Developmental Data and Phylogenetic Systematics: Evolution of the Vertebrate Limb

Among the primary contributions of phylogenetic systematicsto the synthesis of developmental biology and evolution arephylogenetic hypotheses. Phylogenetic hypotheses are criticalin interpreting the patterns of evolution of developmental genesand processes, as are morphological data. Using a robust phylogeny,the evolutionary history of individual morphological or developmentalfeatures can be traced and ancestral conditions inferred. Multiplecharacters (e.g., morphological and developmental) can be mappedtogether on the phylogeny, and patterns of character associationcan be quantified and tested for correlation. Using the vertebrate forelimb as an example, I show that bymapping accurate morphological data (homologous skeletal elementsof the vertebrate forelimb) onto a phylogeny, an alternativeinterpretation of Hox gene expression emerges. Teleost fishesand tetrapods may share no homologous skeletal elements in theirforelimbs, and thus similarities and differences in Hox patternsduring limb development must be reinterpreted. Specifically,the presence of the phase III Hox pattern in tetrapods may notbe correlated with digits but rather may simply be the normalexpression pattern of a metapterygium in fishes. This exampleillustrates the rigorous hypotheses that can be developed usingmorphological data and phylogenetic methods. "Creating a general reference system and investigating the relationsthat extend from it to all other possible and necessary systemsin biology is the task of systematics." (Hennig, 1966, p.7)     

Evolutionary Developmental Biology and Human Language Evolution: Constraints on Adaptation

A tension has long existed between those biologists who emphasize the importance of adaptation by natural selection and those who highlight the role of phylogenetic and developmental constraints on organismal form and function. This contrast has been particularly noticeable in recent debates concerning the evolution of human language. Darwin himself acknowledged the existence and importance of both of these, and a long line of biologists have followed him in seeing, in the concept of ??descent with modification??, a framework naturally able to incorporate both adaptation and constraint. Today, the integrated perspective of modern evolutionary developmental biology (??evo-devo??) allows a more subtle and pluralistic approach to these traditional questions, and has provided several examples where the traditional notion of ??constraint?? can be cashed out in specific, mechanistic terms. This integrated viewpoint is particularly relevant to the evolution of the multiple mechanisms underlying human language, because of the short time available for novel aspects of these mechanisms to evolve and be optimized. Comparative data indicate that many cognitive aspects of human language predate humans, suggesting that pre-adaptation and exaptation have played important roles in language evolution. Thus, substantial components of what many linguists call ??Universal Grammar?? predate language itself. However, at least some of these older mechanisms have been combined in ways that generate true novelty. I suggest that we can insightfully exploit major steps forward in our understanding of evolution and development, to gain a richer understanding of the principles that underlie human language evolution.     

Developmental Aspects of Vertebrate Chromatophores

Melanophores, xanthophores, and iridophores are fundamentallydistinct chromatophores in their appearance, composition, andfunction. All migrate from their neural crest site of originto populate the integument. Their respective pigments, melanins,ptendines, and purines are found in organelles designated respectivelyas melanosomes, pterinosomes and reflecting platelets. Theseorganelles are all derived from an endoplasmic reticular vesicle.This is in keeping with a hypothesis about the common originof pigment cells from a stem cell containing a primordial organellewith the potential of becoming any of the circumscribed pigmentaryorganelles. It is believed that chromatoblasts may not be specificallydetermined until they reach a final destination where they willdifferentiate in accordance with a pattern already specifiedin the integument. In leopard frogs, it appears that the initialinduction of pattern in the skin is general, but later it becomeshighly specific.     

Comparable Rates of Gene Loss and Functional Divergence after Genome Duplications Early in Vertebrate Evolution

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2(n), where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3, . . . , 2(n), reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.     

脊椎动物线粒体DNA的基因重排

将GenBank上已公布的321种脊椎动物mtDNA全序列,按纲整理归类,绘制基因排布图并进行比对。比对结果表明：81个物种的mtDNA中观察到基因重排现象,涉及脊椎动物各纲,其中9个物种同时存在基因顺序变化和基因倒置现象,所有的基因重排都涉及tRNA的变化。脊椎动物mtDNA基因顺序变化可分为3类：1)邻接的基因或片段的位置交换;2)接近于控制序列或轻链起始位点的基因或片段的位置变化,有时还伴随着控制序列的倍增;3)I-Q-M区域的变化。所有鸟类、蛇类、鳄类和有袋类的mtDNA具有各自独特的基因排列顺序。基因倒置现象常见于鱼类和哺乳类,且多表现为tRNA从轻链往重链上迁移。本文就这些基因重排现象、发生重排的机制和mtDNA基因重排在系统发生研究中的应用做一简要概述。     

