Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation,loss of sex and post-mating genetic incompatibilities

Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.     

Autoregulation of the nar operon encoding nitrate reductase in Escherichia coli

Summary Nitrate reductase is demonstrated to exert an autogenous control on its own synthesis. This effect requires the participation of the molybdenum cofactor. Use of strains in which the control region of the nar operon is mutated reveals two loci in this region: one, affected in strain LCB94, is common to both autoregulation and induction by nitrate while the other, mutated in strain LCB188, is specific for the induction by nitrate. It is proposed that the autogenous control prevents the unnecessary accumulation of the nitrate reductase subunits in the cytoplasm.     

Transforming growth factor beta induces rosettes of podosomes in primary aortic endothelial cells

Cytoskeletal rearrangements are central to endothelial cell physiology and are controlled by soluble factors, matrix proteins, cell-cell interactions, and mechanical forces. We previously reported that aortic endothelial cells can rearrange their cytoskeletons into complex actin-based structures called podosomes when a constitutively active mutant of Cdc42 is expressed. We now report that transforming growth factor beta (TGF-beta) promotes podosome formation in primary aortic endothelial cells. TGF-beta-induced podosomes assembled together into large ring- or crescent-shaped structures. Their formation was dependent on protein synthesis and required functional Src, phosphatidylinositide 3-kinase, Cdc42, RhoA, and Smad signaling. MT1-MMP and metalloprotease 9 (MMP9), both upregulated by TGF-beta, were detected at sites of podosome formation, and MT1-MMP was found to be involved in the local degradation of extracellular matrix proteins beneath the podosomes and required for the invasion of collagen gels by endothelial cells. We propose that TGF-beta plays an important role in endothelial cell physiology by inducing the formation of podosomal structures endowed with metalloprotease activity that may contribute to arterial remodeling.     

Do elephants prevent other African herbivores from using waterholes in the dry season?

In some African protected areas, concerns have arisen about the influence of locally high elephant numbers on other forms of biodiversity. In arid and semi-arid savannas, surface-water resources are scarce and agonistic interactions between elephants and other herbivores have been reported at waterholes, yet surprisingly very little is known about the impact of elephants on the use of waterholes by other herbivores. Here, we test whether when there are elephants at a waterhole, other herbivores (1) do not change their drinking behaviour; (2) spend shorter time around the water because they are disturbed by elephants’ presence and consequently have to leave the waterhole area probably without having met their water requirements, or (3) spend more time around the water probably owing to an increase in vigilance activities or because the presence of elephants may signal safety from predators. Results show that all species spend longer time around water when there are elephants at the waterhole, although the difference is not large. Consequently, this study strongly suggests that elephants do not prevent other herbivores from drinking (time at waterholes is not shortened when elephants are around). Further, if the additional time spent to drink is linked to an increased vigilance, the difference is not large, and hence unlikely to affect the population dynamics of other herbivores.     

Abundance and site fidelity of bottlenose dolphins off a remote oceanic island (Reunion Island,southwest Indian Ocean)

This study represents the first comprehensive assessment of the population dynamics and residency of common bottlenose dolphin around Reunion Island (southwest Indian Ocean). Understanding dynamics and movement patterns of this local population is essential to guide effective conservation efforts, notably in a context of growing dolphin-watching activities. Dedicated surveys based on photo-identification methods were conducted over 6 years (2010–2015). The species was present year-round, in groups of 25 individuals on average (1–150). Jolly-Seber mark-recapture models resulted in a population estimate of 254 individuals (95% CI = 191–337) and an apparent annual survival rate of 0.83. The population was almost equally split into three residency patterns: residents (33.1%), long-term visitors (32.6%), and short-term visitors (34.3%, including transients, i.e., individuals only seen once [14.9%]), suggesting that the majority of the population showed a moderate-to-high level of residency in the study area. Individuals from the three residency patterns associated randomly, mixing together and forming a single community. Models based on the lagged identification rate indicated emigration and reimmigration to the survey area, with some individuals occupying the study area for about 2 years (832 days), and remaining outside for an average of 276 days, probably exhibiting larger home ranges and extensive movement behavior.     

