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PubMed2003

Evolution of placental specializations in viviparous African and South American lizards.

Phylogenetic information offers an important resource in analyses of reproductive diversity, including interpretations of fetal membrane evolution. In this paper, we draw upon ongoing studies of South American and African lizards to consider the value of combining phylogenetic and reproductive evidence in the construction of evolutionary interpretations. South American lizards of the genus Mabuya exhibit several reproductive specializations that are convergent on those of eutherian mammals, including viviparity, long gestation periods, ovulation of tiny eggs, and placental supply of the nutrients for development. Studies of placental morphology and development indicate that New World Mabuya share several other derived features, including chorionic areolae and a "Type IV" epitheliochorial placenta with a villous, mesometrial placentome. Some characteristics of these lizards are shared by two African skinks, M. ivensii and Eumecia anchietae, including minuscule eggs, placentotrophy, an absorptive chorioallantois, and features of the yolk sac. Available evidence is consistent with two explanations: (1) placentotrophy originated in Africa, predating a trans-Atlantic colonization by Mabuya of the New World; and (2) placentotrophy arose two or three separate times among these closely related skinks. As illustrated by analysis of these animals, not only can data on fetal membrane morphology yield phylogenetic information, but phylogenetic evidence in turn provides a valuable way to reconstruct the evolution of fetal membranes in a biogeographic context. When appropriately interpreted, morphological and phylogenetic evidence can be combined to yield robust evolutionary conclusions that avoid the pitfalls of circular reasoning.

Allantois↗
PubMed1999

Genetic and biochemical comparison of 2-aminophenol 1,6-dioxygenase of Pseudomonas pseudoalcaligenes JS45 to meta-cleavage dioxygenases: divergent evolution of 2-aminophenol meta-cleavage pathway.

Nitrobenzene is degraded to pyruvate and acetaldehyde by Pseudomonas pseudoalcaligenes JS45 via a reductive pathway, and by Comamonas sp. JS765 via an oxidative pathway. Although the initial reactions in the degradation of nitrobenzene by the two bacteria are totally different, the lower pathways are similar and converge at the level of 4-oxalocrotonate. In order to further investigate the biochemical properties and reveal the evolutionary relationships between the two lower pathways, the genes encoding the 2-aminophenol 1,6-dioxygenase were cloned and sequenced. 2-Aminophenol 1,6-dioxygenase from P. pseudoalcaligenes JS45 and catechol 2,3-dioxygenase from Comamonas sp. JS765 were able to act on both catechol and 2-aminophenol, but catechol was a suicide substrate of 2-aminophenol 1,6-dioxygenase. The activity of 2-aminophenol 1,6-dioxygenase was restored after removal of catechol and incubation with ascorbate and FeCl(2). Both the alpha-subunit (AmnA) and the beta-subunit (AmnB) of the dioxygenase from P. pseudoalcaligenes JS45 show a high degree of identity to the corresponding subunits of the ring-fission dioxygenase from Pseudomonas sp. AP-3: 67% for the alpha-subunit, and 84% for the beta-subunit. Sequence similarity studies suggest that the beta-subunits of both 2-aminophenol 1,6-dioxygenases are distantly related to homoprotocatechuate 2,3-dioxygenase from Escherichia coli strains W and C and then to catechol 2, 3-dioxygenase from Alcaligenes eutrophus. Four active-site-relevant histidines are conserved in AmnB, but not in AmnA. The lack of conserved histidines indicates the absence of an Fe(2+) binding site in AmnA, which explains the previous observations of only approximately one Fe(2+) per two subunits in the 2-aminophenol 1, 6-dioxygenases from P. pseudoalcaligenes JS45. The 2-aminophenol 1, 6-dioxygenase genes are located upstream of the 2-aminomuconic semialdehyde dehydrogenase gene, and a putative member of the YjgF protein family is upstream of the dioxygenase genes. Transcriptional analysis indicates that the YjgF-like protein, 2-aminophenol 1, 6-dioxygenase, and 2-aminomuconic semialdehyde dehydrogenase are coordinately transcribed. A putative ORF similar to part of the RNA helicase genes is downstream of the dehydrogenase gene. Both the novel organization of the genes and the phylogeny of the dioxygenases and dehydrogenase indicate that the 2-aminophenol pathway in P. pseudoalcaligenes JS45 represents an example of a distant divergent evolution of meta-cleavage pathways.

