Mutational patterns in RNA secondary structure evolution examined in three RNA families

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution.     

The evolution of rbcL: A methodology to follow the evolution patterns of Medicago and Sulla (Fabaceae) genera

The chloroplast rbcL gene is selected to be a standard barcode for the phylogenetic analyses of several land plants. Using universal primers pair, the 3’ frame was used to assess the phylogeny of the two Legume genera Medicago and Sulla and the evolution of the translated protein. The multiple alignment exhibited high conservation rates (97.56% and 96.43% for Medicago and Sulla respectively), which might be a brake for the phylogenetic assessment. Nevertheless, the topologies of the cladograms drawn using Maximum Likelihood method, showed a low intraspecific divergence and a slightly high interspecific variation, which confirms the efficiency of rbcL for such characterization’ analyses. Besides, the composition and the patterns of the Amino-Acid sequence and the deduced Codon Usage, highlighted a non-aleatoire distribution of the codons. Thus, the non-synonymous substitutions rates traduced a positive selection occurring in the rbcL of the Medicago and Sulla species.     

Plant evolution: pulses of extinction and speciation in gymnosperm diversity

Living gymnosperms represent the survivors of ancient seed plant lineages whose fossil record reaches back 270 million years. Two recent studies find that recent pulses of extinction and speciation have shaped today's gymnosperm diversity, contradicting the widespread assumption that gymnosperms have remained largely unchanged for tens of millions of years.     

Hominin cognitive evolution: identifying patterns and processes in the fossil and archaeological record

As only limited insight into behaviour is available from the archaeological record, much of our understanding of historical changes in human cognition is restricted to identifying changes in brain size and architecture. Using both absolute and residual brain size estimates, we show that hominin brain evolution was likely to be the result of a mix of processes; punctuated changes at approximately 100 kya, 1 Mya and 1.8 Mya are supplemented by gradual within-lineage changes in Homo erectus and Homo sapiens sensu lato. While brain size increase in Homo in Africa is a gradual process, migration of hominins into Eurasia is associated with step changes at approximately 400 kya and approximately 100 kya. We then demonstrate that periods of rapid change in hominin brain size are not temporally associated with changes in environmental unpredictability or with long-term palaeoclimate trends. Thus, we argue that commonly used global sea level or Indian Ocean dust palaeoclimate records provide little evidence for either the variability selection or aridity hypotheses explaining changes in hominin brain size. Brain size change at approximately 100 kya is coincident with demographic change and the appearance of fully modern language. However, gaps remain in our understanding of the external pressures driving encephalization, which will only be filled by novel applications of the fossil, palaeoclimatic and archaeological records.     

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the can...     

Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae)

The RuBisCO large subunit gene (rbcL) has been the focus of numerous plant phylogenetic studies and studies on molecular evolution in parasitic plants. However, there has been a lack of investigation of photosynthesis gene molecular evolution in fully mycoheterotrophic plants. These plants invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi, from which they obtain fixed carbon and nutrients. The mycoheterotrophic orchid Corallorhiza contains both green (photosynthetic) and non-green (putatively nonphotosynthetic) species. We sequenced rbcL from 31 accessions of eight species of Corallorhiza and hypothesized that some lineages would have pseudogenes resulting from relaxation of purifying selection on RuBisCO's carboxylase function. Phylogenetic analysis of rbcL+ITS gave high jackknife support for relationships among species. We found evidence of pseudogene formation in all lineages of the Corallorhiza striata complex and in some lineages of the C. maculata complex. Evidence includes: stop codons, frameshifts, decreased d(S)/d(N) ratios, replacements not observed in photosynthetic species, rate heterogeneity, and high likelihood of neutral evolution. The evolution of rbcL in Corallorhiza may serve as an exemplary system in which to study the effects of relaxed evolutionary constraints on photosynthesis genes for >400 documented fully mycoheterotrophic plant species.     

