How do SNP ascertainment schemes and population demographics affect inferences about population history?

Background

The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F_ST and principal components analysis (PCA).

Results

Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of F_ST between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong.

Conclusions

Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of F_ST, time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1469-5) contains supplementary material, which is available to authorized users.     

Statistical indicators and state–space population models predict extinction in a population of bobwhite quail

Early warning systems of extinction thresholds have been developed for and tested in microcosm experiments, but have not been applied to populations of wild animals. We used state–space population models and a statistical indicator to detect a transcritical bifurcation extinction threshold in a population of bobwhite quail (Colinus virginianus) located in an agricultural region experiencing habitat deterioration and loss. The extinction threshold was detectible using two independent data sets. We compared predictions from state–space population models to predictions from a statistical indicator and found that predictions were corroborated. Using state–space population models, we estimated that our study population crossed the extinction threshold in 2010 (2002–2036; 95 % confidence intervals [CI]) using the whistle count (WC) data set and in 2008 (1999–2064; 95 % CI) using the Breeding Bird Survey (BBS) data. With the statistical indicator, we estimated that the extinction threshold will be crossed in 2018 (2004–2031; 95 % CI) using the WC data and will be crossed in 2012 (2006–2018; 95 % CI) using the BBS data. We expect extinction in our study population soon after crossing the extinction threshold, but the time to extinction and potential reversibility of the threshold are unknown. Our results suggest that neither small nor decreasing population size will warn of the transcritical bifurcation extinction threshold. We suggest that managers of wildlife populations in regions experiencing land use change should try to predict extinction thresholds and make management decisions to ensure the persistence of the species.     

Dimensions of global population projections: what do we know about future population trends and structures?

The total size of the world population is likely to increase from its current 7 billion to 8–10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA.     

β-thalassemia mutations in the Portuguese population

Summary In this study we have carried out haplotype analysis on the -globin gene cluster and characterized the -thalassemia mutation by oligonucleotide hybridization in 14 patients with thalassemia major and 5 with sickle cell/-thalassemia originating from southern Portugal. We found that three mutations, namely the °-39, ° IVS-1 nt 1 and ⁺ IVS-1 nt 110 are prevalent accounting for 53%, 32% and 10% of the -thalassemia chromosomes respectively. In general each mutation was associated with a specific chromosomal haplotype; the ° mutation, however, was linked to three different haplotypes. These results indicate that three oligo-probes complementary to the most common mutations allow prenatal diagnosis by oligonucleotide analysis in 96% of the couples at risk of having offspring with thalassemia major in southern Portugal.     

α-Thalassemia haplotypes in the Algerian population

Summary DNA mapping was performed in seven unrelated HbH patients and nine carriers for -thalassemia trait originating from Algeria. This study has allowed us to identify four -thalassemia haplotypes: the (–^3.7) haplotype, which is the most frequent (18 of 23 -thalassemic chromosomes), the (–()^20.5) haplotype, a (--) haplotype, and an ()^T haplotype. Our results also show that the (–^3.7) haplotypes encountered in the Algerian population are heterogeneous and differ by the site of the unequal crossover responsible for the 3.7-kb deletion and the size of the interzeta fragment. In addition, during this survey we observed that normal chromosomes bearing a polymorphic BglII site are associated with different interzeta fragments.     

Does population ecology have general laws?

There is a widespread opinion among ecologists that ecology lacks general laws. In this paper the author argues that this opinion is mistaken. Taking the case of population dynamics, the author points out that there are several very general law-like propositions that provide the theoretical basis for most population dynamics models that were developed to address specific issues. Some of these foundational principles, like the law of exponential growth, are logically very similar to certain law of physics (Newton's law of intertia, for example, is almost a direct analogue of exponential growth). The author discusses two other principles (population self-limitation and resource-consumer oscillations), as well as the more elementary postulates that underlie them. None of the "laws" that the author proposes for population ecology are new. Collectively ecologists have been using these general principles in guiding development of their models and experiments since the days of Lotka, Volterra, and Gause.     

What limits the Serengeti zebra population?

The populations of the ecologically dominant ungulates in the Serengeti ecosystem (zebra, wildebeest and buffalo) have shown markedly different trends since the 1960s: the two ruminants both irrupted after the elimination of rinderpest in 1960, while the zebras have remained stable. The ruminants are resource limited (though parts of the buffalo population have been limited by poaching since the 1980s). The zebras resource acquisition tactics should allow them to outcompete the ruminants, but their greater spatial dispersion makes them more available to predators, and it has been suggested that this population is limited by predation. To investigate the mechanisms involved in the population dynamics of Serengeti zebra, we compared population dynamics among the three species using demographic models based on age-class-specific survival and fecundity. The only major difference between zebra and the two ruminants occurred in the first-year survival. We show that wildebeest have a higher reproductive potential than zebra (younger age at first breeding and shorter generation time). Nevertheless, these differences in reproduction cannot account for the observed differences in the population trends between the zebra and the ruminants. On the other hand, among-species differences in first-year survival are great enough to account for the constancy of zebra population size. We conclude that the very low first-year survival of zebra limits this population. We provide new data on predation in the Serengeti and show that, as in other ecosystems, predation rates on zebras are high, so predation could hold the population in a predator pit. However, lion and hyena feed principally on adult zebras, and further work is required to discover the process involved in the high mortality of foals.     

Seasonal variation in the population growth rate of a dominant zooplankter: what determines its population dynamics?

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