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PubMed2005

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus).

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.

Animals↗
PubMed2006

Pattern and process in the ecological biogeography of European freshwater fish.

1. Species lists for regions of Europe defined by Illies (1978, Limnofauna Europaea, 2nd edn. Gustav Fischer Verlag, Stuttgart), and augmented by information from Maitland (2000, Guide to Freshwater Fish of Britain and Europe. Hamlyn, London), are used to describe patterns in freshwater fish species richness and to examine the contribution of habitat preference, migration, body size and glacial history to these patterns. 2. The number of non-endemic species declines to the north and west, with increasing distance from the Ponto-Caspian region, the main source area, whereas endemic species richness declines only with latitude. 3. Habitat generalists tend to be migratory while riverine specialists are usually resident. Similar numbers of riverine species and generalists occur in Europe as a whole but generalists dominate in regional faunas and, to an increasing extent, in more isolated, formerly glaciated areas. Very few lacustrine specialists were found, reflecting the geologically ephemeral nature of lakes. Only 8% of riverine species have colonized glaciated areas, compared with more than half the generalist species, and the number declines rapidly with increasing distance from the source area. 4. Diadromous species show no geographical variation in species richness but potamodromous and resident species are affected by glaciation and by mountain and marine barriers. 5. The mean body size of regional faunas increases with latitude because there are relatively fewer small species in more distant, glaciated areas. 6. About half the species occurring in Europe are restricted to one region and the majority of these endemics occur in barrier regions with Mediterranean climates. Species in glaciated regions have much larger range sizes. Habitat preference and migration type, not body size, are the main determinants of range size. 7. Freshwater habitat availability varies across Europe with glaciated areas having more lakes of a given size than unglaciated areas. Catchment size is greatest at mid-latitudes. For a given catchment size rivers in glaciated areas are shorter. 8. The results support the notion that habitat variability, on both short and long time scales, favours colonization ability, which requires large body size. 9. As a result of their limited vagility northern fish faunas are depauperate, show high levels of plasticity and polymorphism and may show elevated speciation rates. The isolated southern faunas of the Iberian and Italian peninsulas and the Balkans are rich in endemic species but may be subject to extinctions because of the spread of the highly seasonal Mediterranean climate.

Animal Migration↗
PubMed2003

Molecular evidence reveals a polyphyletic origin and chromosomal speciation of Lake Baikal's endemic asellid isopods.

The six endemic isopod species of Lake Baikal have been regarded as a small species flock with uncertain affinities to related asellids. We provide evidence from 16S rRNA sequences for polyphyletic origins of Baikalian Asellidae. One clade of two species is related to the Eurasian genus Asellus. The other clade, Baicalasellus, shows affinities to North American asellids and may have a long evolutionary history within the lake basin. Some speciation events within Baicalasellus clearly have a chromosomal basis. In contrast with numerous taxa exhibiting monophyletic radiations in ancient lakes, the endemic Baikalian isopods arose by multiple invasions and chromosomal mechanisms.

Animals↗
PubMed2002

Molecular phylogeny of Japanese Leporidae, the Amami rabbit Pentalagus furnessi, the Japanese hare Lepus brachyurus, and the mountain hare Lepus timidus, inferred from mitochondrial DNA sequences.

We determined mitochondrial 12S ribosomal RNA (rRNA) and cytochrome b (cyt b) gene sequences in three leporid species of Japan, the Amami rabbit Pentalagus furnessi from the Ryukyu Islands, the Japanese hare Lepus brachyurus from Honshu, and a Japanese form of the mountain hare Lepus timidus ainu from Hokkaido. We compared the sequences with those of other taxa of leporids available in databases. Phylogenetic trees of the 12S rRNA gene sequences indicated that the lineage of P. furnessi diversified during the generic radiation of the leporids at an ancient time, which was estimated to have been the middle Miocene. Cyt-b gene trees revealed that the lineage of L. brachyurus branched off at an early stage in the speciation of Lepus, probably at the beginning of the Pliocene. The cyt b sequences of L. t. ainu were somewhat distinct from those of continental conspecific populations; this lineage divergence is likely to have occurred during the middle or late Pleistocene. The results show that the three regions of the Japanese archipelago, Ryukyu, Honshu-Shikoku-Kyushu, and Hokkaido, now preserve their own leporid taxa, each with a different extent of genetic endemicity. It is possible that the zoogeographic traits of the Japanese leporids are a consequence of the evolutionary dynamics of leporids in East Asia, in that the radiation centers of leporids are likely to have shifted from tropical, through temperate, to arctic zones.