Molecular evolution of the ZFY and ZNF6 gene families

Members of the ZFY and ZNF6 gene families have been cloned from species representing different taxa and different modes of sex determination. Comparisons of these genes show the ZFY-like and ZNF6 sequences to be strongly conserved across marsupials, birds, and lepidosaurians. Sequence analyzed by neighbor-joining indicated that both gene families are monophyletic with a high bootstrap value. Pairing of sequences from males and females of nonmammalian species showed there to be no significant difference between male and female sequences from a single species, consistent with autosomal locations. The molecular distances between murine Zfy-1, Zfy-2, and other ZFY-like sequences suggested that Zfy genes have undergone a period of rapid evolutionary change not seen in human ZFY.      

中国裸子植物的物种多样性格局及其影响因子

物种多样性的大尺度空间格局是宏观生态学和生物地理学研究的核心问题之一。本文利用中国裸子植物分布数据, 结合气候、地形等环境信息, 分析了中国裸子植物物种多样性的大尺度格局及其影响因素, 比较了不同类群之间物种多样性格局和主导因子的差异, 并探讨了裸子植物在植物区系中所占比重的地理格局。结果表明, 中国裸子植物的物种多样性总体上呈现南高北低的趋势, 物种多样性在横断山区最高。在裸子植物的三个主要类群中, 松柏亚纲的物种多样性格局与整体相似, 买麻藤亚纲的多样性高值区则出现在中国西北部的干旱地区, 苏铁亚纲的分布区较为狭窄, 主要集中在南方地区。线性回归分析结果表明, 空间异质性和降水因子对中国裸子植物多样性格局的解释率最高, 末次冰期以来的气温变化、海拔高差和能量因子次之。这表明中国裸子植物物种多样性的格局受到了多种因素的影响, 其中空间异质性和降水因子影响最大。进一步分析发现, 物种多样性格局的主导因子在不同类群之间具有显著差异, 这可能反映了这些类群的进化历史以及生理适应的差异。裸子植物与被子植物的比例具有明显的空间格局: 在东部、南部气候环境优越的地区, 裸子植物与被子植物的比例低于0.06; 而在西部、北部等气候环境比较恶劣的地区, 裸子植物的比例则显著上升。回归分析表明, 能量和水分因子显著影响了裸子植物与被子植物的比例。随着能量的降低和降水的减少, 裸子植物与被子植物的比例会显著升高, 这可能是由于被子植物在温暖湿润地区具有较强竞争优势, 但裸子植物对极端环境具有更好的适应。     

Molecular population genetics and the search for adaptive evolution in plants

The first papers on plant molecular population genetics were published approximately 10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these studies focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding the detection of selection, with focus on plant populations, and we also summarize the empirical plant molecular population genetics literature. At face value, the literature suggests that a history of balancing or positive selection in plant genes is rampant. In two well-studied taxa (maize and Arabidopsis) over 20% of studied genes have been interpreted as containing the signature of selection. We argue that this is probably an overstatement of the prevalence of natural selection in plant genomes, for two reasons. First, demographic effects are difficult to incorporate and have generally not been well integrated into the plant population genetics literature. Second, the genes studied to date are not a random sample, so selected genes may be overrepresented. The next generation of studies in plant molecular population genetics requires additional sampling of local populations, explicit comparisons among loci, and improved theoretical methods to control for demography. Eventually, candidate loci should be confirmed by explicit consideration of phenotypic effects.     

Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes

Analyses of complete cytochrome b sequences from all species of cranes (Aves: Gruidae) reveal aspects of sequence evolution in the early stages of divergence. These DNA sequences are > or = 89% identical, but expected departures from random substitution are evident. Silent, third- position pyrimidine transitions are the dominant substitution type, with transversion comprising only a small fraction of sequence differences. Substitution patterns are not clearly manifested until divergence has reached a moderate level (> 3%), as expected for a stochastic process. Variation in the frequency of mismatch types among lineages decreases at larger divergences, but the level of bias does not decay. Divergence varies up to fivefold among gene regions but is not correlated with structural domain. All protein structural domains except extramembrane 4 display < 20% variable residues. Regions corresponding to putative functional domains show the excepted conservation of amino acids, although the C-terminal portion of the Q0 reaction center displays several nonconservative replacements. Phylogenetic analyses incorporating substitution asymmetries produced mixed results. Distances estimated with multiple parameters (transition, codon-position, composition, and pyrimidine-transition biases) yielded identical additive tree topologies with comparable bootstrap values, all consistent with uncontroversial species relationships. Maximum likelihood analysis incorporating these biases, as well as equally weighted parsimony analysis, produced similar results. Static, differential weighting for parsimony did not improve the phylogenetic signal but produced unusual trees with low bootstraps. The overall rate of nucleotide substitution varies slightly but significantly among cranes, and calibration of distances against fossil dates suggests divergence rates of 0.7%-1.7% per million years.      

