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At least 1,369 records · Page 76Linked to original sources
PubMed2003

Patterning mechanisms in the evolution of derived developmental life histories: the role of Wnt signaling in axis formation of the direct-developing sea urchin Heliocidaris erythrogramma.

A number of echinoderm species have replaced indirect development with highly modified direct-developmental modes, and provide models for the study of the evolution of early embryonic development. These divergent early ontogenies may differ significantly in life history, oogenesis, cleavage pattern, cell lineage, and timing of cell fate specification compared with those of indirect-developing species. No direct-developing echinoderm species has been studied at the level of molecular specification of embryonic axes. Here we report the first functional analysis of Wnt pathway components in Heliocidaris erythrogramma, a direct-developing sea urchin. We show by misexpression and dominant negative knockout construct expression that Wnt8 and TCF are functionally conserved in the generation of the primary (animal/vegetal) axis in two independently evolved direct-developing sea urchins. Thus, Wnt pathway signaling is an overall deeply conserved mechanism for axis formation that transcends radical changes to early developmental ontogenies. However, the timing of expression and linkages between Wnt8, TCF, and components of the PMC-specification pathway have changed. These changes correlate with the transition from an indirect- to a direct-developing larval life history.

Animals↗
PubMed1983

Evolution of immunoglobulin V genes: evidence indicating that recently duplicated human V kappa sequences have diverged by gene conversion.

We have analyzed several closely related members of the gene family encoding the variable regions of human immunoglobulin kappa light chains (V kappa genes). Two of these genes differ at a single nucleotide out of 940 bases sequenced, and are believed to be alleles of a locus called HK 101. This substitution results in an amino acid replacement in the first complementarity-determining region of the kappa chain. We also compared the structures of two nonallelic human V kappa loci (HK 101 and HK 137) and found a high degree of sequence homology over a region at least 13.5 kb long. This long block of homology indicates that these two loci arose from a recent gene duplication. The DNA sequences of these two nonallelic V kappa genes exhibit a very unusual distribution of nucleotide substitutions. Seven of the ten substitutions found among 940 bases are clustered in a 39 base stretch encoding the first complementarity-determining region and the second framework region of the protein. We suggest that this cluster of substitutions was generated by a gene conversion in which a small segment of one gene was replaced with the homologous segment from another V kappa gene.

Alleles↗
PubMed2005

[Divergence of the polytene chromosome banding sequences as a reflection of evolutionary rearrangements of the genome linear structure].

Banding sequences of five chromosomal arms (A, C, D, E, and F), accounting for about 70% of the total genome size in 63 Chironomus species, were used as phylogenetic markers to analyze divergence patterns of the linear genome structure during the evolution. The number of chromosomal breakpoints between the pairs of banding sequences compared served as a measure of divergence. It was demonstrated that the greater the divergence between the species compared, the higher the number of chromosomal breakpoints and the smaller the size of the conserved chromosomal regions. A banding sequences comparison in sibling species demonstrated a lower number of chromosomal breakpoints; the breakpoint number was maximum in a comparison of the banding sequences in the subgenera Chironomus and Camptochironomus. The use of the number of chromosomal breakpoints as a divergence measure provided establishment of phylogenetic relationships between 63 Chironomus species and discrimination of sibling species groups and cytocomplexes on a phylogenetic tree.

Animals↗
PubMed1998

The molecular clock runs at different rates among closely related members of a gene family.

The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor. From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise to the vitamin D-binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin (ALB) gene and a common precursor to alpha-fetoprotein (AFP) and alpha-albumin (ALF). This precursor itself duplicated about 250 Myr ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from albumin. Although individual family members display an approximate clock-like evolution, there are significant deviations-the rates of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions concerning whether it can be used to infer evolutionary time from contemporary sequence differences.

Albumins↗
PubMed2004

Clustered organization of reproductive genes in the C. elegans genome.

Defining the forces that sculpt genome organization is fundamental for understanding the origin, persistence, and diversification of species. The genomic sequences of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae provide an excellent opportunity to explore the dynamics of chromosome evolution. Extensive chromosomal rearrangement has accompanied divergence from their common ancestor, an event occurring roughly 100 million years ago (Mya); yet, morphologically, these species are nearly indistinguishable and both reproduce primarily by self-fertilization. Here, we show that genes expressed during spermatogenesis (sperm genes) are nonrandomly distributed across the C. elegans genome into three large clusters located on two autosomes. In addition to sperm genes, these chromosomal regions are enriched for genes involved in the hermaphrodite sperm/oocyte switch and in the reception of sperm signals that control fertilization. Most loci are present in single copy, suggesting that cluster formation is largely due to gene aggregation and not to tandem duplication. Comparative mapping indicates that the C. briggsae genome differs dramatically from the C. elegans genome in clustering. Because clustered genes have a direct role in reproduction and thus fitness, their aggregated pattern might have been shaped by natural selection, perhaps as hermaphroditism evolved.

