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  • ItemAccepted versionOpen Access
    Ancient genomes show social and reproductive behavior of early Upper Palaeolithic foragers
    (American Association for the Advancement of Science, 2017-11-03) Sikora, M; Seguin-Orlando, A; Sousa, VC; Albrechtsen, A; Korneliussen, T; Ko, A; Rasmussen, S; Dupanloup, I; Nigst, PR; Bosch, MD; Renaud, G; Allentoft, ME; Margaryan, A; Vasilyev, SV; Veselovskaya, EV; Borutskaya, SB; Deviese, T; Comeskey, D; Higham, T; Manica, A; Foley, RA; Meltzer, DJ; Nielsen, R; Excoffier, L; Mirazon Lahr, M; Orlando, L; Willerslev, E; Nigst, Philip [0000-0001-7330-8768]; Bosch, Dorothea [0000-0002-2829-3832]; Manica, Andrea [0000-0003-1895-450X]; Foley, Robert [0000-0003-0479-3039]; Mirazon Lahr, Marta [0000-0001-5752-5770]; Willerslev, Eske [0000-0002-7081-6748]
    Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. Wedemonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.
  • ItemPublished versionOpen Access
    The coevolution of play and the cortico-cerebellar system in primates.
    (Springer Science and Business Media LLC, 2017-10) Kerney, Max; Smaers, Jeroen B; Schoenemann, P Thomas; Dunn, Jacob C; Kerney, Max [0000-0003-4996-3839]
    Primates are some of the most playful animals in the natural world, yet the reason for this remains unclear. One hypothesis posits that primates are so playful because playful activity functions to help develop the sophisticated cognitive and behavioural abilities that they are also renowned for. If this hypothesis were true, then play might be expected to have coevolved with the neural substrates underlying these abilities in primates. Here, we tested this prediction by conducting phylogenetic comparative analyses to determine whether play has coevolved with the cortico-cerebellar system, a neural system known to be involved in complex cognition and the production of complex behaviour. We used phylogenetic generalised least squares analyses to compare the relative volume of the largest constituent parts of the primate cortico-cerebellar system (prefrontal cortex, non-prefrontal heteromodal cortical association areas, and posterior cerebellar hemispheres) to the mean percentage of time budget spent in play by a sample of primate species. Using a second categorical data set on play, we also used phylogenetic analysis of covariance to test for significant differences in the volume of the components of the cortico-cerebellar system among primate species exhibiting one of three different levels of adult-adult social play. Our results suggest that, in general, a positive association exists between the amount of play exhibited and the relative size of the main components of the cortico-cerebellar system in our sample of primate species. Although the explanatory power of this study is limited by the correlational nature of its analyses and by the quantity and quality of the data currently available, this finding nevertheless lends support to the hypothesis that play functions to aid the development of cognitive and behavioural abilities in primates.
  • ItemAccepted versionOpen Access
    Migrating microbes: what pathogens can tell us about population movements and human evolution
    (Taylor & Francis, 2017-08) Houldcroft, CJ; Ramond, J-B; Rifkin, RF; Underdown, SJ; Houldcroft, Charlotte [0000-0002-1833-5285]
    Background: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen’s genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. Methods: This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. Results: Three stories are then presented of germs on a journey. The first is the story of HIV’s spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. Conclusions: Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.
  • ItemPublished versionOpen Access
    The study of human Y chromosome variation through ancient DNA
    (Springer, 2017-03-04) Kivisild, T; Kivisild, Toomas [0000-0002-6297-7808]
    High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.
  • ItemAccepted versionOpen Access
    Clinical and biological insights from viral genome sequencing
    (Nature Publishing Group, 2017-03-01) Houldcroft, CJ; Beale, MA; Breuer, J; Houldcroft, Charlotte [0000-0002-1833-5285]
    Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
  • ItemPublished versionOpen Access
    Hunter-Gatherers and the Origins of Religion.