Amino Acid Sequence↗
PubMed1988

[Extra-osseous and intra-osseous microvascularization of the sternum of the child].

The microvascularization of the sternum of the child has been studied by a method of India ink injection and by histology. Extra-osseous vasculature includes vascular pedicles and sternal vascular networks. Vascular anterior and posterior pedicles issue from internal mammary vessels. Sternal anterior and posterior networks are disposed on the faces of the sternum and are divided in a superficial one and a deep one; both are included in the perichondrium. In newborns and in young infants, vascular structures looking like baskets are affixed to the deep sternal network. It is unlikely that they intervene in the constitution of the adult pattern of the sternal vasculature. The early complete development of sternal networks contrasts with the existence of evolutive characteristics of the intra-osseous vasculature. Intra-osseous vasculature includes the cartilage canal vessels and the vessels of the ossification centers. Cartilage canals are provided with an axial artery, issued from the deep sternal network, which produces short capillaries which continue in peripheral sinuses. Cartilage canals permit the penetration of perichondral tissue deep in the cartilage of the developing sternum, allowing the formation of the ossification center. The ossification center is vascularized by centrifugal arteries, issued from the cartilage canal artery, and disposed in a radiant pattern. They continue, through a conical progressive dilatation, into a sinusoid network, which presents a convergent disposition towards the center of the ossification point. Vascular events precede ossification. Hematopoietic development is consecutive to the vascular events too. The slenderness of vascular pedicles contrasts in neonates with the wide development of the sinusoid network. Adipose tissue is rare in the bone marrow sternum of the child. Secondary evolution of the ossification center vasculature permits its connections with the deep sternal vascular network, with adjacent cartilage canals, and with adjacent ossification centers. Progressively, the number and the importance of the peripheral pedicles of the ossification centers increase. Thus, a multiple and centripetal vascular provision takes the place of the initial, unique, centrifugal one. These modifications correspond to the transition from the vascular pattern of an expanding structure (the ossification center) to the one which is adapted to the full expression of its hematopoietic function.

Adolescent↗
PubMed2006

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

BACKGROUND: Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. RESULTS: We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/samo/ and http://intelligent.eic.osaka-sandai.ac.jp/chenen/samo.htm. CONCLUSION: A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven.

Algorithms↗
PubMed2004

Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss.

Despite the prominence of Caenorhabditis elegans as a major developmental and genetic model system, its phylogenetic relationship to its closest relatives has not been resolved. Resolution of these relationships is necessary for studying the steps that underlie life history, genomic, and morphological evolution of this important system. By using data from five different nuclear genes from 10 Caenorhabditis species currently in culture, we find a well resolved phylogeny that reveals three striking patterns in the evolution of this animal group: (i) Hermaphroditism has evolved independently in C. elegans and its close relative Caenorhabditis briggsae; (ii) there is a large degree of intron turnover within Caenorhabditis, and intron losses are much more frequent than intron gains; and (iii) despite the lack of marked morphological diversity, more genetic disparity is present within this one genus than has occurred within all vertebrates.

Animals↗
PubMed1984

The evolution of multigene families under intrachromosomal gene conversion.

A model for the evolution of the probabilities of genetic identity within and between loci of a multigene family in a finite population is formulated and investigated. Unbiased intrachromosomal gene conversion, equal crossing over between tandemly repeated genes, random genetic drift and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. Formulas for the equilibrium values of the probabilities of identity and a cubic equation for the rate of convergence are deduced. Numerical examples indicate the following. The amount of homology at equilibrium generally decreases as the mutation rate, the population size and the number of repeats increase; it may increase or decrease with increasing crossover rate. The intralocus homology has an intermediate minimum, whereas the interlocus homology increases, as the rate of gene conversion increases. The intralocus homology decreases, whereas the interlocus homology increases, as the proportion of symmetric heteroduplexes increases. The characteristic convergence time can be sufficiently short to imply that intrachromosomal gene conversion may be an important mechanism for maintaining sequence homogeneity among repeated genes. The convergence time decreases as the conversion rate and the proportion of symmetric heteroduplexes increase; although exceptions occur, it generally increases as the population size and the number of repeats increase; it may increase or decrease with increasing crossover rate.