Animals↗
PubMed2005

Molecular and evolutionary characterization of the GnRH-II gene in the chicken: distinctive genomic organization, expression pattern, and precursor sequence.

Of all the structural variants of GnRH (gonadotropin-releasing hormone), GnRH-II has been found to be universally present in and uniquely conserved among jawed vertebrates without any sequence substitutions. Our previous study found that the GnRH-II precursor sequences have become divergent in the lineage of eutherian mammals, based on a comparison between reptilian and mammalian GnRH-II. To elucidate the molecular evolution of GnRH-II throughout amniotes, we have performed the first identification of the avian GnRH-II cDNA/gene from the chicken, the species used for the initial discovery of GnRH-II peptide. Gene arrangement around the GnRH-II in the chicken was similar to that in mammals; however, a gene MRPS26 was partly overlapped with the downstream part of the GnRH-II in the chicken. It was identified that the GnRH-II/MRPS26 locus generated at least five distinct types of transcripts with different expression patterns and three of them may produce functional GnRH-II decapeptide. Sequence comparison revealed that the prepro-GnRH-II polypeptide of the chicken was substantially different from those of other species regarding the length and similarity. The present results strongly indicated that considerable variations were generated in the precursor sequence of the evolutionarily conserved GnRH-II during amniote evolution. It was also suggested that the sequence divergence seen in the chicken may have occurred independently of that in the mammalian lineage.

5' Untranslated Regions↗
PubMed2005

Lack of mitochondrial DNA divergence between chromosome races of the common shrew, Sorex araneus, in Sweden. Implications for interpreting chromosomal evolution and colonization history.

The common shrew, Sorex araneus, has one of the most variable karyotypes among mammals, displaying numerous chromosome races throughout its distribution. The six chromosome races present in Sweden can be categorized in two different karyotypic groups, the west and north European karyotypic groups (western and northern). Three races belonging to the western group are considered to have arisen through whole arm reciprocal translocations (WARTs). Race formation through this process requires a bottleneck event. In the present study we sequenced a part of the mitochondrial DNA (mtDNA) genome to investigate molecular differences between the chromosome races in Sweden. We found no mtDNA differentiation between the mainland chromosome races or the karyotypic groups. Genetic variation is as large between populations within a race as between populations among the races or karyotypic groups, suggesting that the karyotypic groups might have originated in a common glacial refugium. The noticeable exception is the Oland race, which shows higher mtDNA diversity compared to the other Swedish races, indicating a divergent origin difficult to explain. Mitochondrial DNA variation in Sweden suggests that most haplotypes arose in situ and that the populations has undergone a rapid size expansion. Altogether, the mtDNA data are in agreement with the WART hypothesis, which still holds as the most plausible variant of karyotype evolution for three of the chromosome races of the common shrew in Sweden.

Animals↗
PubMed1998

The fate of duplicated genes: loss or new function?

Gene duplication events are important sources of novel gene functions. However, more often than not, a duplicate gene may lose its function and become a pseudogene. What is the relative frequency of these two scenarios: functional divergence versus gene loss? Given that most non-neutral mutations are deleterious, gene loss should be far more frequent than divergence. However, a recent empirical study suggests that about 50% of all gene duplications will lead to functional divergence. The study infers the frequency of functional divergence from the size distribution of gene families produced by two successive genome duplications early in vertebrate evolution. Reasons for this unexpectedly high frequency of functional divergence are discussed.

Animals↗
PubMed2002

Comparative endocrinology of the insulin-like growth factor-binding protein.