    (Springer Science and Business Media LLC, 2016-09) Peoples, Hervey C; Duda, Pavel; Marlowe, Frank W
    Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait "high gods" stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion.
  • ItemOpen Access
    Early Life Conditions and Physiological Stress following the Transition to Farming in Central/Southeast Europe: Skeletal Growth Impairment and 6000 Years of Gradual Recovery.
    (Public Library of Science (PLoS), 2016) Macintosh, Alison A; Pinhasi, Ron; Stock, Jay T; Macintosh, Alison [0000-0003-2914-5206]; Stock, Jay [0000-0003-0147-8631]
    Early life conditions play an important role in determining adult body size. In particular, childhood malnutrition and disease can elicit growth delays and affect adult body size if severe or prolonged enough. In the earliest stages of farming, skeletal growth impairment and small adult body size are often documented relative to hunter-gatherer groups, though this pattern is regionally variable. In Central/Southeast Europe, it is unclear how early life stress, growth history, and adult body size were impacted by the introduction of agriculture and ensuing long-term demographic, social, and behavioral change. The current study assesses this impact through the reconstruction and analysis of mean stature, body mass, limb proportion indices, and sexual dimorphism among 407 skeletally mature men and women from foraging and farming populations spanning the Late Mesolithic through Early Medieval periods in Central/Southeast Europe (~7100 calBC to 850 AD). Results document significantly reduced mean stature, body mass, and crural index in Neolithic agriculturalists relative both to Late Mesolithic hunter-gatherer-fishers and to later farming populations. This indication of relative growth impairment in the Neolithic, particularly among women, is supported by existing evidence of high developmental stress, intensive physical activity, and variable access to animal protein in these early agricultural populations. Among subsequent agriculturalists, temporal increases in mean stature, body mass, and crural index were more pronounced among Central European women, driving declines in the magnitude of sexual dimorphism through time. Overall, results suggest that the transition to agriculture in Central/Southeast Europe was challenging for early farming populations, but was followed by gradual amelioration across thousands of years, particularly among Central European women. This sex difference may be indicative, in part, of greater temporal variation in the social status afforded to young girls, in their access to resources during growth, and/or in their health status than was experienced by men.
  • ItemOpen Access
    Spatial and temporal variation of body size among early Homo.
    (Academic Press, 2015-05) Will, Manuel; Stock, Jay T; Stock, Jay [0000-0003-0147-8631]
    The estimation of body size among the earliest members of the genus Homo (2.4-1.5Myr [millions of years ago]) is central to interpretations of their biology. It is widely accepted that Homo ergaster possessed increased body size compared with Homo habilis and Homo rudolfensis, and that this may have been a factor involved with the dispersal of Homo out of Africa. The study of taxonomic differences in body size, however, is problematic. Postcranial remains are rarely associated with craniodental fossils, and taxonomic attributions frequently rest upon the size of skeletal elements. Previous body size estimates have been based upon well-preserved specimens with a more reliable species assessment. Since these samples are small (n < 5) and disparate in space and time, little is known about geographical and chronological variation in body size within early Homo. We investigate temporal and spatial variation in body size among fossils of early Homo using a 'taxon-free' approach, considering evidence for size variation from isolated and fragmentary postcranial remains (n = 39). To render the size of disparate fossil elements comparable, we derived new regression equations for common parameters of body size from a globally representative sample of hunter-gatherers and applied them to available postcranial measurements from the fossils. The results demonstrate chronological and spatial variation but no simple temporal or geographical trends for the evolution of body size among early Homo. Pronounced body size increases within Africa take place only after hominin populations were established at Dmanisi, suggesting that migrations into Eurasia were not contingent on larger body sizes. The primary evidence for these marked changes among early Homo is based upon material from Koobi Fora after 1.7Myr, indicating regional size variation. The significant body size differences between specimens from Koobi Fora and Olduvai support the cranial evidence for at least two co-existing morphotypes in the Early Pleistocene of eastern Africa.
