Relation of population changes to the distribution of genetic factors

Abstract

During the 1800's, the population of Ireland underwent a rapid increase and subsequent decrease in population size. The effects of this change upon population structure were assessed using a simulation of the isolation by distance model and comparing the results to those obtained assuming constant population size. These results indicate that changes in within‐group genetic similarity (kinship) brought about by a rapid increase in population size are cancelled by the effects of a rapid decrease in population size. Parameters of the isolation by distance model are hardly affected by population size changes. These results suggest that violation of the assumption of constant population size for population structure models may not be that serious when population size changes rapidly and in both directions.     

Some Notes on David Nicholson's Contributions to Modelling Adsorption

Abstract

During his career David has built up a very large number of scientific contacts throughout the world. Many of these became friends and collaborators. Imperial College was, of course, a good place to start from: R.M. Barrer was from New Zealand and John Petropoulos from Greece. Subsequently, he collaborated with scientists from other European Union countries, especially from France and Germany as well as more researchers from Greece. He also made many contacts in the US. A very important example was the sabbatical he had with W.A. Steele at Penn State, where he made his first big incursion into intermolecular forces. He also had very useful exchanges of visits with K.E. Gubbins, which led to joint work. More recently he developed working relationships with scientists from Japan and from South Korea. The scientific value of these contacts may be gauged from the large number of his publications, which involve researchers from these countries as co-authors. However, I am sure the readiness with which overseas researchers participated was in part also due to the friendly and helpful manner with which David received them here.     

Challenges Faced by Behavioral Genetic Studies: Researchers Perspective from the MENA Region

BackgroundBehavioral genetic studies are important for the understanding of the contribution of genetic variations to human behavior. However, such studies might be associated with some ethical concerns.MethodsIn the current study, ethical challenges related to studies of genetic variations contributing to human behavior were examined among researchers. To achieve the study purpose, the Middle East and North Africa (MENA) region researchers were taken as an example, where the after- mentioned ethical challenges were discussed among a group of researchers, who were the participants of an online forum. Discussions and responses of the participants were monitored and were later qualitatively analyzed.ResultsDiscussions revealed that several ethical challenges, including subjects’ recruitment, the difficulty of obtaining informed consents, and issues of privacy and confidentiality of obtained data as information leakage, in this case, will lead to social stigma and isolation of the participants and their immediate family members. Jordanian social and cultural norms, faith, and the tribal nature of the population were raised as a major challenge that might face conducting behavioral genetic studies in the Arab populations of the MENA. The lack of regulation related to the conduction of genetic studies, misunderstanding, and misuse of genetic information are other challenges. A full explanation of genetic research and the current and future possible benefits/risks of such research could be potential solutions.ConclusionIn conclusion, the MENA populations are tackled with major challenges in relation to conducting research studies in genetics/antisocial behavior field/s. Establishment of guidelines related to genetic studies, capacity building, increasing public awareness about the importance of genetic testing, and enhancing responsible conduct of research will facilitate the conduct of such sensitive studies in the future in the region.     

Expert,healer, reassurer,hero and prophet: framing genetics and medical scientists in television news

Abstract

This paper is concerned with representations of the human genome and medical applications of modern biotechnology in Finnish television news. The main focus is on the way that news stories are framed by various linguistic and visual means and on how scientists appearing in the news are positioned. The qualitative analysis shows that in the national frame, biotechnology was treated as a field with great future promise, weighing the prospects of Finnish scientists to succeed in international competition. In the disease frame, the focus was on the achievements of genetic research in the treatment of serious diseases. In the breakthrough frame, it was predicted that genetics will revolutionise the treatment of diseases in ‘the near future’. Finally, news stories presented in the threat frame were mainly concerned to predict and avert problems arising from the potential abuse of genetic research. The analysis suggests that these frames implied certain speaking positions to the scientists appearing in the news stories.     