Animals↗
PubMed2003

Analysis of microsatellites in 13 hemiascomycetous yeast species: mechanisms involved in genome dynamics.

We have analyzed all di-, tri-, and tetranucleotide repeats in the partially sequenced genomes of 13 hemiascomycetous yeast species, and compared their sequences, lengths, and distributions to those observed in the genome of Saccharomyces cerevisiae. We found that most of the 13 species exhibit a unique distribution of microsatellites, not correlated to the base composition of their genome. Species close to S. cerevisiae exhibit a similar distribution, while species more distantly related show a more divergent distribution. We propose that de novo formation and continuous loss of microsatellites are active processes generating new DNA sequences. We also show that hemiascomycete-specific genes encoding transcription factors contain trinucleotide repeats more frequently than expected from their average frequency distribution. These transcription factors might play an important role in the speciation process, by regulating gene expression through DNA-protein or protein-protein interactions mediated by stretches of charged amino acids encoded by trinucleotide repeats.

Amino Acid Sequence↗
PubMed2003

Lead speciation in artificial human digestive fluid.

For children, soil ingestion via hand-to-mouth behavior can be a main route of exposure to contaminants such as lead. The ingested lead can be mobilized from the soil and form new species during the digestion process. Speciation is known to affect the availability of metals for transport across biological membranes. In the present study, in vitro digestions were performed with (artificially contaminated) standard soil. Lead speciation was investigated in the artificial human intestinal fluid, i.e., chyme, to gain insight into the lead species and lead fractions that may be available for transport across the intestinal epithelium. To that end, both a lead ion selective electrode (Pb-ISE) and a voltammetric technique (differential pulse anodic stripping voltammetry, DPASV) were used. The results indicate that in chyme only a negligible lead fraction is present as free Pb(2+), whereas lead phosphate and lead bile complexes are important fractions. The lead phosphate complexes appear to be voltammetrically labile, i.e., in dynamic equilibrium with Pb(2+). Labile complexes can dissociate and the produced metal ions can subsequently be transported across the intestinal epithelium. Lead bile complexes may behave in a similar manner, or this organometal complex may be able to traverse the intestinal membrane. Therefore, substantially more than only the free metal ion should be considered available for transport across the intestinal epithelium.

Administration, Oral↗
PubMed2003

A direct experimental test of founder-flush effects on the evolutionary potential for assortative mating.

Founder-flush speciation models propose that population bottlenecks can enhance evolutionary potential for reproductive isolation. To test this prediction, we subjected bottlenecked (three-pair founder-flush) and nonbottlenecked populations of the housefly to 18 generations of selection for assortative mating. After the selection regime, we analysed videotaped courtship bouts in these lines to identify correlated responses to the selection protocol. The realized heritabilities for assortative mating for both the bottlenecked and nonbottlenecked treatments were very low, but still significant. The founder-flush populations had thus responded to selection as well as the nonbottlenecked populations, although not significantly greater (i.e. total increases in assortative mating were 9.6 and 8.6%, respectively). Multivariate analyses on the courtship repertoires found that, although both bottlenecked and nonbottlenecked treatments attained similar levels of assortative mating, the treatments exhibited different evolutionary solutions in their correlated responses. Specifically, the bottlenecked lines demonstrated a significantly more diverse set of evolutionary trajectories (i.e. significant shifts along the second principal component for courtship). This suggests that the bottlenecked lines had greater potential for the evolution of novel phenotypes as predicted by founder-induced speciation models. Our results, however, cannot distinguish whether the more variable evolutionary responses resulted from increased heritabilities in courtship components, reduced potential to follow the convergent evolutionary trajectories noted for the nonbottlenecked lines, or some combination of both general processes in determining the resultant multivariate phenotype.