Genetic Constraints on Protein Evolution

ABSTRACT

Evolution requires the generation and optimization of new traits (“adaptation”) and involves the selection of mutations that improve cellular function. These mutations were assumed to arise by selection of neutral mutations present at all times in the population. Here we review recent evidence that indicates that deleterious mutations are more frequent in the population than previously recognized and that these mutations play a significant role in protein evolution through continuous positive selection. Positively selected mutations include adaptive mutations, i.e. mutations that directly affect enzymatic function, and compensatory mutations, which suppress the pleiotropic effects of adaptive mutations. Compensatory mutations are by far the most frequent of the two and would allow potentially adaptive but deleterious mutations to persist long enough in the population to be positively selected during episodes of adaptation. Compensatory mutations are, by definition, context-dependent and thus constrain the paths available for evolution. This provides a mechanistic basis for the examples of highly constrained evolutionary landscapes and parallel evolution reported in natural and experimental populations. The present review article describes these recent advances in the field of protein evolution and discusses their implications for understanding the genetic basis of disease and for protein engineering in vitro.     

Evolution of Vertebrate Indoleamine 2,3-Dioxygenases

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the same reaction, the first step in tryptophan catabolism via the kynurenine pathway. TDO is widely distributed among life-forms, being found not only in eukaryotes but also in bacteria. In contrast, IDO has been found only in mammals and yeast to date. However, recent genome and EST projects have identified IDO homologues in non-mammals and found an IDO paralogue that is expressed in mice. In this study, we cloned the frog and fish IDO homologues and the mouse IDO paralogue, and characterized their enzymatic properties using recombinants. The IDOs of lower vertebrates and the mouse IDO paralogue had IDO activity but had 500–1000 times higher K _m values and very low enzyme efficiency compared with mammalian IDOs. It appears that L-Trp is not a true substrate for these enzymes in vivo, although their actual function is unknown. On the phylogenetic tree, these low-activity IDOs, which we have named “proto-IDOs,” formed a cluster that was distinct from the mammalian IDO cluster. The IDO and proto-IDO genes are present tandemly on the chromosomes of mammals, including the marsupial opossum, whereas only the proto-IDO gene is observed in chicken and fish genomes. These results suggest that (mammalian) IDOs arose from proto-IDOs by gene duplication that occurred before the divergence of marsupial and eutherian (placental) mammals in mammalian evolutionary history.     

Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth

With a remarkable increase in genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-organizing map (SOM) is a powerful tool for clustering high-dimensional data on one plane. For oligonucleotide compositions handled as high-dimensional data, we have previously modified the conventional SOM for genome informatics: BLSOM. In the present study, we constructed BLSOMs for oligonucleotide compositions in fragment sequences (e.g. 100 kb) from a wide range of vertebrates, including coelacanth, and found that the sequences were clustered primarily according to species without species information. As one of the nearest living relatives of tetrapod ancestors, coelacanth is believed to provide access to the phenotypic and genomic transitions leading to the emergence of tetrapods. The characteristic oligonucleotide composition found for coelacanth was connected with the lowest dinucleotide CG occurrence (i.e. the highest CG suppression) among fishes, which was rather equivalent to that of tetrapods. This evident CG suppression in coelacanth should reflect molecular evolutionary processes of epigenetic systems including DNA methylation during vertebrate evolution. Sequence of a de novo DNA methylase (Dntm3a) of coelacanth was found to be more closely related to that of tetrapods than that of other fishes.     

Structural Constraints on RNA Virus Evolution

The recently discovered hepatitis G virus (HGV) or GB virus C (GBV-C) is widely distributed in human populations, and homologues such as HGV/GBV-CCPZ and GBV-A are found in a variety of different primate species. Both epidemiological and phylogenetic analyses support the hypothesis that GB viruses coevolved with their primate hosts, although their degree of sequence similarity appears incompatible with the high rate of sequence change of HGV/GBV-C over short observation periods. Comparison of complete coding sequences (8,500 bases) of different genotypes of HGV/GBV-C showed an excess of invariant synonymous sites (at 23% of all codons) compared with the frequency expected by chance (10%). To investigate the hypothesis that RNA secondary-structure formation through internal base pairing limited sequence variability at these sites, an algorithm was developed to detect covariant sites among HGV/GBV-C sequences of different genotypes. At least 35 covariant sites that were spatially associated with potential stem-loop structures were detected, whose positions correlated with positions in the genome that showed reductions in synonymous variability. Although the functional roles of the predicted secondary structures remain unclear, the restriction of sequence change imposed by secondary-structure formation provides a mechanism for differences in net rate of accumulation of nucleotide substitutions at different sites. However, the resulting disparity between short- and long-term rates of sequence change of HGV/GBV-C violates the assumptions of the "molecular clock." This places a major restriction on the use of nucleotide or amino acid sequence comparisons to calculate times of divergence of other viruses evolving under the same structural constraints as GB viruses.     