Phylogeography,genetic structure,and conservation of the endangered Caspian brown trout, <Emphasis Type="Italic">Salmo trutta caspius</Emphasis> (Kessler, 1877), from Iran

The Caspian Sea, the largest inland closed water body in the world, has numerous endemic species. The Caspian brown trout (Salmo trutta caspius) is considered as endangered according to IUCN criteria. Information on phylogeography and genetic structure is crucial for appropriate management of genetic resources. In spite of the huge number of studies carried out in the Salmo trutta species complex across its distribution range, very few data are available on these issues for S. trutta within the Caspian Sea. Mitochondrial (mtDNA control region) and nuclear (major ribosomal DNA internal transcribed spacer 1, ITS-1, and ten microsatellite loci) molecular markers were used to study the phylogeography, genetic structure, and current captive breeding strategies for reinforcement of Caspian trout in North Iranian rivers. Our results confirmed the presence of Salmo trutta caspius in this region. Phylogenetic analysis demonstrated its membership to the brown trout Danubian (DA) lineage. Genetic diversity of Caspian brown trout in Iranian Rivers is comparable to the levels usually observed in sustainable anadromous European brown trout populations. Microsatellite data suggested two main clusters connected by gene flow among river basins likely by anadromous fish. No genetic differences were detected between the hatchery sample and the remaining wild populations. While the current hatchery program has not produced detectable genetic changes in the wild populations, conservation strategies prioritizing habitat improvement and recovering natural spawning areas for enhancing wild populations are emphasized.     

Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.     

Hasty generalisation and exaggerated certainties: reporting genetic findings in health disparities research

Abstract

In the United States, research that examines potential genetic contributions to health disparities often relies on racial categories. Some see benefit in this research especially for conditions where disparities in health status seem strongly associated with racial identity, such as heart disease and prostate cancer. But this research calls for close scrutiny. First, despite common optimism about genetic research, it may not be the most productive way to examine health disparities. And second, this research has the potential to contribute to racial stereotypes, arguably a prime cause of the health disparities the genetic research actually seeks to ameliorate. Two articles reporting results about genetics and heart disease are used to illustrate these concerns. Both report strong correlations between increased vulnerability to heart disease and black racial identity. Despite serious sampling and analysis problems in these articles, the findings rapidly entered the scientific and popular literature. A possible reason for their ready acceptance is their congruence with stereotypes that attribute poor health and genetic inferiority to minority US populations.     

African Origin and Europe-Mediated Global Dispersal of The Cyanobacterium Microcystis aeruginosa

Microcystis aeruginosa is a bloom-forming cyanobacteria, which currently has a cosmopolitan distribution. Since M. aeruginosa can produce toxic compounds across all continents that it inhabits, it is of major public health relevance to assess its origin and dispersal. Thus, we conducted a worldwide study using 29 isolates representative of all the main continents, and used a concatenated genetic system for phylogenetic analyses consisting of four genetic markers (spanning ca. 3,485 bp). Our results support an early origin of M. aeruginosa in the African continent, with a subsequent dispersal to establish a second genetic pool in the European continent, from where M. aeruginosa then colonized the remaining continental regions. Our findings indicate that the European population has a cosmopolitan distribution, and is genetically closer to populations from Africa and North America. Our study also highlights the utility of using a concatenated dataset for phylogenetic inferences in cyanobacteria.     

Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south‐eastern United States and Caribbean Islands

Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south‐east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south‐east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south‐east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south‐east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south‐east US and the Caribbean island to be the admixture hot zone where distinctly African‐like Caribbean flies become genomically more similar to European‐like south‐east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection.     