Animals↗
PubMed2005

Patterns of speciation in endemic Mexican Goodeid fish: sexual conflict or early radiation?

Currently there is much interest in the potential for sexual selection or conflict to drive speciation. Theory proposes that speciation will be accelerated where sexual conflict is strong, particularly if females are ahead because mate choice will accentuate divergence by limiting gene flow. The Goodeinae are a monophyletic group of endemic Mexican fishes with an origin at least as old as the Miocene. Sexual selection is important in the Goodeinae and there is substantial interspecific variability in body morphology, which influences mate choice, allowing inference of the importance of female mate choice. We therefore used this group to test the relationship between sexual dimorphism and speciation rate. We quantified interspecific variation in sexual dimorphism amongst 25 species using a multivariate measure of total morphological differentiation between the sexes that accurately reflects sexual dimorphism driven by female mate choice and also used a mtDNA-based phylogeny to examine speciation rates. Comparative analyses failed to support a significant association between sexual dimorphism and speciation rate. In addition, variation in the time course of speciation throughout the whole clade was also examined using a similar tree containing 34 extant species. A constant rates model for the growth of this clade was rejected, but analyses instead indicated a decline in the rate of speciation over time. These results support the hypothesis of an early expansion of the group, perhaps due to an early radiation influenced by the key innovation of live bearing, or the prevalence of Miocene volcanism. In general, support for the role of sexual selection in generating patterns of speciation is proving equivocal and we argue that vicariance biogeography and adaptive radiations remain the most likely determinants of major patterns of diversification of continental organisms.

Animals↗
PubMed1994

Shared sequence variants of Mus spretus LINE-1 elements tracing dispersal to within the last 1 million years.

LINE-1 repetitive sequences contain a record of an evolving population of transposons within the mammalian genome. Of the 100,000 copies of LINE-1 sequences per genome there are many shared sequence variants representing changes occurring within the propagating LINE-1 elements themselves, rather than changes that occur during retrotransposition or after an element inserts in the genome. These shared sequence variants define families of LINE-1 elements which have spread within specific periods of time. We have been interested in studying events in LINE-1 evolution since the speciation of Mus spretus and Mus domesticus approximately 3 million years (Myr) ago. To do this, we have collected LINE-1 sequences that have shared sequence variants specific to M. spretus. The sampled LINE-1 elements were sequenced at their extreme 3' ends, where the density of sequence variants is highest. The new sequences define six new M. spretus-specific sequence variants. Of these, we have found one that could be used to screen for LINE-1 elements arising in the last 1 Myr, which we argue is a critical sample for understanding the dynamics of LINE-1 propagation.

Animals↗
PubMed2003

Changes in cyanoprokaryote populations, Microcystis morphology, and microcystin concentrations in Lake Elphinstone (Central Queensland, Australia).

Lake Elphinstone is a tropical inland water body in the far north of the Fitzroy Catchment in Central Queensland, Australia, and has experienced recurrent toxic cyanoprokaryote blooms since 1997. This article reports on an examination of the environmental conditions of the lake and the concurrent cyanoprokaryote species together with their toxicity. The lake was sampled three times during periods of high cyanoprokaryote cell concentrations. Successive changes in the dominant Microcystis species were accompanied by variation in the concentration of the hepatotoxin microcystin. Environmental parameters recorded during dominance by both the highly toxic species Microcystis panniformis and the nontoxic M. botrys are provided. Nutrient status, temperature, and light conditions were associated with species change within the blooms. Variation of microcystin concentrations coincided with speciation change (i.e., morphological variation) within the blooms. Also discussed is the environmental impact of toxin production by M. panniformis with respect to influence on cell division, energy states, and toxin photodegradation. Lake Elphinstone is the first Australian location reported to have M. panniformis.