  • ItemPublished versionOpen Access
    Lower limb biomechanics and habitual mobility among mid-Holocene populations of the Cis-Baikal
    (Elsevier BV, 2016) Stock, JT; Macintosh, AA; Stock, JT [0000-0003-0147-8631]
    The mid-Holocene hunteregatherer populations of the Cis-Baikal represent long-term occupation by the Early Neolithic Kitoi Culture (6800e4900 B.C.) and the Middle Neolithic and Bronze Age Isakovo, Serovo and Glazkovo (ISG) cultures (4200e1000 B.C.). While there is considerable evidence for cultural and genetic discontinuity between these populations, differences in habitual activity between these periods remain poorly understood. The current study uses cross sectional geometric (CSG) properties of the femur and tibia in the lower limb, to investigate variation in mechanical loading and terrestrial locomotion between the Kitoi and ISG cultural groups. The results demonstrate a significant decrease in femoral rigidity and a trend towards more circular femoral diaphyses among the later ISG groups which suggests that there was a significant decrease in terrestrial mobility across this transition. This trend is accompanied by significant declines in tibial rigidity among females, resulting in greater sexual dimorphism among the ISG than the Kitoi. This indicates a shift towards a sexual division of labour which involved greater sedentism of the ISG than Kitoi women. Overall, the results suggest that shifts in habitual activity throughout the mid-Holocene of the Cis-Baikal involved both increased sedentism, and an increase in sexual differences in logistical mobility.
  • ItemOpen Access
    Divergence in male and female manipulative behaviors with the intensification of metallurgy in Central Europe.
    (Public Library of Science (PLoS), 2014) Macintosh, Alison A; Pinhasi, Ron; Stock, Jay T; Macintosh, Alison [0000-0003-2914-5206]; Stock, Jay [0000-0003-0147-8631]
    Humeral morphology has been shown to reflect, in part, habitual manipulative behaviors in humans. Among Central European agricultural populations, long-term social change, increasing task specialization, and technological innovation all had the potential to impact patterns of habitual activity and upper limb asymmetry. However, systematic temporal change in the skeletal morphology of agricultural populations in this region has not been well-characterized. This study investigates diachronic patterns in humeral biomechanical properties and lengths among 174 adult Central European agriculturalists through the first ∼ 5400 years of farming in the region. Greater asymmetry in biomechanical properties was expected to accompany the introduction of metallurgy, particularly in males, while upper limb loading patterns were expected to be more similar between the Bronze and Iron Ages. Results revealed a divergence in the lateralization of upper limb biomechanical properties by sex between the Early/Middle Neolithic and Early/Middle Bronze Age. Neolithic females had significantly more variable properties than males in both humeri, while Bronze Age female properties became homogeneous and very symmetrical relative to the right-biased lateralization of contemporaneous males. The Bronze Age to Iron Age transition was associated with morphological change among females, with a significant increase in right-biased asymmetry and a concomitant reduction in sexual dimorphism. Relative to biomechanical properties, humeral length variation and asymmetry were low though some significant sexual dimorphism and temporal change was found. It was among females that the lateralization of humeral biomechanical properties, and variation within them, changed most profoundly through time. This suggests that the introduction of the ard and plow, metallurgical innovation, task specialization, and socioeconomic change through ∼ 5400 years of agriculture impacted upper limb loading in Central European women to a greater extent than men.
  • ItemOpen Access
    Relationships of maternal and paternal anthropometry with neonatal body size, proportions and adiposity in an Australian cohort.
