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Results for “ecological speciation”

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PubMed2006

Sequences, sequence clusters and bacterial species.

Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

Bacteria↗

PubMed2005

Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae).

To study the consequences of hybridization and genome duplication on polyploid genome evolution and adaptation, we used independently formed hybrids (Spartina x townsendii and Spartina x neyrautii) that originated from natural crosses between Spartina alterniflora, an American introduced species, and the European native Spartina maritima. The hybrid from England, S. x townsendii, gave rise to the invasive allopolyploid, salt-marsh species, Spartina anglica. Recent studies indicated that allopolyploid speciation may be associated with rapid genetic and epigenetic changes. To assess this in Spartina, we performed AFLP (amplified fragment length polymorphism) and MSAP (methylation sensitive amplification polymorphism) on young hybrids and the allopolyploid. By comparing the subgenomes in the hybrids and the allopolyploid to the parental species, we inferred structural changes that arose repeatedly in the two independently formed hybrids. Surprisingly, 30% of the parental methylation patterns are altered in the hybrids and the allopolyploid. This high level of epigenetic regulation might explain the morphological plasticity of Spartina anglica and its larger ecological amplitude. Hybridization rather than genome doubling seems to have triggered most of the methylation changes observed in Spartina anglica.

DNA Methylation↗

PubMed2006

Molecular diversity after a range expansion in heterogeneous environments.

Recent range expansions have probably occurred in many species, as they often happen after speciation events, after ice ages, or after the introduction of invasive species. While it has been shown that range expansions lead to patterns of molecular diversity distinct from those of a pure demographic expansion, the fact that many species do live in heterogeneous environments has not been taken into account. We develop here a model of range expansion with a spatial heterogeneity of the environment, which is modeled as a gamma distribution of the carrying capacities of the demes. By allowing temporal variation of these carrying capacities, our model becomes a new metapopulation model linking ecological parameters to molecular diversity. We show by extensive simulations that environmental heterogeneity induces a loss of genetic diversity within demes and increases the degree of population differentiation. We find that metapopulations with low average densities are much more affected by environmental heterogeneity than metapopulations with high average densities, which are relatively insensitive to spatial and temporal variations of the environment. Spatial heterogeneity is shown to have a larger impact on genetic diversity than temporal heterogeneity. Overall, temporal heterogeneity and local extinctions are not found to leave any specific signature on molecular diversity that cannot be produced by spatial heterogeneity.

Computer Simulation↗

PubMed2005

Adaptation and speciation: what can F(st) tell us?

A useful way of summarizing genetic variability among different populations is through estimates of the inbreeding coefficient, F(st). Several recent studies have tried to use the distribution of estimates of F(st) from individual genetic loci to detect the effects of natural selection. However, the promise of this approach has yet to be fully realized owing to the pervasive dogma that this distribution is highly dependent on demographic history. Here, I review recent theoretical results that indicate that the distribution of estimates of F(st) is generally expected to be robust to the vagaries of demographic history. I suggest that analyses based on it provide a useful first step for identifying candidate genes that might be under selection, and explore the ways in which this information can be used in ecological and evolutionary studies.

Journal Article↗

PubMed2000

Adaptive dynamics in diploid, sexual populations and the evolution of reproductive isolation.

Evolutionary branching is the process whereby an initially monomorphic population evolves to a point where it undergoes disruptive selection and splits up into two phenotypically diverging lineages. We studied evolutionary branching in three models that are ecologically identical but that have different genetic systems. The first model is clonal, the second is sexual diploid with additive genetics on a single locus and the third is like the second but with an additional locus for mate choice. Evolutionary branching occurred under exactly the same ecological circumstances in all three models. After branching the evolutionary dynamics may be qualitatively different. In particular, in the diploid, sexual models there can be multiple evolutionary outcomes whereas in the corresponding clonal model there is only one. We showed that evolutionary branching favours the evolution of (partial) assortative mating and that this in turn effectively restores the results from the clonal model by rendering the alternative outcomes unreachable except for the one that also occurs in the clonal model. The evolution of assortative mating during evolutionary branching can be interpreted as the initial phase of sympatric speciation with phenotypic divergence and partial reproductive isolation.

Adaptation, Physiological↗

PubMed1998

Using metal-ligand binding characteristics to predict metal toxicity: quantitative ion character-activity relationships (QICARs).