Environmental Monitoring↗
PubMed2003

Early hominin speciation at the Plio/Pleistocene transition.

Over the last half-decade or so, there has been an explosion in the recognition of hominin genera and species. We now have the late Miocene genera Orrorin and Sahelanthropus, the mid Pliocene genus Kenyanthropus, three new Pliocene species of Australopithecus (A. anamensis, A. garhi and A. bahrelghazali) and a sub species of Ardipithecus (Ar. r. kadabba) to contend with. Excepting also the more traditional species allocated to Paranthropus, Australopithecus and early Homo we are approaching around 15 species over 5 million years (excluding hominin evolution over the last one million years). Can such a large number of hominin species be justified? An examination of extant hominid (Gorilla gorilla, Pan troglodytes, and Pan paniscus) anatomical variability indicates that the range of fossil hominin variability supports the recognition of this large number of fossil species. It is also shown that not all hominins are directly related to the emergence of early Homo and as such have become extinct. Indeed the traditional australopithecine species 'A'. anamensis, 'A'. afarensis and 'A'. garhi are considered here to belong to a distinct genus Praeanthropus. They are also argued not be hominins, but rather an as yet undefined hominid group from which the more derived hominins evolved. The first hominin is represented by A. africanus or a hominin very much like it. The Paranthropus clade is defined by a derived heterochronic condition of peramorphosis, associated with sequential progenesis (contraction of successive growth stages) in brain and dental development, but a mixture of peramorphic and paedomorphic features in its craniofacial anatomy. Conversely, Kenyanthropus and Homo both share a pattern of peramorphosis, associated with sequential hypermorphosis (prolongation of successive growth stages) in brain development, and paedomorphosis processes in cranial, facial and dental development. This suggests, that these two clades share an important synapomorphy not recognised in the parsimony analyses, suggesting that they may form a sister group relationship to the exclusion of Paranthropus. This highlights the need to re-interpret phylogenetic results in terms of function and development. The rapid speciation and extinction as argued here is in keeping with other fossil groups in Africa at the Plio/Pleistocene transition. This emphasises that we must approach the pre-australopithecines and hominins as part of the endemic African fauna, and not in isolation to the evolutionary and climatic processes that were operating all around them.

Africa↗
PubMed1992

Speciation of tissue and cellular iron with on-line detection by inductively coupled plasma-mass spectrometry.

Iron accumulating to excess in tissues of humans and animal models occurs mainly as complexes with transferrin, ferritin, other hemoproteins, and insoluble hemosiderin particles. To determine the distribution of Fe amongst these molecular species, we have used inductively coupled plasma-mass spectrometry as a means of on-line, isotope-specific detection for their liquid chromatographic separation. The stable isotope 57Fe is a suitable isotope for monitoring the Fe content of each fraction, and its availability at high isotopic enrichment makes it an attractive choice for tracer studies when the use of a radioisotope is undesirable, e.g., in human subjects. The detection system offers the advantages of high sensitivity (detection limits in the parts per billion range), a wide dynamic range (linearity of the calibration curve over several orders of magnitude), and on-line analysis facilitating real-time evaluation of the chromatographic separation, in addition to isotope-specific information. The Fe distributions in healthy rat livers, liver and heart tissue from Fe-loaded human subjects, and human hepatocyte cultures are reported. The ferritin:hemosiderin ratio in these samples is shown to be an indicator of the degree of Fe loading and correlates well with that determined by Zeeman-corrected electrothermal atomic absorption as an alternative means of detection.

Animals↗
PubMed2005

Computer simulations of sympatric speciation in a simple food web.

Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with the formation of the species. Inspired by them, in this paper we investigate the process of sympatric speciation in a simple food web model. For that we modify the individual-based Penna model that has been widely used to study aging as well as other evolutionary processes. Initially, our web consists of a primary food source and a single herbivore species that feeds on this resource. Subsequently we introduce a predator that feeds on the herbivore. In both instances we manipulate directly a basal resource distribution and monitor the changes in the populations. Sympatric speciation is obtained for the top species in both cases, and our results suggest that the speciation velocity depends on how far up, in the food chain, the focus population is feeding. Simulations are done with three different sexual imprinting-like mechanisms, in order to discuss adaptation by natural selection.

