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PubMed2006

Habitat type predicts genetic population differentiation in freshwater invertebrates.

A basic challenge in evolutionary biology is to establish links between ecology and evolution of species. One important link is the habitat template. It has been hypothesized, that the spatial and temporal settings of a habitat strongly influence the evolution of species dispersal propensity. Here, we evaluate the importance of the habitat type on genetic population differentiation of species using freshwater habitats as a model system. Freshwater habitats are either lentic (standing) or lotic (running). On average, lotic habitats are more stable and predictable over space and time than lentic habitats. Therefore, lentic habitats should favour the evolution of higher dispersal propensity which ensures population survival of lentic species. To test for such a relationship, we used extensive data on species' genetic population differentiation of lentic and lotic freshwater invertebrates retrieved from published allozyme studies. Overall, we analysed more than 150 species from all over the world. Controlling for several experimental, biological and geographical confounding effects, we always found that lentic invertebrates exhibit, on average, lower genetic population differentiation than lotic species. This pattern was consistent across insects, crustaceans and molluscs. Our results imply fundamental differences in genetic population differentiation among species adapted to either lentic or lotic habitats. We propose that such differences should occur in a number of other habitat types that differ in spatio-temporal stability. Furthermore, our results highlight the important role of lotic habitats as reservoirs for evolutionary processes and the potential for rapid speciation.

Animals↗
PubMed2006

The evolution of plant-insect mutualisms.

Mutualisms (cooperative interactions between species) have had a central role in the generation and maintenance of life on earth. Insects and plants are involved in diverse forms of mutualism. Here we review evolutionary features of three prominent insect-plant mutualisms: pollination, protection and seed dispersal. We focus on addressing five central phenomena: evolutionary origins and maintenance of mutualism; the evolution of mutualistic traits; the evolution of specialization and generalization; coevolutionary processes; and the existence of cheating. Several features uniting very diverse insect-plant mutualisms are identified and their evolutionary implications are discussed: the involvement of one mobile and one sedentary partner; natural selection on plant rewards; the existence of a continuum from specialization to generalization; and the ubiquity of cheating, particularly on the part of insects. Plant-insect mutualisms have apparently both arisen and been lost repeatedly. Many adaptive hypotheses have been proposed to explain these transitions, and it is unlikely that any one of them dominates across interactions differing so widely in natural history. Evolutionary theory has a potentially important, but as yet largely unfilled, role to play in explaining the origins, maintenance, breakdown and evolution of insect-plant mutualisms.

Animals↗
PubMed2002

Complete genomic sequence of an Epstein-Barr virus-related herpesvirus naturally infecting a new world primate: a defining point in the evolution of oncogenic lymphocryptoviruses.

Callitrichine herpesvirus 3 (CalHV-3) was isolated from a B-cell lymphoma arising spontaneously in the New World primate Callithrix jacchus, the common marmoset. Partial genomic sequence analysis definitively identified CalHV-3 as a member of the Epstein-Barr virus (EBV)-related lymphocryptovirus (LCV) genus and extended the known host range of LCVs beyond humans and Old World nonhuman primates. We have now completed the first genomic sequence of an LCV infecting a New World primate by describing the unique short region, the major internal repeat, and a portion of the unique long region. This portion of the genome contains the putative latent origin of replication and 13 additional open reading frames (ORFs), 5 of which show no homology to any viral or cell genes. One of the novel genes, C5, is a positional homologue for the transformation-essential EBV gene EBNA-2. The marmoset LCV genome is also notable for the absence of viral interleukin-10 and small nonpolyadenylated RNA homologues. Marmoset LCV transcripts encoding putative latent infection nuclear proteins have a common leader sequence that is spliced from the major internal repeat in a manner similar to that of the EBV EBNA-LP, suggesting strong conservation of a common promoter and splicing of these latent infection mRNAs. An EBV LMP2A-like spliced transcript crossing the terminal repeats encodes a unique ORF, C7, with multiple transmembrane domains and tyrosine kinase phosphorylation sites functionally reminiscent of EBV LMP2A. However, the carboxy-terminal location of the candidate phosphotyrosine residues is more reminiscent of the Kaposi's sarcoma-associated herpesvirus K15 gene and provides potential evidence of an evolutionary transition from rhadinoviruses to lymphocryptoviruses. The unusual gene repertoire of the marmoset LCV differentiates ancestral viral genes likely present in an LCV progenitor from viral genes acquired later as primates and LCV coevolved, providing a defining point in the evolution of oncogenic LCVs.

