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At least 811 records · Page 45Linked to original sources
PubMed2004

Evolution of a climbing habit promotes diversification in flowering plants.

Key innovations are traits that are associated with the particular evolutionary 'success' of some taxonomic groups. Climbing plants depend on the availability of physical support to reach the canopy and thereby prevent shading by neighbouring plants. The present article shows that the evolution of a climbing habit in flowering plants constitutes a key innovation. A literature survey identified 48 pairs of sister groups from 45 families of flowering plants for which information on phylogenetic relationships, growth habit and species richness was available. In 38 cases, the climbing taxa were more diverse than their non-climbing sister groups. This pattern was highly significant. The same result was found when separate analyses were carried out for herbaceous and woody climbing plants, which differ in their constraints for successfully reaching a support.

Biological Evolution↗
PubMed2005

Morphological evolution, ecological diversification and climate change in rodents.

Among rodents, the lineage from Progonomys hispanicus to Stephanomys documents a case of increasing size and dental specialization during an approximately 9 Myr time-interval. On the contrary, some contemporaneous generalist lineages like Apodemus show a limited morphological evolution. Dental shape can be related to diet and can be used to assess the ecological changes along the lineages. Consequently, size and shape of the first upper molar were measured in order to quantify the patterns of morphological evolution along both lineages and compare them to environmental trends. Climatic changes do not have a direct influence on evolution, but they open new ecological opportunities by changing vegetation and allow the evolution of a specialist like Stephanomys. On the other hand, environmental changes are not dramatic enough to destroy the habitat of a long-term generalist like Apodemus. Hence, our results exemplify a case of an influence of climate on the evolution of specialist species, although a generalist species may persist without change.

Analysis of Variance↗
PubMed2006

A newly recognized fossil coelacanth highlights the early morphological diversification of the clade.

Previously considered an actinopterygian or an osteichthyan incertae sedis, the Devonian (Givetian-Frasnian) Holopterygius nudus is reinterpreted as a coelacanth. This genus is among the oldest coelacanths known from articulated remains, but its eel-like morphology marks a considerable departure from the conventional coelacanth body plan. A cladistic analysis places Holopterygius as the sister taxon of the Carboniferous (Serpukhovian) genus Allenypterus. Despite the specialized morphology of these genera, they occupy a surprisingly basal position in coelacanth phylogeny; only Diplocercides and Miguashaia are further removed from the crown. A morphometric analysis reveals that coelacanths were anatomically disparate early in their history. Conflicts between this result and those of previous studies challenge the adequacy of systematic character sets for describing historical patterns of morphological variety. Coelacanths have long had an iconic place in the study of vertebrate evolution for their apparent anatomical conservatism over geological time, but Holopterygius provides clear evidence for rapid morphological evolution early in the history of this clade.

Animals↗
PubMed2007

Opsin gene duplication and diversification in the guppy, a model for sexual selection.

Identification of genes that control variation in adaptive characters is a prerequisite for understanding the processes that drive sexual and natural selection. Male coloration and female colour perception play important roles in mate choice in the guppy (Poecilia reticulata), a model organism for studies of natural and sexual selection. We examined a potential source for the known variation in colour perception, by analysing genomic and complementary DNA sequences of genes that code for visual pigment proteins. We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. Alleles with non-synonymous changes that suggest dissimilar spectral tuning properties occur in the same population and even in the same individual, and the high frequency of non-synonymous substitutions argues for diversifying selection acting on these proteins. Therefore, variability in tuning amino acids is partitioned within individuals and populations of the guppy, in contrast to variability for LWS at higher taxonomic levels in cichlids, a second model system for differentiation owing to sexual selection. Since opsin variability parallels the extreme male colour polymorphism within guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species.

Alleles↗
PubMed2025

Ancestral complexity and constrained diversification of the ant olfactory system.

Communication is a cornerstone of social living, allowing the exchange of information to align goals and synchronize behaviour. Ants, a group of highly successful social insects, have heightened olfactory abilities that are integral to their evolutionary success. Essential for colony cohesion and cooperation, a female-specific olfactory subsystem processes information about nestmate recognition cues (cuticular hydrocarbons), including basiconic sensilla on the antenna and a cluster of specific glomeruli in the antennal lobe. While it has often been linked to ants' social lifestyle, the evolutionary origins and phylogenetic distribution of this system remain unknown. We conducted a comparative exploration of the ant olfactory system across eight major subfamilies, integrating neuroanatomical, chemical and behavioural analyses. Our findings reveal that sophistication of the ant olfactory system has deep evolutionary roots. Moreover, antennal lobe investment is not associated with social traits such as colony size, polygyny or foraging strategies, but correlates with cuticular hydrocarbon profile complexity. Despite neuroanatomical differences, different ant species consistently excel in nestmate discrimination, indicating adaptation to chemical diversity while maintaining reliable social recognition. This suggests that cuticular hydrocarbon profile and neuronal investment in olfactory neuropil have co-evolved to sustain discrimination performance.

