Current Population Genetics Research Articles

Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene.

Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.

Pleistocene Glacial Refugia in the Don River Basin: Witness from the Endangered Depressed River Mussel

The depressed river mussel Pseudanodonta complanata (Rossmässler, 1835) is an endangered freshwater bivalve with sparse distribution across Europe. Despite its high conservation priority, available data on the current population genetics and biogeography of P. complanata are very limited. In this paper, we studied the genetic diversity and differentiation of P. complanata based on newly sequenced COI and ND1 gene fragments, and on available sequences from the NCBI GenBank. We discovered a localized and highly divergent lineage in the Don River basin and a widespread but low diversified lineage distributed from the Volga River basin to the Oise River in France. A star-like haplotype network, results of mismatch analysis, and significant negative values of neutrality tests reveal that the pan-European lineage went through a bottleneck event. The discovery of the separate lineage in the Don River basin is and additional evidence of the existence of Pleistocene glacial refugia in the south of the Russian Plain. Moreover, this finding confirms the significance of the Azov Sea drainage as a freshwater biodiversity hotspot of great conservation importance.

HLA haplotype frequency estimation for heterogeneous populations using a graph-based imputation algorithm

HLA haplotype frequencies are estimated from ambiguous unphased HLA genotyping data using Expectation-Maximization (EM) algorithms. Current population genetics methods require independent EM frequency estimates for each population, and assume that each population is in Hardy-Weinberg Equilibrium (HWE). The HWE assumption of EM has thus far resulted in the exclusion of individuals from mixed or unknown ethnic backgrounds from reference datasets. Multi-region populations are currently poorly served by stem cell donor registry HLA imputation and matching implementations due to the inability of such algorithms to incorporate admixture into their population genetics models. To address this unmet need, we have expanded the imputation component of our GRaph IMputation and Matching (GRIMM) framework, where imputation becomes the expectation step in an iterative EM algorithm. Our novel multi-region EM implementation considers region as a Bayesian prior, enabling integration of HLA information from multiple single-region population groups, and for the first time including individuals with ambiguous or mixed ethnic backgrounds. We show that our multi-region EM produces much higher likelihood values and better haplotype recovery as measured by Kullback-Leibler divergence than all evaluated EM implementations when tested on real datasets of US donor registry HLA typings as well as simulated multi-region datasets of ambiguous HLA typings.

Would tropical climatic variations impact the genetic variability of triatomines: Rhodnius ecuadoriensis, principal vector of Chagas disease in Ecuador?

Rhodnius ecuadoriensis is one of the most important vector species of Chagas disease in Ecuador. This species is distributed in the Central coast region and in the south Andean region, and an incipient speciation process between these geographical populations was previously proposed. The current population genetics study only focused on the Central coast region and analyzed 96 sylvatic specimens of R. ecuadoriensis associated with Phytelephas aequatorialis palm trees. We used Cytb and 16S-rRNA sequences and a Cytb-16S-rRNA concatenated set to explore (i) the genetic variability, spatial structuring, and demographic history of R. ecuadoriensis, and to determine (ii) the relationship between the genetic and climatic variabilities. A particularly high genetic variability was observed without detectable general genetic structure; only some terminal genetic clusters were observed. We did not observe isolation by geographical distance (IBD), and it is likely that ancient expansion occurred, according to Fs index and mismatch distribution for Cytb-16S-rRNA concatenated sequences. Hierarchical clustering showed that the current locality origins of the bugs were grouped into four bioclimatic clusters. Genetic and bioclimatic distances were not correlated, but some genetic clusters were associated with bioclimatic ones. The results showed an ancient evolution of the species in the region with a possible old expansion. The absence of spatial genetic structure could be due to climatic conditions (possible selection of singular genotypes) and to passive transportation of palms tree materials where R. ecuadoriensis are living.

Current population genetics of Japanese harbor seals: Two distinct populations found within a small area

AbstractWe used microsatellite loci to understand the current population genetics of Japanese harbor seals, and found that they were subdivided into two distinct populations, one in Erimo and the other in eastern Hokkaido, despite being only 150 km apart and having no obvious geographical boundaries between them. Strong population subdivision between the two areas may be due to the small number of haul‐out sites and population size, and that a single habitat type is used for haul‐out sites in Japan. Also, at Erimo, there are numerous rocky reefs at a single haul‐out site that stretch up to 1.3 km offshore from land, while 10 haul‐out sites in eastern Hokkaido, separated by a maximum of 30 km, are interspersed along 75 km of the coast. The direction in which the rocky reefs stretch away from land or in which the haul‐out sites are facing may be limiting the movement of Japanese harbor seals and causing strong population subdivision between Erimo and eastern Hokkaido. No recent genetic bottlenecks were detected, although the seals in Erimo and eastern Hokkaido were reported to have experienced declines in population size over the past few decades.

HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations.

The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and the FST value support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes the FST outliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60–95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript.

‘We Are All the Same, We All Are Mestizos’: Imagined Populations and Nations in Genetics Research in Colombia

In Colombia, as in other Latin American countries, current population genetics research is based on the understanding that Colombians constitute a mestizo nation, given the admixture process that took place between Africans, Amerindians, and Europeans during colonial times. The mestizo is a pervasive category used by geneticists to conduct, organise, and publish research studies that deal with the continent's peopling process and the genetic makeup of its contemporary population(s). It is also the dominant imaginary for the Colombian population and a key nation-building ideology. By tracing how this category moves and is used across four Colombian genetics laboratories, it is possible to discern that despite its apparently clear-cut boundaries, the mestizo is contingent, contested, and flexible, allowing for multiple understandings and usages. This flexibility and multiplicity are visible in the quantification of genetic ancestry, the divisions of geographical location, and the understanding of gender. Such understandings allow one to think about a homogeneous nation (inclusive) that is simultaneously heterogeneous (exclusive); they provide multiple but not necessarily contradictory possibilities of being mestizo, allowing the coexistence of images of the nation that could otherwise seem contradictory; and they permit navigation around contested terms such as race, while simultaneously thinking of mixed races or racialised individuals. Finally, these flexible and multiple constructions of the mestizo (re)produce various subjects as ‘other’, whether they are women, the Indigenous, the black/dark, or the poor.

Phylogeography of the Eurasian green woodpecker (Picus viridis)

Aim In this paper we investigate the evolutionary history of the Eurasian green woodpecker (Picus viridis) using molecular markers. We specifically focus on the respective roles of Pleistocene climatic oscillations and geographical barriers in shaping the current population genetics within this species. In addition, we discuss the validity of current species and subspecies limits. Location Western Palaearctic: Europe to western Russia, and Africa north of the Sahara. Methods We sequenced two mitochondrial genes and five nuclear introns for 17 Eurasian green woodpeckers. Multilocus phylogenetic analyses were conducted using maximum likelihood and Bayesian algorithms. In addition, we sequenced a fragment of the cytochrome b gene (cyt b, 427 bp) and of the Z-linked BRM intron 15 for 113 and 85 individuals, respectively. The latter data set was analysed using population genetic methods. Results Our phylogenetic results support the monophyly of Picus viridis and suggest that this taxon comprises three allopatric/parapatric lineages distributed in North Africa, the Iberian Peninsula and Europe, respectively. The North African lineage split from the Iberian/European clade during the early Pleistocene (1.6–2.2 Ma). The divergence event between the Iberian and the European lineages occurred during the mid-Pleistocene (0.7–1.2 Ma). Our results also support a post-glacial range expansion of these two lineages from distinct refugia located in the Iberian Peninsula and possibly in eastern Europe or Anatolia, which led to the establishment of a secondary contact zone in southern France. Main conclusions Our results emphasize the crucial role of both Pleistocene climatic oscillations and geographical barriers (Strait of Gibraltar, Pyrenees chain) in shaping the current genetic structure of the Eurasian green woodpecker. Our molecular data, in combination with diagnosable plumage characters, suggest that the North African green woodpecker (Levaillant’s woodpecker) merits species rank as Picus vaillantii (Malherbe, 1847). The two European lineages could be distinguished by molecular and phenotypic characters over most of their respective geographical ranges, but they locally exchange genes in southern France. Consequently, we prefer to treat them as subspecies (P. viridis viridis, P. viridis sharpei) pending further studies.

Bottlenecks and multiple introductions: population genetics of the vector of avian malaria in Hawaii.

Avian malaria has had a profound impact on the demographics and behaviour of Hawaiian forest birds since its vector, Culex quinquefasciatus the southern house mosquito, was first introduced to Hawaii around 1830. In order to understand the dynamics of the disease in Hawaii and gain insights into the evolution of vector-mediated parasite-host interactions in general we studied the population genetics of Cx. quinquefasciatus in the Hawaiian Islands. We used both microsatellite and mitochondrial loci. Not surprisingly we found that mosquitoes in Midway, a small island in the Western group, are quite distinct from the populations in the main Hawaiian Islands. However, we also found that in general mosquito populations are relatively isolated even among the main islands, in particular between Hawaii (the Big Island) and the remaining Hawaiian Islands. We found evidence of bottlenecks among populations within the Big Island and an excess of alleles in Maui, the site of the original introduction. The mitochondrial diversity was typically low but higher than expected. The current distribution of mitochondrial haplotypes combined with the microsatellite information lead us to conclude that there have been several introductions and to speculate on some processes that may be responsible for the current population genetics of vectors of avian malaria in Hawaii.

Polymorphism for Y-linked suppressors of sex-ratio in two natural populations of Drosophila mediopunctata.

In several Drosophila species there is a trait known as "sex-ratio": males carrying certain X chromosomes (called "SR") produce female biased progenies due to X-Y meiotic drive. In Drosophila mediopunctata this trait has a variable expression due to Y-linked suppressors of sex-ratio expression, among other factors. There are tow types of Y chromosomes (suppressor and nonsuppressor) and two types of SR chromosomes (suppressible and unsuppressible). Sex-ratio expression is suppressed in males with the SRsuppressible/Ysuppressor genotype, whereas the remaining three genotypes produce female biased progenies. Now we have found that approximately 10-20% of the Y chromosomes from two natural populations 1500 km apart are suppressors of sex-ratio expression. Preliminary estimates indicate that Ysuppressor has a meiotic drive advantage of 6% over Ynonsuppressor. This Y polymorphism for a nonneutral trait is unexpected under current population genetics theory. We propose that this polymorphism is stabilized by an equilibrium between meiotic drive and natural selection, resulting from interactions in the population dynamics of X and Y alleles. Numerical simulations showed that this mechanism may stabilize nonneutral Y polymorphisms such as we have found in D. mediopunctata.

The evolutionary design of error-rates, and the fast fixation enigma.

Genetic and non-genetic error-rates are analyzed in parallel for a lower and a higher organism (E. coli and man, respectively). From the comparison of mutation with fixation rates, contrasting proposals are made, concerning the arrangement of error-rates in the two organisms. In E. coli, reproduction is very conservative, but genetic variability is high within populations. Most mutations are discarded by selection, yet single mutational variants of a gene have, on average, little impact on fitness. In man, the mutation rate per generation is high, the variability generated in the population is comparatively low, and most mutations are fixed by drift rather than selection. The variants of a gene are in general more deleterious than in E. coli. There is a discrepancy in the published mutation rates: the rate of mutation fixations in human populations is twice or four times higher than the individual rate of mutation production, a feature which is not consistent with current population genetics models. Two, not mutually exclusive, hypotheses may explain this 'fast fixation enigma': (i) Mutation rates have substantially decreased in recent human evolution and (ii) A substantial fraction of the fixed mutations were generated in a process-such as gene conversion-that violates the principle of independence of mutation events.

The Spatial Scale of Genetic Differentiation in a Hummingbird-Pollinated Plant: Comparison with Models of Isolation by Distance

We examined patterns of genetic differentiation at isozyme loci in natural populations of Ipomopsis aggregata, for which distances of gene flow had been previously estimated. Using genetic neighborhood areas based on direct estimates of gene flow to define subpopulations, we found that FST values (the inbreeding coefficient of a subpopulation relative to the total population) were consistently positive but small. Allele frequencies were spatially autocorrelated at distances of less than 5 m only. Both measures of genetic structure indicate some isolation by distance but less than predicted by current population genetics theory. Subpopulation size derived from realized gene flow estimates from paternity analysis produced a slightly better fit to theory than did using estimates from tracking pollen dispersal to stigmas. Discrepancies between observation and theory may also arise from other sources including occasional long-distance gene flow that is difficult to observe.

Evaluation of Current Population Genetics Theory

My aim is to give a partial evaluation or critique of the state of population genetics theory. A decent theory must include the following components: the development of concepts of fitness that have demonstrated epistemic correlations, life tables, mating, fecundity, finite (even if large) niche size, and, of course, Mendelism and mutation. It must in the end also include varying environment and competition between species. The extent to which the desiderata are met is discussed. The big lacunae in the whole theory appear to be the inadequate treatment of fitness and the ignoring of niche capacity. Some theorems that are given as fundamental must be questioned and even discarded. Integration of ideas of simple Mendelism, quantitative genetic variation, and ecology is the big task ahead. It is critical that more complete theory be developed.

Population Genetics Theory: Another View

In this reply to Kempthorne's critique of current population genetics theory (this symposium), I describe the differences in viewpoint and in choice of evidence which lead me to a more favorable conclusion. Kempthorne's attacks on the general selection model and on Fisher's Fundamental Theorem of Natural Selection have considerable justification; in both cases, however, qualification is preferable to demolition. Furthermore, recent advances in selection theory really meet Kempthorne's well-founded objections. Finally, the most substantial point in Kempthorne's critique is not that current population genetics theory is inoperable, but that it is practically impossible to apply to life-history problems. Computers, properly programmed, may provide a valuable way around this impasse. In addition, the necessity and the difficulty of manipulating one variable at a time have been with science for a long and exasperating time.

A two loci viability matrix with implications in current population genetics models

Some equilibrium properties of a two loci deterministic system subject to a postulated viability matrix are given. Two conclusions are reached: i) linkage can not stabilize additive equally contributing two-loci systems under optimizing selection. ii) Hybrid protein superiority can not be invoked for the maintenance of polymorphisms shared by duplicated structural loci.