Amino Acid Sequence↗
PubMed2006

Docking protein domains in contact space.

BACKGROUND: Many biological processes involve the physical interaction between protein domains. Understanding these functional associations requires knowledge of the molecular structure. Experimental investigations though present considerable difficulties and there is therefore a need for accurate and reliable computational methods. In this paper we present a novel method that seeks to dock protein domains using a contact map representation. Rather than providing a full three dimensional model of the complex, the method predicts contacting residues across the interface. We use a scoring function that combines structural, physicochemical and evolutionary information, where each potential residue contact is assigned a value according to the scoring function and the hypothesis is that the real configuration of contacts is the one that maximizes the score. The search is performed with a simulated annealing algorithm directly in contact space. RESULTS: We have tested the method on interacting domain pairs that are part of the same protein (intra-molecular domains). We show that it correctly predicts some contacts and that predicted residues tend to be significantly closer to each other than other pairs of residues in the same domains. Moreover we find that predicted contacts can often discriminate the best model (or the native structure, if present) among a set of optimal solutions generated by a standard docking procedure. CONCLUSION: Contact docking appears feasible and able to complement other computational methods for the prediction of protein-protein interactions. With respect to more standard docking algorithms it might be more suitable to handle protein conformational changes and to predict complexes starting from protein models.

Algorithms↗
PubMed2001

Genome trees constructed using five different approaches suggest new major bacterial clades.

BACKGROUND: The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes. RESULTS: Five largely independent approaches were employed to construct trees for completely sequenced bacterial and archaeal genomes: i) presence-absence of genomes in clusters of orthologous genes; ii) conservation of local gene order (gene pairs) among prokaryotic genomes; iii) parameters of identity distribution for probable orthologs; iv) analysis of concatenated alignments of ribosomal proteins; v) comparison of trees constructed for multiple protein families. All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. Beyond these obvious groupings, the trees made with different methods appeared to differ substantially in terms of the relative contributions of phylogenetic relationships and similarities in gene repertoires caused by similar life styles and horizontal gene transfer to the tree topology. The trees based on presence-absence of genomes in orthologous clusters and the trees based on conserved gene pairs appear to be strongly affected by gene loss and horizontal gene transfer. The trees based on identity distributions for orthologs and particularly the tree made of concatenated ribosomal protein sequences seemed to carry a stronger phylogenetic signal. The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. The latter group also appeared to join the low-GC Gram-positive bacteria at a deeper tree node. These new groupings of bacteria were supported by the analysis of alternative topologies in the concatenated ribosomal protein tree using the Kishino-Hasegawa test and by a census of the topologies of 132 individual groups of orthologous proteins. Additionally, the results of this analysis put into question the sister-group relationship between the two major archaeal groups, Euryarchaeota and Crenarchaeota, and suggest instead that Euryarchaeota might be a paraphyletic group with respect to Crenarchaeota. CONCLUSIONS: We conclude that, the extensive horizontal gene flow and lineage-specific gene loss notwithstanding, extension of phylogenetic analysis to the genome scale has the potential of uncovering deep evolutionary relationships between prokaryotic lineages.

Bacteria↗
PubMed2004

Direct selection on male attractiveness and female preference fails to produce a response.

BACKGROUND: Theoretical studies suggest that direct and indirect selection have the potential to cause substantial evolutionary change in female mate choice. Similarly, sexual selection is considered a strong force in the evolution of male attractiveness and the exaggeration of secondary sexual traits. Few studies have, however, directly tested how female mate choice and male attractiveness respond to selection. Here we report the results of a selection experiment in which we selected directly on female mating preference for attractive males and, independently, on male attractiveness in the guppy, Poecilia reticulata. We measured the direct and correlated responses of female mate choice and male attractiveness to selection and the correlated responses of male ornamental traits, female fecundity and adult male and female survival. RESULTS: Surprisingly, neither female mate choice nor male attractiveness responded significantly to direct or to indirect selection. Fecundity did differ significantly among lines in a way that suggests a possible sexually-antagonistic cost to male attractiveness. CONCLUSIONS: The opportunity for evolutionary change in female mate choice and male attractiveness may be much smaller than predicted by current theory, and may thus have important consequences for how we understand the evolution of female mate choice and male attractiveness. We discuss a number of factors that may have constrained the response of female choice and male attractiveness to selection, including low heritabilities, low levels of genetic (co)variation in the multivariate direction of selection, sexually-antagonistic constraint on sexual selection and the "environmental covariance hypothesis".

Animals↗
PubMed2000

A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster.

BACKGROUND: Non-long terminal repeat (non-LTR) retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate. We have performed a systematic search for sequences matching the characteristic reverse transcriptase domain of non-LTR retrotransposons in the sequenced regions of the Drosophila melanogaster genome. RESULTS: In addition to previously characterized BS, Doc, F, G, I and Jockey elements, we have identified new non-LTR retrotransposons: Waldo, You and JuanDm. Waldo elements are related to mosquito RTI elements. You to the Drosophila I factor, and JuanDm to mosquito Juan-A and Juan-C. Interestingly, all JuanDm elements are highly homogeneous in sequence, suggesting that they are recent components of the Drosophila genome. CONCLUSIONS: The genome of D. melanogaster contains at least ten families of non-site-specific non-LTR retrotransposons representing three distinct clades. Many of these families contain potentially active members. Fine evolutionary analyses must await the more accurate sequences that are expected in the next future.

Amino Acid Sequence↗
PubMed2005

Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle.

Prior to human settlement 700 years ago New Zealand had no terrestrial mammals--apart from three species of bats--instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10-15 kg; 2-3 m wingspan) was 30%-40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.

Animals↗
PubMed2024

Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed neotropical river.

The striped catfish Pseudoplatystoma magdaleniatum is a large-sized migratory species from the north Andes region, endemic to Magdalena basin and one of the major fishery resources. Despite the estimated reduction of over 80% of the fisheries production of this species throughout the basin in recent decades, its population in the lower Magdalena-Cauca basin showed healthy genetics after molecular analyses. However, the current conservation status of this species and several habitat disturbances demand the re-evaluation of its population genetics to infer evolutionary risks and assess potential changes. This work analyzed a total of 164 samples from the Cauca River collected downstream the Ituango Dam between 2019-2021 using species-specific microsatellite markers to compare the genetic diversity and structure in samples collected between 2010-2014 from the lower Magdalena-Cauca basin, previously analyzed. Our results showed a relatively stable panmictic population over time (4 to 10 years), with high genetic diversity and evidence of recent bottleneck. Promoting habitat connectivity to conserve gene flow, characterizing diversity and genetic structure over the entire basin, and integrating the results with future monitoring are important aspects for the management planning for P. magdaleniatum in the Magdalena-Cauca basin.

Animals↗
PubMed2005

[Molecular evidence for origin of plastid-like organelle apicoplast: a review].

Apicomplexan protozoa contains a highly reduced plastid-like organelle termed apicoplast. The research on evolutionary origin of apicoplast is a topic of long-term intense debate, by far, hasn't still reached congruent conclusion though a variety of molecular technologies were employed, so that it become a typical case in plastid origin field. In this paper , we reviewed the molecular evidence for apicoplast evolutionary origin, predicting the potential source of novel molecular evidence as clues for further studying.

Animals↗
PubMed1999

Bi-penta-bi-decaradial symmetry: A review of evolutionary and developmental trends in holothuroidea (echinodermata)

Holothuroidea, comprising the sea cucumbers, is the least studied class of extant echinoderms, yet this group possesses a wealth of features of potential interest to developmental and evolutionary biologists. Holothuroids include the most morphologically derived echinoderms, including pelagic species and spheroid, plated taxa with mouth and anus adjacent at the end of a long, flexible stalk. To begin investigating this diversity of body form, we first estimated evolutionary relationships in the class Holothuroidea based on maximum parsimony analyses of 1,075 nt of the nuclear small subunit rDNA (for six species in four orders) and on 52 informative morphological characters (for the 25 extant families). Both the morphological and molecular evidence suggests almost an inversion of the prevailing higher level classification. Character-state optimizations indicated that pronounced adult bilateral symmetry evolved three times. In one group even a regain of secondary radial symmetry is found. Respiratory trees, structures unique to holothuroids, are a relatively late innovation, are ectodermally derived, and are bilaterally symmetric, supporting the possibility that the secondary gain of bilateral symmetry in holothuroids is ectodermally derived analogous to, say, the derivation of vertebrate limb dorso-ventral axis. The test of imbricating plates found in 10% of living holothuroids is apparently not homologous with that of other heavily armored echinoderms, evolving much later and at least twice. Indirectly developing larvae, auriculariae, occur in two evolutionarily disparate clades and unlike echinoids comprise a minority of clades. We suggest that this implies the parallel convergent evolution of this larval type or, more speculatively, some form of retention of developmental constraints. J. Exp. Zool. (Mol. Dev. Evol.) 285:93-103, 1999. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗
PubMed2002

Sexual selection and speciation in mammals, butterflies and spiders.

Recently refined evolutionary theories propose that sexual selection and reproductive conflict could be drivers of speciation. Male and female reproductive optima invariably differ because the potential reproductive rate of males almost always exceeds that of females: females are selected to maximize mate 'quality', while males can increase fitness through mate 'quantity'. A dynamic, sexually selected conflict therefore exists in which 'competitive' males are selected to override the preference tactics evolved by 'choosy' females. The wide variation across taxa in mating systems therefore generates variance in the outcome of intrasexual conflict and the strength of sexual selection: monandry constrains reproductive heterozygosity and allows female choice to select and maintain particular (preferred) genes; polyandry promotes reproductive heterozygosity and will more likely override female choice. Two different theories predict how sexual selection might influence speciation. Traditional ideas indicate that increased sexual selection (and hence conflict) generates a greater diversity of male reproductive strategies to be counteracted by female mate preferences, thus providing elevated potentials for speciation as more evolutionary avenues of male-female interaction are created. A less intuitively obvious theory proposes that increased sexual selection and conflict constrains speciation by reducing the opportunities for female mate choice under polyandry. We use a comparative approach to test these theories by investigating whether two general measures of sexual selection and the potential for sexual conflict have influenced speciation. Sexual size dimorphism (across 480 mammalian genera, 105 butterfly genera and 148 spider genera) and degree of polyandry (measured as relative testes size in mammals (72 genera) and mating frequency in female butterflies (54 genera)) showed no associations with the variance in speciosity. Our results therefore show that speciation occurs independently of sexual selection.

Animals↗
PubMed2001

Host-plant adaptation in an herbivorous marine amphipod: genetic potential not realized in field populations.

Evolutionary responses of herbivores to their host plants depend not only on selection from plants, but also on the genetic basis of traits relating to host use. The genetic basis of such traits has been investigated extensively among terrestrial insect herbivores, but has received almost no attention among marine herbivores. We tested whether performance traits in the herbivorous marine amphipod Peramphithoe parmerong display heritable variation and, for the first time for a marine herbivore, whether selection has resulted in local adaptation to host plants on two spatial scales. Peramphithoe parmerong displayed heritable genetic variation for survival on two host macroalgae, the high-quality Sargassum linearifolium and the poor-quality Padina crassa, and for growth on S. linearifolium. Differences in performance on different hosts thus have the potential to select for differential use of hosts by this amphipod. Despite this potential, there was no evidence among field populations of local adaptation to host algae on either scale tested: between hosts within a site or among sites differing in algal species composition. Within a site, amphipods were not more likely to prefer or perform better on the host on which they were collected. Similarly, amphipods collected from sites in which P. crassa was present were not more likely to perform well on this host than amphipods collected from sites where this alga was not found. Ecological factors that may explain the persistence of P. parmerong on P. crassa and the possibility of phylogenetic constraints on host use by P. parmerong are discussed.

Adaptation, Physiological↗
PubMed2026

Genomic-Environmental Integration Predicts Climate Vulnerability and Adaptive Potential of Tibetan Plateau Herpetofauna.

The herpetofauna of the Tibetan Plateau, home to Earth's highest-elevation ectothermic vertebrates, face escalating threats from rapid climate change. However, conventional conservation strategies often overlook intraspecific genetic variation and adaptive potential, limiting their predictive accuracy and effectiveness. Here, we integrate whole-genome resequencing data with environmental modeling to assess climate vulnerability in two endemic species: Nanorana parkeri (Tibetan frog) and Thermophis baileyi (hot-spring snake). Results suggest that the western populations of the two species exhibit higher genomic offsets under future climate, while some eastern populations of the Tibetan frog face a decrease in niche suitability, and the hot-spring snake will experience varying degrees of loss of suitable habitats. Furthermore, heterozygosity, genetic diversity, and genetic load demonstrate significant correlations with genomic offsets, suggesting that low genetic diversity and high genetic load may weaken the potential to adapt to environmental changes. Based on a genome-niche index that combines genomic offsets with niche suitability change, we identified evolutionary rescue populations that are potentially tolerant to climate change. Our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive potential and enable effective conservation management of high-altitude herpetofauna under rapid climate change.

