Model of interaction between learning and evolution. Computer simulation and analytical results

The evolution of fruit-fly biology

Demographic uncertainty in ecological risk assessments

BackgroundThe cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique.ResultsWe conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4–7.8%) while that of nuclear genes was low (0.06–0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.ConclusionsOur research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.

Global phylogeography of the dolphinfish ( Coryphaena hippurus): The influence of large effective population size and recent dispersal on the divergence of a marine pelagic cosmopolitan species

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 x 10(4) to 10.9 x 10(4)) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.

Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. This phenomenon is thought to be driven by selection for translational efficiency. As the efficacy of selection is proportional to the effective population size, species with large population sizes, such as phytoplankton, are expected to have strong codon bias. To test this, we measured codon bias in 215 strains from Haptophyta, Chlorophyta, Ochrophyta (except diatoms that were studied previously), Dinophyta, Cryptophyta, Ciliophora, unicellular Rhodophyta and Chlorarachniophyta. Codon bias is modest in most groups, despite the astronomically large population sizes of marine phytoplankton. The strength of the codon bias, measured with the effective number of codons, is the strongest in Haptophyta and the weakest in Chlorarachniophyta. The optimal codons are GC-ending in most cases, but several shifts to AT-ending codons were observed (mainly in Ochrophyta and Ciliophora). As it takes a long time to reach a new equilibrium after such shifts, species having AT-ending codons show a lower frequency of optimal codons compared to other species. Genetic diversity, calculated for species with more than three strains sequenced, is modest, indicating that the effective population sizes are many orders of magnitude lower than the astronomically large census population sizes, which helps to explain the modest codon bias in marine phytoplankton. This study represents the first comparative analysis of codon bias across multiple major phytoplankton groups.

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 × 104 to 10.9 × 104) during 0.74–1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.Corresponding Editor: S. Edwards

Author response: Dynamics of immune memory and learning in bacterial communities

Editor's evaluation: Dynamics of immune memory and learning in bacterial communities

Decision letter: Dynamics of immune memory and learning in bacterial communities

The model of interaction between learning and evolutionary optimization is designed and investigated. The evolving population of modeled organisms is considered. The mechanism of genetic assimilation of the acquired features during a number of generations of Darwinian evolution is studded. The genetic assimilation means that individually acquired features are “re-invented” by evolution and recorded directly into the genotypes of organisms. It is shown that the genetic assimilation takes place as follows: the organism distribution moves towards the optimum at learning and further selection; then genotypes of selected organisms also move towards the optimum. The mechanism of influence of the learning load is analyzed. It is shown that the learning load leads to a significant acceleration of evolution. The hiding effect is also studied; this effect means that a strong learning inhibits the evolutionary search in some situations.

The lecture characterizes the following main properties of interaction between learning and evolution: (1) the mechanism of the genetic assimilation, (2) the hiding effect, (3) the role of the learning load at investigated processes of learning and evolution. During the genetic assimilation, phenotypes of modeled organisms move towards the optimum at learning; after this, genotypes of selected organisms also move towards the optimum. The hiding effect means that strong learning can inhibit the evolutionary search for the optimal genotype. The learning load can lead to a significant acceleration of evolution.

The classical theory about effects of high residential density is "negative," stating that high density produces negative social attitudes and undesirable behaviors. Yet empirical re search usually finds density only weakly related to individuals' attitudes and behavior. A survey was conducted in Baltimore for three purposes: to test "negative" hypotheses for new dependent variables; to determine if negative density effects appear only when certain "buffers" are weak; and to test hypotheses about "positive" effects of density. Results show that large population size and feelings that an area is overpopulated produce frustrations about the environment. Objective density has some negative and positive effects, but it is less important than population size, subjective appraisal of population, and population composition. Compared to prior research, the special contributions of the Baltimore study are examination of (1) population size, (2) "positive" consequences of high density and large size, and (3) effects in three distinct residential areas.

IntroductionAs anthropogenic change alters and fragments habitats, it is apparent that evolutionary change can co-occur with ecological change, though the scale and consequences of this contemporary evolution remain unclear. In coastal salt marshes of eastern North America, the flood tolerant low elevation marsh grass (Spartina alterniflora), is displacing Spartina patens, the flood intolerant high elevation marsh grass. Rising seas restrict S. patens, once occupying large areas of many hectares, to increasingly small patches, some as small as a few square meters. MethodsUsing nine microsatellite loci, we examined the genetic diversity and population structure of Tumidagena minuta, a minute, flightless planthopper and specialist herbivore of S. patens. We sampled T. minuta from S. patens habitat patches of varying radius (3–82 meters) and distances (54–1,100 meters) to test how landscape variation affects population genetic parameters associated with microevolutionary processes. We sampled and genotyped 142 T. minuta individuals across six S. patens patches in a single marsh in New Jersey, USA. ResultsWe observed high polymorphism, observing between 7 and 28 alleles per locus and an average of 13.3 alleles per locus. We observed no genetic differentiation among sampled patches (RST = −0.0109). The contemporary genetic effective population size (Ne) was estimated at approximately 360 (95% confidence interval: 208–1325) based on two-locus linkage disequilibrium. Based on an estimate of Nem = 32.4 in the finite island model, the estimated gene flow rate among these patches was 0.09 migrants per generation. DiscussionThese estimates, which are rarely produced for non-model insects, suggest that, despite rapid and precipitous decreases in habitat size and connectivity, T. minuta populations have remained large and have experienced little genetic differentiation due to drift. Ecological changes in patch size and isolation at this scale have not influenced population genetic processes like effective migration rate for T. minuta, consistent with our expectations for an insect with a large population size.

Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.