Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter‐gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high‐coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter‐gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter‐gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease‐mediated pH regulation as candidate adaptations of the microbiome to the hunter‐gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.     

Periosteal versus true cross‐sectional geometry: A comparison along humeral,femoral, and tibial diaphyses

Cross‐sectional geometric (CSG) properties of human long bone diaphyses are typically calculated from both periosteal and endosteal contours. Though quantification of both is desirable, periosteal contours alone have provided accurate predictions of CSG properties at the midshaft in previous studies. The relationship between CSG properties calculated from external contours and “true” (endosteal and periosteal) CSG properties, however, has yet to be examined along the whole diaphysis. Cross‐sectional computed tomography scans were taken from 21 locations along humeral, femoral, and tibial diaphyses in 20 adults from a late prehistoric central Illinois Valley cemetery. Mechanical properties calculated from images with (a) artificially filled medullary cavities (“solid”) and (b) true unaltered cross‐sections were compared at each section location using least squares regression. Results indicate that, in this sample, polar second moments of area (J), polar section moduli (Z_p), and cross‐sectional shape (I_max/I_min) calculated from periosteal contours correspond strongly with those calculated from cross‐sections that include the medullary cavity. Correlations are high throughout most of the humeral diaphysis and throughout large portions of femoral and tibial diaphyses (R² = 0.855–0.998, all P < 0.001, %SEE ≤ 8.0, %PE ≤ 5.0), the major exception being the proximal quarter of the tibial diaphysis for J and Z_p. The main source of error was identified as variation in %CA. Results reveal that CSG properties quantified from periosteal contours provide comparable results to (and are likely to detect the same differences among individuals as) true CSG properties along large portions of long bone diaphyses. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Genetic perspectives on forager‐farmer interaction in the Luangwa Valley of Zambia

The transformation from a foraging way of life to a reliance on domesticated plants and animals often led to the expansion of agropastoralist populations at the expense of hunter‐gatherers (HGs). In Africa, one of these expansions involved the Niger‐Congo Bantu‐speaking populations that started to spread southwards from Cameroon/Nigeria ～4,000 years ago, bringing agricultural technologies. Genetic studies have shown different degrees of gene flow (sometimes involving sex‐biased migrations) between Bantu agriculturalists and HGs. Although these studies have covered many parts of sub‐Saharan Africa, the central part (e.g. Zambia) was not yet studied, and the interactions between immigrating food‐producers and local HGs are still unclear. Archeological evidence from the Luangwa Valley of Zambia suggests a long period of coexistence (～1,700 years) of early food‐producers and HGs. To investigate if this apparent coexistence was accompanied by genetic admixture, we analyzed the mtDNA control region, Y chromosomal unique event polymorphisms, and 12 associated Y‐ short tandem repeats in two food‐producing groups (Bisa and Kunda) that live today in the Luangwa Valley, and compared these data with available published data on African HGs. Our results suggest that both the Bisa and Kunda experienced at most low levels of admixture with HGs, and these levels do not differ between the maternal and paternal lineages. Coalescent simulations indicate that the genetic data best fit a demographic scenario with a long divergence (62,500 years) and little or no gene flow between the ancestors of the Bisa/Kunda and existing HGs. This scenario contrasts with the archaeological evidence for a long period of coexistence between the two different communities in the Luangwa Valley, and suggests a process of sociocultural boundary maintenance may have characterized their interaction. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Technical note: The effect of midshaft location on the error ranges of femoral and tibial cross‐sectional parameters

In comparing long‐bone cross‐sectional geometric properties between individuals, percentages of bone length are often used to identify equivalent locations along the diaphysis. In fragmentary specimens where bone lengths cannot be measured, however, these locations must be estimated more indirectly. In this study, we examine the effect of inaccurately located femoral and tibial midshafts on estimation of geometric properties. The error ranges were compared on 30 femora and tibiae from the Eneolithic and Bronze Age. Cross‐sections were obtained at each 1% interval from 60 to 40% of length using CT scans. Five percent of deviation from midshaft properties was used as the maximum acceptable error. Reliability was expressed by mean percentage differences, standard deviation of percentage differences, mean percentage absolute differences, limits of agreement, and mean accuracy range (MAR) (range within which mean deviation from true midshaft values was less than 5%). On average, tibial cortical area and femoral second moments of area are the least sensitive to positioning error, with mean accuracy ranges wide enough for practical application in fragmentary specimens (MAR = 40–130 mm). In contrast, tibial second moments of area are the most sensitive to error in midshaft location (MAR = 14–20 mm). Individuals present significant variation in morphology and thus in error ranges for different properties. For highly damaged fossil femora and tibiae we recommend carrying out additional tests to better establish specific errors associated with uncertain length estimates. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

The influence of size on body shape diversification across Indo‐Pacific shore fishes*

Understanding the causes of body shape variability across the tree of life is one of the central issues surrounding the origins of biodiversity. One potential mechanism driving observed patterns of shape disparity is a strongly conserved relationship between size and shape. Conserved allometry has been shown to account for as much as 80% of shape variation in some vertebrate groups. Here, we quantify the amount of body shape disparity attributable to changes in body size across nearly 800 species of Indo‐Pacific shore fishes using a phylogenetic framework to analyze 17 geometric landmarks positioned to capture general body shape and functionally significant features. In marked contrast to other vertebrate lineages, we find that changes in body size only explain 2.9% of the body shape variation across fishes, ranging from 3% to 50% within our 11 sampled families. We also find a slight but significant trend of decreasing rates of shape evolution with increasing size. Our results suggest that the influence of size on fish shape has largely been overwhelmed by lineage‐specific patterns of diversification that have produced the modern landscape of highly diverse forms that we currently observe in nature.     

Effects of ornamentation and phylogeny on the evolution of wing shape in stalk‐eyed flies (Diopsidae)

Exaggerated male ornaments are predicted to be costly to their bearers, but these negative effects may be offset by the correlated evolution of compensatory traits. However, when locomotor systems, such as wings in flying species, evolve to decrease such costs, it remains unclear whether functional changes across related species are achieved via the same morphological route or via alternate changes that have similar function. We conducted a comparative analysis of wing shape in relation to eye‐stalk elongation across 24 species of stalk‐eyed flies, using geometric morphometrics to determine how species with increased eye span, a sexually selected trait, have modified wing morphology as a compensatory mechanism. Using traditional and phylogenetically informed multivariate analyses of shape in combination with phenotypic trajectory analysis, we found a strong phylogenetic signal in wing shape. However, dimorphic species possessed shifted wing veins with the result of lengthening and narrowing wings compared to monomorphic species. Dimorphic species also had changes that seem unrelated to wing size, but instead may govern wing flexion. Nevertheless, the lack of a uniform, compensatory pattern suggests that stalk‐eyed flies used alternative modifications in wing structure to increase wing area and aspect ratio, thus taking divergent morphological routes to compensate for exaggerated eye stalks.     

The influence of male age on within‐pair and extra‐pair paternity in passerines

Although male age has often been found to predict success in gaining extra‐pair paternity, it is unclear whether this gain is associated with an individual’s success in avoiding cuckoldry. We examined the relationship between male age and both within‐ and extra‐pair paternity in passerines using a meta‐analytical approach. There was a positive correlation between male age and success in extra‐pair paternity but little evidence for an association between male age and within‐pair paternity. In addition, effect sizes for male within‐pair paternity and male extra‐pair paternity were not significantly correlated. Thus, factors that predict success in obtaining extra‐pair paternity, such as male age, may not necessarily predict success in avoiding cuckoldry.     

Sexual dimorphism in steppe tortoises (Testudo horsfieldii): influence of the environment and sexual selection on body shape and mobility

Selective forces shape sexes differently, with male body proportions facing strong selection to enhance mate searching and male-to-male combat traits, and female fitness being influenced by the ability to assimilate large amounts of nutrients necessary for vitellogenesis (and/or gestation), and their ability to carry the eggs or embryos. We evaluated the sexual dimorphism of body proportion of more than 800 wild steppe tortoises (Testudo horsfieldii) in Uzbekistan. The thick, well-developed shell offers protection from predators but pronounced digging habits probably also constrain body shape (e.g. a shell that is dorso-ventrally flattened, although round from a dorsal view helps to penetrate into, and move within the soil). Thus, in this species, natural selection might favour a heavy and flat shell that is 'closed' with small openings for appendages. In males, these environmental influences appear to be countered by sexual selection. Compared to females, they weigh less (absolutely and relative to shell dimensions), have longer legs, have shell structure allowing wider movements for their legs, and they walk faster. Males were also able to right themselves more quickly than females did in experimental tests. This quick righting ability is critical because intra-sexual combats frequently result in males being flipped onto their backs and becoming prone to hyperthermia or predation. Females are heavily built, with wide shells (relative to male shells), which may provide space for carrying eggs. From our results, a number of simple hypotheses can be tested on a wide range of chelonian species.     

P‐glycoprotein (ABCB1) inhibited network of mitochondrion transport along microtubule and BMP signal‐induced cell shape in chimpanzee left cerebrum by systems‐theoretical analysis

