Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.     

胡颓子科叶绿体基因组系统发育分析与演化趋势推断

【目的】为探索胡颓子科叶绿体基因组演化趋势,从而为胡颓子科植物物种鉴定以及资源开发利用提供理论依据。【方法】研究从头组装并注释了沙棘属（Hippophae）和野牛果属（Shepherdia）共4个类群的叶绿体基因组,结合已发表的叶绿体基因组序列,比较了胡颓子科各类群叶绿体基因组的基因构成、重复序列和结构特征,建立了系统发育树,并通过高分化区定位了该科叶绿体基因组的潜在DNA条形码区域。【结果】胡颓子科各属叶绿体基因组在四分体结构、基因数量和排列上高度相似;沙棘属和野牛果属的反向重复区（IR）和整个基因组重复序列数目较胡颓子属有扩张和增加的趋势。基于胡颓子科18个类群的叶绿体全基因组序列的系统发育树中,胡颓子属、沙棘属和野牛果属各自聚为一支,前者先分化出来,沙棘属和野牛果属有最近共同祖先;从长单拷贝区（LSC）和短单拷贝区（SSC）筛选出3个DNA条形码候选区,其中ycf1基因的鉴定效果最佳,基于此构建的各类群系统发育关系与基于全基因组序列的结果一致。【结论】胡颓子科的叶绿体基因组结构保守,但其非编码区序列在各属间存在明显差异,且IR区序列与重复序列在演化过程中分别有扩张和增多的趋势。研究选定的DNA条形码序列能很好区分胡颓子科各属之间以及胡颓子属内物种间关系。     

Gene duplication,transfer, and evolution in the chloroplast genome

In addition to the nuclear genome, organisms have organelle genomes. Most of the DNA present in eukaryotic organisms is located in the cell nucleus. Chloroplasts have independent genomes which are inherited from the mother. Duplicated genes are common in the genomes of all organisms. It is believed that gene duplication is the most important step for the origin of genetic variation, leading to the creation of new genes and new gene functions. Despite the fact that extensive gene duplications are rare among the chloroplast genome, gene duplication in the chloroplast genome is an essential source of new genetic functions and a mechanism of neo-evolution. The events of gene transfer between the chloroplast genome and nuclear genome via duplication and subsequent recombination are important processes in evolution. The duplicated gene or genome in the nucleus has been the subject of several recent reviews. In this review, we will briefly summarize gene duplication and evolution in the chloroplast genome. Also, we will provide an overview of gene transfer events between chloroplast and nuclear genomes.     

基于叶绿体基因多样性的中国水稻起源进化研究

针对目前亚洲栽培稻起源地和进化途径学说众多、分歧巨大的现状,本研究选择原产中国的98份亚洲栽培稻和125份普通野生稻为材料,对叶绿体中atpA序列、rps16内含子序列、trnP-rpl33间隔区、trnG-trnfM序列、trnT-trnL间隔区序列的五段高突变序列进行测序,利用生物信息学方法进行比对分析,绘制Network网络图,构建系统发育树。结果表明,普通野生稻的Indel和SNP数目均比亚洲栽培稻多,序列多样性丰富;基于单倍型的Network网络图和系统发育树可将所有参试材料归为3个类群,类群I主要为粳稻与普通野生稻,类群II主要为籼稻,类群III主要为普通野生稻,而类群II和类群III亲缘关系较近,提示粳、籼两个亚种可能由偏粳、偏籼的普通野生稻分别进化而来,支持二次起源学说;所有与亚洲栽培稻亲缘关系较近的普通野生稻均来源于华南地区,支持华南地区为我国亚洲栽培稻起源中心的论点。     

Evolution of disintegrin cysteine-rich and mammalian matrix-degrading metalloproteinases: Gene duplication and divergence of a common ancestor rather than convergent evolution

The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution. Correspondence to: J.M. Crampton     

Phylogeny and the Evolution of the <Emphasis Type="Italic">Amylase</Emphasis> Multigenes in the <Emphasis Type="Italic">Drosophila montium</Emphasis> Species Subgroup

