Genetic variants determining survival and fertility in an adverse African environment: a population-based large-scale candidate gene association study.

Human survival probability and fertility decline strongly with age. These life history traits have been shaped by evolution. However, research has failed to uncover a consistent genetic determination of variation in survival and fertility. As an explanation, such genetic determinants have been selected in adverse environments, in which humans have lived during most of their history, but are almost exclusively studied in populations in modern affluent environments. Here, we present a large-scale candidate gene association study in a rural African population living in an adverse environment. In 4387 individuals, we studied 4052 SNPs in 148 genes that have previously been identified as possible determinants of survival or fertility in animals or humans. We studied their associations with survival comparing newborns, middle-age adults, and old individuals. In women, we assessed their associations with reported and observed numbers of children. We found no statistically significant associations of these SNPs with survival between the three age groups nor with women's reported and observed fertility. Population stratification was unlikely to explain these results. Apart from a lack of power, we hypothesise that genetic heterogeneity of complex phenotypes and gene-environment interactions prevent the identification of genetic variants explaining variation in survival and fertility in humans.

Ancestral stories of Ghanaian Bimoba reflect millennia-old genetic lineages.

Oral history and oral genealogies are mechanisms of collective memory and a main cultural heritage of many populations without a writing system. In the effort to analytically address the correspondence between genetic data and historical genealogies, anthropologists hypothesised that genealogies evolve through time, ultimately containing three parts: literal--where the most recent ancestry is truthfully represented; intended--ancestry is inferred and reflects political relations among groups; and mythical--that does not represent current social reality. While numerous studies discuss oral genealogies, to our knowledge no genetic studies have been able to investigate to what extent genetic relatedness corresponds to the literal and intended parts of oral genealogies. We report on the correspondence between genetic data and oral genealogies among Bimoba males in a single village in North-Eastern Ghana. We compared the pairwise mismatch distribution of Y chromosome short tandem repeat (Y-STR) haplotypes among all lineages present in this village to the self-reported (oral) relatedness. We found that Bimoba are able to correctly identify unrelated individuals in 92% of the cases. In contrast, they are able to correctly identify related individuals only in 38% of the cases, which can be explained by three processes: (1) the compression of genealogies, leading to increasing inaccuracy with increasing genealogical distance, (2) inclusions into the lineage from intended relations such as clan co-option or adoptions, and (3) false paternities, which in this study were found to have a minor effect on the correspondence between genetic data and oral genealogies. In addition, we observed that 70% of unrelated pairs have from six to eight Y-STR differences, a diversification peak which we attribute to an ancient West African expansion dating around 9454 years ago. We conclude that, despite all caveats, oral genealogies are reflecting ancient lineages more accurately than previously thought.

Indian Ocean crossroads: human genetic origin and population structure in the Maldives.

The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago.

The influence of clan structure on the genetic variation in a single Ghanaian village.

Socioeconomic and cultural factors are thought to have an important role in influencing human population genetic structure. To explain such population structure differences, most studies analyse genetic differences among widely dispersed human populations. In contrast, we have studied the genetic structure of an ethnic group occupying a single village in north-eastern Ghana. We found a markedly skewed male population substructure because of an almost complete lack of male gene flow among Bimoba clans in this village. We also observed a deep male substructure within one of the clans in this village. Among all males, we observed only three Y-single-nucleotide polymorphism (SNP) haplogroups: E1b1a*-M2, E1b1a7a*-U174 and E1b1a8a*-U209, P277, P278. In contrast to the marked Y-chromosomal substructure, mitochondrial DNA HVS-1 sequence variation and autosomal short-tandem repeats variation patterns indicate high genetic diversities and a virtually random female-mediated gene flow among clans. On the extreme micro-geographical scale of this single Bimoba village, correspondence between the Y-chromosome lineages and clan membership could be due to the combined effects of the strict patrilocal and patrilineal structure. If translated to larger geographic scales, our results would imply that the extent of variation in uniparentally inherited genetic markers, which are typically associated with historical migration on a continental scale, could equally likely be the result of many small and different cumulative effects of social factors such as clan membership that act at a local scale. Such local scale effects should therefore be considered in genetic studies, especially those that use uniparental markers, before making inferences about human history at large.

Mosaic segmental uniparental isodisomy and progressive clonal selection: a common mechanism of late onset ß-thalassemia major.

Genomic DNA of 3 patients, born as healthy carriers and developing a late-onset severe transfusion-dependent beta-thalassemia major was studied by high-density genome wide SNP array analysis. A mosaic loss of heterozygosity for almost the entire 11p was found, not attributable to deletions but involving mosaicism for segmental paternal isodisomy of 11p. Mitotic recombination leading to mosaic segmental uniparental isodisomy on chromosome 11p in multiple tissues has been described as a molecular disease mechanism for a subset of sporadic Beckwith-Wiedemann syndrome cases. A similar mechanism also seems to be involved in causing late-onset disease in carriers of recessive mutations in other genes located in 11p, such as late-onset beta-thalassemia major and sickle cell disease. We suggest that the loss of maternally imprinted IGF-2 and H19 genes may account for the selective advantage of hematopoietic cells containing this segmental paternal isodisomy of 11p carrying the ß-thalassemia mutation.

A sensitive method to extract DNA from biological traces present on ammunition for the purpose of genetic profiling.

Exploring technological limits is a common practice in forensic DNA research. Reliable genetic profiling based on only a few cells isolated from trace material retrieved from a crime scene is nowadays more and more the rule rather than the exception. On many crime scenes, cartridges, bullets, and casings (jointly abbreviated as CBCs) are regularly found, and even after firing, these potentially carry trace amounts of biological material. Since 2003, the Forensic Laboratory for DNA Research is routinely involved in the forensic investigation of CBCs in the Netherlands. Reliable DNA profiles were frequently obtained from CBCs and used to match suspects, victims, or other crime scene-related DNA traces. In this paper, we describe the sensitive method developed by us to extract DNA from CBCs. Using PCR-based genotyping of autosomal short tandem repeats, we were able to obtain reliable and reproducible DNA profiles in 163 out of 616 criminal cases (26.5%) and in 283 out of 4,085 individual CBC items (6.9%) during the period January 2003-December 2009. We discuss practical aspects of the method and the sometimes unexpected effects of using cell lysis buffer on the subsequent investigation of striation patterns on CBCs.

Changed gene expression for candidate ageing genes in long-lived Bicyclus anynana butterflies.

Candidate genes for the regulation of lifespan have emerged from studies that use mutants and genetically manipulated model organisms. However, it is rarely addressed whether these genes contribute to lifespan variation in populations of these species that capture natural standing genetic variation. Here, we explore expression variation in three candidate ageing genes, Indy, sod2, and catalase, in Bicyclus anynana, a butterfly with well understood ecology. We used lines established from natural populations and artificially selected for increased adult starvation resistance. They show a considerable increase in adult lifespan under both starvation and optimal food conditions. We measured adult butterflies of various ages, under a range of optimal and starvation diets, from two selected populations and one unselected control population. In all lines, Indy and catalase are up-regulated in response to starvation while this is not evident for sod2. Under starvation, Indy and catalase are up-regulated in, while this is not evident for sod2. Under optimal food conditions, Indy is down-regulated at a later age, with Indy expression showing relatively high inter-individual variation. We find differences between the selected lines and the unselected line. Under starvation conditions, expression is higher for catalase in one, and for sod2 in both selected lines. Importantly, sod2 expression is also higher in the selected populations under optimal food conditions. We conclude that sod2, but not Indy, is involved in the response to artificial selection for increased starvation resistance. The role of catalase is less clear because of the differences between the two selected lines. Moreover, sod2 appears to be a candidate gene that underpins the genetic correlation between starvation resistance and longevity. Our study indicates that some, but not all, genes identified through mutant screens in other organisms may underpin standing genetic variation for ageing-related traits in stocks of Bicyclus butterflies established from natural populations. Clearly, this needs to be investigated in other organisms as well, especially in the organisms to which mutants screens were applied. This information will narrow down the list of genes that underpin variation in lifespan and ageing in extant populations of organisms, and which may serve as candidate genes in humans.

Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA.

The current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with self-declared ancestry we have analyzed paternally, maternally and bi-parentally inherited DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification.

Increased life span in a polyphenic butterfly artificially selected for starvation resistance.

Starvation resistance is closely associated with fitness in natural populations of many organisms. It often co-varies with longevity and is a relevant target for understanding the evolution of aging. We selected for increased starvation resistance in the seasonally polyphenic butterfly Bicyclus anynana in a warm, wet-seasonal environment over 17 generations. We measured the response to selection for two selected lines compared to that of an unselected stock. Results show an increase in survival under adult starvation of 50%-100%. In addition, selection lines showed an increase in life span under normal adult feeding of 30%-50%. Female reproduction was changed toward laying fewer but larger eggs. The results indicate a sex-specific response to selection: females reallocated resources toward a more durable body, whereas males appeared to increase starvation resistance through changed metabolic rate. The phenotype produced by artificial selection resembles the form that occurs in the cool, dry-season environment, which suggests that selection has targeted the regulatory mechanisms for survival that are also involved in the suite of traits (including starvation resistance) central to the adaptive plastic response of this butterfly to seasonal conditions. In general, these results imply that the regulation of life span involves mechanisms of phenotypic plasticity.