Animals↗
PubMed2005

Ecological speciation in tropical reef fishes.

The high biodiversity in tropical seas provides a long-standing challenge to allopatric speciation models. Physical barriers are few in the ocean and larval dispersal is often extensive, a combination that should reduce opportunities for speciation. Yet coral reefs are among the most species-rich habitats in the world, indicating evolutionary processes beyond conventional allopatry. In a survey of mtDNA sequences of five congeneric west Atlantic reef fishes (wrasses, genus Halichoeres) with similar dispersal potential, we observed phylogeographical patterns that contradict expectations of geographical isolation, and instead indicate a role for ecological speciation. In Halichoeres bivittatus and the species pair Halichoeres radiatus/brasiliensis, we observed strong partitions (3.4% and 2.3% divergence, respectively) between adjacent and ecologically distinct habitats, but high genetic connectivity between similar habitats separated by thousands of kilometres. This habitat partitioning is maintained even at a local scale where H. bivittatus lineages are segregated between cold- and warm-water habitats in both Bermuda and Florida. The concordance of evolutionary partitions with habitat types, rather than conventional biogeographical barriers, indicates parapatric ecological speciation, in which adaptation to alternative environmental conditions in adjacent locations overwhelms the homogenizing effect of dispersal. This mechanism can explain the long-standing enigma of high biodiversity in coral reef faunas.

Adaptation, Biological↗
PubMed2006

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution.

To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed 'community phylogeny' approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.

Bacteria↗
PubMed2004

Relative contribution of dispersal and natural selection to the maintenance of a hybrid zone in Littorina.

Habitat preference behavior may play an important role in nonallopatric speciation. However, most examples of habitat preference contributing to differentiation within natural populations correspond to parasites or herbivores living in the discrete environments constituted by their animal or plant hosts. In the present study we investigated migration guided by habitat preference in the intertidal snail Littorina saxatilis in a hybrid zone associated with an ecotone across the shore, which is therefore a continuously varying environment. First, we found evidence for this behavior in one of the two locations studied. Second, we made reciprocal transplants to suppress the phenotypic gradient observed across the hybrid zone and measured the relative contributions of selection and migration to its regeneration. Selection played an important role at the two locations studied, but migration was only important at one, where it accounted for between a third and a half of the regenerated gradient. This overall minor effect of migration was relevant for theoretical models dealing with nonallopatric speciation, because it suggested that variation for habitat preference did not have an important role in the initiation of the differentiation process. The preference behavior observed in the hybrid zone would have evolved secondarily, as a consequence of habitat-dependent fitness differences between phenotypes.

Animals↗
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

A triple-layer model of the surface electrochemical properties of clay minerals.

We propose an electrical triple-layer model (TLM) to describe the electrochemical properties of clay minerals. This model includes a speciation model of the active crystallographic surface sites plus a classical description of the Stern and diffuse layers. In addition to the surface charges associated with the surface groups (aluminols, silanols, and Al--O--Si sites), the model takes into account the degree of isomorphic substitution rate inside the crystalline network. The model computes both the zeta potential and the low-frequency (few kHz) surface conductivity as these two properties are equally important to interpret electrokinetic properties of colloids and clay-rich porous materials. For surface conductivity, the model comprises two contributions; one is associated with the Stern layer (dynamic Stern layer) and the second is associated with the excess of counterions located in the diffuse Gouy-Chapman layer. The parameters of the TLM model are optimized using the Simplex algorithm. Comparison between the model and the experimental data shows good agreement for a reasonable choice of parameters close to the a priori values determined from quartz and gibbsite. Surface conductivity of smectite appears rather independent of salinity, while for kaolinite, surface conductivity increases with salinity. In both cases, the Stern layer contribution to surface conductivity dominates but the contribution associated with the diffuse layer cannot be neglected.

Journal Article↗