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Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection
03-22-2013 03-21-2013
High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.
Data from: Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas
03-19-2013 05-23-2013
Background: The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations of C. pallasii are also present in the border waters of the North-East Atlantic in Europe. These populations show considerable regional and life history differentiation and have been recognized in subspecies classification. The chronology of the inter-oceanic invasions and genetic basis of the phenotypic structuring however remain unclear. Results: The Atlantic and Pacific herrings both feature high mtDNA diversities (large long-term population sizes) in their native basins, but an ocean-wide homogeneity of C. harengus is contrasted by deep east-west Pacific subdivision within Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe are identified as members of the western Pacific C. pallasii clade, with some retained inter-oceanic haplotype sharing. They have lost diversity in colonization bottlenecks, but have also thereafter accumulated abundant new variation. The data delineate three phylogeographic groups within the European C. pallasii: herring from the inner White Sea; herring from the Mezen and Chesha Bays; and a strongly bottlenecked peripheral population in Balsfjord of the Norwegian Sea. Conclusions: The NE European outposts of C. pallasii are judged to be early post-glacial colonists from the NW Pacific. A strong regional substructure has evolved since that time, in contrast to the apparent broad-scale uniformity maintained by herrings in their native basins. The structure only partly matches the previous biological concepts based on seasonal breeding stocks or geographical subspecies designations. The trans-Arctic herring phylogeography is notably similar to those of the amphi-boreal mollusk taxa Macoma and Mytilus, suggesting similar histories of inter-oceanic connections. We also considered the time dependency of molecular rates, critical for interpreting timing of relatively recent biogeographical events, by comparing the estimates from coding and non-coding mitochondrial regions of presumably different mutation dynamics.
Data from: Historic disturbance regimes promote tree diversity only under low browsing regimes in eastern deciduous forest
02-01-2013 02-01-2014
Eastern deciduous forests are changing in species composition and diversity outside of classical successional trajectories. Three disturbance mechanisms appear central to this phenomenon: fire frequency is reduced, canopy gaps are smaller, and browsers are more abundant. Which factor is most responsible is a matter of great debate and remains unclear, at least partly because few studies have simultaneously investigated more than one process. We conducted a large-scale experiment in mesophytic forests of West Virginia, USA, to test three key hypotheses: (1) the fire hypothesis (fire suppression limits diversity to few shade-tolerant, fire-intolerant species that replace and suppress many fire-tolerant species); (2) the gap hypothesis (small gaps typical of today's forests promote dominance of a few shade-tolerant species); and (3) the browsing hypothesis (overbrowsing by deer limits diversity to a few unpalatable species). We tested these hypotheses using a factorial experiment that manipulated surface fire, large canopy gap formation (gap size 255 m2), and browsing by deer, and we followed the fates of >28 000 seedlings and saplings for five years. Understory tree communities in control plots were dominated (up to 90%) by Fagus grandifolia, averaging little more than two species, whereas overstories were diverse, with 10–15 species. Fire, large canopy gaps, and browsing all dramatically affected understory composition. However, our findings challenge views that fire and large canopy gaps can maintain or promote diversity, because browsers reduced the benefits of gaps and created depauperate understories following fire. Consequently, two major disturbances that once promoted tree diversity no longer do so because of browsing. Our findings appear to reconcile equivocal views on the role of fire and gaps. If browsers are abundant, these two disturbances either depress diversity or are less effective. Alternatively, with browsers absent, these disturbances promote diversity (three- to fivefold). Our results apply to large portions of eastern North America where deer are overabundant, and we provide compelling experimental evidence that historical disturbance regimes in combination with low browsing regimes typical of pre-European settlement forests could maintain high tree species diversity. However, restoring disturbances without controlling browsing may be counterproductive.
