Population structure of graptolite assemblages

Graptolite rhabdosomes display a diverse suite of morphologies. The range of morphotypes present within most moderate to high diversity assemblages from the Ordovician and Silurian is similar, despite the different taxonomic composition of the faunas at different times. Survivorship analyses of graptolite faunas from the Ordovician and Silurian demonstrate strong similarities in the mortality rates of unrelated graptolites of similar functional morphology. It also shows a strong correlation of decreasing mortality rates amongst more mature colonies with increasing rhabdosome complexity. This similarity in both functional morphology and life history of graptolites suggests that they lived within a very stable planktic community structure

The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages

The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intra-group but limited inter-group recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly over-represented in Group A compared to Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly over-represented in Group B compared to Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts

Evolutionary dynamics on any population structure

Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been absent for a long time, but have recently emerged for special structures where all individuals have the same number of neighbors. But the problem of determining which trait is favored by selection in the natural case where the number of neighbors can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class which suggests there is no efficient algorithm. Whether there exists a simple solution for weak selection was unanswered. Here we provide, surprisingly, a general formula for weak selection that applies to any graph or social network. Our method uses coalescent theory and relies on calculating the meeting times of random walks. We can now evaluate large numbers of diverse and heterogeneous population structures for their propensity to favor cooperation. We can also study how small changes in population structure---graph surgery---affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.Comment: 68 pages, 10 figure

Gene-history correlation and population structure

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.Comment: Revised and extended version: 26 pages, 5 figures, 1 tabl

The scale of population structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales