Preferential retention of the slowly evolving gene in pairs of duplicates in angiosperm genomes

Gene duplication provides raw material for functional innovation, but gene duplicability varies considerably. Previous studies have found widespread asymmetrical sequence evolution between paralogs. However, it remains unknown whether the rate of evolution among paralogs affects their propensity of being retained after another round of whole-genome duplication (WGD). In this study, we investigated gene groups that have experienced two successive WGDs to determine which of two older duplicates with different evolutionary rates was more likely to retain both younger duplicates. To uncouple the measurement of evolutionary rates from any assignment of duplicate or singleton status, we measured the evolutionary rates of singleton genes in out-lineages but classified these singleton genes according to whether they are retained or not in a crown group of species. We found that genes that retained younger duplicates in the crown group of genomes were more constrained prior to the younger duplication event than those that failed to leave duplicates. In addition, we also found that the retained clades have more genes in out-lineages. Subsequent analyses showed that genes in the retained clades were expressed more broadly and highly than genes in the singleton clades. We concluded that the set of repeatedly retained genes after two WGDs is biased toward slowly evolving genes in angiosperms, suggesting that the potential of genes for both functional conservation and divergence likely affects their propensity of being retained after WGD in angiosperms.     

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.     

A diffusion model for the fate of tandem gene duplicates in diploids

Suppose one chromosome in one member of a population somehow acquires a duplicate copy of the gene, fully linked to the original gene's locus. Preservation is the event that eventually every chromosome in the population is a descendant of the one which initially carried the duplicate. For a haploid population in which the absence of all copies of the gene is lethal, the probability of preservation has recently been estimated via a diffusion approximation. That approximation is shown to carry over to the case of diploids and arbitrary strong selection against the absence of the gene. The techniques used lead to some new results. In the large population limit, it is shown that the relative probability that descendants of a small number of individuals carrying multiple copies of the gene fix in the population is proportional to the number of copies carried. The probability of preservation is approximated when chromosomes carrying two copies of the gene are subject to additional, fully non-functionalizing mutations, thereby modelling either an additional cost of replicating a longer genome, or a partial duplication of the gene. In the latter case the preservation probability depends only on the mutation rate to null for the duplicated portion of the gene.     

Pigmentary function and evolution of tyrp1 gene duplicates in fish

The function of the tyrosinase‐related protein 1 (Tyrp1) has not yet been investigated in vertebrates basal to tetrapods. Teleost fishes have two duplicates of the tyrp1 gene. Here, we show that the teleost tyrp1 duplicates have distributed the ancestral gene expression in the retinal pigment epithelium (RPE) and melanophores in a species‐specific manner. In medaka embryos, tyrp1a expression is found in the RPE and in melanophores while tyrp1b is only expressed in melanophores. In zebrafish embryos, expression of tyrp1 paralogs overlaps in the RPE and in melanophores. Knockdown of each zebrafish tyrp1 duplicate alone does not show pigmentary defects, but simultaneous knockdown of both tyrp1 genes results in the formation of brown instead of black eumelanin accompanied by severe melanosome defects. Our study suggests that the brown melanosome color in Tyrp1‐deficient vertebrates is an effect of altered eumelanin synthesis. Black eumelanin formation essentially relies on the presence of Tyrp1 and some of its function is most likely conserved from the common ancestor of bony vertebrates.     

Quantifying asymmetry: Ratios and alternatives

Traditionally, the study of metric skeletal asymmetry has relied largely on univariate analyses, utilizing ratio transformations when the goal is comparing asymmetries in skeletal elements or populations of dissimilar dimensions. Under this approach, raw asymmetries are divided by a size marker, such as a bilateral average, in an attempt to produce size‐free asymmetry indices. Henceforth, this will be referred to as “controlling for size” (see Smith: Curr Anthropol 46 (2005) 249‐273). Ratios obtained in this manner often require further transformations to interpret the meaning and sources of asymmetry. This model frequently ignores the fundamental assumption of ratios: the relationship between the variables entered in the ratio must be isometric. Violations of this assumption can obscure existing asymmetries and render spurious results. In this study, we examined the performance of the classic indices in detecting and portraying the asymmetry patterns in four human appendicular bones and explored potential methodological alternatives. Examination of the ratio model revealed that it does not fulfill its intended goals in the bones examined, as the numerator and denominator are independent in all cases. The ratios also introduced strong biases in the comparisons between different elements and variables, generating spurious asymmetry patterns. Multivariate analyses strongly suggest that any transformation to control for overall size or variable range must be conducted before, rather than after, calculating the asymmetries. A combination of exploratory multivariate techniques, such as Principal Components Analysis, and confirmatory linear methods, such as regression and analysis of covariance, appear as a promising and powerful alternative to the use of ratios. Am J Phys Anthropol 154:498–511, 2014. © 2014 Wiley Periodicals, Inc.     