    (Wiley, 2015-04) Pomeroy, Emma; Wells, Jonathan CK; Cole, Tim J; O'Callaghan, Michael; Stock, Jay T; Pomeroy, Emma [0000-0001-6251-2165]; Stock, Jay [0000-0003-0147-8631]
    The patterns of association between maternal or paternal and neonatal phenotype may offer insight into how neonatal characteristics are shaped by evolutionary processes, such as conflicting parental interests in fetal investment and obstetric constraints. Paternal interests are theoretically served by maximizing fetal growth, and maternal interests by managing investment in current and future offspring, but whether paternal and maternal influences act on different components of overall size is unknown. We tested whether parents' prepregnancy height and body mass index (BMI) were related to neonatal anthropometry (birthweight, head circumference, absolute and proportional limb segment and trunk lengths, subcutaneous fat) among 1,041 Australian neonates using stepwise linear regression. Maternal and paternal height and maternal BMI were associated with birthweight. Paternal height related to offspring forearm and lower leg lengths, maternal height and BMI to neonatal head circumference, and maternal BMI to offspring adiposity. Principal components analysis identified three components of variability reflecting neonatal "head and trunk skeletal size," "adiposity," and "limb lengths." Regression analyses of the component scores supported the associations of head and trunk size or adiposity with maternal anthropometry, and limb lengths with paternal anthropometry. Our results suggest that while neonatal fatness reflects environmental conditions (maternal physiology), head circumference and limb and trunk lengths show differing associations with parental anthropometry. These patterns may reflect genetics, parental imprinting and environmental influences in a manner consistent with parental conflicts of interest. Paternal height may relate to neonatal limb length as a means of increasing fetal growth without exacerbating the risk of obstetric complications.
  • ItemOpen Access
    A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.
    (Elsevier BV, 2014-11-06) Clemente, Florian J; Cardona, Alexia; Inchley, Charlotte E; Peter, Benjamin M; Jacobs, Guy; Pagani, Luca; Lawson, Daniel J; Antão, Tiago; Vicente, Mário; Mitt, Mario; DeGiorgio, Michael; Faltyskova, Zuzana; Xue, Yali; Ayub, Qasim; Szpak, Michal; Mägi, Reedik; Eriksson, Anders; Manica, Andrea; Raghavan, Maanasa; Rasmussen, Morten; Rasmussen, Simon; Willerslev, Eske; Vidal-Puig, Antonio; Tyler-Smith, Chris; Villems, Richard; Nielsen, Rasmus; Metspalu, Mait; Malyarchuk, Boris; Derenko, Miroslava; Kivisild, Toomas; Cardona, Alexia [0000-0002-7877-5565]; Jacobs, Guy [0000-0002-4698-7758]; Eriksson, Anders [0000-0003-3436-3726]; Manica, Andrea [0000-0003-1895-450X]; Raghavan, Maanasa [0000-0003-1997-0739]; Willerslev, Eske [0000-0002-7081-6748]; Vidal-Puig, Antonio [0000-0003-4220-9577]; Kivisild, Toomas [0000-0002-6297-7808]
    Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.
  • ItemOpen Access
    Resistance to antibiotics of clinical relevance in the fecal microbiota of Mexican wildlife.
    (Public Library of Science (PLoS), 2014) Cristóbal-Azkarate, Jurgi; Dunn, Jacob C; Day, Jennifer MW; Amábile-Cuevas, Carlos F
    There are a growing number of reports of antibiotic resistance (ATBR) in bacteria living in wildlife. This is a cause for concern as ATBR in wildlife represents a potential public health threat. However, little is known about the factors that might determine the presence, abundance and dispersion of ATBR bacteria in wildlife. Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys (Alouatta palliata), spider monkeys (Ateles geoffroyi), tapirs (Tapirus bairdii) and felids (jaguars, Panthera onca; pumas, Puma concolor; jaguarundis, Puma yagouaroundi; and ocelots, Leopardus pardalis) living freely in two regions of the Mexican state of Veracruz under different degrees of human influence. Overall, our study shows that ATBR is commonplace in bacteria isolated from wildlife in southeast Mexico. Most of the resistances were towards old and naturally occurring antibiotics, but we also observed resistances of potential clinical significance. We found that proximity to humans positively affected the presence of ATBR and that ATBR was higher in terrestrial than arboreal species. We also found evidence suggesting different terrestrial and aerial routes for the transmission of ATBR between humans and wildlife. The prevalence and potential ATBR transfer mechanisms between humans and wildlife observed in this study highlight the need for further studies to identify the factors that might determine ATBR presence, abundance and distribution.
