Differences In Evolutionary Rates Research Articles

Evolutionary rates for multivariate traits: the role of selection and genetic variation.

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders' equation (Δz(-)=Gβ), which predicts evolutionary change for a suite of phenotypic traits (Δz(-)) as a product of directional selection acting on them (β) and the genetic variance-covariance matrix for those traits (G ). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.

The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.

Acquisition of germ plasm accelerates vertebrate evolution.

Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates of evolution appear to cause phylogenetic incongruence in protein-coding sequence comparisons between vertebrate taxa. Our results support the hypothesis that germ plasm liberates constraints on somatic development and that enhanced evolvability drives the evolution of germ plasm.

The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates

In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing-associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates.

Annonaceae substitution rates: a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Linking Life-History Traits, Ecology, and Niche Breadth Evolution in North American Eriogonoids (Polygonaceae)

Macroevolutionary and microevolutionary studies provide complementary explanations of the processes shaping the evolution of niche breadth. Macroevolutionary approaches scrutinize factors such as the temporal and spatial environmental heterogeneities that drive differentiation among species. Microevolutionary studies, in contrast, focus on the processes that affect intraspecific variability. We combine these perspectives by using macroevolutionary models in a comparative study of intraspecific variability. We address potential differences in rates of evolution of niche breadth and position in annual and perennial plants of the Eriogonoideae subfamily of the Polygonaceae. We anticipated higher rates of evolution in annuals than in perennials owing to differences in generation time that are paralleled by rates of molecular evolution. Instead, we found that perennial eriogonoid species present greater environmental tolerance (wider climate niche) than annual species. Niche breadth of perennial species has evolved two to four times faster than in annuals, while niche optimum has diversified more rapidly among annual species than among perennials. Niche breadth and average elevation of species are correlated. Moreover, niche breadth increases more rapidly with mean species elevation in perennials than in annuals. Our results suggest that both environmental gradients and life-history strategy influence rates and patterns of niche breadth evolution.

A novel regulatory element for Shh expression in the lung and gut of mouse embryos

Hedgehog (Hh) signaling plays pivotal roles in morphogenesis of several embryonic tissues, including the primitive gut. In the mouse embryo, Sonic hedgehog (Shh) is expressed in endodermal epithelia from the oral cavity to the intestine, and contributes to cell proliferation in the underlying mesenchyme and subsequent differentiation into the gastrointestinal smooth muscle. Three evolutionary conserved non-coding sequences in the region upstream of the Shh coding sequence contain endoderm-specific enhancers for Shh expression. Although Shh expression in the endodermal epithelial lining is mostly attributed to these three enhancers, none of them regulates gene expression in the gastroesophageal epithelium. Here, we found that a 1.7Kb fragment located 100Kb upstream of the Shh coding sequence contains a functional element for Shh expression in endodermal organs, including the esophagus and stomach. Compared with the three known endodermal enhancers, this novel enhancer shows less evolutionary conservation, even among rodents. In mouse embryonic endodermal tissues, the seamless expression of Shh is achieved by a patchwork of multiple enhancers with different rates of evolution.

Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms

The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.

Evolutionary trend of the small subunit nuclear ribosomal DNAs (SSU rDNAs) of wood-feeding Cryptocercus cockroaches (Blattaria: Cryptocercus)

The objective of this study is to elucidate the evolutionary rate of Cryptocercus SSU rDNAs based on the relative rate test (RRT) and comparative analysis of the primary sequences. In the RRTs, the evolutionary rate differences (dKs) of the Cryptocercus SSU rDNAs were not statistically significant (0.107 <P<0.996) in all cases, although an Asian Cryptocercus appeared to evolve more slowly than a North American Cryptocercus as indicated by the negative signs of dKs. Contrary to the RRT, the comparative analysis of SSU rDNA sequences revealed some interesting aspects in the evolutionary rates of Cryptocercus SSU rDNAs. In comparison with those of closely (Mastotermes darwiniensis and Tenodera aridifolia) or more distantly related taxa (Locusta migratoria), the SSU rDNAs of the genus Cryptocercus showed that insertions are progressing in a variable region (HV2). The SSU rDNA of Calymmaderus punctulatus species complex (Mountain Lake Biological Station, VA), a North American species, was unusually more elongated in the HV2 than those of the reference taxa or the other congeneric species.

Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza

BackgroundReassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds.ResultsBy extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (dN/dS), we found the average dN/dS across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of dN/dS values for each subtype on a site-by-site basis indicated that the elevated dN/dS on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint.ConclusionsOur results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.

Differences in Evolution Rates among Eudicotyledon Species Observed by Analysis of Protein Divergence

Genome evolution rates can vary considerably among plants. In particular, a correlation has often been reported between the evolution rate and annual/perennial habit, possibly associated with differences in generation time. For example, among the rosid species whose genome is fully sequenced, Vitis vinifera, a perennial species, was shown to have the genome that evolved the slowest. In order to extend knowledge of evolution rates to the asterid clade, one of the two major clades of core eudicotyledonous, the protein evolution rates in three asterid species, one perennial (Coffea canephora) and two annual species (Solanum lycopersicum and Mimulus guttatus), were investigated and compared with V. vinifera. Significant differences were observed among these species, and the proteins that evolved the most slowly were those of V. vinifera. Among the species belonging to the asterid clade, C. canephora appears to have evolved more slowly than the others. These findings are consistent with a correlation between perennial habit and slow evolution rates. The C. canephora genome seems to be an appropriate model for paleogenomic studies of asterids.

Evolutionary rate of human tissue-specific genes are related with transposable element insertions

The influence of transposable elements (TEs) on genome evolution has been widely studied. However, it remains unclear whether TE insertions also impact on evolutionary rate of human genes. In this study, we have compared the differences in TEs and evolutionary rates between human tissue-specific genes. Our results showed that various functional categories of human tissue-specific genes contained different TE numbers and divergent values of Ka/Ks, with human nucleic acid binding transcription factor activity genes having the fewest TE density and Ka/Ks value. Interestingly, we also found that human tissue-specific genes with TEs have also undergone faster evolution than those without TEs. Therefore, TEs have significant impact on the evolutionary rates of human tissue-specific genes. Furthermore, local genomic properties such as gene length, GC content and recombination rate may reflect a true transpositional bias for the particular TEs. Our results may provide important insights for further elucidating the evolution of human tissue-specific genes.

Comparative study of the complete mitochondrial genomes of the bronze gudgeon (Coreius heterodon) and largemouth bronze gudgeon (Coreius guichenoti)

The bronze gudgeon (Coreius heterodon) and the congeneric species largemouth bronze gudgeon (Coreius guichenoti), two endemic fish species in China, are important economic fishes in local areas. The bronze gudgeon is distributed in Yangtze River and Huanghe River basin, whereas the largemouth bronze gudgeon is distributed only in the middle and upper reaches of Yangtze River. Here, we sequenced the complete mitochondrial genomes of the two species and compared the evolutionary rate differences between the two species. The complete mitochondrial genomes of C. heterodon and C. guichenoti are 16,611 and 16,612 bp, respectively. Both of the complete mitogenome sequences contain 13 protein-coding genes, 2 rRNA subunits, 22 tRNAs and 1 non-coding control region, which are typical vertebrate mitogenomes. The relative rate test shows that the mitochondrial genome of C. heterodon evolves nearly threefold faster than that of C. guichenoti, which is mostly caused by the higher substitution rates in rRNAs and especially in tRNAs in C. heterodon.

A Comment on the Use of Stochastic Character Maps to Estimate Evolutionary Rate Variation in a Continuously Valued Trait