The role of gene flow asymmetry along an environmental gradient in constraining local adaptation and range expansion

Theoretically, asymmetric gene flow along an environmental gradient can limit species range expansion by keeping peripheral populations from locally adapting. However, few empirical studies have examined this potentially fundamental evolutionary mechanism. We address this possibility in the cricket Allonemobius socius, which exist along a season‐length gradient where the probability of producing a single generation per year (univoltinism) increases with latitude. As the probability of univoltinism increases northwards, populations are expected to hedge their bets by producing a greater proportion of diapause eggs when exposed to a mild diapause cue. However, gene flow from southern populations may disrupt local adaptation in the north by reducing the proportion of diapause eggs (expected to be 100% in pure univoltine environments). This may limit range expansion along the northern periphery where A. socius compete with A. fasciatus, a sister species that exhibits an invariant diapause‐only egg‐laying strategy. To assess the potential for range limitation, we examined diapause incidence (the proportion of diapause eggs produced under diapause conditions), gene flow symmetry and population structure across nine A. socius populations. We found that gene flow was asymmetric and biased northwards towards the periphery. Furthermore, peripheral populations that inhabited pure univoltine environments produced numerous nondiapause eggs (a southern, bivoltine diapause phenotype), which we assume to be a suboptimal phenotype. These patterns suggest that asymmetric gene flow along the gradient constrains adaptation in peripheral populations, potentially constraining species range expansion.     

Not all anthocyanins are born equal: distinct patterns induced by stress in Arabidopsis

Main Conclusion

Different abiotic stress conditions induce distinct sets of anthocyanins, indicating that anthocyanins have different biological functions, or that decoration patterns of each anthocyanin are used for unique purposes during stress. The induction of anthocyanin accumulation in vegetative tissues is often considered to be a response of plants to biotic or abiotic stress conditions. Arabidopsis thaliana (Arabidopsis) accumulates over 20 anthocyanins derived from the anthocyanidin cyanidin in an organ-specific manner during development, but the anthocyanin chemical diversity for their alleged stress protective functions remains unclear. We show here that, when grown in various abiotic stress conditions, Arabidopsis not only often accumulates significantly higher levels of total anthocyanins, but different stress conditions also favor the accumulation of different sets of anthocyanins. For example, the anthocyanin patterns of seedlings grown at pH 3.3 or in media lacking phosphate are very similar and characterized by relatively high levels of the anthocyanins A8 and A11. In contrast, anthocyanin inductive conditions (AIC) provided by high sucrose media are characterized by high accumulation of A9* and A5 relative to other stress conditions. The modifications present in each condition correlate reasonably well with the induction of the respective anthocyanin modification enzymes. Taken together, our results suggest that Arabidopsis anthocyanin profiles provide ‘fingerprints’ that reflect the stress status of the plants.     

Characterizing gene movements between chromosomes in Drosophila

Drosophila have a variety of innate immune strategies for defending itself from infection, including humoral and cell mediated responses to invading microorganisms. At the front lines of these responses, are a diverse group of pattern recognition receptors that recognize pathogen associated molecular patterns. These patterns include bacterial lipopolysaccharides, peptidoglycans, and fungal β?1,3 glucans. Some of the receptors catalytically modify the pathogenic determinant, but all are responsible for directly facilitating a signaling event that results in an immune response. Some of these events require multiple pattern recognition receptors acting sequentially to activate a pathway. In some cases, a signaling pathway may be activated by a variety of different pathogens, through parallel receptors detecting different pathogenic determinants. In this chapter, we review what is known about pattern recognition receptors in Drosophila, and how those lessons may be applied towards a broader understanding of immunity.     