Data from: Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions
03-13-2013 07-22-2013
The life history of the fruit fly (Drosophila melanogaster) is well understood, but fitness components are rarely measured by following single individuals over their lifetime, thereby limiting insights into lifetime reproductive success, reproductive senescence and post-reproductive lifespan. Moreover, most studies have examined long-established laboratory strains rather than freshly caught individuals and may thus be confounded by adaptation to laboratory culture, inbreeding or mutation accumulation. Here, we have followed the life histories of individual females from three recently caught, non-laboratory-adapted wild populations of D. melanogaster. Populations varied in a number of life-history traits, including ovariole number, fecundity, hatchability and lifespan. To describe individual patterns of age-specific fecundity, we developed a new model that allowed us to distinguish four phases during a female's life: a phase of reproductive maturation, followed by a period of linear and then exponential decline in fecundity and, finally, a post-ovipository period. Individual females exhibited clear-cut fecundity peaks, which contrasts with previous analyses, and post-peak levels of fecundity declined independently of how long females lived. Notably, females had a pronounced post-reproductive lifespan, which on average made up 40% of total lifespan. Post-reproductive lifespan did not differ among populations and was not correlated with reproductive fitness components, supporting the hypothesis that this period is a highly variable, random ‘add-on’ at the end of reproductive life rather than a correlate of selection on reproductive fitness. Most life-history traits were positively correlated, a pattern that might be due to genotype by environment interactions when wild flies are brought into a novel laboratory environment but that is unlikely explained by inbreeding or positive mutational covariance caused by mutation accumulation.
Data from: Disentangling the effects of mating systems and mutation rates on cytoplamic diversity in gynodioecious Silene nutans and dioecious Silene otites
04-17-2013 07-18-2013
Many flowering plant species exhibit a variety of distinct sexual morphs, the two most common cases being the co- occurrence of females and males (dioecy) or the co-occurrence of hermaphrodites and females (gynodioecy). In this study we compared DNA sequence variability of the three genomes (nuclear, mitochondrial and chloroplastic) of a gynodioecious species, Silene nutans, with that of a closely related dioecious species, Silene otites. In the light of theoretical models, we expect cytoplasmic diversity to differ between the two species due to the selective dynamics that acts on cytoplasmic genomes in gynodioecious species: under an epidemic scenario, the gynodioecious species is expected to exhibit lower cytoplasmic diversity than the dioecious species, while the opposite is expected in the case of balancing selection maintaining sterility cytoplasms in the gynodioecious species. We found no difference between the species for nuclear gene diversity, but, for the cytoplasmic loci, the gynodioecious S. nutans had more haplotypes, and higher nucleotide diversity, than the dioecious relative, S. otites, even though the latter has a relatively high rate of mitochondrial synonymous substitutions, and therefore presumably a higher mutation rate. Therefore, since the mitochondrial mutation rate cannot account for the higher cytoplasmic diversity found in S. nutans, our findings support the hypothesis that gynodioecy in S. nutans has been maintained by balancing selection rather than by epidemic-like dynamics.
Data from: Royal dynasties as human inbreeding laboratories: the Habsburgs
04-10-2013 07-18-2013
The European royal dynasties of the Early Modern Age provide a useful framework for human inbreeding research. In this article, consanguineous marriage, inbreeding depression and the purging of deleterious alleles within a consanguineous population are investigated in the Habsburgs, a royal dynasty with a long history of consanguinity over generations. Genealogical information from a number of historical sources was used to compute kinship and inbreeding coefficients for the Habsburgs. Marriages contracted by the Habsburgs from 1450 to 1750 presented an extremely high mean kinship (0.0628 {plus minus} 0.009), which was the result of the matrimonial policy conducted by the dynasty to establish political alliances through marriage. A strong inbreeding depression for both infant and child survival was detected in the progeny of 71 Habsburg marriages in the period 1450-1800. The inbreeding load for child survival experienced a pronounced decrease from 3.98 {plus minus} 0.87 in the period 1450-1600 to 0.93 {plus minus} 0.62 in the period 1600-1800, temporal changes in the inbreeding depression for infant survival were not detected. Such reduction of inbreeding depression for child survival in a relatively small number of generations could be caused by elimination of deleterious alleles of large effects according with predictions from purging models. The differential purging of the infant and child inbreeding loads suggests that the genetic basis of inbreeding depression was probably very different for infant and child survival in the Habsburg lineage. Our findings provide empirical support that human inbreeding depression for some fitness components might be purged by selection within consanguineous populations.