Ecological risk assessment can be enhanced with predictive models for metal toxicity. Modelings of published data were done under the simplifying assumption that intermetal trends in toxicity reflect relative metal-ligand complex stabilities. This idea has been invoked successfully since 1904 but has yet to be applied widely in quantitative ecotoxicology. Intermetal trends in toxicity were successfully modeled with ion characteristics reflecting metal binding to ligands for a wide range of effects. Most models were useful for predictive purposes based on an F-ratio criterion and cross-validation, but anomalous predictions did occur if speciation was ignored. In general, models for metals with the same valence (i.e., divalent metals) were better than those combining mono-, di-, and trivalent metals. The softness parameter (sigma p) and the absolute value of the log of the first hydrolysis constant ([symbol: see text] log KOH [symbol: see text]) were especially useful in model construction. Also, delta E0 contributed substantially to several of the two-variable models. In contrast, quantitative attempts to predict metal interactions in binary mixtures based on metal-ligand complex stabilities were not successful.

Algorithms↗

PubMed2004

Prevalence of interspecific hybrids amongst asexual fungal endophytes of grasses.

Epichloë endophytes are fungal symbionts of grasses that span a continuum including asexual mutualists that are vertically transmitted, obligately sexual pathogens that are horizontally transmitted, and mixed-strategy symbionts with both mutualistic and pathogenic capabilities. Here we show that processes of genome evolution differ markedly for the different symbiont types. Genetic and phylogenetic analysis was conducted of a broad taxonomic, ecological and geographical sample of sexual and asexual isolates, in which were identified and sequenced alleles of genes for beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1), and microsatellite alleles were identified by length polymorphisms. The majority of asexual isolates had two or three alleles of most loci, but every sexual isolate had only single alleles for each locus. Phylogenetic analysis of tub2 and tef1 indicated that in all instances of multiple alleles in an isolate, the alleles were derived from different sexual species. It is concluded that, whereas horizontally transmissible species had haploid genomes and speciation occurred cladistically, most of the strictly seedborne mutualists were interspecific hybrids with heteroploid (aneuploid or polyploid) genomes. Furthermore, the phylogenetic evidence indicated that, in at least some instances, hybridization followed rather than caused evolution of the strictly seedborne habit. Therefore, the abundance of hybrid species among grass endophytes, and their prevalence in many host populations suggests a selective advantage of hybridization for the mutualistic endophytes.

Base Sequence↗

PubMed2026

The History of Transposable Element Invasions in Drosophila melanogaster.

As a fundamental biological principle, genomic information is typically transmitted vertically from parent to offspring. Occasionally, however, genetic material is transferred horizontally between species. Transposable elements (TEs) are frequently involved in such horizontal transfer (HT), possibly due to their ability to move in genomes. HT has been particularly well-studied in Drosophila melanogaster, a key model organism for evolutionary and ecological research. Recent studies have revealed that HT triggered the invasion of 12 different TEs in the D. melanogaster genome over the past 200 years. This finding challenges our traditional view of genome evolution, suggesting that TE invasions may not only be isolated events that can be ignored as rare exceptions but could represent recurrent events that continuously reshape genomes. In this review, we trace the history of how these 12 invasions were discovered and outline the lines of evidence supporting them. We also discuss the potential evolutionary consequences of these TE invasions, including their roles in adaptation, genome evolution, speciation, and extinction risk. Finally, we highlight open questions and directions for future research. In particular, it will be essential to test whether other organisms also exhibit similarly high rates of recent TE invasions and to assess whether human activity triggered the high rate of invasions.

Journal Article↗

PubMed2006

Arsenic and selenium in microbial metabolism.

Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

Amino Acid Sequence↗

PubMed2002

Polymerase chain reaction-single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complex.

Independent lines of evidence support an Australian origin for the Mediterranean populations of the tropical alga Caulerpa taxifolia. To complement previous biogeographical studies based on nuclear rDNA internal transcribed spacer (ITS), a new chloroplast marker was developed--the cp 16S rDNA intron-2. Sequence variability for both nuclear and chloroplast markers were assessed in 110 individuals using single strand conformation polymorphism. Comparison of intrapopulation genetic diversity between invasive Mediterranean and 'native' Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped nontropical invasive populations with inshore-mainland populations from Australia, while the second clustered all offshore-island populations studied so far. Despite our finding of nine distinct nuclear and five distinct chloroplast profiles, a single nucleocytoplasmic combination was characteristic of the invasive populations and sexual reproduction was found to be very rare. C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies.

Australia↗

PubMed2004

Climate change and evolving human diversity in Europe during the last glacial.