Molecular diversity and conformity of neurohormonal peptides: clues to an adaptive role in evolution

Peptide regulators are probably the most widely distributed signalling agents in the animal kingdom. They are found in both invertebrates and vertebrates where they are produced in endocrine, neuroendocrine and neuronal tissues. As more of these ubiquitous messengers have been characterized it has become evident that they may be grouped into families with clearly defined relationships. Amino acid sequences of the mature, final product indicate relationships between for example cholecystokinin (CCK) and gastrin. More detailed examination of peptide precursors can give further insights into family trees and in the case of the secretin-vasoactive intestinal polypeptide family result in the identification of a novel co-coded peptide. Such dual coding has led to the hypothesis of gene-duplication in peptide evolution, a phenomenon admirably exemplified by the glucagon family and the opioid family. A further example of peptide diversity is evident when mRNA processing is examined. Here a single gene encoding two (or more) structural sequences can produce multiple mRNAs, each encoding a unique peptide sequence. The mRNA produced varies according to the tissue site. The calcitonin and Tachykinin family are fine examples with different peptides produced in neurones and endocrine tissues. A remarkable conservatism of peptide sequences is found in the insulin family where distinct relationships are evident between insulin, insulin-related growth factors (IGF) and insect prothoracicotrophic hormone. Such relationships are supported by examination of the genes for insulin and IGF. Peptide regulators do not evolve in isolation and it is clear that their receptors are also exposed to adaptive pressures. Receptor classes for the Tachykinin family are well characterized, with receptors being identified as falling into two categories, SP-P type and SP-E type. Similar situations obtain for the opioids. Much of this information is based on mammalian studies, however recent work on gastrin/CCK receptors in a range of vertebrates indicates a phylogenetic diversity between brain and gut receptors.     

Molecular systematics and evolution of the Ptinidae (Coleoptera: Bostrichoidea) and related families

The Ptinidae (Coleoptera: Bostrichoidea) are a cosmopolitan, ecologically diverse, but poorly known group of Coleoptera and, excluding a few economic pests, species are rarely encountered. This first broad phylogenetic study of the Ptinidae s.l. (i.e. including both the spider beetles and anobiids) examines relationships based on DNA sequence data from two mitochondrial genes (16S and COI) and one nuclear gene (28S), using out‐group taxa from both the Bostrichidae and Dermestidae. Topologies varied depending on the genes used and whether data were analysed with either parsimony or Bayesian methods. Generally the two mitochondrial genes supported relationships near the tips of the phylogeny, whereas the nuclear gene supported the basal relationships. The monophyly of the Ptinidae was not inferred by all of the gene combinations and analysis methods, although the combined Ptinidae and Bostrichidae have a single origin in all cases. Alternative relationships include the Ptinidae s.s. (i.e. Ptininae and Gibbiinae) as sister to the anobiids (i.e. the nine remaining subfamilies of Ptinidae s.l.) + Bostrichidae, or the Bostrichidae as sister to the Ptinidae s.s.+ anobiids. Most of the larger subfamilies within the Ptinidae are not monophyletic. Further analysis with more taxa and more genes will be required to clarify and decide upon the best hypothesis of relationships found within the clades of the Bostrichidae and Ptinidae. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 88–108.     

Physicochemical evolution and positive selection of the gymnosperm matK proteins

It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified from 27 Taxaceae and 12 Cephalotaxaceae species. matK sequences of 19 Pinaceae species were retrieved from GenBank. The phylogenetic tree was generated using conceptual-translated amino acid sequences. Selective influences were investigated using standard d _N/d _S ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a phylogenetic context. Analyses revealed the presence of positive selection in matKs (N-terminal region, RT domain and domain X) of Taxaceae and Pinaceae, and found positive destabilizing selection in N-terminal region and RT domain of Cephalotaxaceae matK. Moreover, various amino acid properties were found to be influenced by destabilizing positive selection. Amino acid sites relating to these properties and to different secondary structures were found and have the potential to affect group II intron maturase function. Despite the evolutionary constraint on the rapidly evolving matK, this protein evolves under positive selection in gymnosperm. Several regions of matK have experienced molecular adaptation which fine-tunes maturase performance.     

Molecular adaptive evolution of SARS-COV-2 spike protein in Saudi Arabia

The sequences of SARS-CoV-2 spike (S) from Saudi Arabia along with SARS-CoV and bat SARS-like CoVs were obtained. Positive selection analysis and secondary structure investigation of spike sequences were performed. Adaptive molecular evolution was observed in SARS-CoV-2 displayed by positive selection pressure at N-terminal domain (NTD; codons 41, 163, 174 and 218), Receptor binding domain (RBD; codons 378 and 404) and S1/S2 Cleavage site (codon 690). Furthermore, the spike protein secondary structure depicted by the homo-trimer structure showed a high similarity between Saudi SARS-CoV-2 isolate and the parental strain (bat SL-COVZC45). Despite the high similarity depicted in the spike sequence model alignment, it displayed a significant difference when each chain was treated solely owing to 7 motif differences in the three composing chains. In addition, SARS-CoV-2 S trimer model uncovered the presence of N-acetyl glucosamine ligands. Eventually, 3C-like proteinase cleavage site was observed in S2 domain could be used as a site for drug discovery. Genetics and molecular evolutionary facts are useful for assessment of evolution, host adaptation and epidemic patterns ultimately helpful for adaptation of control strategies.     

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.     

Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences

Phylogenetic analyses of DNA nucleotide sequences from the plastid genes rbcL and matK were employed to investigate intergeneric relationships within Malpighiaceae. Cladistic relationships generated from the independent data matrices for the family are generally in agreement with those from the combined matrix. At the base of Malpighiaceae are several clades mostly representing genera from a paraphyletic subfamily Byrsonimoideae. Intergeneric relationships among these byrsonimoid malpighs are well supported by the bootstrap, and the tribe Galphimeae is monophyletic. There is also a well-supported clade of genera corresponding to tribes Banisterieae plus Gaudichaudieae present in all trees, and many of the relationships among these banisterioid malpighs are well supported by the bootstrap. However, tribes Hiraeae and Tricomarieae (the hiraeoid malpighs) are paraphyletic and largely unresolved. Species of Mascagnia are distributed throughout these hiraeoid clades, confirming the suspected polyphyly of this large genus. Optimization of selected morphological characters on these trees demonstrates clear phylogenetic trends such as the evolution of globally symmetrical from radially symmetrical pollen, increased modification and sterilization of stamens, and switch from base chromosome number n = 6 to n = 10.     

Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus

Marine unicellular cyanobacteria, represented by Synechococcus and Prochlorococcus, dominate the total phytoplankton biomass and production in oligotrophic ocean. In this study, we employed comparative genomics approaches to extensively investigate synonymous codon usage bias and evolutionary rates in a large number of closely related species of marine unicellular cyanobacteria. Although these two groups of marine cyanobacteria have a close phylogenetic relationship, we find that they are highly divergent not only in codon usage patterns but also in the driving forces behind the diversification. It is revealed that in Prochlorococcus, mutation and genome compositional constraints are the main forces contributing to codon usage bias, whereas in Synechococcus, translational selection. In addition, nucleotide substitution rate analysis indicates that they are not evolving at a constant rate after the divergence and that the average d_N/d_S values of core genes in Synechococcus are significantly higher than those in Prochlorococcus. Our evolutionary genomic analysis provides the first insight into codon usage, evolutionary genetic mechanisms and environmental adaptation of Synechococcus and Prochlorococcus after divergence.