  • ItemOpen Access
    Host genetics of Epstein-Barr virus infection, latency and disease.
    (Wiley, 2015-03) Houldcroft, Charlotte J; Kellam, Paul; Houldcroft, Charlotte [0000-0002-1833-5285]
    Epstein-Barr virus (EBV) infects 95% of the adult population and is the cause of infectious mononucleosis. It is also associated with 1% of cancers worldwide, such as nasopharyngeal carcinoma, Hodgkin's lymphoma and Burkitt's lymphoma. Human and cancer genetic studies are now major forces determining gene variants associated with many cancers, including nasopharyngeal carcinoma and Hodgkin's lymphoma. Host genetics is also important in infectious disease; however, there have been no large-scale efforts towards understanding the contribution that human genetic variation plays in primary EBV infection and latency. This review covers 25 years of studies into host genetic susceptibility to EBV infection and disease, from candidate gene studies, to the first genome-wide association study of EBV antibody response, and an EBV-status stratified genome-wide association study of Hodgkin's lymphoma. Although many genes are implicated in EBV-related disease, studies are often small, not replicated or followed up in a different disease. Larger, appropriately powered genomic studies to understand the host response to EBV will be needed to move our understanding of the biology of EBV infection beyond the handful of genes currently identified. Fifty years since the discovery of EBV and its identification as a human oncogenic virus, a glimpse of the future is shown by the first whole-genome and whole-exome studies, revealing new human genes at the heart of the host-EBV interaction.
  • ItemOpen Access
    Effect of daily versus weekly home fortification with multiple micronutrient powder on haemoglobin concentration of young children in a rural area, Lao People's Democratic Republic: A randomised trial
    (Springer Nature, 2011-11-24) Kounnavong, S; Sunahara, T; Mascie-Taylor, CGN; Hashizume, M; Okumura, J; Moji, K; Boupha, B; Yamamoto, T
    Abstract Background Multiple micronutrient deficiencies, in particular iron deficiency anaemia (IDA) is a severe public health problem in Lao People's Democratic Republic (Lao PDR). Because of the practical difficulties encountered in improving the nutritional adequacy of traditional complementary foods and the limitations associated with the use of liquid iron supplementation for the treatment and prevention of IDA in infants and young children, recently, home-fortification with multivitamins and minerals sprinkles was recommended. This study aims to compare the effect of twice weekly versus daily supplementation with multivitamins and minerals powder (MMP) on anaemia prevalence, haemoglobin concentration, and growth in infants and young children in a rural community in Lao PDR. Methods A randomized trial was conducted in six rural communities. Children aged 6 to 52 months (n = 336) were randomly assigned to a control group (n = 110) or to one of two intervention groups receiving either two sachets per week (n = 115) or a daily sachet (n = 111) of MMP for 24 weeks; 331 children completed the study. A finger prick of blood was taken at baseline, at week 12, and again at week 24 to determine haemoglobin concentration. Anthropometric measurements were taken every 4 weeks. The McNemar test was used to assess within group differences at three time points in the study subjects with anaemia and one-way ANOVA was used to assess changes in mean haemoglobin concentration in the treatment groups. Results MMP supplementation resulted in significant improvements in haemoglobin concentration and in the reduction of anaemia prevalence in the two treatment groups compared with the control group (p <0.001). The severely to moderately anaemic children (Hb <100 g/L) on daily supplementation recovered faster than those on twice weekly supplementation. MMP was well accepted and compliance was high in both treatment groups. Overall, the improvement in the weight for age Z-score was very small and not statistically significant across the three study groups. Conclusions MMP supplementation had positive effects in reduction of anaemia prevalence and in improving haemoglobin concentration. For severely to moderately anaemic children, daily MMP supplementation was more effective in improving haemoglobin concentration and reducing anaemia prevalence. A longer intervention period is probably needed to have a positive effect on growth.