Current depression among adult cancer survivors: Findings from the 2010 Behavioral Risk Factor Surveillance System

BackgroundA cancer diagnosis and subsequent treatments constitute a significantly increased psychological burden among cancer patients. This study examined the prevalence of current depression and the risk factors associated with a high burden of depression among cancer survivors in the US.MethodsWe analyzed data from 3550 cancer survivors (aged ≥18 years) and 26,917 adults without cancer who participated in the 2010 Behavioral Risk Factor Surveillance System. Depressive symptoms were assessed by the Patient Health Questionnaire-8 diagnostic algorithm. Participants with a total depression severity score of ≥10 were defined as having current depression. Prevalence and prevalence ratios were estimated by conducting log-linear regression analysis while controlling for potential confounders.ResultsOverall, 13.7% of cancer survivors (vs. 8.9% of adults without cancer, P < 0.001) reported having current depression; the prevalence varied significantly by cancer category. Among cancer survivors, after multivariate adjustment for covariates, cancer diagnosis within a year, being in ‘other’ racial/ethnic group, divorced, separated, widowed, or never married, current or former smoker, or having histories of diabetes, disability, or depression were associated with significantly higher prevalence ratios for current depression; whereas being at an advanced age (≥60 years old), attaining educational levels of >high school graduate, or engaging in leisure-time physical activity were associated with significantly lower prevalence ratios for current depression.ConclusionOur results indicate that cancer survivors are at increased risk of current depression. Targeting cancer survivors at high risk of depressive issues may be especially important for clinical support and interventions aimed at improving mental well-being.     

Broadening the genetic base of European maize heterotic pools with US Cornbelt germplasm using field and molecular marker data

Maize (Zea mays L.) breeders are concerned about the narrowing of the genetic base of elite germplasm. To reverse this trend, elite germplasm from other geographic regions can be introgressed, but due to lack of adaptation it is difficult to assess their breeding potential in the targeted environment. The objectives of this study were to (1) investigate the relationship between European and US maize germplasm, (2) examine the suitability of different mega-environments and measures of performance to assess the breeding potential of exotics, and (3) study the relationship of genetic distance with mid-parent heterosis (MPH). Eight European inbreds from the Dent and Flint heterotic groups, 11 US inbreds belonging to Stiff Stalk (SS), non-Stiff Stalk (NSS), and CIMMYT Pool 41, and their 88 factorial crosses in F₁ and F₂ generations were evaluated for grain yield and dry matter concentration. The experiments were conducted in three mega-environments: Central Europe (target mega-environment), US Cornbelt (mega-environment where donor lines were developed), and Southeast Europe (an intermediate mega-environment). The inbreds were also fingerprinted with 266 SSR markers. Suitable criteria to identify promising exotic germplasm were F₁ hybrid performance in the targeted mega-environment and F₁ and parental performance in the intermediate mega-environment. Marker-based genetic distances reflected relatedness among the inbreds, but showed no association with MPH. Based on genetic distance, MPH, and F₁ performance, we suggest to introgress SS germplasm into European Dents and NSS into European Flints, in order to exploit the specific adaptation of European flint germplasm and the excellent combining ability of US germplasm in European maize breeding programs.     

Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe

Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (H_o = 0.005) and very high levels of inbreeding (F_IS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations of this highly endangered species of European Community interest.     

Meeting report of the European mouse complex genetics network SYSGENET

The second scientific meeting of the European systems genetics network for the study of complex genetic human disease using genetic reference populations (SYSGENET) took place at the Center for Cooperative Research in Biosciences in Bilbao, Spain, December 10–12, 2012. SYSGENET is funded by the European Cooperation in the Field of Scientific and Technological Research (COST) and represents a network of scientists in Europe that use mouse genetic reference populations (GRPs) to identify complex genetic factors influencing disease phenotypes (Schughart, Mamm Genome 21:331–336, 2010). About 50 researchers working in the field of systems genetics attended the meeting, which consisted of 27 oral presentations, a poster session, and a management committee meeting. Participants exchanged results, set up future collaborations, and shared phenotyping and data analysis methodologies. This meeting was particularly instrumental for conveying the current status of the US, Israeli, and Australian Collaborative Cross (CC) mouse GRP. The CC is an open source project initiated nearly a decade ago by members of the Complex Trait Consortium to aid the mapping of multigenetic traits (Threadgill, Mamm Genome 13:175–178, 2002). In addition, representatives of the International Mouse Phenotyping Consortium were invited to exchange ongoing activities between the knockout and complex genetics communities and to discuss and explore potential fields for future interactions.     

A comprehensive human leukocyte antigen analysis of 36 782 cord blood units stored in the Australian Public Cord Blood Banking Network

Background and aimsThe network of public cord blood banks (CBBs) in Australia, known as AusCord, comprises CBBs located in Brisbane, Sydney and Melbourne. A novel comprehensive analysis has been performed to determine whether the cryopreserved, searchable cord blood unit (CBU) inventory of approximately 36 000 units share similar tissue types or haplotypes.MethodsHuman leukocyte antigen (HLA) data was analysed using Microsoft Excel following standardisation of typing data.ResultsThe analysis has found that the majority of stored, searched and released CBU exhibit a tissue type that is unique within and between the CBBs. Therefore, each collection performed by the CBBs is likely to comprise a tissue type that is not already stored among the total AusCord inventory. HLA alleles (HLA-A*34, HLA-B*56, HLA-DRB1*08:03), which are uncommon in European populations, were associated with Pacific Islander and/or Indigenous Australian populations and confirmed to be more frequent among donors who, when screened, self-identified as these ethnicities.ConclusionsThese data indicate that (i) continued addition of CBU to existing inventories is likely to further increase the HLA diversity and (ii) screening donors for ethnicity or strategically locating collection sites where ethnic minorities reside can successfully result in collection of rare HLA associated with ethnic minority groups for whom finding donors might otherwise be more difficult.     

Genetic diversity of Trypanosoma cruzi parasites infecting dogs in southern Louisiana sheds light on parasite transmission cycles and serological diagnostic performance

BackgroundChagas disease is a neglected zoonosis of growing concern in the southern US, caused by the parasite Trypanosoma cruzi. We genotyped parasites in a large cohort of PCR positive dogs to shed light on parasite transmission cycles and assess potential relationships between parasite diversity and serological test performance.Methodology/principal findingsWe used a metabarcoding approach based on deep sequencing of T. cruzi mini-exon marker to assess parasite diversity. Phylogenetic analysis of 178 sequences from 40 dogs confirmed the presence of T. cruzi discrete typing unit (DTU) TcI and TcIV, as well as TcII, TcV and TcVI for the first time in US dogs. Infections with multiple DTUs occurred in 38% of the dogs. These data indicate a greater genetic diversity of T. cruzi than previously detected in the US. Comparison of T. cruzi sequence diversity indicated that highly similar T. cruzi strains from these DTUs circulate in hosts and vectors in Louisiana, indicating that they are involved in a shared T. cruzi parasite transmission cycle. However, TcIV and TcV were sampled more frequently in vectors, while TcII and TcVI were sampled more frequently in dogs.Conclusions/significanceThese observations point to ecological host-fitting being a dominant mechanism involved in the diversification of T. cruzi-host associations. Dogs with negative, discordant or confirmed positive T. cruzi serology harbored TcI parasites with different mini-exon sequences, which strongly supports the hypothesis that parasite genetic diversity is a key factor affecting serological test performance. Thus, the identification of conserved parasite antigens should be a high priority for the improvement of current serological tests.     

Population genomics and the causes of local differentiation

Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock‐full of genetic variation. This variation was a surprise that required a re‐thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range‐wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high‐throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.     

Racial Disparities in Prostate Cancer Mortality in the 50 Largest US Cities

IntroductionThis paper presents race-specific prostate cancer mortality rates and the corresponding disparities for the largest cities in the US over two decades.MethodsThe 50 largest cities in the US were the units of analysis. Data from two 5-year periods were analyzed: 1990–1994 and 2005–2009. Numerator data were abstracted from national death files where the cause was malignant neoplasm of prostate (prostate cancer) (ICD9 = 185 and ICD10 = C61). Population-based denominators were obtained from US Census data. To measure the racial disparity, we calculated non-Hispanic Black: non-Hispanic White rate ratios (RRs), rate differences (RDs), and corresponding confidence intervals for each 5-year period. We also calculated correlation and unadjusted regression coefficients for 11 city-level variables, such as segregation and median income, and the RDs.ResultsAt the final time point (2005–2009), the US and all 41 cities included in the analyses had a RR greater than 1 (indicating that the Black rate was higher than the White rate) (range = 1.13 in Minneapolis to 3.24 in Los Angeles), 37 of them statistically significantly so. The US and 26 of the 41 cities saw an increase in the Black:White RR between the time points. The level of disparity within a city was associated with the degree of Black segregation.ConclusionThis analysis revealed large disparities in Black:White prostate cancer mortality in the US and many of its largest cities over the past two decades. The data show considerable variation in the degree of disparity across cities, even among cities within the same state. This type of specific city-level data can be used to motivate public health professionals, government officials, cancer control agencies, and community-based organizations in cities with large or increasing disparities to demand more resources, focus research efforts, and implement effective policy and programmatic changes in order to combat this highly prevalent condition.     

Seasonal variation of circulating plasma carotenoids in Mediterranean Great Tit males Parus major

Capsule Mediterranean Great Tits showed a marked increase in levels of circulating carotenoids during moult and autumn.

Aims To study seasonal variation in plasma carotenoid content during a whole annual cycle for Great Tits Parus major inhabiting a Mediterranean woodland.

Methods We used a sample of 71 adult male Great Tits captured in NE Spain during a whole year. Data were organized into four seasons (winter, breeding, moult and autumn). We sampled blood to extract plasma. Carotenoid plasma concentrations were analysed by High-performance liquid chromatography (HPLC).

Results Lutein and zeaxanthin content varied seasonally, with a marked increase in levels during moult and autumn. Within the moulting period, levels increased gradually as the season progressed. This pattern differed significantly from that previously described in northern European populations, where high values appear mainly in the breeding season. Carotenoid concentrations (lutein: 1.2?±?0.25, zeaxanthin: 0.07?±?0.03?µg mL^?1) were also lower than in northern Europe.

Conclusion Mediterranean Great Tits show a very different pattern of circulating carotenoids and lower levels than northern European populations. The increasing pattern of carotenoid availability found within the moulting period raises the need to control for the effect of sampling date when analysing data on carotenoid concentrations at different times of year.     

Some butterflies do not care much about topography: a single genetic lineage of Erebia euryale (Nymphalidae) along the northern Iberian mountains

The phylogeography of montane species often reveals strong genetic differentiation among mountain ranges. Both classic morphological and genetic studies have indicated distinctiveness of Pyrenean populations of the butterfly Erebia euryale. This hypothesis remained inconclusive until data from the westernmost populations of the distribution area (Cantabrian Mountains) were analysed. In the present study, we set out to describe the population structure of Erebia euryale in western Cantabria, where the species occurs in scattered localities. For this goal, we estimate the genetic diversity and differentiation found in 218 individuals from six Cantabrian (North Spain) localities genotyped by 17 allozyme loci. We also sequence 816 bp of the cytochrome oxidase subunit I mitochondrial gene in 49 individuals from Cantabrian localities and 41 specimens from five other European sites. Mitochondrial data support the recognition of four major genetic groups previously suggested for the European populations based on allozyme polymorphisms. Both mitochondrial and nuclear markers reveal genetic distinctiveness of a single Pyrenean–Cantabrian lineage of E. euryale. The lack of geographical structure and the star‐like topology displayed by the mitochondrial haplotypes indicate a pattern of demographic expansion in northern Iberia, probably related to Upper Pleistocene climatic oscillations. By contrast, within the Pyrenean–Cantabrian lineage, Cantabrian samples are genetically structured in nuclear datasets. In particular, San Isidro is significantly differentiated from the other five populations, which cluster into two groups. We recognize an evolutionary significant unit for Pyrenean–Cantabrian populations of Erebia euryale. Our results also illustrate that the evolutionary history of a species may be shaped by processes undetectable by using mtDNA alone.