Phylogenetic comparative biology has progressed considerably in recent years (e.g., Butler and King 2004; Rabosky 2006; Bokma 2008; Alfaro et al. 2009; Stadler 2011; Slater et al. 2012). One of the most important developments has been the application of likelihood-based methods to fit alternative models for trait evolution in a phylogenetic treewith branch lengths proportional to time (e.g., Butler andKing2004;O’Meara et al. 2006; Thomas et al. 2006; Revell and Collar 2009; Beaulieu et al. 2012). An important example of this type of method is O’Meara et al. (2006) “noncensored” test for variation in the evolutionary rate for a continuously valued character trait through time or across the branches of a phylogenetic tree (also see Thomas et al. 2006 for a closely related approach). According to this method, we first hypothesize evolutionary rate regimes on the tree (called “painting” in Butler and King 2004); and then we fit an evolutionary model, specifically the popular Brownian model (Cavalli-Sforza and Edwards 1967; Felsenstein 1973, 1985), in which the instantaneous variance of the Brownian random diffusion process has different values in different parts of the phylogeny (O’Meara et al. 2006). In their original article, O’Meara et al. (2006) did not focus specifically on how to hypothesize evolutionary regimes on the tree. The authors did, however, suggest that to test the hypothesis that a discrete character state had influenced the rate of a continuous character, one could use the approach of (Nielsen 2002; Huelsenbeck et al. 2003; Bollback 2006) to first stochastically map the discretely valued trait, and then “test to see whether the portions of the tree with one state for the discrete character have a different rate of evolution for the continuous character than portions of the tree to which the other discrete state has beenmapped” (O’Meara et al. 2006, p. 931). Indeed, this has become common practice for this and other closely related methods (e.g., Collar et al. 2009, 2010; Revell and Collar 2009; Martin and Wainwright 2011; Price et al. 2011). Normally, then, the set of evolutionary rate estimates from the stochastically mapped trees are averaged across all the trees in the sample. This is presented as a method of obtaining rate estimates that “integrate over uncertainty in...ancestral states” (Collar et al. 2010, p. 1035). Figure 1 illustrates this analysis pipeline. a)

Continuous characters in phylogenetic analyses: patterns of corolla tube length evolution in LithospermumL. (Boraginaceae)

The present study comprises an analysis of six different scoring schemes and eight different types of analytic methods aiming to investigate the evolution of a continuous character (i.e. corolla tube length) in Lithospermum L. (Boraginaceae). Corolla tube length in the genus is quite variable, ranging from 1 mm to 75 mm, and the length of the corolla tube has implications for pollination biology, such as longer corolla tubes (> 25 mm in length) being pollinated by hummingbirds or moths. In general, the various methods resolve similar ancestral character states; however, different states are reconstructed at nodes in which the descendants greatly differ in corolla tube length. Additionally, it is suggested that all of the variation of a continuous character should be included in analyses, and this may necessitate multiple analyses with different partitions of the data. The various analyses provide evidence that two maximum parsimony methods, linear parsimony and the TNT method, minimize the number of different rates of evolution. In Lithospermum, six origins of corolla tubes > 20 mm in length are resolved, and these origins occurred at two different times periods: (1) in the shadow of hummingbird diversification in North America (approximately 6–8 Mya) and (2) more recently (approximately 1–1.5 MyA). Four substantial decreases in corolla tube length also are reconstructed, and these may be associated with the origin of self-pollination. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains

Toll-like receptors (TLRs) that initiate an innate immune response contain an extracellular leucine rich repeat (LRR) domain and an intracellular Toll IL-receptor (TIR) domain. There are fifteen different TLRs in vertebrates. The LRR domains, which adopt a solenoid structure, usually have higher rates of evolution than do the TIR globular domains. It is important to understand the molecular evolution and functional roles of TLRs from this standpoint. Both pairwise genetic distances and Ka/Ks's (the ratios between non synonymous and synonymous substitution rates) were compared between the LRR domain and the TIR domain of 366 vertebrate TLRs from 96 species (from fish to primates). In fourteen members (TLRs 1, 2, 3, 4, 5, 6, 7, 8, 9, 11/12, 13, 14, 21, and 22/23) the LRR domains evolved significantly more rapidly than did the corresponding TIR domains. The evolutionary rates of the LRR domains are significantly different among these members; LRR domains from TLR3 and TLR7 from primates to fishes have the lowest rate of evolution. In contrast, the fifteenth member, TLR10, shows no significant differences; its TIR domain is not highly conserved. The present results suggest that TLR10 may have a different function in signaling from those other members and that a higher conservation of TLR3 and TLR7 may reflect a more ancient mechanism and/or structure in the innate immune response system. Gene conversions are suggested to have occurred in platypus TLR6 and TLR10. This study provides new insight about structural and functional diversification of vertebrate TLRs.