Animals↗
PubMed1987

The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.

The DNA sequence of the mitochondrial large subunit (LSU) rRNA gene of Schizosaccharomyces pombe has been determined. In the direction of transcription, this gene is located between the gene coding for subunit II of cytochrome oxidase and a cluster of three tRNA genes. Both the 5' and 3' ends of the LSU rRNA have been mapped precisely: whereas the 5' end can be assigned unambiguously to a single nucleotide position, multiple 3' ends occur within a run of eight U residues. Based on these results, the S. pombe LSU rRNA is between 2818 and 2826 nucleotides long. A sequence motif immediately upstream of the 5' end of the gene resembles that of the mitochondrial promoter motif of Saccharomyces cerevisiae; however, the sequence at the 3' end of the gene is not similar to any of the motifs implicated as processing signals in other mitochondrial systems. Unlike its counterparts in S. cerevisiae and Aspergillus nidulans, the mitochondrial LSU rRNA gene of S. pombe does not contain an intron. Comparison of potential secondary structure among the three fungal mitochondrial and Escherichia coli LSU rRNAs has defined a common secondary structure core, held together by long-range hydrogen-bonding interactions. A 5.8S-like structure is present within the 5'-terminal region of all three fungal mitochondrial LSU rRNAs; in contrast, no 4.5S-like structure is evident at the 3' end of these molecules. An evolutionary evaluation of highly conserved regions of a small set of LSU rRNA sequences suggests that S. pombe mitochondria diverged from a mitochondrial proto-fungal branch earlier than either A. nidulans or S. cerevisiae mitochondria. This result, considered in conjunction with the patterns of genome organization and codon usage in fungal mitochondria, points to a slower evolutionary clock speed in the mitochondrial genome of S. pombe.

Base Sequence↗
PubMed1998

[Progressive study of EEG and evoked potentials in Lafora disease].

OBJECTIVE: The aim of this paper is to present a simultaneous evolutionary study of EEG and multimodality evoked potentials (EP) in a patient with progressive myoclonus epilepsy (PME) with Lafora bodies in the sweat glands from the axillary skin biopsy. CLINICAL CASE: The EEG showed progressive deterioration characteristic of this entity. Epileptiform activity was modified in distribution and morphology throughout the sickness. Abnormalities appeared in serial sleep records, although with acceptable preservation of its structure. The EEG findings supported the diagnosis of PME prior to clinical suspicion. A gradual increase in the somatosensory EP amplitude was observed, leading to an early giant configuration. However, an asymmetry persisted between both hemispheres, with the right cortex being more affected. Recording simultaneously on C3 and C4 after unilateral stimulation, a high-amplitude ipsilateral response was found in both hemispheres, suggesting hyperexcitability of cortical and subcortical neural structures. CONCLUSION: These somatosensory EP findings--progressive deterioration, interhemispheric asymmetry and ipsilateral giant response--have not, to our knowledge, been previously described.

Adolescent↗
PubMed2003

Evolutionary consequences of Wolbachia infections.

The past decade has revealed the bacterium Wolbachia as the most widespread symbiont of arthropods and nematodes. Behind this evolutionary success is an remarkable variety of effects on host biology, ranging from manipulation of reproduction in favor of females to more classical mutualistic interactions. Here we discuss the potential of Wolbachia for promoting evolutionary changes in its hosts.

Animals↗
PubMed1992

On the potential of simple repetitive DNA for fingerprinting in clinical, forensic, and evolutionary dynamic studies.

The purpose of this review is to discuss critically the practical meaning of a specific genome component, simple repetitive desoxyribonucleic acid (DNA) sequences as clinical and forensic and diagnostic and research tools. Previously, multilocus DNA fingerprinting was the major technology employed to visualize such simple repeat sequences. This technique enables many polymorphic loci to be simultaneously detected thus yielding vast amounts of information. With the advent of enzymatic DNA amplification via the polymerase chain reaction (PCR), individual simple repeat loci can be demonstrated, theoretically even from single DNA molecules and so a wealth of additional approaches have also become feasible. In general investigating, small, known, single copy parts of genomes have not posed truly insurmountable problems if enough material was available. There have even been a few (anecdotal) reports on the amplification of simple repeats from ancient DNA (see, e.g. [30]. Here we would like to after a solid basis for an earnest discussion of the applications of these simple repetitive sequences using various methodological approaches relevant for clinical diagnosis, setting aside the obvious unsolved mysteries of their biology.

Animals↗