Potential constraints on evolution: sexual dimorphism and the problem of protandry in the butterfly Bicyclus anynana.

The earlier mean adult emergence between males and females, protandry, has been well studied mathematically and in comparative studies. However, quantitative and evolutionary genetic research on protandry is scarce. The butterfly, Bicyclus anynana exhibits protandry and here we selected for each of the different combinations of male and female development time in this species, thus including direct selection on protandry (i.e., FAST, fast males and fast females; SLOW, slow males and slow females; FMSF, fast males and slow females; and SMFF, slow males and fast females). After eight generations of selection there was no significant response for increased or decreased protandry, whereas selection for increased or decreased development time in both sexes (FAST or SLOW) was successful. Continued selection (> 30 generations) for decreased or increased protandry showed a significant difference between the FMSFC and SMFFC lines (subscript c for continued selection), which was of the same magnitude as the nonsignificant difference observed between the FMSF and SMFF lines at generation eight. This indicated that the initial selection was successful, but that the difference between the lines did not increase with continued selection. Our results also indicate that the genetic covariance across sexes for development time is near unity. Interestingly, lines selected for decreased protandry (SMFF) had lower egg-to-adult survival, and broods from these lines had lower rates of egg hatching. This suggests that interactions with fertility might constrain certain directions of change in patterns of protandry. Moreover, selection yielded a change in the ratio of male to female development time for slow lines, suggesting that some amount of sex-specific genetic variance for development time is still present in this population. The FMSFC line showed the largest effect of selection on protandry, mainly through an effect on female developmental time. Lastly, our results show that temperature has an effect on the amount of protandry in the selected lines. These results are discussed in relation to the ecology of this species and the evolution of protandry.

Developmental plasticity and acclimation both contribute to adaptive responses to alternating seasons of plenty and of stress in Bicyclus butterflies.

Plasticity is a crucial component of the life cycle of invertebrates that live as active adults throughout wet and dry seasons in the tropics. Such plasticity is seen in the numerous species of Bicyclus butterflies in Africa which exhibit seasonal polyphenism with sequential generations of adults with one or other of two alternative phenotypes. These differ not only in wing pattern but in many other traits. This divergence across a broad complex of traits is associated with survival and reproduction either in a wet season that is favourable in terms of resources, or mainly in a dry season that is more stressful. This phenomenon has led us to examine the bases of the developmental plasticity in a model species, B.anynana, and also the evolution of key adult life history traits, including starvation resistance and longevity. We now understand something about the processes that generate variation in the phenotype,and also about the ecological context of responses to environmental stress. The responses clearly involve a mix of developmental plasticity as cued by different environments in pre-adult development,and the acclimation of life history traits in adults to their prevailing environment.

Consequences of artificial selection on pre-adult development for adult lifespan under benign conditions in the butterfly Bicyclus anynana.

The genetic architecture underlying the regulation of lifespan is shaped by evolutionary history, thus, including selection in past environments. In particular, the developmental environment is important, because selection pressure for survival is highest during development. From this life-history point of view, the ageing phenotype is the outcome of these factors, and links between the developmental and adult life stage are expected. In this study, we specifically address whether genetic variation in pre-adult traits affects adult lifespan. We use lines artificially selected for divergence in development time, pupal mass or egg size, thus, exploiting the standing genetic variation in pre-adult traits present in natural populations of Bicyclus anynana. We then reared individuals from each line and the unselected base population in a common environment, and recorded each selected trait and adult longevity. In general, differences in adult lifespan across selection lines were small. This is not surprising given the benign conditions used here. The minor differences in adult survival were only partially the result of environmental influences, as indicated by low phenotypic correlations. However, significant genetic correlations point to possible intrinsic mechanisms involved in lifespan regulation. Genetic variation in egg mass or pupal mass did not contribute to variation in lifespan. However, we found a negative genetic correlation between developmental time and lifespan, suggesting a genetic coupling of faster development with a longer adult lifespan in this species. A follow-up study with an identical set-up that introduces stress during development should give a more detailed insight into the role of development in the regulation of lifespan.