A link between climate change and human evolution during the Pleistocene has often been assumed but rarely tested. At the macro-evolutionary level Foley showed for hominids that extinction, rather than speciation, correlates with environmental change as recorded in the deep sea record. Our aim is to examine this finding at a smaller scale and with high-resolution environmental and archaeological archives. Our interest is in changing patterns of human dispersal under shifting Pleistocene climates during the last glacial period in Europe. Selecting this time frame and region allows us to observe how two hominid taxa, Neanderthals and Crô-Magnons, adapted to climatic conditions during oxygen isotope stage 3. These taxa are representative of two hominid adaptive radiations, termed terrestrial and aquatic, which exhibited different habitat preferences but similar tolerances to climatic factors. Their response to changing ecological conditions was predicated upon their ability to extend their societies in space and time. We examine this difference further using a database of all available radiocarbon determinations from western Europe in the late glacial. These data act as proxies for population history, and in particular the expansion and contraction of regional populations as climate changed rapidly. Independent assessment of these processes is obtained from the genetic history of Europeans. The results indicate that climate affects population contraction rather than expansion. We discuss the consequences for genetic and cultural diversity which led to the legacy of the Ice Age: a single hominid species, globally distributed.

Adaptation, Biological↗

PubMed1999

Brain size is not correlated with forelimb dexterity in fissiped carnivores (Carnivora): A comparative test of the principle of proper mass.

To test the hypothesis that brain size and forelimb dexterity are positively correlated, the relative brain size of 41 species of fissiped (terrestrial) carnivores (Order: Carnivora) was examined with respect to their forelimb use during feeding. With the use of a newly derived dexterity index, the forelimb dexterity executed by each of the species was calculated as a single, continuous variable which was then regressed against the residuals of brain size. To account for confounding effects of phylogenetic inertia, the analysis was performed with independent contrasts analysis using a speciational model of evolutionary change (i.e. equal branch lengths). The results suggest that relative brain size and isocortex size are not correlated with the dexterity of the proximal or distal segments or a combination of the two (total forelimb dexterity). The presence of species with widely different brain sizes and similar dexterities, and vice versa, suggests that an increase in the amount of neural substrate might not be necessary for the production of finely coordinated forelimb movements. It is suggested that this outcome is representative of the plasticity of both mammalian brain size and behavior and that variations in brain size and forelimb dexterity could be linked to disparate ecological and phylogenetic factors which act in concert to promote or constrain neural development and behavior in different species.

Animals↗

PubMed2004

Ice sheets promote speciation in boreal birds.

The premise that Pleistocene ice ages played an important role in generating present-day species diversity has been challenged by genetic data indicating that most of the youngest terrestrial species on Earth coalesced long before major glacial advances. However, study has been biased towards faunas distributed at low latitudes that were not directly fragmented by advancing ice sheets. Using mitochondrial sequence divergence and a molecular clock, we compared the coalescence times of pairs of avian species belonging to superspecies complexes from the high-latitude boreal forest with those of sub-boreal and tropical avifaunas of the New World. Remarkably, all coalescence events in boreal superspecies date to the Pleistocene, providing direct evidence that speciation was commonly initiated during recent glacial periods. A pattern of endemism in boreal superspecies plausibly links the timing of divergence to the fragmentation of the boreal forest by ice sheets during the Mid- and Late Pleistocene. In contrast to the boreal superspecies, only 56% of sub-boreal and 46% of tropical superspecies members coalesced during the Pleistocene, suggesting that avifaunas directly fragmented by ice sheets experienced rapid rates of diversification, whereas those distributed farther south were affected to a lesser extent. One explanation for the absence of pre-Pleistocene superspecies in boreal avifaunas is that strong selection pressures operated in boreal refugia, causing superspecies members to achieve ecological differentiation at an accelerated rate.

Animals↗

PubMed2000

Nested cladistic analysis, phylogeography and speciation in the Timarcha goettingensis complex (Coleoptera, chrysomelidae).

The Timarcha goettingensis complex is a monophyletic assemblage of closely related leaf beetles (Chrysomelidae), distributed from the north half of the Iberian Peninsula to Central Europe. Oligophagy, mountainous habitat and apterism are factors which are assumed to promote speciation in these beetles. We have used cytochrome oxidase subunit II mitochondrial DNA genealogies obtained from 31 sampling localities and a nested geographical distance analysis to assess the population structure and demographic factors explaining the geographical distributions of the mtDNA haplotypes in the T. goettingensis complex. The results show that there is a significant association between genetic structuring and geography. Inferences about the historical population processes in the species complex are discussed, being in general in accordance with contiguous range expansions and past fragmentations. The use of the cohesion species concept approach suggests the existence of several systematic ranks among the different T. goettingensis populations, which is in part supported by ecological traits such as trophic selection and altitudinal distribution.