Abstract To investigate the phylogenetic relationships and molecular evolution of α-amylase (Amy) genes in the Drosophila montium species subgroup, we constructed the phylogenetic tree of the Amy genes from 40 species from the montium subgroup. On our tree the sequences of the auraria, kikkawai, and jambulina complexes formed distinct tight clusters. However, there were a few inconsistencies between the clustering pattern of the sequences and taxonomic classification in the kikkawai and jambulina complexes. Sequences of species from other complexes (bocqueti, bakoue, nikananu, and serrata) often did not cluster with their respective taxonomic groups. This suggests that relationships among the Amy genes may be different from those among species due to their particular evolution. Alternatively, the current taxonomy of the investigated species is unreliable. Two types of divergent paralogous Amy genes, the so-called Amy1- and Amy3-type genes, previously identified in the D. kikkawai complex, were common in the montium subgroup, suggesting that the duplication event from which these genes originate is as ancient as the subgroup or it could even predate its differentiation. Thc Amy1-type genes were closer to the Amy genes of D. melanogaster and D. pseudoobscura than to the Amy3-type genes. In the Amy1-type genes, the loss of the ancestral intron occurred independently in the auraria complex and in several Afrotropical species. The GC content at synonymous third codon positions (GC3s) of the Amy1-type genes was higher than that of the Amy3-type genes. Furthermore, the Amy1-type genes had more biased codon usage than the Amy3-type genes. The correlations between GC3s and GC content in the introns (GCi) differed between these two Amy-type genes. These findings suggest that the evolutionary forces that have affected silent sites of the two Amy-type genes in the montium species subgroup may differ.     

miR156靶基因SPL在植物中的系统分布和进化模式分析

Squamosa promoterbinding proteinlike genes （SPLs）在植物发育过程中具有重要作用。很多SPLs被miR156调节,然而,对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类,苔藓,石松,单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现,藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II,表明它们有着共同的祖先。Group II进一步分为7个亚支（IIaIIg）,miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中,它们可能发生外显子的丢失且伴随MRE的丢失。另外,基因重复对SPL靶基因的丰度变化影响很大,尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。     

Multiple Gene Duplication and Rapid Evolution in the groEL Gene: Functional Implications

The chaperonins, GroEL and GroES, are present ubiquitously and provide a paradigm in the understanding of assisted protein folding. Due to its essentiality of function, GroEL exhibits high sequence conservation across species. Complete genome sequencing has shown the occurrence of duplicate or multiple copies of groEL genes in bacteria such as Mycobacterium tuberculosis and Corynebacterium glutamicum. Monophyly of each bacterial clade in the phylogenetic tree generated for the GroEL protein suggests a lineage-specific duplication. The duplicated groEL gene in Actinobacteria is not accompanied by the operonic groES despite the presence of upstream regulatory elements. Our analysis suggests that in these bacteria the duplicated groEL genes have undergone rapid evolution and divergence to function in a GroES-independent manner. Evaluation of multiple sequence alignment demonstrates that the duplicated genes have acquired mutations at functionally significant positions including those involved in substrate binding, ATP binding, and GroES binding and those involved in inter-ring and intra-ring interactions. We propose that the duplicate groEL genes in different bacterial clades have evolved independently to meet specific requirements of each clade. We also propose that the groEL gene, although essential and conserved, accumulates nonconservative substitutions to exhibit structural and functional variations. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Bhattacharya]     

Evolution of the Vertebrate Cytosolic Malate Dehydrogenase Gene Family: Duplication and Divergence in Actinopterygian Fish

Abstract A general correlation between neural expression and negative charge in isozymes suggests charge represents an adaptation to the neural environment. Interestingly, a notable exception exists in teleost fish. Two cytosolic malate dehydrogenase (MDH) isozymes have different spatial expression patterns in certain fishes: one is expressed in all tissues and the second is expressed primarily in the eye and skeletal muscle. While the neural MDH isozyme is negatively charged, the difference in charge between the two isozymes is not as pronounced as that observed in other gene families (e.g., triosephosphate isomerase and lactate dehydrogenase). Most tetrapods express a single cytosolic MDH isozyme, and it has been demonstrated recently that the pair of isozymes found in teleosts results from a gene duplication sometime after the separation of teleosts and tetrapods, although the exact timing of this duplication has not been inferred. Phylogenetic analyses suggest that the duplication of teleost isozymes occurred during the radiation of actinopterygian fish, consistent with the timing of duplication at other loci. Using inferred amino acid sequences, we examine the pattern of change following the duplication and across the rest of the MDH gene tree. Comparison between the MDH gene family and another gene family that shows a larger charge differential among members (triosephosphate isomerase) indicates that the smaller charge difference between MDH isozymes is best explained by greater constraint on amino acid change directly following the duplication, not greater constraint across the entire gene tree. This difference in constraint might result from the wider pattern of expression of the “neural” MDH isozyme.     

miR156靶基因SPL在植物中的系统分布和进化模式分析

Squamosa promoter binding protein like genes (SPLs)在植物发育过程中具有重要作用。很多SPLs被miR156调节,然而,对于它们在植物中的系统分布和进化模式还知之甚少。本文对9个测序物种（藻类,苔藓,石松,单子叶和双子叶植物）的183个SPLs进行了生物信息学分析。结果表明miR156应答元件（MREs）仅在陆生植物SPLs中发现,藻类中不存在。系统进化分析显示陆生植物SPLs分为两大分支：group I和group II。 MiR156靶基因仅分布于group II,表明它们有着共同的祖先。Group II进一步分为7个亚支(IIa IIg),miR156靶基因分布在除IId外的其余6个亚支的特定SPLs。系统分类与基因结构的相关性反映了SPL靶基因结构上的变化。在进化过程中,它们可能发生外显子的丢失且伴随MRE的丢失。另外,基因重复对SPL靶基因的丰度变化影响很大,尤其是被子植物与低等植物分歧后它们数量明显增加。以拟南芥为模式植物分析发现串联重复和片段重复是SPL靶基因扩张的主要机制。     

Unraveling the Distribution and Evolution of miR156 targeted SPLs in Plants by Phylogenetic Analysis

Squamosa promoter binding protein like genes (SPLs) are critical during plant development and mostly regulated by miR156. However, little is known about phylogenetic distribution and evolutionary patterns of miR156 targeted SPLs. In this study, 183 SPLs from nine genome sequenced species representing algae, bryophytes, lycophyte, monocots, and eudicots were computationally analyzed. Our results showed that miR156 responsive elements (MREs) on SPLs were present in land plants but absent from unicellular green algae. Phylogenetic analysis revealed that miR156 targeted SPLs only distributed in group II not group I of land plants, suggesting they originated from a common ancestor. In addition, group II were further divided into seven subgroups (IIa IIg) and miR156 targeted SPLs distributed in some specific members of SPLs from six subgroups except subgroup IId. Such distribution pattern was well elucidated by gene structure evolution of miR156 targeted SPLs based on the correlation of phylogenetic classification and gene structure. They could suffer from the exon loss events combined with MREs loss during evolution. Moreover, gene duplication contributed to the abundance of miR156 targeted SPLs, which had significantly increased after angiosperms and lower plants split. With Arabidopsis as the model species, we found segmental and tandem gene duplications predominated during miR156 targeted SPLs expansion. Taken together, these results provide better insights in understanding the function diversity and evolution of miR156 targeted SPLs in plants.     

Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model

The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system. The wild-type TEM-1 β-lactamase gene confers resistance to ampicillin but not to cefotaxime. Point mutations confer cefotaxime resistance, but they compromise ampicillin resistance. Thus, selection for both drug resistances in a bacterium with two copies of β-lactamase should favor the divergence of one copy to improve cefotaxime resistance while maintaining the other copy to preserve ampicillin resistance. This selection was performed on a bacterium with identical sequences of β-lactamase on two separate, compatible plasmids. As expected, one plasmid evolved increased cefotaxime resistance when appropriately strong cefotaxime selection was applied. However, the cefotaxime-resistant plasmid maintained sufficient ampicillin resistance to tolerate the concentration of ampicillin used, and the other plasmid was lost. Hosts carrying both the cefotaxime-resistant and wild-type plasmids were then subjected to various higher concentrations of both drugs to find conditions that would ensure the maintenance of both plasmids. In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. Reviewing Editor: Dr. Margaret Riley     