The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility

Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individuals are heterozygous at the S locus and recombination is suppressed in the S-locus region, it has been suggested that deleterious mutations could accumulate at genes linked to the S locus, generating a “sheltered load.” In this article, we first theoretically investigate the conditions generating sheltered load in SSI. We show that deleterious mutations can accumulate in linkage with specific S alleles, and particularly if those S alleles are dominant. Second, we looked for the presence of sheltered load in Arabidopsis halleri using CO₂ gas treatment to overcome self-incompatibility. By examining the segregation of S alleles and measuring the relative fitness of progeny, we found significant sheltered load associated with the most dominant S allele (S15) of three S alleles tested. This sheltered load seems to be expressed at several stages of the life cycle and to have a larger effect than genomic inbreeding depression.THE main genetic mechanism causing inbreeding depression is believed to be the expression of recessive mildly deleterious mutations in inbred individuals (Charlesworth and Charlesworth 1999). These deleterious mutations are generally supposed to be distributed throughout the genome. However, some genomic regions where loci under balancing selection are present may be more inclined than others to accumulate deleterious mutations and could lead to the formation of what is generally called a “sheltered load” (Uyenoyama 1997; van Oosterhout 2009). The sheltered load has been suggested as a potential reason why MHC genes, mating-type systems in fungi, and self-incompatibility systems in plants generally show longer terminal branches in their genealogies than expected (Richman 2000). Despite its potential importance, the extent of the sheltered load is still largely unknown.Homomorphic self-incompatibility is widely distributed among angiosperm families (de Nettancourt 2001; Igic et al. 2008). Self-incompatibility (SI) is controlled by genes under strong balancing selection. SI prevents self-fertilization and promotes outcrossing by the presence of a gamete recognition system involving proteins expressed in both the pollen and the pistil. The proteins controlling the recognition system are generally encoded by genes located in a single genomic region, the S locus. Each plant in a self-incompatible population expresses an S specificity and is unable to mate with other plants expressing the same specificity. In species with gametophytic self-incompatibility (GSI), the S specificity is controlled by interactions between protein expressed in the pollen''s haploid genome, the male gametophyte, and the pistil''s diploid genome. In species with sporophytic self-incompatibility (SSI), S specificity is controlled by interactions between gene products of the diploid sporophyte expressed on the pollen coat and those on the stigmatic surface. In this mating system, three reasons may facilitate the accumulation of recessive deleterious mutations in this region, namely a sheltered load (Uyenoyama 1997). First, high heterozygote frequencies are expected in populations at the S locus but also at other linked loci in the S-locus genomic region (Kamau et al. 2007). Second, negative frequency-dependent selection, a form of balancing selection, is the main selective force acting on the S locus and on linked genes (Castric and Vekemans 2004). Third, the recombination rate is low in the S-locus region (Casselman et al. 2000; Charlesworth et al. 2003). Such a sheltered load may have important evolutionary consequences for SI evolution: it can slow down the rate of emergence of new S alleles (Uyenoyama 2003), considerably extend the conditions for the persistence of GSI (Porcher and Lande 2005), and, finally, substantially increase the inbreeding depression in a small population (Glémin et al. 2001), which can have large consequences for endangered species and the viability of their populations.The magnitude of the sheltered load should depend on the size of the genomic region in which heterozygosity is enforced because of linkage to the S locus and also on the number of genes affecting fitness in that region. From an analysis of recombination rates in the S-locus genomic region in Arabidopsis lyrata, a species with SSI, Kawabe et al. (2006) suggested that the number of genes in the S-genomic region is probably not high enough for a large sheltered load to have an impact on fitness compared to the overall genomic load. Dowd et al. (2000) indeed found only 13 genes near the S locus in Petunia inflata. However, two studies have demonstrated the existence of transmission ratio distortion of some S alleles in A. lyrata (Bechsgaard et al. 2004; Leppala et al. 2008). The authors proposed that this could be indirect evidence of the existence of a sheltered load. To the best of our knowledge, the existence of sheltered load in SI species was specifically demonstrated so far only in Solanum carolinense, a species with GSI: Stone (2004) crossed individuals sharing alleles at the S locus, using bud pollination to overcome self-incompatibility. By looking at seed number and genotype of the progeny, a sheltered load linked to only two of seven S alleles investigated was detected. Direct evidence and estimations of the extent of the sheltered load are thus lacking.In SSI, complex dominance interactions among S alleles are usually observed [Ipomoea trifida (Kowyama et al. 1994), Brassica campestris (Hatakeyama et al. 1998), A. lyrata (Mable et al. 2003), and A. halleri (Llaurens et al. 2008a)]. The effect of these dominance interactions on the occurrence of a sheltered genetic load has not been investigated either theoretically or empirically, but may potentially be large. Indeed, recessive S alleles are expected to be more often homozygous in natural populations than dominant alleles (Schierup et al. 1997), and so may rapidly purge strongly deleterious recessive mutations, and thus should limit the sheltering effect. The sheltered load could thus differ depending on the dominance levels of the associated S alleles.In this study, we first investigated the theoretical conditions for the accumulation of a sheltered load in a SSI system, using stochastic simulations. Then, we empirically tested the existence and strength of an S-linked sheltered load in relation to dominance levels in SSI. We focused on A. halleri, a member of the Brassicaceae family. In this family, the S-locus region includes two major genes: SCR (also called SP-11), encoding a cysteine-rich protein of the pollen envelope, and SRK, encoding a receptor kinase located across the membrane of the papilla cells. High heterozygote frequencies at the S locus have been found in several species like B. insularis (Glémin et al. 2005) or A. lyrata (Schierup et al. 2006). The SRK and SCR genes are tightly linked, since they are located close to each other, and recombination suppression in the S-locus region has been suggested in several studies: in Brassica (Casselman et al. 2000) and in A. lyrata (Kamau and Charlesworth 2005; Kawabe et al. 2006). The conditions thus may be suitable for the existence of sheltered genetic load in A. halleri. We performed controlled pollinations in A. halleri to specifically measure the magnitude of the potential sheltered load of three S alleles with different dominance levels: a dominant, an intermediate, and a recessive allele. To evaluate the effect of the sheltered load on these crosses, we looked at the number of seeds produced, as well as at the development and the genotype at the S locus of the progeny.     

Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Lemniscomys striatus and to evaluate the relative roles of ecological change, habitat patchiness, rivers and geological barriers in structuring patterns of diversity. Location Sub‐Saharan Africa. Methods The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene) were addressed in a survey of 128 individuals of L. striatus from 42 localities. Using maximum parsimony, maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intraspecific relationships and tested hypotheses for historical patterns of gene flow within L. striatus. Results Our results identified four major geographical clades within L. striatus: a West African clade, a Benin‐Nigeria clade, a Central African clade, and an East African clade. Several subclades were identified within these four major clades. Restricted gene flow with isolation by distance was recorded, which is congruent with the low dispersal ability of such a small murid rodent. No clear signal of population expansion was detected within clades or subclades. Main conclusions The western rift system and the Volta and Niger rivers may have acted as long‐term extrinsic barriers to gene flow, resulting in the emergence of the four main clades of L. striatus. The observed pattern of mitochondrial variation observed within each clade probably results from late Pleistocene climatic and vegetation changes: during adverse conditions (forest expansion), L. striatus may have survived only in refugia, and then experienced range expansion under favourable conditions (savanna expansion).     

The toxofilin-actin-PP2C complex of Toxoplasma: identification of interacting domains

Toxofilin is a 27 kDa protein isolated from the human protozoan parasite Toxoplasma gondii, which causes toxoplasmosis. Toxofilin binds to G-actin, and in vitro studies have shown that it controls elongation of actin filaments by sequestering actin monomers. Toxofilin affinity for G-actin is controlled by the phosphorylation status of its Ser53, which depends on the activities of a casein kinase II and a type 2C serine/threonine phosphatase (PP2C). To get insights into the functional properties of toxofilin, we undertook a structure-function analysis of the protein using a combination of biochemical techniques. We identified a domain that was sufficient to sequester G-actin and that contains three peptide sequences selectively binding to G-actin. Two of these sequences are similar to sequences present in several G- and F-actin-binding proteins, while the third appears to be specific to toxofilin. Additionally, we identified two toxofilin domains that interact with PP2C, one of which contains the Ser53 substrate. In addition to characterizing the interacting domains of toxofilin with its partners, the present study also provides information on an in vivo-based approach to selectively and competitively disrupt the protein-protein interactions that are important to parasite motility.