We constructed the significant low‐expression P‐glycoprotein (ABCB1) inhibited transport and signal network in chimpanzee compared with high‐expression (fold change ≥2) the human left cerebrum in GEO data set, by using integration of gene regulatory activated and inhibited network inference method with gene ontology (GO) analysis. Our result showed that ABCB1 transport and signal upstream network RAB2A inhibited ABCB1, and downstream ABCB1‐inhibited SMAD1_2, NCK2, SLC25A46, GDF10, RASGRP1, EGFR, LRPPRC, RASSF2, RASA4, CA2, CBLB, UBR5, SLC25A16, ITGB3BP, DDIT4, PDPN, RAB2A in chimpanzee left cerebrum. We obtained that the different biological processes of ABCB1 inhibited transport and signal network repressed carbon dioxide transport, ER to Golgi vesicle‐mediated transport, folic acid transport, mitochondrion transport along microtubule, water transport, BMP signaling pathway, Ras protein signal transduction, transforming growth factor beta receptor signaling pathway in chimpanzee compared with the inhibited network of the human left cerebrum, as a result of inducing inhibition of mitochondrion transport along microtubule and BMP signal‐induced cell shape in chimpanzee left cerebrum. Our hypothesis was verified by the same and different biological processes of ABCB1 inhibited transport and signal network of chimpanzee compared with the corresponding activated network of chimpanzee and the human left cerebrum, respectively. Copyright © 2012 John Wiley & Sons, Ltd.     

Evolution of skull and body shape in Triturus newts reconstructed from three‐dimensional morphometric data and phylogeny

To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well‐studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three‐dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 243–255.     

The importance of accounting for the area of the medullary cavity in cross‐sectional geometry: A test based on the femoral midshaft

In cross‐sectional geometric (CSG) studies, both the subperiosteal and endosteal contours are considered important factors in determining bone bending rigidity. Recently, regression equations predicting CSG properties from a section's external dimensions were developed in a world‐wide sample of human long bones. The results showed high correlations between some subperiosteally derived and actual CSG parameters. We present a theoretical model that further explores the influence of endosteal dimensions on CSG properties. We compare two hypothetical femoral midshaft samples with the same total subperiosteal area but with percentages of cortical bone at the opposite ends of published human variation for population sample means. Even in this relatively uncommon scenario, the difference between the samples in the resultant means for predicted femoral polar second moment of area (J) appears to be modest: power analysis indicates that a minimum sample size of 61 is needed to detect the difference 90% of the time via a t‐test. Moreover, endosteal area can be predicted—although with substantial error—from periosteal area. Despite this error, including this relationship in subperiosteally derived estimates of J produces sample mean estimates close to true mean values. Power analyses reveal that when similar samples are used to develop prediction equations, a minimum sample of hundreds or more may be needed to distinguish a predicted mean J from the true mean J. These results further justify the use of regression equations estimating J from periosteal contours when analyzing behaviorally induced changes in bone rigidity in ancient populations, when it is not possible to measure endosteal dimensions. However, in other situations involving comparisons of individual values, growth trends, and senescence, where relative cortical thickness may vary greatly, inclusion of endosteal dimensions is still important. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

The influence of macro‐litterfall and forest structure on litterfall damage to seedlings

Abstract Microdisturbance to seedlings is important because it can differentially affect the mortality and recruitment of seedlings of forest tree species and thereby ultimately affect community composition. Microdisturbance due to litterfall has been shown to vary greatly in its influence on seedling survival among and within forests, and yet there have been no previous studies that investigate the cause of these differences. In this study the influence of macro‐litterfall on seedling damage is investigated in five complex temperate forests in New Zealand. Litterfall damage to artificial seedlings in these forests was strongly correlated with macro‐leaf‐fall (leaves > 30 cm × 1.5 cm) dry weight and total macro‐litterfall (leaves and deadwood > 30 cm × 1.5 cm) surface area (R² = 0.99, P < 0.005 for each). Protective vegetation within 2 m of the ground (mostly lianes and woody shrubs) reduced the risk of litterfall damage by up to 84%. Hitherto unexplained differences in litterfall damage to seedlings found among, and within, forests (tropical and temperate) may therefore be due to differences in rates of macro‐leaf‐fall and forest structure. These results are important because they suggest that subtle differences in forest structure, and species composition, may influence regeneration patterns through the litterfall microdisturbance regime.     

The influence of tetrad shape and intersporal callose wall formation on pollen aperture pattern ontogeny in two eudicot species

Background and Aims

In flowering plants, microsporogenesis is accompanied by various types of cytoplasmic partitioning (cytokinesis). Patterns of male cytokinesis are suspected to play a role in the diversity of aperture patterns found in pollen grains of angiosperms. The relationships between intersporal wall formation, tetrad shape and pollen aperture pattern ontogeny are studied.

Methods

A comparative analysis of meiosis and aperture distribution was performed within tetrads in two triporate eudicot species with contrasting aperture arrangements within their tetrads [Epilobium roseum (Onagraceae) and Paranomus reflexus (Proteaceae)].

Key Results and Conclusions

Intersporal wall formation is a two-step process in both species. Cytokinesis is first achieved by the formation of naked centripetal cell plates. These naked cell plates are then covered by additional thick, localized callose deposits that differ in location between the two species. Apertures are finally formed in areas in which additional callose is deposited on the cell plates. The recorded variation in tetrad shape is correlated with variations in aperture pattern, demonstrating the role of cell partitioning in aperture pattern ontogeny.