Data from: Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele
04-10-2013 07-18-2013
The Mexican tetra, Astyanax mexicanus, comprises 29 populations of cave-adapted fish distributed across a vast karst region in northeastern Mexico. These populations have a complex evolutionary history, having descended from "old" and "young" ancestral surface-dwelling stocks that invaded the region ~8 MYa and ~2.1 MYa, respectively. This study investigates a set of captive, pigmented Astyanax cavefish collected from the Micos cave locality in 1970, in which albinism appeared over the last two decades. We combined novel coloration analyses, coding sequence comparisons, and mRNA expression level studies to investigate the origin of albinism in captive-bred Micos cavefish. We discovered albino Micos cavefish harbor two copies of a loss-of-function Oca2 allele previously identified in the geographically distant Pachón cave population. This result suggests that phylogenetically young Micos cavefish and phylogenetically old Pachón fish inherited this Oca2 allele from the ancestral surface-dwelling taxon. This likely resulted from the presence of the loss-of-function Oca2 haplotype in the "young" ancestral surface-dwelling stock that colonized the Micos cave, and also introgressed into the ancient Pachón cave population. The appearance of albinism in captive Micos cavefish, caused by the same loss-of-function allele present in Pachón cavefish, implies that geographically and phylogenetically distinct cave populations can evolve the same troglomorphic phenotype from standing genetic variation present in the ancestral taxon.
Data from: Evolutionary hotspots in the Mojave Desert
04-15-2013 05-21-2013
Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.
Data from: Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence
06-28-2013 07-01-2013
BACKGROUND: Heroin dependence is a debilitating psychiatric disorder with complex inheritance. Since the dopaminergic system has a key role in rewarding mechanism of the brain, which is directly or indirectly targeted by most drugs of abuse, we focus on the effects and interactions among dopaminergic gene variants. OBJECTIVE: To study the potential association between allelic variants of dopamine D2 receptor (DRD2), ANKK1 (ankyrin repeat and kinase domain containing 1), dopamine D4 receptor (DRD4), Catechol-O-methyl transferase (COMT) and dopamine transporter (SLC6A3) genes and heroin dependence in Hungarian patients. METHODS: 303 heroin dependent subjects and 555 healthy controls were genotyped for 7 single nucleotide polymorphisms (SNPs): rs4680 of the COMT gene; rs1079597 and rs1800498 of the DRD2 gene; rs1800497 of the ANKK1 gene; rs1800955, rs936462 and rs747302 of the DRD4 gene. Four variable number of tandem repeats (VNTRs) were also genotyped: 120 bp duplication and 48 bp VNTR in exon 3 of DRD4 and 40 bp VNTR and intron 8 VNTR of SLC6A3. We also provide a multivariate model for the associations among them implying Bayesian networks in Bayesian multilevel analysis. FINDINGS AND CONCLUSIONS: In single marker analysis the TaqIA (rs1800497) and TaqIB (rs1079597) variants were associated with heroin dependence. Moreover, -521 C/T SNP (rs1800955) of the DRD4 gene showed nominal association with a possible protective effect of the C allele. After applying the Bonferroni correction TaqIB was still significant suggesting that the minor (A) allele of the TaqIB SNP is a risk component in the genetic background of heroin dependence. The findings of the additional multiple marker analysis are consistent with the results of the single marker analysis, but this method was able to reveal an indirect effect of a promoter polymorphism (rs936462) of the DRD4 gene and this effect is mediated through the -521 C/T (rs1800955) polymorphism in the promoter.