Mixture analysis of asymmetry: modelling directional asymmetry, antisymmetry and heterogeneity in fluctuating asymmetry

The occurrence of different forms of asymmetry complicates the analysis and interpretation of patterns in asymmetry. Furthermore, between-individual heterogeneity in developmental stability (DS) and thus fluctuating asymmetry (FA), is required to find relationships between DS and other factors. Separating directional asymmetry (DA) and antisymmetry (AS) from real FA and understanding between-individual heterogeneity in FA is therefore crucial in the analysis and interpretation of patterns in asymmetry. In this paper we introduce and explore mixture analysis to (i) identify FA, DA and AS from the distribution of the signed asymmetry, and (ii) to model and quantify between-individual heterogeneity in developmental stability and FA. In addition, we expand mixtures to the estimation of the proportion of variation in the unsigned FA that can be attributed to between-individual heterogeneity in the presumed underlying developmental stability (the so-called hypothetical repeatability). Finally, we construct weighted normal probability plots to investigate the assumption of underlying normality of the different components. We specifically show that (i) model selection based on the likelihood ratio test has the potential to yield models that incorporate nearly all heterogeneity in FA; (ii) mixtures appear to be a powerful and sensitive statistical technique to identify the different forms of asymmetry; (iii) restricted measurement accuracy and the occurrence of many zero observations results in an overestimation of the hypothetical repeatability on the basis of the model parameters; and (iv) as judged from the high correlation coefficients of the normal probability plots, the underlying normality assumption appears to hold for the empirical data we analysed. In conclusion, mixtures provide a useful statistical tool to study patterns in asymmetry.     

Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth

Gene duplication plays important roles in organismal evolution, because duplicate genes provide raw materials for the evolution of mechanisms controlling physiological and/or morphological novelties. Gene duplication can occur via several mechanisms, including segmental duplication, tandem duplication and retroposition. Although segmental and tandem duplications have been found to be important for the expansion of a number of multigene families, the contribution of retroposition is not clear. Here we show that plant SKP1 genes have evolved by multiple duplication events from a single ancestral copy in the most recent common ancestor (MRCA) of eudicots and monocots, resulting in 19 ASK (Arabidopsis SKP1-like) and 28 OSK (Oryza SKP1-like) genes. The estimated birth rates are more than ten times the average rate of gene duplication, and are even higher than that of other rapidly duplicating plant genes, such as type I MADS box genes, R genes, and genes encoding receptor-like kinases. Further analyses suggest that a relatively large proportion of the duplication events may be explained by tandem duplication, but few, if any, are likely to be due to segmental duplication. In addition, by mapping the gain/loss of a specific intron on gene phylogenies, and by searching for the features that characterize retrogenes/retrosequences, we show that retroposition is an important mechanism for expansion of the plant SKP1 gene family. Specifically, we propose that two and three ancient retroposition events occurred in lineages leading to Arabidopsis and rice, respectively, followed by repeated tandem duplications and chromosome rearrangements. Our study represents a thorough investigation showing that retroposition can play an important role in the evolution of a plant gene family whose members do not encode mobile elements.     

Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae

The role of sequence divergence in functional divergence of duplicate genes is a topic of great interest. In this study, we compare the numbers of amino acid substitutions in each sequence since two yeast duplicates diverged, using a preduplication ancestral outgroup. Using this strategy, we explored the relationship between sequence divergence and functional divergence between duplicate partners. We show that the degree of relative functional asymmetry between duplicate proteins is proportional to the relative sequence divergence between them. Furthermore, of the two duplicates, the copy closer to their ancestral sequence (fewer number of amino acid substitutions) interacts with more proteins and affects fitness more severely when deleted. Therefore, asymmetric sequence divergence between duplicates is correlated with asymmetric functional divergence and may underlie the duplicate's role in genetic robustness against mutations. Among the functional traits considered, protein abundance appears to have the strongest correlation with the nonsynonymous divergence between duplicates. Taken together with the results from whole-genome analyses, our results indicate that within-species duplicates are subject to the same evolutionary force that acts on interspecific sequence and functional divergence. In particular, we detect signs of purifying selection on the more slowly evolving duplicate.     

Prenatal stress and increased fluctuating asymmetry in the parietal bones of neonatal rats

Recent studies have reported increased fluctuating dental and long bone asymmetry in neonates as a function of prenatal stress. The present study was designed to assess the effects of prenatal stress on a third calcium-dependent system, membranous bone. Pregnant rats were exposed to cold, heat, or noise from conception through parturition. Bilateral parietal bone lengths were measured in the term neonates. Levels of fluctuating asymmetry were found to be significantly increased (p less than .001) in all three stressed groups compared to unstressed controls. Results support the concept of a generalized stress response, and suggestions are offered for human osteological application.     