The Pattern of Evolution of Smaller-Scale Gene Duplicates in Mammalian Genomes is More Consistent with Neo- than Subfunctionalisation

Gene duplication and the accompanying release of negative selective pressure on the duplicate pair is thought to be the key process that makes functional change in the coding and regulatory regions of genomes possible. However, the nature of these changes remains unresolved. There are a number of models for the fate of gene duplicates, the two most prominent of which are neofunctionalisation and subfunctionalisation, but it is still unclear which is the dominant fate. Using a dataset consisting of smaller-scale (tandem and segmental) duplications identified from the genomes of four fully sequenced mammalian genomes, we characterise two key features of smaller-scale duplicate evolution: the rate of pseudogenisation and the rate of accumulation of replacement substitutions in the coding sequence. We show that the best fitting model for gene duplicate survival is a Weibull function with a downward sloping convex hazard function which implies that the rate of pseudogenisation of a gene declines rapidly with time since duplication. Our analysis of the accumulation of replacement substitutions per replacement site shows that they accumulate on average at 64% of the neutral expectation immediately following duplication and as high as 73% in the human lineage. Although this rate declines with time since duplication, it takes several tens of millions of years before it has declined to half its initial value. We show that the properties of the gene death rate and of the accumulation of replacement substitutions are more consistent with neofunctionalisation (or subfunctionalisation followed by neofunctionalisation) than they are with subfunctionalisation alone or any of the other alternative modes of evolution of smaller-scale duplicates. Electronic Supplementary Material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Evolution of Growth Hormone in Primates: The GH Gene Clusters of the New World Monkeys Marmoset (Callithrix jacchus) and White-Fronted Capuchin (Cebus albifrons)

The GH gene cluster in marmoset, Callithrix jacchus, comprises eight GH-like genes and pseudogenes and appears to have arisen as a consequence of gene duplications occurring independently of those leading to the human GH gene cluster. We report here the complete sequence of the marmoset GH gene locus, including the intergenic regions and 5′ and 3′ flanking sequence, and a study of the multiple GH-like genes of an additional New World monkey (NWM), the white-fronted capuchin, Cebus albifrons. The marmoset sequence includes 945 nucleotides (nt) of 5′ flanking sequence and 1596 nt of 3′ flanking sequence that are “unique”; between these are eight repeat units, including the eight GH genes/pseudogenes. The breakpoints between these repeats are very similar, indicating a regular pattern of gene duplication. These breakpoints do not correspond to those found in the much less regular human GH gene cluster. This and phylogenetic analysis of the repeat units within the marmoset gene cluster strongly support the independent origin of these gene clusters, and the idea that the episode of rapid evolution that occurred during GH evolution in primates preceded the gene duplications. The marmoset GH gene cluster also differs from that of human in having fewer and more evenly distributed Alu sequences (a single pair in each repeat unit) and a “P-element” upstream of every gene/pseudogene. In human there is no P-element upstream of the gene encoding pituitary GH, and these elements have been implicated in placental expression of the other genes of the cluster. The GH gene clusters in marmoset and capuchin appear to have arisen as the consequence of a single-gene duplication event, but in capuchin there was then a remarkable expansion of the GH locus, giving at least 40 GH-like genes and pseudogenes. Thus even among NWMs the GH gene cluster is very variable. [Reviewing Editor: Nicolas Galtier]     

Adaptive Evolution and Frequent Gene Conversion in the Brain Expressed X-Linked Gene Family in Mammals