Data from: The fate of phosphorus fertilizer in Amazon soya bean fields
04-22-2013 05-20-2013
Fertilizer-intensive soya bean agriculture has recently expanded in southeastern Amazônia, and whereas intensive fertilizer use in the temperate zone has led to widespread eutrophication of freshwater ecosystems, the effects in tropical systems are less well understood. We examined the fate of fertilizer P by comparing P forms and budgets across a chronosequence of soya bean fields (converted to soya beans between 2003 and 2008) and forests on an 800 km2 soya bean farm in Mato Grosso, Brazil. Soya bean fields were fertilized with 50 kg P ha-1 yr-1 (30 kg P ha-1 y-1 above what is removed in crops). We used modified Hedley fractionation to quantify soil P pools and found increases in less-plant-available inorganic pools and decreases in organic pools in agricultural soils compared with forest. Fertilizer P did not move below 20 cm. Measurements of P sorption capacity suggest that while fertilizer inputs quench close to half of the sorption capacity of fast-reacting pools, most added P is bound in more slowly reacting pools. Our data suggest that this agricultural system currently has a low risk of P losses to waterways and that long time-scales are required to reach critical soil thresholds that would allow continued high yields with reduced fertilizer inputs.
Data from: Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms
04-17-2013 06-18-2013
The recent emergence of barcoding approaches coupled to those of Next Generation Sequencing (NGS) have raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL, and cox1), and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. In the goal to detect methodological biases, one sample was constituted directly from pooled cultures, whereas the others consisted of pooled PCR products. The NGS reads obtained by pyrosequencing (Roche 454) were compared first to a DNA reference library including the sequences of all the species used to constitute the mock community, and secondly to a complete DNA reference library with a larger taxonomic coverage. A stringent taxonomic assignation, gave inventories that were compared to the real one. We detected biases due to DNA extraction and to PCR amplification that resulted in false-negatives detection. Conversely, pyrosequencing errors appeared to generate false-positives, especially in case of closely allied species. The taxonomic coverage of DNA reference libraries appears to be the most crucial factor, together with marker polymorphism which is essential to identify taxa at the species level. RbcL offers a high resolving power which, together with its large DNA reference library. Though needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.
Data from: Parsimonious inference of hybridization in the presence of incomplete lineage sorting
06-04-2013 08-12-2013
Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analysing a yeast data set, we demonstrate issues that arise when analysing real data sets. Although a probabilistic approach was recently introduced for this problem, and although parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS.
Data from: Genetic architecture underlying morning and evening circadian phenotypes in fruit flies Drosophila melanogaster
04-24-2013 09-19-2013
Circadian rhythms are perhaps among the genetically best characterised behaviours. Several mutations with drastic effects on circadian processes have been identified and models developed to explain how clock genes and their products generate self-sustained oscillations. While natural variations in circadian phenotypes have been studied extensively, the genetic basis of such adaptive variations remains largely unknown. Here we report the results of a preliminary genetic analysis of adaptive divergence of circadian phenotypes in populations of fruit flies Drosophila melanogaster. Two sets of populations- early and late were created in a long-term laboratory selection for morning and evening emergence with four independent replicates each. Over the course of ~55 generations, the early flies evolved increased morning emergence and shorter circadian period, while late flies evolved increased evening emergence and longer period. To examine the genetic basis of circadian phenotypes, we set-up crosses between early and late flies and monitored emergence and activity/rest rhythms in the F1, backcrossed and F2 progeny. Our analysis suggests that the genetic basis of divergent circadian phenotypes in early and late stocks is primarily autosomal. Line-cross analysis revealed that additive and non-additive genetic effects contribute to the divergence of circadian phenotypes in early and late flies.