Emerging early in chordate evolution, the IGF-regulatory axis diverged from an insulin-like predecessor into a vertebrate regulatory system specializing in cell growth activation and allied anabolic functions. Essential to the divergence of the IGF and insulin systems was an early presence of soluble IGF-binding proteins (IGFBPs), which bind IGF peptides at much higher affinity than that of the insulin receptor but at comparable affinities to that of the IGF receptor. IGFBPs have no homology with IGF receptors. Instead, IGFBPs are a derived group of proteins within a superfamily of cysteine-rich growth factors, whose members are found throughout the animal taxa. While blocking IGF actions through the insulin receptor is a fundamental role, IGFBPs evolved within the vertebrate line into centralized, 'integrators' of the endocrine growth-regulatory apparatus. IGFBPs have substantial influences on the distribution and bioavailability of IGF peptides in the cellular and physiological environments, but they have a variety of other properties. The six principal mammalian IGFBPs exhibit an array of specialized properties that appear to be derived from a complex evolutionary history (including cell membrane association, interaction with proteins that post-translationally modify them, direct IGF-independent effects on cells, and others) and they are regulated by a diversity of 'outside' factors (e.g. other hormones, metabolic status, stress). Thus, IGFBPs are multifunctional integrators having diverse physiological 'agendas'. Much less is known about IGFBPs and their properties in the other vertebrate taxa. Increasingly, however, it is being recognized that they play equally important endocrine roles, in both conserved and non-conserved ways, when compared with those currently defined in mammals. This review highlights selected 'comparative aspects' in current IGFBP research, in an attempt to view this essential group of endocrine regulators from a wider, biological perspective.

Animals↗
PubMed1999

Mutation, recombination, and incipient speciation of bacteria in the laboratory.

Mutations in the DNA mismatch repair system increase mutation and recombination. They may thereby promote the genetic divergence that underlies speciation, after which the reacquisition of a functional repair system may sustain that divergence by creating a barrier to recombination. We tested several lines of Escherichia coli, derived from a common ancestor and evolved for 20,000 generations, for their recombination ability. Some lines, but not others, had become mismatch repair-defective mutators during experimental evolution, providing different opportunities for DNA sequence divergence. We knocked out the repair system in lines that had retained this function, and we restored function to those lines that had become defective. We then estimated recombination rates in various crosses between these repair-deficient and -proficient strains. The effect of the mismatch repair system on recombination was greatest in those lines that had evolved nonfunctional repair, indicating they had undergone more sequence divergence and, consequently, were more sensitive to the recombination-inhibiting effect of a functional repair system. These results demonstrate the establishment of an incipient genetic barrier between formerly identical lines, and they support a model in which the mismatch repair system can influence speciation dynamics through its simultaneous effects on mutation and recombination.

Biological Evolution↗
PubMed2005

Molecular evolution of the ankyrin gene family.

Ankyrins are membrane adaptor molecules that play important roles in coupling integral membrane proteins to the spectrin-based cytoskeleton network. Human mutations of ankyrin genes lead to severe genetic diseases such as fatal cardiac arrhythmias and hereditary spherocytosis. To elucidate the evolutionary history of ankyrins, we have identified novel ankyrin sequences in insect, fish, frog, chicken, dog, and chimpanzee genomes and explored the phylogenetic relationships of the ankyrin gene family. Our data demonstrate that duplication of ankyrin genes occurred at two different stages. The first duplication resulted from an independent evolution event specific in Arthropoda after its divergence from Chordata. Following the separation from Urochordata, expansion of ankyrins in vertebrates involved ancestral genome duplications. We did not find evidence of coordinated arrangements of gene families of ankyrin-associated membrane proteins on paralogous chromosomes. In addition, evolution of the 24 ANK-repeats strikingly correlated with the exon boundary sites of ankyrin genes, which might have occurred before its duplication in vertebrates. Such correlation is speculated to bring functional diversity and complexity. Moreover, based on the phylogenetic analysis of the ANK-repeat domain, we put forward a novel model for the putative primordial ankyrin that contains the fourth six-ANK-repeat subdomain and the spectrin-binding domain. These findings will provide guides for future studies concerning structure, function, evolutionary origins of ankyrins, and possibly other cytoskeletal proteins.

Animals↗
PubMed2003

Evolutionary experimentation through hybridization under laboratory condition in Drosophila: evidence for recombinational speciation.

