Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Gut microbial composition depends on different dietary habits just as health depends on microbial metabolism, but the association of microbiota with different diets in human populations has not yet been shown. In this work, we compared the fecal microbiota of European children (EU) and that of children from a rural African village of Burkina Faso (BF), where the diet, high in fiber content, is similar to that of early human settlements at the time of the birth of agriculture. By using high-throughput 16S rDNA sequencing and biochemical analyses, we found significant differences in gut microbiota between the two groups. BF children showed a significant enrichment in Bacteroidetes and depletion in Firmicutes (P < 0.001), with a unique abundance of bacteria from the genus Prevotella and Xylanibacter, known to contain a set of bacterial genes for cellulose and xylan hydrolysis, completely lacking in the EU children. In addition, we found significantly more short-chain fatty acids (P < 0.001) in BF than in EU children. Also, Enterobacteriaceae (Shigella and Escherichia) were significantly underrepresented in BF than in EU children (P < 0.05). We hypothesize that gut microbiota coevolved with the polysaccharide-rich diet of BF individuals, allowing them to maximize energy intake from fibers while also protecting them from inflammations and noninfectious colonic diseases. This study investigates and compares human intestinal microbiota from children characterized by a modern western diet and a rural diet, indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide.

/pdf/impact-of-diet-in-shaping-gut-microbiota-revealed-by-a-35b0ym235k.pdf

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

/pdf/the-impact-of-diet-in-shaping-gut-microbiota-revealed-by-a-3gi1n03d19.pdf

The impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and Rural Africa

Hybrid zones are, roughly speaking, narrow regions in which genetically distinct populations meet, mate, and produce hybrids. They are often only a few hundred meters wide and yet may be several hundred kilometers long. They are found in a wide variety of organisms: Tables 1 and 2 list about 150 reasonably clear examples, in which there is a spatial transition between two hybridizing forms. Such a widespread and striking phenomenon requires explanation; more importantly, it offers us several ways of understanding the nature and origin of species. First, hybrid zones pose interesting questions for the taxonomist, for they contrast two views of the species: as a set of populations delimited by genetic barriers to gene exchange; and as a set of populations maintained in a particular stable equilibrium by selection. Second, the wide range of genotypes found in a hybrid zone can be used to analyze the genetic differences and selective forces that separate the taxa involved. This may allow some inferences about the way these differences evolved and, by extrapolation, about the way fully isolated species diverge from each other. Finally, models of parapatric speciation, and of Wright's "shifting balance," involve the formation, move­ ment, and modification of hybrid zones. Hybrid zones must be understood before the plausibility of these models can be judged. After clarifying our terminology, we will summarize the relevant theory and then see how this can be used to make inferences from field data. A notable increase in the number of detailed genetic studies of hybrid zones occurred over

Analysis of Hybrid Zones

Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

https://science.sciencemag.org/content/sci/298/5591/129.full.pdf

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Speciation in the Anopheles gambiae complex is reviewed and discussed with emphasis on the patterns of chromosomal differentiation, particularly at the intraspecific level. The significance of inversion polymorphism in gambiae and arabiensis (the two species of greatest medical importance) is evaluated with reference to recent field investigations carried out in Nigeria. In both sibling species some of the inversions show clinical geographical changes in frequencies, with evident correlations with climatic conditions and vegetation zones. Microgeographical variations in species distribution and in intraspecific inversion frequencies are also present, which appear mostly related to man-made environmental contrasts. Parallel indoor-/outdoor collections of samples from polymorphic populations of arabiensis and gambiae show that adult mosquitoes carrying certain inversion karyotypes do not distribute at random in relation to the human environment, being significantly more frequent in outdoor than in indoor samples, or vice-versa. Optimal habitat choice appears to be involved in such variations of indoor resting behaviour, since the chromosomal types carried by less endophilic individuals are those more adapted to humid climates, i.e. those which tend to avoid the higher nocturnal saturation deficit of the indoor environment. This phenomenon, producing non-uniform exposure of the vector population to residual insecticides sprayed in houses, might explain the mediocrity of the results of malaria control projects based on house-spraying against endophilic vectors in the African savannas.

Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex

Field-collected specimens of all known taxa in the Anopheles gambiae complex were analyzed on the basis of chromosome inversions with reference to a standard polytene chromosome map. The phylogenetic relationships among the seven described species in the complex could be inferred from the distribution of fixed inversions. Nonrandom patterns of inversion distribution were observed and, particularly on chromosome arm 2R, provided evidence for genetically distinct populations in A. gambiae, A. arabiensis, and A. melas. In A. gambiae from Mali, stable genetic differentiation was observed even in populations living in the same region, suggesting a process of incipient speciation which is being confirmed by studies with molecular markers. The possible role of chromosome differentiation in speciation of the A. gambiae complex and in the emergence of distinct chromosomal forms within the nominal species is discussed in relation to human malaria.

https://science.sciencemag.org/content/sci/298/5597/1415.full.pdf

A Polytene Chromosome Analysis of the Anopheles gambiae Species Complex

Polytene chromosome studies on the Afrotropical mosquitoes of the Anopheles gambiae complex show that the rearrangements of the banding pattern are all based on paracentric inversions. Some of these occur at the homozygous state only (fixed inversions) and are used for cytotaxonomic identification of the six sibling species. Others occur as intraspecific chromosomal polymorphisms which are frequent particularly in An. gambiae and An. arabiensis, the two taxa showing the widest distribution and the closest association with man and man-made breeding places. A particularly high level of chromosome differentiation has been recorded in Anpoheles gambiae (the most anthropophilic taxon of the complex and possibly the one most recently evolved) which can be split into forest and savanna chromosomal forms. The forest form seems chromosomally uniform, being characterized in all the rain forest areas by the chromosome-2 standard arrangement, probably one of the most primitive in the complex. The forest form...

Chromosomal inversion intergradation and incipient speciation in Anopheles gambiae

We karyotyped and identified by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis Anopheles gambiae s.s. samples collected in several African countries. The data show the existence of two non-panmictic molecular forms, named S and M, whose distribution extended from forest to savannahs. Mosquitoes of the S and M forms are homosequential standard for chromosome-2 inversions in forest areas. In dry savannahs, S is characterized mainly by inversion polymorphisms typical of Savanna and Bamako chromosomal forms, while M shows chromosome-2 arrangements typical of Mopti and/or Savanna and/or Bissau, depending on its geographical origin. Chromosome-2 inversions therefore seem to be involved in ecotypic adaptation rather than in mate-recognition systems. Strong support for the reproductive isolation of S and M in Ivory Coast comes from the observation that the kdr allele is found at high frequencies in S specimens and not at all in chromosomal identical M specimens. However, the kdr allele does not segregate with molecular forms in Benin.

Molecular evidence of incipient speciation within Anopheles gambiae s.s. in West Africa.

Data from polytene chromosome studies on the Anopheles gambiae complex in Mali were reviewed. The banding pattern was successfully scored in 17,705 specimens from 76 sampling sites representing the main ecological strata of the country. Two members of the complex, namely An. arabiensis and An. gambiae, were found widespread and frequently sympatric, with the latter prevalent in most localities. Population genetic analysis of the inversion polymorphisms indicated the existence of panmictic conditions for An. arabiensis only, whereas the parallel study of An. gambiae supported its splitting into at least three reproductive units, characterized by different 2R chromosome arrangements, designated Bamako, Mopti and Savanna. The chromosomal evidence was consistent with the hypothesis of complete reproductive isolation between Bamako and Mopti. Partial isolation between these two taxa and Savanna was suggested by the scoring of hypothetical hybrid 2R heterokaryotypes in various samples, but the actual hybrid origin of these specimens was not confirmed. Different patterns of geographical and seasonal distribution were shown as follows. An. arabiensis prevails in arid savannas (Sahel and Northern Sudan savanna) out of the flooded or irrigated zones; it is able to withstand the most arid conditions of Saharan localities and its breeding might extend throughout the dry season. An. gambiae Savanna and Bamako prevail in relatively humid savannas (Southern Sudan savanna) and their breeding generally occurs only during the rainy season. The Savanna taxon was almost absent in flooded or irrigated zones and in riverine localities; the Bamako taxon is distributed along the upper river Niger and its tributaries. An. gambiae Mopti extends its range in all ecological zones present in Mali including the Sahel and predesertic areas, showing high relative frequencies up to absolute dominance in flooded or irrigated areas; its breeding is highly successful also during the dry season. Rainfall at the sampling sites was found to correlate positively with the frequency of Savanna and negatively with the frequency of Mopti. The remarkable ecological flexibility of the latter was found associated with wide seasonal and geographical variations in its 2R inversion polymorphism bc/u. Higher frequencies of the bc arrangement were recorded both in the Southern localities during the dry season and in the Northern more arid localities during the rainy season. The absence or scarcity of An. arabiensis and An. gambiae Savanna in most flooded or irrigated zones suggests their competitive exclusion by An. gambiae Mopti.

Vincenzo Petrarca

Papers

Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex

A Polytene Chromosome Analysis of the Anopheles gambiae Species Complex

Chromosomal inversion intergradation and incipient speciation in Anopheles gambiae

Molecular evidence of incipient speciation within Anopheles gambiae s.s. in West Africa.

The distribution and inversion polymorphism of chromosomally recognized taxa of the Anopheles gambiae complex in Mali, West Africa.