Diversity of Lactase Persistence Alleles in Ethiopia: Signature of a Soft Selective Sweep

The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (−13910^∗T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (−13907^∗G, rs41525747; −13915^∗G, rs41380347; −14010^∗C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, −14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the −14009^∗G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep.     

Behavioural changes and the adaptive diversification of pigeons and doves

What factors determine the extent of evolutionary diversification remains a major question in evolutionary biology. Behavioural changes have long been suggested to be a major driver of phenotypic diversification by exposing animals to new selective pressures. Nevertheless, the role of behaviour in evolution remains controversial because behavioural changes can also retard evolutionary change by hiding genetic variation from selection. In the present study, we apply recently implemented Ornstein–Uhlenbeck evolutionary models to show that behavioural changes led to associated evolutionary responses in functionally relevant morphological traits of pigeons and doves (Columbiformes). Specifically, changes from terrestrial to arboreal foraging behaviour reconstructed in a set of phylogenies brought associated shorter tarsi and longer tails, consistent with functional predictions. Interestingly, the transition to arboreality accelerated the rates of evolutionary divergence, leading to an increased morphological specialization that seems to have subsequently constrained reversals to terrestrial foraging. Altogether, our results support the view that behaviour may drive evolutionary diversification, but they also highlight that its evolutionary consequences largely depend on the limits imposed by the functional demands of the adaptive zone.     

Early lipoic acid intake protects retina of diabetic mice

The aim of this study was to test the effect of lipoic acid treatment on the retina after a short diabetic insult. Diabetes was induced by alloxan and mice were divided into sub-groups; control, diabetic, diabetic+insulin and all groups received±lipoic acid (100 mg/kg body weight) for 3 weeks. GSH content, MDA concentration, GPx activity were measured and electroretinograms (ERG) were recorded. Early administration of lipoic acid to diabetic mice prevented the statistically significant decreases of GSH content and GPx activity and normalized MDA concentration. Moreover, lipoic acid restored electroretinogram b-wave amplitude of diabetic animals to control values. Lipoic acid has a protective effect on the diabetic retina.     

Streamlined Development of Targeted Mass Spectrometry‐Based Method Combining Scout‐MRM and a Web‐Based Tool Indexed with Scout Peptides

MS‐based targeted proteomics is a relevant technology for sensitive and robust relative or absolute quantification of proteins biomarker candidates in complex human biofluids or tissue extracts. Performing a multiplex assay imposes time scheduling of peptide monitoring only around their expected retention time that needs to be defined with synthetic peptide. Time‐scheduled monitoring is clearly a constraint that precludes from straightforward assay transfer between biological matrices or distinct experimental setup. Any unexpected retention time (RT) shift challenges assay robustness and its implementation for large‐scale analysis. Recently, Scout‐multiple reaction monitoring that fully releases multiplexed targeted acquisition from RT scheduling by successively monitoring complex transition groups triggered with sentinel molecules called Scout has been introduced. It is herein documented how Peptide Selector database and tool streamlines the building of a multiplexed method thanks to RT indexation relative to Scout peptides. This case study deals with surrogate peptides of biomarker candidates related to drug‐induced liver and vascular injury, running such on‐line built method (eight Scouts triggering the monitoring of a total of 692 transitions) enables 100% recovery of a panel of 93 spiked‐in heavy labeled standards, despite significant RT shifts between serum, plasma, or urine. This result illustrates the simplicity of automatically building and deploying robust proteomics targeted assay.     

Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest‐agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F_ST = 0.072) to an extent close to what has been reported (F_ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.     

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo‐communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead‐beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica‐solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size‐selection of low molecular‐weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead‐beating, DNA binding in silica‐solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data‐processing protocol should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.     

Life-history traits of two Mediterranean lizard populations: a possible example of countergradient covariation

The trade-off between clutch and offspring size, which is a central topic in life-history research, is shaped by natural selection to maximize the number of surviving offspring, but it also depends on the resources available for reproduction. Conspecific populations living in different environments may differ in adult body size, clutch mass, clutch size, offspring size, and/or post-natal growth rates, due either to phenotypic plasticity or to local adaptation. Here, we compare these traits and their relationships between two populations of the lizard Psammodromus algirus separated by a 600-m altitudinal gradient. We used a common garden design to control incubation temperature and food availability, with two different feeding treatments. Females were larger at the high-elevation site. Although SVL-adjusted clutch mass did not differ between populations, high-elevation females laid more but smaller eggs than low-elevation ones. Hatchlings were larger at lower elevation. Our common garden experiment revealed that low-elevation hatchlings grew faster than high-elevation hatchlings under both feeding treatments. However, higher food availability at higher altitude allows high-elevation lizards to grow faster and attain larger adult sizes, especially in the case of females. The two key adaptations of low-elevation lizards, large eggs and hatchlings and the ability to grow rapidly after hatching, are likely to enhance survival in low-productivity Mediterranean lowlands. Our data support the hypothesis that the reproductive strategies of these populations provide an example of countergradient variation, because the genotypes that encode for fast growth and large body size occurred in low food availability habitats where juveniles grew slowly and attained small adult sizes.     

Disproportionate effects of non‐colonial small herbivores on structure and diversity of grassland dominated by large herbivores

The response of semiarid grasslands to small, non‐colonial herbivores has received little attention, focusing primarily on the effects of granivore assemblages on annual plant communities. We studied the long‐term effects of both small and large herbivores on vegetation structure and species diversity of shortgrass steppe, a perennial semiarid grassland considered marginal habitat for small mammalian herbivores. We hypothesized that 1) large generalist herbivores would affect more abundant species and proportions of litter‐bare ground‐vegetation cover through non‐selective herbivory, 2) small herbivores would affect less common species through selective but limited consumption, and 3) herbivore effects on plant richness would increase with increasing aboveground net primary production (ANPP). Plant community composition was assessed over a 14‐year period in pastures grazed at moderate intensities by cattle and in exclosures for large (cattle) and large‐plus‐small herbivores (additional exclusion of rabbits and rodents). Exclusion of large herbivores affected litter and bare ground and basal cover of abundant, common and uncommon species. Additional exclusion of small herbivores did not affect uncommon components of the plant community, but had indirect effects on abundant species, decreased the cover of the dominant grass Bouteloua gracilis and total vegetation, and increased litter and species diversity. There was no relationship between ANPP and the intensity of effects of either herbivore body size on richness. Exclusion of herbivores of both body sizes had complementary and additive effects which promoted changes in vegetation composition and physiognomy that were linked to increased abundance of tall and decreased abundance of short species. Our findings show that small mammalian herbivores had disproportionately large effects on plant communities relative to their small consumption of biomass. Even in small‐seeded perennial grasslands with a long history of intensive grazing by large herbivores, non‐colonial small mammalian herbivores should be recognized as an important driver of grassland structure and diversity.