Animals↗
PubMed1999

Homology and convergence in vertebrate and invertebrate nervous systems.

Each year the meeting of the American Neuroscience Society attracts over 20,000 members, reflecting the explosion of interest in this field that has occurred over the past few decades. Researchers from many disciplines are focusing their skills on the investigation of every aspect of nervous systems, and neuroscience now encompasses the entire range of endeavour from the study of the single molecules that make up neural membranes to the non-invasive observation of neural function in animals behaving in their natural environments. Advances over the past three decades in our understanding of nervous systems are impressive and come from a multifaceted approach to the study of both vertebrate and invertebrate animals. An almost unexpected by-product of the parallel investigation of vertebrate and invertebrate nervous systems that is explored in this article is the emergent view of an intricate web of evolutionary homology and convergence exhibited in the structure and function of the nervous systems of these two large, paraphyletic groups of animals.

Animals↗
PubMed2002

Was our ancestor a hyperthermophilic procaryote?

In this paper we critically review the 'classical' model for the emergence of the three domains (Archaea, Bacteria, Eucarya), which presents hyperthermophilic procaryotes as the ancestors of all life on this planet. We come to the conclusion that our last common ancestor is likely to have been rather a non-hyperthermophilic protoeucaryote endowed with sn-1,2 glycerol ester lipids (as in modern Bacteria and Eucarya), from which Archaea emerged by streamlining under pressure for adapting to heat, a process which involved an important molecular innovation: the advent of sn-2,3 glycerol ether lipids. The nature of the primeval bacterial lines of descent is less clear; it would appear, nevertheless, that the first extreme- and hyperthermophilic Bacteria emerged by converging mechanisms; lateral gene transfer from Archaea may have played a role in this adaptation.

Animals↗
PubMed2005

Effects of perceived risk and strength of affiliation on decisions to help others: toward a convergence of evolutionary and social psychology.

In this study, the influence of perceived affiliation with a target and perceived risk on decisions to act altruistically were investigated. These are variables which have been suggested by the social and evolutionary psychology literatures, respectively. 12 participants responded to automobile accident scenarios that combined risk and affiliation with a target in descriptions of opportunities to render aid. Participants reported a lower likelihood to help when perceived risk was high, but only if their perceived affiliation with the targets was low or moderate; tendency to help highly affiliated targets was uniformly high throughout all risk conditions. Participants' ratings of certainty in their decisions to render aid were directly related to both perceived risk and perceived affiliation with a target. Decisions were arrived at more slowly when perceived risk and perceived affiliation were both moderate. Therefore, both risk and affiliation were considered by participants when deciding whether to act altruistically. This illustrates a convergence of predictions from social and evolutionary psychology.

Accidents, Traffic↗
PubMed1988

Evolution of tropomyosin functional domains: differential splicing and genomic constraints.

We have cloned and determined the nucleotide sequence of a complementary DNA (cDNA) encoded by a newly isolated human tropomyosin gene and expressed in liver. Using the least-square method of Fitch and Margoliash, we investigated the nucleotide divergences of this sequence and those published in the literature, which allowed us to clarify the classification and evolution of the tropomyosin genes expressed in vertebrates. Tropomyosin undergoes alternative splicing on three of its nine exons. Analysis of the exons not involved in differential splicing showed that the four human tropomyosin genes resulted from a duplication that probably occurred early, at the time of the amphibian radiation. The study of the sequences obtained from rat and chicken allowed a classification of these genes as one of the types identified for humans. The divergence of exons 6 and 9 indicates that functional pressure was exerted on these sequences, probably by an interaction with proteins in skeletal muscle and perhaps also in smooth muscle; such a constraint was not detected in the sequences obtained from nonmuscle cells. These results have led us to postulate the existence of a protein in smooth muscle that may be the counterpart of skeletal muscle troponin. We show that different kinds of functional pressure were exerted on a single gene, resulting in different evolutionary rates and different convergences in some regions of the same molecule. Codon usage analysis indicates that there is no strict relationship between tissue types (and hence the tRNA precursor pool) and codon usage. G + C content is characteristic of a gene and does not change significantly during evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2006

Directed evolution of a bacterial efflux pump: adaptation of the E. coli TolC exit duct to the Pseudomonas MexAB translocase.

