that may influence spectral absorption tuning of chromophores.     

Sorghum phosphoenolpyruvate carboxylase gene family: structure,function and molecular evolution

Although housekeeping functions have been shown for the phosphoenolpyruvate carboxylase (EC 4.1.1.31, PEPC) in plants and in prokaryotes, PEPC is mainly known for its specific role in the primary photosynthetic CO₂ fixation in C4 and CAM plants. We have shown that in Sorghum, a monocotyledonous C4 plant, the enzyme is encoded in the nucleus by a small multigene family. Here we report the entire nucleotide sequence (7.5 kb) of the third member (CP21) that completes the structure of the Sorghum PEPC gene family. Nucleotide composition, CpG islands and GC content of the three Sorghum PEPC genes are analysed with respect to their possible implications in the regulation of expression. A study of structure/function and phylogenetic relationships based on the compilation of all PEPC sequences known so far is presented. Data demonstrate that (1) the different forms of plant PEPC have very similar primary structures, functional and regulatory properties, (2) neither apparent amino acid sequences nor phylogenetic relationships are specific for the C4 and CAM PEPCs and (3) expression of the different genes coding for the Sorghum PEPC isoenzymes is differently regulated (i.e. by light, nitrogen source) in a spatial and temporal manner. These results suggest that the main distinguishing feature between plant PEPCs is to be found at the level of genes expression rather than in their primary structure.     

A new marker based on the avian spindlin gene that is able to sex most birds,including species problematic to sex with CHD markers

We have developed a new marker (Z43B) that can be successfully used to identify the sex of most birds (69%), including species difficult or impossible to sex with other markers. We utilized the zebra finch Taeniopygia guttata EST microsatellite sequence (CK309496) which displays sequence homology to the 5′ untranslated region (UTR) of the avian spindlin gene. This gene is known to be present on the Z and W chromosomes. To maximize cross‐species utility, the primer set was designed from a consensus sequence created from homologs of CK309496 that were isolated from multiple distantly related species. Both the forward and reverse primer sequences were 100% identical to 14 avian species, including the Z chromosome of eight species and the chicken Gallus gallus W chromosome, as well as the saltwater crocodile Crocodylus porosus. The Z43B primer set was assessed by genotyping individuals of known sex belonging to 61 non‐ratite species and a single ratite. The Z and W amplicons differed in size making it possible to distinguish between males (ZZ) and females (ZW) for the majority (69%) of non‐ratite species tested, comprising 10 orders of birds. We predict that this marker will be useful for obtaining sex‐typing data for ca 6,869 species of birds (69% of non‐ratites but not galliforms). A wide range of species could be sex‐typed including passerines, shorebirds, eagles, falcons, bee‐eaters, cranes, shags, parrots, penguins, ducks, and a ratite species, the brown kiwi, Apteryx australis. Those species sexed include species impossible or problematic to sex‐type with other markers (magpie, albatross, petrel, eagle, falcon, crane, and penguin species). Zoo Biol. 35:533–545, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.     

The evolution of hypervariable sex and supernumerary (B) chromosomes in the relict New Zealand frog,Leiopelma hochstetteri

Chromosomes exhibiting elevated levels of differentiation are termed hypervariable but no proposed mechanisms are sufficient to account for such enhanced evolutionary divergence. Both hypervariable sex and supernumerary (B) chromosomes were investigated in the endemic New Zealand frog, Leiopelma hochstetteri, which is chromosomally polymorphic both within and between populations and has sufficiently elevated variation that different populations can be identified solely by their C-banded karyotypes. This frog is further distinguished by the univalent, female-specific W-chromosome (0W/00 sex determination) uniquely possessed by North Island populations. This sex chromosome exhibited variation in morphology, size, and heterochromatin distribution, sufficient to resolve 11 different types, including isochromosomes. Five of the 12 populations examined also had supernumerary chromosomes that varied in number (up to 15 per individual) and morphology. Specific variations seen among the hypervariable chromosomes could have resulted from heterochromatinisation, chromosome fusions, loss-of-function mutations, deletions, and/or duplications. Frogs of the same species from Great Barrier Island, however, had neither supernumeraries nor the female-specific chromosome. The 0W/00 sex chromosome system must have been derived after the isolation of Great Barrier Island from North Island populations by raised sea levels between 14 000 and 8000 years ago. Furthermore, biochemical divergence between populations is minor and therefore the chromosomal variation seen is comparatively recent in origin. The one characteristic common to all known hypervariable chromosomes is curtailment or lack of recombination. Their accelerated evolution therefore is possible via the mechanism of Muller's ratchet, either alone or in concert with other factors.     

The fucosyltransferase gene family: an amazing summary of the underlying mechanisms of gene evolution

The fucosyltransferase gene family encodes enzymes that transfer fucose in 1,2, 1,3/4 and 1,6 linkages on a large variety of glycans. The most ancient genes harbour a split coding sequence, and encode enzyme that transfer fucose at or near O- and N-peptidic sites (serine, threonine or chitobiose unit). Conversely, the more recent genes have a monoexonic coding sequence, and encode enzymes that transfer fucose at the glycan periphery. All basic mechanisms of gene evolution contribute to this amazing scenario: exon shuffling, transposition, point mutations, and duplication. As typical examples: (i) exon shuffling leads to the ancestral organization of the 1,6 fucosyltransferase gene; (ii) the ancestor of 1,2 fucosyltransferase genes is reshaped by retrotransposition at the same locus; (iii) duplication associated to point mutations leads to the most recent 1,3/4 fucosyltransferase genes.