Animals↗
PubMed1989

Diversification and extinction patterns among Neogene perimediterranean mammals.

The best mammalian fossil record during the Neogene of Western Europe is that of the rodents, the most successful and diversified mammal order. The study of origination and extinction during the Neogene (24-3 Ma BP) in one of the best-documented areas, Spain and southern France, gives an insight into the dynamics of these communities and indicates the possible nature of the driving forces. Three main periods of time show a high rate of origination: the late Burdigalian (17.5 Ma BP), the early Vallesian (11.5-11 Ma BP) and the early Pliocene (4.2-3.8 Ma BP). Two of these high origination-rate periods are immediately followed by important extinction events during which all cohorts are deeply affected (11.5-11 Ma BP and 4.2-3.8 Ma BP). The most important extinction event seems to occur during the early Vallesian (11.5-11 Ma BP), which probably includes the middle/late Miocene boundary. At the Miocene/Pliocene boundary, and during the early Pliocene, the faunal turnover seems to become faster, inducing a strong decrease of the mean species duration. Whereas the main immigration event, which occurs at 17.5 Ma BP, can be related to other faunal migrations in terms of the closure of the Tethys, as it occurs also in eastern Africa and in southwest Asia, the middle/late Miocene boundary event may have been related to a period of ice growth in the Southern Hemisphere. The extinction event that affects the planktonic foraminifera at 12 Ma BP cannot be chronologically correlated to this southwestern European land-mammal extinction event, because the calibration of the marine fossil record during that time-span has to be precise. Some limited terrestrial faunal exchanges that occur during the Messinian between southwestern Europe and northwestern Africa do not deeply affect the general faunal dynamics. Both allochthonous cohorts of immigrants become rapidly extinct. Several endemic rodent faunas, indicating insular conditions, have been reported from the southern edge of the western European continent from the middle Miocene up to the Pliocene. All show low taxonomic diversity, strong endemism and short survival. Some of them, like those of the Gargano Islands during the late Miocene, underwent peculiar morphological changes and also speciation. The large number of rodent genera coevolving in the Gargano Islands is indicative of the large surface areas of these islands. The general geographic pattern of southwestern Europe during the Neogene may therefore correspond to a large continental province including Spain and southern France with some kind of fast-modifying archipelago on its southern rim.

Animals↗
PubMed2006

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

Eukaryotic Cells↗
PubMed1999

Variation of hepatitis C virus following serial transmission: multiple mechanisms of diversification of the hypervariable region and evidence for convergent genome evolution.

We have studied the evolution of hepatitis C virus (HCV) from a common source following serial transmission from contaminated batches of anti-D immunoglobulin. Six secondary recipients were each infected with virus from identifiable primary recipients of HCV-contaminated anti-D immunoglobulin. Phylogenetic analysis of virus E1/E2 gene sequences [including the hypervariable region (HVR)] and part of NS5B confirmed their common origin, but failed to reproduce the known epidemiological relationships between pairs of viruses, probably because of the frequent occurrence of convergent substitutions at both synonymous and nonsynonymous sites. There was no evidence that the rate at which the HCV genome evolves is affected by transmission events. Three different mechanisms appear to have been involved in generating variation of the hypervariable region; nucleotide substitution, insertion/deletion of nucleotide triplets at the E1/E2 boundary and insertion of a duplicated segment replacing almost the entire HVR. These observations have important implications for the phylogenetic analysis of HCV sequences from epidemiologically linked isolates.

Adolescent↗
PubMed2001

Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution.

Evolutionary pathways open to even relatively simple organisms, such as bacteria, may lead to complex and unpredictable phenotypic changes, both adaptive and non-adaptive. The evolutionary pathways taken by 18 populations of Ralstonia strain TFD41 while they evolved in defined environments for 1000 generations were examined. Twelve populations evolved in liquid media, while six others evolved on agar surfaces. Phenotypic analyses of these derived populations identified some changes that were consistent across all populations and others that differed among them. The evolved populations all exhibited morphological changes in their cell envelopes, including reductions of the capsule in each population and reduced prostheca-like surface structures in most populations. Mean cell length increased in most populations (in one case by more than fourfold), although a few populations evolved shorter cells. Carbon utilization profiles were variable among the evolved populations, but two distinct patterns were correlated with genetic markers introduced at the outset of the experiment. Fatty acid methyl ester composition was less variable across populations, but distinct patterns were correlated with the two physical environments. All 18 populations evolved greatly increased sensitivity to bile salts, and all but one had increased adhesion to sand; both patterns consistent with changes in the outer envelope. This phenotypic diversity contrasts with the fairly uniform increases in competitive fitness observed in all populations. This diversity may represent a set of equally probable adaptive solutions to the selective environment; it may also arise from the chance fixation of non-adaptive mutations that hitchhiked with a more limited set of beneficial mutations.

Bacterial Adhesion↗
PubMed2005

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.

By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alternative promoters (PAPs). On average, there were 3.1 PAPs per gene, with the composition of one CpG-island-containing promoter per 2.6 CpG-less promoters. In 17% of the PAP-containing loci, tissue-specific use of the PAPs was observed. The richest tissue sources of the tissue-specific PAPs were testis and brain. It was also intriguing that the PAP-containing promoters were enriched in the genes encoding signal transduction-related proteins and were rarer in the genes encoding extracellular proteins, possibly reflecting the varied functional requirement for and the restricted expression of those categories of genes, respectively. The patterns of the first exons were highly diverse as well. On average, there were 7.7 different splicing types of first exons per locus partly produced by the PAPs, suggesting that a wide variety of transcripts can be achieved by this mechanism. Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans.

Base Sequence↗
PubMed1999

Identification of three novel Ca(2+) channel gamma subunit genes reveals molecular diversification by tandem and chromosome duplication.

Gene duplication is believed to be an important evolutionary mechanism for generating functional diversity within genomes. The accumulated products of ancient duplication events can be readily observed among the genes encoding voltage-dependent Ca(2+) ion channels. Ten paralogous genes have been identified that encode isoforms of the alpha(1) subunit, four that encode beta subunits, and three that encode alpha(2)delta subunits. Until recently, only a single gene encoding a muscle-specific isoform of the Ca(2+) channel gamma subunit (CACNG1) was known. Expression of a distantly related gene in the brain was subsequently demonstrated upon isolation of the Cacng2 gene, which is mutated in the mouse neurological mutant stargazer (stg). In this study, we sought to identify additional genes that encoded gamma subunits. Because gene duplication often generates paralogs that remain in close syntenic proximity (tandem duplication) or are copied onto related daughter chromosomes (chromosome or whole-genome duplication), we hypothesized that the known positions of CACNG1 and CACNG2 could be used to predict the likely locations of additional gamma subunit genes. Low-stringency genomic sequence analysis of targeted regions led to the identification of three novel Ca(2+) channel gamma subunit genes, CACNG3, CACNG4, and CACNG5, on chromosomes 16 and 17. These results demonstrate the value of genome evolution models for the identification of distantly related members of gene families.

Amino Acid Sequence↗
PubMed2006

Functional diversification of acyl-coenzyme A oxidases in jasmonic acid biosynthesis and action.

The biosynthesis of jasmonic acid (JA) in plant peroxisomes requires the action of acyl-coenzyme A oxidase (ACX). Among the five expressed members (ACX1-5) of the ACX gene family in Arabidopsis (Arabidopsis thaliana), only ACX1 is known to serve a role in JA production. Here, we used transgenic promoter-reporter lines to show that ACX1 is highly expressed in mature and germinating pollen, stem epidermal cells, and other tissues in which jasmonate-signaled processes occur. Wound-induced JA accumulation was reduced in a mutant that is defective in ACX1 and was abolished in a mutant that is impaired in both ACX1 and its closely related paralog, ACX5. The severe JA deficiency in acx1/5 double mutants was accompanied by decreased resistance to the leaf-eating insect Trichoplusia ni. The double mutant also showed reduced pollen viability and fecundity. Treatment of acx1/5 plants with JA restored both protection against T. ni larvae and normal seed set. Unexpectedly, acx1/5 plants accumulated JA in response to infection by the necrotrophic fungal pathogen Alternaria brassicicola. In contrast to mutants that are impaired in jasmonate perception or early steps of the JA biosynthetic pathway, acx1/5 plants maintained resistance to A. brassicicola infection. These results indicate that ACX1/5-mediated JA synthesis is essential for resistance to chewing insects and male reproductive function and further suggest that other ACX isozymes contribute to JA production in response to A. brassicicola challenge. Thus, different types of biotic stress may induce JA synthesis via distinct enzymatic routes.

Acyl-CoA Oxidase↗