This work examines the molecular evolution of a brain-expressed X-linked gene family in the mammalian genomes of human, chimp, macaque, mouse, rat, dog, and cow. The gene structures are well conserved across family members and among the mammals in that all five members have three exons with the first two exons untranslated. Furthermore, the five members are arranged tandemly on chromosome X with Bex5, Bex1, Bex2 on the negative strand and Bex4, Bex3 on the positive strand, and this physical arrangement remains conserved among species. Sequence analyses indicate that gene conversion has been frequent and ongoing among Bex1-4, occurring in multiple species independently. All gene conversions in different species between Bex1 and Bex4, and between Bex2 and Bex3, appear to be limited to the upstream regions of the third exon, whereas the gene conversions occurred independently in different species between Bex1 and Bex2 and cover only the third exon. Bex5 appears to have little exchange of genetic information with other members, possibly due to its distance from other members. The GC content decreases from 5′-UTR, intron 1, intron 2, coding region, to 3′-UTR, reflecting faithfully the frequency of gene conversion in different regions of the Bex genes. Sequence analyses also suggest that both relaxed selective constraint and positive selection have acted on the Bex members after duplication. In particular, Bex3 shows strong evidence of positive selection and seems to have evolved a new gene function after gene duplication.     

拟南芥花药绒毡层细胞中具有基因簇特征的基因进化和功能分析

在植物基因组中, 除了同源基因成簇现象外, 近年来还发现一些具有共表达特性的异源基因也能够以基因簇形式存在, 但这些异源基因簇的进化和生物学功能尚不清楚。花药发育和花粉形成是植物进化出的特有的生殖生物学过程, 同时产生了一些在花药绒毡层中特异表达和特定功能的基因簇基因。该研究通过筛选和分析花药绒毡层中基因簇基因的分子特性、表达调控、基因年龄和基因重复进化等信息, 探讨花药基因簇基因与植物开花功能进化之间的关系。结果表明, 在拟南芥(Arabidopsis thaliana)中共筛选到84个(13个基因簇)花药绒毡层特异高表达的基因簇基因, 它们主要产生于串联重复事件, 76%的基因出现在开花植物分化后的阶段, 主要参与生殖发育、花粉鞘组成和脂代谢等生物学过程。研究初步解析了拟南芥花药绒毡层中基因簇基因的基本特征、生物学功能和基因进化机制, 为深入揭示植物基因簇基因的遗传学功能奠定了基础。     

Molecular Evolution of a Small Gene Family of Wound Inducible Kunitz Trypsin Inhibitors in Populus

Maximum likelihood models of codon substitutions were used to analyze the molecular evolution of a Kunitz trypsin inhibitor (KTI) gene family in Populus and Salix. The methods support previous assertions that the KTI genes comprise a rapidly evolving gene family. Models that allow for codon specific estimates of the ratio of nonsynonymous to synonymous substitutions (ω) among sites detect positive Darwinian selection at several sites in the KTI protein. In addition, branch-specific maximum likelihood models show that there is significant heterogeneity in ω among branches of the KTI phylogeny. In particular, ω is substantially higher following duplication than speciation. There is also evidence for significant rate heterogeneity following gene duplication, suggesting different evolutionary rates in newly arisen gene duplicates. The results indicate uneven evolutionary rates both between sites in the KTI protein and among different lineages in the KTI phylogeny, which is incompatible with a neutral model of sequence evolution. [Reviewing Editor: Dr. Willie J. Swanson]     

Phylogeny of Plastids Based on Cladistic Analysis of Gene Loss Inferred from Complete Plastid Genome Sequences

Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the primary photosynthetic eukaryotes (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the loss of plastid genes after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean (Chlamydomonas) lineage, and the secondary plastids from the diatom (Odontiella) and cryptophyte (Guillardia) were monophyletic within the red lineage.     

甘蓝型油菜主要农艺性状的遗传模型和基因效应分析

本文以甘蓝型优质油菜(81008×Tower)正反交各12个世代的资料,按照4种不同的遗传模型,对包括单株产量在内的8个农艺性状的遗传方式进行了详尽地分析。结果表明:所有性状的遗传皆不符合简单的加性-显性模型,上位性效应普遍存在,且对世代平均数有较大影响;单株产量及几个产量性状的遗传均受重复型互作基因的控制,杂种优势需利用三基因或多基因间的互作效应。