Data from: Linking the evolution of body shape and locomotor biomechanics in bird-line archosaurs
04-24-2013 05-14-2013
Locomotion in living birds (Neornithes) has two remarkable features: feather-assisted flight, and the use of unusually crouched hindlimbs for bipedal support and movement. When and how these defining functional traits evolved remains controversial. However, the advent of computer modelling approaches and the discoveries of exceptionally preserved key specimens now make it possible to use quantitative data on whole-body morphology to address the biomechanics underlying this issue. Here we use digital body reconstructions to quantify evolutionary trends in locomotor biomechanics (whole-body proportions and centre-of-mass position) across the clade Archosauria. We use three-dimensional digital reconstruction to estimate body shape from skeletal dimensions for 17 archosaurs along the ancestral bird line, including the exceptionally preserved, feathered taxa Microraptor, Archaeopteryx, Pengornis and Yixianornis, which represent key stages in the evolution of the avian body plan. Rather than a discrete transition from more-upright postures in the basal-most birds (Avialae) and their immediate outgroup deinonychosauria, our results support hypotheses of a gradual, stepwise acquisition of more-crouched limb postures across much of theropod evolution, although we find evidence of an accelerated change within the clade Maniraptora (birds and their closest relatives, such as deinonychosaurs). In addition, whereas reduction of the tail is widely accepted to be the primary morphological factor correlated with centre-of-mass position and, hence, evolution of hindlimb posture, we instead find that enlargement of the pectoral limb and several associated trends have a much stronger influence. Intriguingly, our support for the onset of accelerated morpho-functional trends within Maniraptora is closely correlated with the evolution of flight. Because we find that the evolution of enlarged forelimbs is strongly linked, via whole-body centre of mass, to hindlimb function during terrestrial locomotion, we suggest that the evolution of avian flight is linked to anatomical novelties in the pelvic limb as well as the pectoral.
Data from: Cortisol awakening response is linked to disease course and progression in multiple sclerosis
04-16-2013 05-22-2013
OBJECTIVES: Dysregulation of the hypothalamus-pituitary-adrenal (HPA) axis has frequently been reported in multiple sclerosis (MS). So far, HPA axis function in MS has predominantly been studied under pharmacological stimulation which is associated with a series of methodological caveats. Knowledge of circadian cortisol patterns and cortisol awakening response (CAR) is still limited. METHODS: A total of 77 MS patients (55 relapsing-remitting MS (RRMS) / 22 secondary-progressive MS (SPMS)) as well as 34 healthy control (HC) subjects were enrolled. Diurnal cortisol release was assessed by repeated salivary cortisol sampling. Neurological disability was rated by the Kurtzke’s Expanded Disability Status Scale (EDSS). Depressive symptoms and perceived stress were assessed by self-report measures. RESULTS: RRMS but not SPMS patients differed in circadian cortisol release from HC subjects. Differences in cortisol release were restricted to CAR. Treated and treatment naïve RRMS patients did not differ in CAR. In a RRMS follow-up cohort (nine months follow-up), RRMS patients with EDSS progression (≥ 0.5) expressed a significantly greater CAR compared to HC subjects. RRMS patients with a stable EDSS did not differ from HC subjects. Neither depressive symptoms nor perceived stress ratings were associated with CAR in RRMS patients. In a step-wise regression analysis, EDSS at baseline and CAR were predictive of EDSS at follow-up (R² = 67 %) for RRMS patients. CONCLUSIONS: Circadian cortisol release, in particular CAR, shows a course specific pattern with most pronounced release in RRMS. There is also some evidence for greater CAR in RRMS patients with EDSS progression. As a consequence, CAR might be of predictive value in terms of neurological disability in RRMS patients. The possible role of neuroendocrine-immune interactions in MS pathogenesis is further discussed.
Data from: Genomic islands of divergence are not affected by geography of speciation in sunflowers.
05-07-2013 07-07-2014
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.