  • ItemOpen Access
    A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar.
    (Springer Science and Business Media LLC, 2009-12-14) Ricaut, François-X; Razafindrazaka, Harilanto; Cox, Murray P; Dugoujon, Jean-M; Guitard, Evelyne; Sambo, Clement; Mormina, Maru; Mirazon-Lahr, Marta; Ludes, Bertrand; Crubézy, Eric
    BACKGROUND: Current models propose that mitochondrial DNA macrohaplogroups M and N evolved from haplogroup L3 soon after modern humans left Africa. Increasingly, however, analysis of isolated populations is filling in the details of, and in some cases challenging, aspects of this general model. RESULTS: Here, we present the first comprehensive study of three such isolated populations from Madagascar: the Mikea hunter-gatherers, the neighbouring Vezo fishermen, and the Merina central highlanders (n = 266). Complete mitochondrial DNA genome sequences reveal several unresolved lineages, and a new, deep branch of the out-of-Africa founder clade M has been identified. This new haplogroup, M23, has a limited global distribution, and is restricted to Madagascar and a limited range of African and Southwest Asian groups. CONCLUSIONS: The geographic distribution, phylogenetic placement and molecular age of M23 suggest that the colonization of Madagascar was more complex than previously thought.
  • ItemOpen Access
    A female signal reflects MHC genotype in a social primate.
    (Springer Science and Business Media LLC, 2010-04-07) Huchard, Elise; Raymond, Michel; Benavides, Julio; Marshall, Harry; Knapp, Leslie A; Cowlishaw, Guy
    BACKGROUND: Males from many species are believed to advertise their genetic quality through striking ornaments that attract mates. Yet the connections between signal expression, body condition and the genes associated with individual quality are rarely elucidated. This is particularly problematic for the signals of females in species with conventional sex roles, whose evolutionary significance has received little attention and is poorly understood. Here we explore these questions in the sexual swellings of female primates, which are among the most conspicuous of mammalian sexual signals and highly variable in size, shape and colour. We investigated the relationships between two components of sexual swellings (size and shape), body condition, and genes of the Major Histocompatibility Complex (MHC) in a wild baboon population (Papio ursinus) where males prefer large swellings. RESULTS: Although there was no effect of MHC diversity on the sexual swelling components, one specific MHC supertype (S1) was associated with poor body condition together with swellings of small size and a particular shape. The variation in swelling characteristics linked with the possession of supertype S1 appeared to be partially mediated by body condition and remained detectable when taking into account the possession of other supertypes. CONCLUSIONS: These findings suggest a pathway from immunity genes to sexual signals via physical condition for the first time in females. They further indicate that mechanisms of sexual selection traditionally assigned to males can also operate in females.
  • ItemOpen Access
    Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.
    (Springer Science and Business Media LLC, 2008-08-04) Chaubey, Gyaneshwer; Karmin, Monika; Metspalu, Ene; Metspalu, Mait; Selvi-Rani, Deepa; Singh, Vijay Kumar; Parik, Jüri; Solnik, Anu; Naidu, B Prathap; Kumar, Ajay; Adarsh, Niharika; Mallick, Chandana Basu; Trivedi, Bhargav; Prakash, Swami; Reddy, Ramesh; Shukla, Parul; Bhagat, Sanjana; Verma, Swati; Vasnik, Samiksha; Khan, Imran; Barwa, Anshu; Sahoo, Dipti; Sharma, Archana; Rashid, Mamoon; Chandra, Vishal; Reddy, Alla G; Torroni, Antonio; Foley, Robert A; Thangaraj, Kumarasamy; Singh, Lalji; Kivisild, Toomas; Villems, Richard; Foley, Robert [0000-0003-0479-3039]; Kivisild, Toomas [0000-0002-6297-7808]
    BACKGROUND: Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East. RESULTS: Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of approximately 12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages. CONCLUSION: Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.