Bacterial multidrug efflux pumps operate by periplasmic recruitment and opening of TolC family outer membrane exit ducts by cognate inner membrane translocases. Directed evolution of active hybrid pumps was achieved by challenging a library of mutated, shuffled TolC variants to adapt to the non-cognate Pseudomonas MexAB translocase, and confer resistance to the efflux substrate novobiocin. Amino acid substitutions in MexAB-adapted TolC variants that endowed high resistance were recreated independently, and revealed that MexAB-adaptation was conferred only by substitutions located in the lower alpha-helical barrel of TolC, specifically the periplasmic equatorial domain and entrance coiled coils. These changes converge to the native MexAB partner OprM, and indicate an interface key to the function and diversity of efflux pumps.

Anti-Bacterial Agents↗
PubMed2006

Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion.

In Saccharomyces, an ancient whole-genome duplication (WGD) and widespread duplicate gene deletion resulted in extensive reorganization of adjacent gene relationships. We have studied the evolution of adjacent gene pairs' identity, orientation, and spacing following whole-genome duplication and deletion (WGD-D) using comparative genomic analyses and simulations. Surveying adjacent gene organization across the Saccharomyces species complex, we find a genome-wide bias toward divergently and convergently transcribed gene pairs in all species but a reduction in this bias in the species that underwent WGD-D. Among neutral models of WGD-D, only single-gene deletion can produce the appropriate reduction in orientation bias and recapitulate the pattern of short, highly dispersed deletions we observe in Saccharomyces cerevisiae. To characterize the dynamics of WGD-D, we trace the conservation and creation of adjacent gene pairs along the S. cerevisiae lineage. We find that newly created adjacencies have a tandem orientation bias, while adjacencies conserved from prior to WGD-D have the same divergent-convergent bias as found in the species that diverged before WGD. We also find that adjacent gene pairs produced by WGD-D gained greater intergenic spacing but that this is reduced in the older adjacencies. Given this, and the preponderance of short deleted blocks, we argue that the deletion phase of WGD-D occurred primarily by small inactivating mutations followed by numerous small deletions. Newly created adjacent gene pairs also have an initial increase in mean log2 expression ratios and maximal expression levels, suggesting that increased intergenic spacing caused a genome-wide reduction in transcriptional interference.

Evolution, Molecular↗
PubMed1996

Long-term evolution of multilocus traits.

We analyze monomorphic equilibria of long-term evolution for one or two continuous traits, controlled by an arbitrary number of autosomal loci and subject to constant viability selection. It turns out that fitness maximization always obtains at long term equilibria, but in the case of two traits, linkage determines the precise nature of the fitness measure that is maximized. We then consider local convergence to long term equilibria, for two multilocus traits subject to either constant or frequency dependent selection. From a model of long-term dynamics near an equilibrium we derive a criterion of local long-term stability for 2-dimensional equilibria. It turns out that mutation can be a decisive factor for stability.

Animals↗
PubMed2006

The evolution of echolocation in bats.

Recent molecular phylogenies have changed our perspective on the evolution of echolocation in bats. These phylogenies suggest that certain bats with sophisticated echolocation (e.g. horseshoe bats) share a common ancestry with non-echolocating bats (e.g. Old World fruit bats). One interpretation of these trees presumes that laryngeal echolocation (calls produced in the larynx) probably evolved in the ancestor of all extant bats. Echolocation might have subsequently been lost in Old World fruit bats, only to evolve secondarily (by tongue clicking) in this family. Remarkable acoustic features such as Doppler shift compensation, whispering echolocation and nasal emission of sound each show multiple convergent origins in bats. The extensive adaptive radiation in echolocation call design is shaped largely by ecology, showing how perceptual challenges imposed by the environment can often override phylogenetic constraints.

Animals↗
PubMed2001

Extreme morphological and ecological homoplasy in tropical salamanders.

Fossorial salamanders typically have elongate and attenuated heads and bodies, diminutive limbs, hands and feet, and extremely elongate tails. Batrachoseps from California, Lineatriton from eastern México, and Oedipina from southern México to Ecuador, all members of the family Plethodontidae, tribe Bolitoglossini, resemble one another in external morphology, which has evolved independently. Whereas Oedipina and Batrachoseps are elongate because there are more trunk vertebrae, a widespread homoplasy (parallelism) in salamanders, the genus Lineatriton is unique in having evolved convergently by an alternate "giraffe-neck" developmental program. Lineatriton has the same number of trunk vertebrae as related, nonelongated taxa, but individual trunk vertebrae are elongated. A robust phylogenetic hypothesis, based on sequences of three mtDNA genes, finds Lineatriton to be deeply nested within a clade characterized by generalized ecology and morphology. Lineatriton lineolus, the only currently recognized taxon in the genus, shows unanticipated genetic diversity. Surprisingly, geographically separated populations of L. lineolus are not monophyletic, but are sister taxa of different species of the morphologically generalized genus Pseudoeurycea. Lineatriton, long thought to be a unique monospecific lineage, is polyphyletic. Accordingly, the specialized morphology of Lineatriton displays homoplasy at two hierarchical levels: (i) with respect to other elongate lineages in the family (convergence), and (ii) within what is currently recognized as a single taxon (parallelism). These evolutionary events are of adaptive significance because to invade the lowland tropics salamanders must be either arboreal or fossorial; the repeated evolution of elongation and attenuation has led to multiple lowland invasions.

Animals↗
PubMed2006

Intercontinental community convergence of ecology and morphology in desert lizards.

Evolutionary ecologists have long debated the extent to which communities in similar environments but different geographic regions exhibit convergence. On the one hand, if species' adaptations and community structure are determined by environmental features, convergence would be expected. However, if historical contingencies have long-lasting effects convergence would be unlikely. Most studies to date have emphasized the differences between communities in similar environments and little quantitative evidence for convergence exists. The application of comparative phylogenetic methods to ecological studies provides an opportunity to further investigate hypotheses of convergence. We compared the evolutionary patterns of structural ecology and morphology of 42 species of iguanian lizards from deserts of Australia and North America. Using a comparative approach, we found that evolutionary convergence of ecology and morphology occurs both in overall, community-wide patterns and in terms of pairs of highly similar intercontinental pairs of species. This result indicates that in these desert lizards, deterministic adaptive evolution shapes community patterns and overrides the historical contingencies unique to particular lineages.

Adaptation, Biological↗
PubMed2006

Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus.

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations.

Animals↗
PubMed2025

De Novo Whole Genome Assemblies of Unusual Case-Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene (h-fibroin).

Trichoptera (caddisflies) is one of the most species-rich orders of aquatic insects. Species of caddisflies cover a broad ecological diversity as exemplified by various uses of underwater silk secretions. Diversity of silk use generally aligns with the evolution of major caddisfly lineages, specifically at the subordinal level: Annulipalpia (retreat makers) and Integripalpia (cocoon and tube-case makers). However, silk use within suborders differs for a few exceptional species in these clades. In this study, we provide the first whole genome assemblies and annotations for two unusual Integripalpia species: Limnocentropus insolitus, whose hard tube-case is anchored to boulders by a rigid, elongated silken stalk, and Phryganopsyche brunnea which builds a "floppy" cylindrical case that lacks the typical robustness of tube-cases. Its texture rather resembles that of the flexible retreats built by Annulipalpia. Using the two high-quality genome assemblies, we identified and annotated the major silk gene, h-fibroin, and compared its amino acid composition across various groups, including retreat, cocoon, and tube-case makers. Our phylogenetic analysis confirmed the phylogenetic position of the two species in the tube-case-making clade. The major silk gene of L. insolitus shows a similar amino acid composition to other tube-case-making species. In contrast, the amino acid composition of P. brunnea resembles that of retreat-making species, in particular with regard to the high content of proline. This is consistent with the hypothesis that proline could be linked to enhanced extensibility of silk fibers. Taken together, our results underscore the role of silk genes in shaping the evolutionary ecology of retreat- and tube-case-making in caddisflies.

Animals↗