Evolutionary conservation and disease gene association of the human genes composing pseudogenes

Pseudogenes, the ‘genomic fossils’ present portrayal of evolutionary history of human genome. The human genes configuring pseudogenes are also now coming forth as important resources in the study of human protein evolution. In this communication, we explored evolutionary conservation of the genes forming pseudogenes over the genes lacking any pseudogene and delving deeper, we probed an evolutionary rate difference between the disease genes in the two groups. We illustrated this differential evolutionary pattern by gene expressivity, number of regulatory miRNA targeting per gene, abundance of protein complex forming genes and lesser percentage of protein intrinsic disorderness. Furthermore, pseudogenes are observed to harbor sequence variations, over their entirety, those become degenerative disease-causing mutations though the disease involvement of their progenitors is still unexplored. Here, we unveiled an immense association of disease genes in the genes casting pseudogenes in human. We interpreted the issue by disease associated miRNA targeting, genes containing polymorphisms in miRNA target sites, abundance of genes having disease causing non-synonymous mutations, disease gene specific network properties, presence of genes having repeat regions, affluence of dosage sensitive genes and the presence of intrinsically unstructured protein regions.

Assessing Determinants of Exonic Evolutionary Rates in Mammals

From studies investigating the differences in evolutionary rates between genes, gene compactness and gene expression level have been identified as important determinants of gene-level protein evolutionary rate, as represented by nonsynonymous to synonymous substitution rate (d(N)/d(S)) ratio. However, the causes of exon-level variances in d(N)/d(S) are less understood. Here, we use principal component regression to examine to what extent 13 exon features explain the variance in d(N), d(S), and the d(N)/d(S) ratio of human-rhesus macaque or human-mouse orthologous exons. The exon features were grouped into six functional categories: expression features, mRNA splicing features, structural-functional features, compactness features, exon duplicability, and other features, including G + C content and exon length. Although expression features are important for determining d(N) and d(N)/d(S) between exons of different genes, structural-functional features and splicing features explained more of the variance for exons of the same genes. Furthermore, we show that compactness features can explain only a relatively small percentage of variance in exon-level d(N) or d(N)/d(S) in either between-gene or within-gene comparison. By contrast, d(S) yielded inconsistent results in the human-mouse comparison and the human-rhesus macaque comparison. This inconsistency may suggest rapid evolutionary changes of the mutation landscape in mammals. Our results suggest that between-gene and within-gene variation in d(N)/d(S) (and d(N)) are driven by different evolutionary forces and that the role of mRNA splicing in causing the variation in evolutionary rates of coding sequences may be underappreciated.

Natural and human-induced coastal dynamics at a back-barrier beach

This study contributes to the understanding of very low-energy fetch-limited environments by reporting the evolution of a back-barrier beach (Ancão Peninsula, southern Portugal). It considers two timescales: a large-scale evolution for the past 60years based on aerial photograph analysis, and a small-scale beach evolution based on monthly topographic surveys performed during three years of monitoring. Each timescale revealed a different rate of evolution, the first reporting a modified beach response-type (from human activities), and the second reporting a natural beach response-type. Human activities caused significant changes in the back-barrier shore, whereas changes under natural forcing were much smaller, were less influential on the area's evolution, and were not sufficient to counteract or mask the consequences of human activities. The findings of the study should contribute to a better understanding about the large- and small- scale changes in other back-barriers characterised by similar very low-energy conditions.

Twenty‐Fold Difference in Evolutionary Rates between the Mitochondrial and Plastid Genomes of Species with Secondary Red Plastids

Within plastid-bearing species, the relative rates of evolution between mitochondrial and plastid genomes are poorly studied, but for the few lineages in which they have been explored, including land plants and green algae, the mitochondrial DNA mutation rate is nearly always estimated to be lower than or equal to that of the plastid DNA. Here, we show that in protists from three distinct lineages with secondary, red algal-derived plastids, the opposite is true: their mitochondrial genomes are evolving 5-30 times faster than their plastid genomes, even when the plastid is nonphotosynthetic. These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode.