Molecular phylogenetic analyses indicate paraphyly of the genus Hybomys (Rodentia: Muridae): Taxonomic implications

Widely distributed in Guineo‐Congolian forests, the genus Hybomys is represented by two species complexes (univittatus and trivirgatus), each restricted to one distinct forest block. In the last revision, these two species complexes were considered as distinct subgenera (Hybomys and Typomys). Previous morphological and karyological studies identified an important divergence between these two subgenera and raised the question of their taxonomic status (subgenus or genus). The number of species within this genus is also a matter of discussion: nine forms were described but only six (H. badius, H. basilii, H. lunaris, H. planifrons, H. trivirgatus, and H. univitttatus) are currently recognized as distinct species, the three others (H. pearcei, H. eisentrauti, and H. rufocanus) being considered as synonyms. The monophyly of the genus and its species have never been previously investigated with DNA sequence data. In this study, we combined mitochondrial and nuclear data (for a total of 3,264 nucleotide characters) to test the monophyly of Hybomys and to assess the specific status of H. eisentrauti and H. rufocanus. Our results highlight the paraphyly of the genus: members of the H. univittatus species complex appeared closely related to the genera Stochomys and Dephomys; representatives of H. trivirgatus are the sister clade of the node grouping Stochomys, Dephomys and member of the H. univittatus species complex. Combined with previous morphological findings, our results suggest that Typomys and Hybomys should be considered as two distinct genera. Based on tree topology and genetic distances, we propose to consider H. rufocanus as a valid species, distinct from H. univittaus, and to consider H. badius and H. eisentrauti as junior synonyms of H. rufocanus.     

Count data in biology—Data transformation or model reformation?

Statistical analyses are an integral component of scientific research, and for decades, biologists have applied transformations to data to meet the normal error assumptions for F and t tests. Over the years, there has been a movement from data transformation toward model reformation—the use of non‐normal error structures within the framework of the generalized linear model (GLM). The principal advantage of model reformation is that parameters are estimated on the original, rather than the transformed scale. However, data transformation has been shown to give better control over type I error, for simulated data with known error structures. We conducted a literature review of statistical textbooks directed toward biologists and of journal articles published in the primary literature to determine temporal trends in both the text recommendations and the practice in the refereed literature over the past 35 years. In this review, a trend of increasing use of reformation in the primary literature was evident, moving from no use of reformation before 1996 to >50% of the articles reviewed applying GLM after 2006. However, no such trend was observed in the recommendations in statistical textbooks. We then undertook 12 analyses based on published datasets in which we compared the type I error estimates, residual plot diagnostics, and coefficients yielded by analyses using square root transformations, log transformations, and the GLM. All analyses yielded acceptable residual versus fit plots and had similar p‐values within each analysis, but as expected, the coefficient estimates differed substantially. Furthermore, no consensus could be found in the literature regarding a procedure to back‐transform the coefficient estimates obtained from linear models performed on transformed datasets. This lack of consistency among coefficient estimates constitutes a major argument for model reformation over data transformation in biology.     

New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa

According to fossil data, the wood mouse arrived in North Africa 7500 ya, while it was present in Europe since Early Pleistocene. Previous molecular studies suggested that its introduction in North Africa probably occurred via the Strait of Gibraltar more than 0.4 Mya ago. In this study, we widely sampled wood mice to get a better understanding of the geographic and demographic history of this species in North Africa and possibly to help resolving the discrepancy between genetic and palaeontological data. Specifically, we wanted to answer the following questions: (1) When and how did the wood mouse arrive in North Africa? and (2) What is its demographic and geographic history in North Africa since its colonization? We collected in the field 438 new individuals and used both mtDNA and six microsatellite markers to answer these questions. Our results confirm that North African wood mice have a south‐western European origin and colonized the Maghreb through the Strait of Gibraltar probably during the Mesolithic or slightly after. They first colonized the Tingitana Peninsula and then expanded throughout North Africa. Our genetic data suggest that the ancestral population size comprised numerous individuals reinforcing the idea that wood mice did not colonize Morocco accidentally through rafting of a few individuals, but via recurrent/multiple anthropogenic translocations. No spatial structuring of the genetic variability was recorded in North Africa, from Morocco to Tunisia.     

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.     

Domestic hens succeed at serial reversal learning and perceptual concept generalisation using a new automated touchscreen device

Improving the welfare of farm animals depends on our knowledge on how they perceive and interpret their environment; the latter depends on their cognitive abilities. Hence, limited knowledge of the range of cognitive abilities of farm animals is a major concern. An effective approach to explore the cognitive range of a species is to apply automated testing devices, which are still underdeveloped in farm animals. In screen-like studies, the uses of automated devices are few in domestic hens. We developed an original fully automated touchscreen device using digital computer-drawn colour pictures and independent sensible cells adapted for cognitive testing in domestic hens, enabling a wide range of test types from low to high complexity. This study aimed to test the efficiency of our device using two cognitive tests. We focused on tasks related to adaptive capacities to environmental variability, such as flexibility and generalisation capacities as this is a good start to approach more complex cognitive capacities. We implemented a serial reversal learning task, categorised as a simple cognitive test, and a delayed matching-to-sample (dMTS) task on an identity concept, followed by a generalisation test, categorised as more complex. In the serial reversal learning task, the hens performed equally for the two changing reward contingencies in only three reversal stages. In the dMTS task, the hens increased their performance rapidly throughout the training sessions. Moreover, to the best of our knowledge, we present the first positive result of identity concept generalisation in a dMTS task in domestic hens. Our results provide additional information on the behavioural flexibility and concept understanding of domestic hens. They also support the idea that fully automated devices would improve knowledge of farm animals’ cognition.     

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.     

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.