A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution

Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, because one of its members is disrupted by a chromosomal translocation in a neuroblastoma patient. The NBPF genes have a repetitive structure with high intragenic and intergenic sequence similarity in both coding and noncoding regions. These similarities might expose these genomic regions to illegitimate recombination, resulting in structural variation in the NBPF genes. The encoded proteins contain a highly conserved domain of unknown function, which we have named the NBPF repeat. In silico analysis combined with the isolation of multiple full-length cDNA clones showed that several members of this gene family are abundantly expressed in a large variety of tissues and cell lines. Strikingly, no discernable orthologues could be identified in the completed genomes of fruit fly, nematode, mouse, or rat, but sequences with low homology could be isolated from the draft canine and bovine genomes. Interestingly, this gene family shows primate-specific duplications that result in species-specific arrays of NBPF homologous sequences. Overall, this novel NBPF family reflects the continuous evolution of primate genomes that resulted in large physiological differences, and its potential role in this process is discussed.     

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

To understand the expansion ofmulticopy microRNA （miRNA） families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miRl60 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.     

The life and death of gene families

One of the unique insights provided by the growing number of fully sequenced genomes is the pervasiveness of gene duplication and gene loss. Indeed, several metrics now suggest that rates of gene birth and death per gene are only 10–40% lower than nucleotide substitutions per site, and that per nucleotide, the consequent lineage‐specific expansion and contraction of gene families may play at least as large a role in adaptation as changes in orthologous sequences. While gene family evolution is pervasive, it may be especially important in our own evolution since it appears that the “revolving door” of gene duplication and loss has undergone multiple accelerations in the lineage leading to humans. In this paper, we review current understanding of gene family evolution including: methods for inferring copy number change, evidence for adaptive expansion and adaptive contraction of gene families, the origins of new families and deaths of previously established ones, and finally we conclude with a perspective on challenges and promising directions for future research.     

Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution

The (asymptotic) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that networks generated by these models are generally similar. In this paper, we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the “right” seed graph (typically a dense subgraph of the protein–protein interaction network analyzed), the duplication model captures many topological features of publicly available protein–protein interaction networks very well.     

落叶松-杨栅锈菌基因复制事件及共线性分析

落叶松-杨栅锈菌是一种分布广且危害严重的林木病原真菌.了解基因组内发生的基因复制事件及基因组间的共线性关系,能为最终理解落叶松-杨栅锈菌适应性进化等生物学问题提供帮助.落叶松-杨栅锈菌全基因组水平上基因复制相关研究未见报道,共线性研究报道也较少.本研究利用落叶松-杨栅锈菌全基因组序列分析其基因复制模式.结果表明,落叶松...     

Conservation and divergence of APETALA1/FRUITFULL-like gene function in grasses: evidence from gene expression analyses

Duplicated APETALA1/FRUITFULL (AP1/FUL) genes show distinct but overlapping patterns of expression within rice (Oryza sativa) and within ryegrass (Lolium temulentum), suggesting discrete functional roles in the transition to flowering, specification of spikelet meristem identity, and specification of floral organ identity. In this study, we analyzed the expression of the AP1/FUL paralogues FUL1 and FUL2 across phylogenetically disparate grasses to test hypotheses of gene function. In combination with other studies, our data support similar roles for both genes in spikelet meristem identity, a general role for FUL1 in floral organ identity, and a more specific role for FUL2 in outer floral whorl identity. In contrast to Arabidopsis AP1/FUL genes, expression of FUL1 and FUL2 is consistent with an early role in the transition to flowering. In general, FUL1 has a wider expression pattern in all spikelet organs than FUL2, but both genes are expressed in all spikelet organs in some cereals. FUL1 and FUL2 appear to have multiple redundant functions in early inflorescence development. We hypothesize that sub-functionalization of FUL2 and interaction of FUL2 with LHS1 could specify lemma and palea identity in the grass floret.     

Left-right asymmetry in embryonic development: a comprehensive review

Embryonic morphogenesis occurs along three orthogonal axes. While the patterning of the anterior-posterior and dorsal-ventral axes has been increasingly well characterized, the left-right (LR) axis has only recently begun to be understood at the molecular level. The mechanisms which ensure invariant LR asymmetry of the heart, viscera, and brain represent a thread connecting biomolecular chirality to human cognition, along the way involving fundamental aspects of cell biology, biophysics, and evolutionary biology. An understanding of LR asymmetry is important not only for basic science, but also for the biomedicine of a wide range of birth defects and human genetic syndromes. This review summarizes the current knowledge regarding LR patterning in a number of vertebrate and invertebrate species, discusses several poorly understood but important phenomena, and highlights some important open questions about the evolutionary origin and conservation of mechanisms underlying embryonic asymmetry.