Selective Pressure on the Allantoicase Gene During Vertebrate Evolution

During vertebrate evolution, the uric acid degradation pathway has been modified and several enzymes have been lost. Consequently, the end product of purine catabolism varies from species to species. In the past few years, we have focused our attention on vertebrate allantoicase (an uricolytic pathway enzyme), whose activity is present in certain fish and amphibians only, but whose mRNA we detected also in mammals. As allantoicase activity disappeared in amniotes, we wonder why these sequences not only remain present in the mammalian genome, but are still transcribed. To elucidate this issue, we have cloned and analyzed comparable cDNA sequences of different organisms from ascidians to mammals. The analysis of the nonsynonymous–synonymous substitution rate that we performed on the coding region comprising exons 3 to 8 by means of maximum likelihood suggested that a certain amount of purifying selection is acting on the allantoicase sequences. Some implications of the preservation of an apparently unnecessary gene in higher vertebrates are discussed.     

Molecular Evolution of Vertebrate Goose-Type Lysozyme Genes

We have found that mammalian genomes contain two lysozyme g genes. To better understand the function of the lysozyme g genes we have examined the evolution of this small gene family. The lysozyme g gene structure has been largely conserved during vertebrate evolution, except at the 5' end of the gene, which varies in number of exons. The expression pattern of the lysozyme g gene varies between species. The fish lysozyme g sequences, unlike bird and mammalian lysozyme g sequences, do not predict a signal peptide, suggesting that the encoded proteins are not secreted. The fish sequences also do not conserve cysteine residues that generate disulfide bridges in the secreted bird enzymes, supporting the hypothesis that the fish enzymes have an intracellular function. The signal peptide found in bird and mammalian lysozyme g genes may have been acquired as an exon in the ancestor of birds and mammals, or, alternatively, an exon encoding the signal peptide has been lost in fish. Both explanations account for the change in gene structure between fish and tetrapods. The mammalian lysozyme g sequences were found to have evolved at an accelerated rate, and to have not perfectly conserved the known active site catalytic triad of the bird enzymes. This observation suggests that the mammalian enzymes may have altered their biological function, as well.     

The Molecular Evolution of the Vertebrate Trypsinogens

We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted. Received: 12 July 1997     

The Origin and Evolution of Vertebrate Glycine Transporters

In the vertebrate central nervous system, glycinergic neurotransmission is regulated by the action of the glycine transporters 1 and 2 (GlyT1 and GlyT2)—members of the solute carrier family 6 (SLC6). Several invertebrate deuterostomes have two paralogous glycine carrier genes, with one gene in the pair having greater sequence identity and higher alignment scores with respect to GlyT1 and the other paralog showing greater similarity to GlyT2. In phylogenetic trees, GlyT2-like sequences from invertebrate deuterostomes form a monophyletic subclade with vertebrate GlyT2, while invertebrate GlyT1-like proteins constitute an outgroup to both the GlyT2-like proteins and to vertebrate GlyT1 sequences. These results are consistent with the hypothesis that vertebrate GlyT1 and GlyT2 are, respectively, derived from GlyT1- and GlyT2-like genes in invertebrate deuterostomes. This implies that the gene duplication which gave rise to these paralogs occurred prior to the origin of vertebrates. GlyT2 subsequently diverged significantly from its invertebrate orthologs (i.e., through the acquisition of a unique N-terminus) as a consequence of functional specialization, being expressed principally in the lower CNS; while GlyT1 has activity in both the lower CNS and several regions of the forebrain.     

Activity Physiology and Evolution of the Vertebrate Skeleton

SYNOPSIS. Vertebrates frequently rely on intramuscular glycolysisas the major source of ATP utilized during bouts of intenseexercise. This is often followed by extended periods of markedsystemic pH fluctuation. Such a pattern of activity physiologyis unique among the Metazoa and probably dates back to the veryearliest vertebrates. The origin of bone may have been necessitated by requirementfor a skeletal matrix with chemical stability over the broadrange of tissue pH associated with vertebrate exercise physiology.