Animals↗

PubMedDate not supplied

[Occurence of Onchocerca tarsicola Bain and Schulz-Key, 1974, in reindeer (author's transl)].

Onchocerca tarsicola is recorded from reindeer (Rangifer tarandus L.). This parasite is originally described from red deer (Cervus elaphus L.). There are indications that reindeer may not be the primary host of O. tarsicola: 1. Reindeer is parasitized only by O, tarsicola whereas red deer, due to speciations, is carrying three related Onchocerca species from the same line. 2. O. tarsicola, usually found along tendons distal of the tarsal and carpal joints, is in reindeer frequently found at aberrant locations which is commonly observed in connection with "transfuga" parasites. 3. Heavy infestations of O. tarsicola in reindeer seem to have started in the late sixties and since then have become more and more extensive.

Animals↗

PubMed2004

The effects of intraspecific competition and stabilizing selection on a polygenic trait.

The equilibrium properties of an additive multilocus model of a quantitative trait under frequency- and density-dependent selection are investigated. Two opposing evolutionary forces are assumed to act: (i) stabilizing selection on the trait, which favors genotypes with an intermediate phenotype, and (ii) intraspecific competition mediated by that trait, which favors genotypes whose effect on the trait deviates most from that of the prevailing genotypes. Accordingly, fitnesses of genotypes have a frequency-independent component describing stabilizing selection and a frequency- and density-dependent component modeling competition. We study how the equilibrium structure, in particular, number, degree of polymorphism, and genetic variance of stable equilibria, is affected by the strength of frequency dependence, and what role the number of loci, the amount of recombination, and the demographic parameters play. To this end, we employ a statistical and numerical approach, complemented by analytical results, and explore how the equilibrium properties averaged over a large number of genetic systems with a given number of loci and average amount of recombination depend on the ecological and demographic parameters. We identify two parameter regions with a transitory region in between, in which the equilibrium properties of genetic systems are distinctively different. These regions depend on the strength of frequency dependence relative to pure stabilizing selection and on the demographic parameters, but not on the number of loci or the amount of recombination. We further study the shape of the fitness function observed at equilibrium and the extent to which the dynamics in this model are adaptive, and we present examples of equilibrium distributions of genotypic values under strong frequency dependence. Consequences for the maintenance of genetic variation, the detection of disruptive selection, and models of sympatric speciation are discussed.

Biological Evolution↗

PubMed2003

Patterns and processes in reef fish diversity.

A central aim of ecology is to explain the heterogeneous distribution of biodiversity on earth. As expectations of diversity loss grow, this understanding is also critical for effective management and conservation. Although explanations for biodiversity patterns are still a matter for intense debate, they have often been considered to be scale-dependent. At large geographical scales, biogeographers have suggested that variation in species richness results from factors such as area, temperature, environmental stability, and geological processes, among many others. From the species pools generated by these large-scale processes, community ecologists have suggested that local-scale assembly of communities is achieved through processes such as competition, predation, recruitment, disturbances and immigration. Here we analyse hypotheses on speciation and dispersal for reef fish from the Indian and Pacific oceans and show how dispersal from a major centre of origination can simultaneously account for both large-scale gradients in species richness and the structure of local communities.

Animals↗

PubMed2004

Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara.

Species in the genus Tangara are distributed throughout the New World tropics and vary in their morphology, behavior, and ecology. We used data from the cytochrome b and ND 2 genes to provide the first phylogenetic perspective on the evolution of this diversity. Reconstructions based on parsimony, maximum likelihood, and Bayesian approaches were largely congruent. The genus is monophyletic and consists of two main clades. Within these clades, DNA sequence data confirm the monophyly of most previously recognized species groups within Tangara, indicating general concordance between molecular data and impressions based on geographic distribution, morphology, and behavior. Within some currently recognized species, levels of DNA sequence variation are larger than expected, suggesting multiple taxa may be involved. In contrast, some currently recognized species are only weakly differentiated from their sister species. Biogeographic analyses indicate that many early speciation events occurred in the Andes. More recently, dispersal events followed by subsequent speciation have occurred in other geographic areas of the Neotropics. Assuming a molecular clock, most speciation events occurred well before Pleistocene climatic cycles. The time frame of Tangara speciation corresponds more closely to a period of continued uplift in the Andes during the late Miocene and Pliocene.

Animals↗