Data from: Identifying loci under selection against gene flow in isolation with migration models
03-02-2013 05-20-2013
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
Data from: Evolution of smooth tubercle bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection
05-21-2013 06-04-2013
Background: PE and PE_PGRS are two mycobateria-restricted multigene families encoding membrane associated and secreted proteins that have expanded mainly in the pathogenic species, notably the Mycobacterium tuberculosis complex (MTBC). Several lines of evidence attribute to PE and PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more insight into the nature of these genes, we sought to address their evolutionary trajectories in the group of smooth tubercle bacilli (STB), the putative ancestor of the clonal MTBC. Methodology/Principal Findings: By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate significant incongruence among single gene genealogies and detect strong signals of recombination using various approaches. Coalescent-based estimation of population recombination and mutation rates (ρ and θ, respectively) indicates that the two mechanisms are of roughly equal importance in generating diversity (ρ/θ = 1.457), a finding in a marked contrast to house keeping genes (HKG) whose evolution is chiefly brought about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times higher mean rate of nonsynonymous substitutions, with strong evidence of positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has previously been shown to be essential for mycobacterial survival in macrophages and granulomas. Imprint of positive selection operating on specific amino acid residues or along branches of PE_PGRS62 phylogenetic tree was further demonstrated using maximum likelihood- and covarion-based approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in present-day MTBC strains. Conclusions/Significance: Overall the data indicate that, in STB, PE/PE_PGRS genes have undergone a strong diversification process that is speeded up by recombination, with evidence of positive selection. The finding that positive selection involved an essential PE_PGRS gene whose sequence appears to be driven to fixation in present-day MTBC strains lends further support to the critical role of PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.
Data from: The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species
03-12-2013 03-15-2013
Background: Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence. The balance between gene flow and selection determines the maintenance of such a structure in sympatry. Studying these two antagonistic forces in plant pathogens is made possible because of the high ability of pathogens to disperse and of the strong selective pressures exerted by their hosts. In this article, we analysed the genetic structure of the population of the apple scab fungus, Venturia inaequalis, in a heterogeneous environment composed of various Malus species. Inferences were drawn from microsatellite and AFLP data obtained from 114 strains sampled in a single orchard on nine different Malus species to determine the forces that shape the genetic structure of the pathogen. Results: Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) an avirulent subpopulation infecting only Malus trees that did not carry this resistance gene. A genome scan of loci on these two subpopulations did not detect any locus under selection. Additionally, we did not detect any other particular substructure linked to different hosts. However, an isolation-by-distance (IBD) pattern at the orchard scale revealed free gene flow within each subpopulation. Conclusions: Our work shows a rare example of a very strong effect of a resistance gene on pathogen populations. Despite the high diversity of Malus hosts, the presence of Rvi6 seems sufficient to explain the observed genetic structure. Moreover, detection of an IBD pattern at the orchard scale revealed a very low average dispersal distance that is particularly significant for epidemiologists and landscape managers for the design of scab control strategies.
Data from: Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiae
04-09-2013 06-05-2013
Multicellular complexity is a central topic in biology, but the evolutionary processes underlying its origin are difficult to study and remain poorly understood. Here we use experimental evolution to investigate the tempo and mode of multicellular adaptation during a de novo evolutionary transition to multicellularity. Multicelled “snowflake” yeast evolved from a unicellular ancestor after 7 days of selection for faster settling through liquid media. Over the next 220 days, snowflake yeast evolved to settle 44% more quickly. Throughout the experiment the clusters evolved faster settling by three distinct modes. The number of cells per cluster increased from a mean of 42 cells after 7 days of selection to 114 cells after 227 days. Between days 28 and 65, larger clusters evolved via a twofold increase in the mass of individual cells. By day 227, snowflake yeast evolved to form more hydrodynamic clusters that settle more quickly for their size than ancestral strains. The timing and nature of adaptation in our experiment suggests that costs associated with large cluster size favor novel multicellular adaptations, increasing organismal complexity.