BACKGROUND: Drosophila nasuta nasuta (2n = 8) and Drosophila nasuta albomicans (2n = 6) are a pair of sibling allopatric chromosomal cross-fertile races of the nasuta subgroup of immigrans species group of Drosophila. Interracial hybridization between these two races has given rise to new karyotypic strains called Cytorace 1 and Cytorace 2 (first phase). Further hybridization between Thailand strain of D. n. albomicans and D. n. nasuta of Coorg strain has resulted in the evolution of two more Cytoraces, namely Cytorace 3 and Cytorace 4 (second phase). The third phase Cytoraces (Cytorace 5 to Cytorace 16) have evolved through interracial hybridization among first, second phase Cytoraces along with parental races. Each of these Cytoraces is composed of recombined genomes of the parental races. Here, we have made an attempt to systematically assess the impact of hybridization on karyotypes, morphometric and life history traits in all 16 Cytoraces. RESULTS: The results reveal that in most cases, the newly evolved Cytoraces, with different chromosome constitutions, exhibit decreased body size, better fitness and live longer than their parents. Particularly, Cytorace 5, 6 and 8 have evolved with very much higher range values of quantitative traits than the parents and other Cytoraces, which suggests the role of transgressive segregation in the evolution of these Cytoraces. CONCLUSION: Thus, the rapid divergence recorded in the chromosomes, karyotypes, body size and fitness traits of Cytoraces exhibit the early event of recombinational raciation / speciation in the evolution of the Cytoraces under laboratory conditions.

Animals↗
PubMed1997

Cloning and characterisation of the gene encoding red deer (Cervus elaphus) growth hormone: implications for the molecular evolution of growth hormone in artiodactyls.

In mammals the structure of pituitary GH is generally strongly conserved, indicating a slow basal rate of molecular evolution. However, on two occasions, during the evolution of primates and of artiodactyls, the rate of evolution has increased dramatically (25- to 50-fold) so that the sequences of human and ruminant GHs differ markedly from those of other mammalian GHs. In order to define further the burst of GH evolution that occurred in artiodactyls we have cloned and characterised the GH gene of red deer (Cervus elaphus) using genomic DNA and a polymerase chain reaction technique. The deduced sequence for the mature GH from red deer is identical to that of bovine GH, indicating that the burst of rapid evolution of GH that occurred in Artiodactyla must have been completed before the divergence of Cervidae and Bovidae and suggesting that the rate of evolution during this burst must have been greater than previously estimated. In other aspects (signal sequence, 5' and 3' sequences, introns and synonymous substitutions in the coding sequence) the red deer GH gene differs considerably from the GH genes of other ruminants. Differences between the signal peptide sequences of red deer and bovid GHs probably explain why N-terminal heterogeneity is seen in bovine, ovine and caprine GHs but not GH from red deer, pig or most other mammals.

Amino Acid Sequence↗
PubMed2004

Karyotypic evolution pathways in medulloblastoma/primitive neuroectodermal tumor determined with a combination of spectral karyotyping, G-banding, and fluorescence in situ hybridization.

Medulloblastomas (MBs) or primitive neuroectodermal tumors (PNETs) represent 15%-30% of pediatric brain tumors and are the most common brain tumors in children; they are rare in adults. Classification of these tumors is based on tissue morphology and is often controversial and problematic. Karyotypic analysis of these tumors using conventional cytogenetic methods is often a difficult process that may be hindered by a limited number of metaphase cells and poor chromosome morphology, often leading to only partial characterization of the chromosomal abnormalities. We investigated three primary human tumors and four cell lines (CHO-707, DAOY, D-341, and PFSK) utilizing a combination of conventional G-banding, spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH) techniques. A high level of intratumoral heterogeneity was seen, with multiple numerical and structural chromosomal aberrations. The chromosomes most frequently involved in structural aberrations were chromosomes 1 (14 rearrangements), 7 (9 rearrangements), and 21 (9 rearrangements). The chromosomes most frequently involved in numerical aberrations were chromosomes 1, 12, and 13 (four cases) and chromosomes 14, 17, 19, 21, 22, and X (three cases). Numerous aberrant chromosomes were characterized only with the SKY analysis, and based on these findings multiple clones were identified, facilitating analysis of karyotypic evolution. The most frequent evolution mechanism was via polyploidization, followed by acquisition of additional numerical or structural aberrations (or both); however, the results showed that the karyotypic evolution process in these tumors is typically divergent and complex.

Adult↗
PubMed2006

Microgeographic evolution of snail shell shape and predator behavior.

Genetic divergence in geographically isolated populations is a prerequisite for allopatric speciation, one of the most common modes of speciation. In ecologically equivalent populations existing within a small, environmentally homogeneous area, an important role for environmentally neutral divergence is often found or inferred. We studied a species complex of conspicuously shaped Opisthostoma land snails on scattered limestone outcrops within a small area of lowland rainforest in Borneo. We used shell morphometrics, mitochondrial and nuclear DNA sequences, and marks of predation to study the factors involved in allopatric divergence. We found that a striking geographic divergence exists in shell morphology, which is partly associated with neutral genetic divergence. We also found geographic differentiation in the behavior of the snails' invertebrate predator and evidence of an evolutionary interaction between aspects of shell shape and predator behavior. Our study shows that adaptation to biotic aspects of the environment may play a more important role in allopatric speciation than previously suspected, even on a geographically very small scale.

Adaptation, Physiological↗
PubMed1999

The variable genes and gene families of the mouse immunoglobulin kappa locus.

In this report 118 mouse Vkappa genes are described which, together with the 22 Vkappa genes reported previously (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458-1466) amount to 140 genes that had been cloned and sequenced in our laboratory. For 73 of them cDNAs are known, i. e. they have to be considered functional genes, although 10 genes of this group have 1-bp deviations from the canonical promoter, splice site or heptanucleotide recombination signal sequences. Twenty Vkappa genes have been defined as only potentially functional since they do not contain any defect, but no cDNAs have been found (yet) for them. Of the 140 Vkappa genes 47 are pseudogenes. There are indications that two to five Vkappa genes or pseudogenes exist in the kappa locus which we have not yet been able to clone. The 140 Vkappa genes and pseudogenes were assigned to 18 gene families, 4 of them being one-member families. This differs from previous enumerations of the families only by the combination of the Vkappa9 and Vkappa10 families and by the addition of the Vkappa dv gene as a new separate family. Sequence identity usually was 80% or above within the gene families and 55-80% between genes of different families. Many of the mouse Vkappa gene families show significant homologies to the human ones, indicating that in evolution Vkappa gene diversification predated the divergence of the primate and rodent clades.

Animals↗
PubMed2006

Genetic basis of olfactory communication in primates.

The genes involved in olfactory communication in mammals via the vomeronasal system are summarized, and studies investigating these genes in primates are reviewed. Only five potentially functional vomeronasal receptor genes (V1RL s) have been found in humans, and only one of these (V1RL1) has been studied in other primates. V1RL1 has become a pseudogene repeatedly during primate evolution, but patterns of natural selection on primate V1RL genes demonstrate that this gene family diverged under natural selection throughout at least part of primate evolution. Evolution of the TRP2 gene, which encodes for an ion channel that is important in vomeronasal organ (VNO) signalling, strongly suggests that this signalling function was lost in ancestral Catarrhines. Overall, much work remains to be done to elucidate the repertoire of genes that are involved in pheromonal communication, particularly in Strepsirhines. Such studies promise unique insights into the evolution of this modality.

Animal Communication↗
PubMed2006

Approaches to defining the ancestral eukaryotic protein complexome.

In this paper, we integrate and summarize the currently available information on the ancestral eukaryotic protein complexome, which is defined as the set of protein complexes that extant eukaryotes inherited from their last common ancestor. From the literature, we compiled lists of complexes with three or more distinct protein components from well-studied eukaryotic model organisms. Combinatorial complexes of membrane-associated signalling proteins and specific transcription factors were disregarded. A stringent but sensitive novel orthology detection algorithm, complemented with manual sequence similarity searches and with published data on whole genome or segmental and tandem gene duplications, enabled us to map the vast majority of these complexes to a virtual primitive eukaryote termed Eukaryotic Virtual Ancestor (EVA). EVA is intended to resemble the last common eukaryotic ancestor and to emulate the biological common denominator of the major extent eukaryotic lineages at the molecular level. The dataset was then used for the functional and domain annotation of the ancestral eukaryotic complexome. Furthermore, we illustrate its usefulness for inferring complexes of poorly studied eukaryotes and for the recognition of highly divergent orthologs. We also discuss the evolution of the circa 1,400 complex-associated ancestral proteins. As about 90% of these proteins have been conserved in all thirteen studied free-living eukaryotes, the evolutionary reduction and loss of complexes seems minimal. Moreover, the available data suggest that, in general, the acquisition of stable complexes of novel design occurs too slowly to be a major contributor to evolutionary innovation. Finally, given the stability of the ancestral eukarotic complexome we propose its use in the formulation of the mathematical systems that aim to simulate biological processes. Our data suggest that these simplified formulations can apply to most free-living model eukaryotes.

Animals↗