Evolution of population structure in a highly social top predator, the killer whale

Intraspecific resource partitioning and social affiliations both have the potential to structure populations, though it is rarely possible to directly assess the impact of these mechanisms on genetic diversity and population divergence. Here, we address this for killer whales (Orcinus orca), which specialize on prey species and hunting strategy and have long-term social affiliations involving both males and females. We used genetic markers to assess the structure and demographic history of regional populations and test the hypothesis that known foraging specializations and matrifocal sociality contributed significantly to the evolution of population structure. We find genetic structure in sympatry between populations of foraging specialists (ecotypes) and evidence for isolation by distance within an ecotype. Fitting of an isolation with migration model suggested ongoing, low-level migration between regional populations (within and between ecotypes) and small effective sizes for extant local populations. The founding of local populations by matrifocal social groups was indicated by the pattern of fixed mtDNA haplotypes in regional populations. Simulations indicate that this occurred within the last 20,000 years (after the last glacial maximum). Our data indicate a key role for social and foraging behavior in the evolution of genetic structure among conspecific populations of the killer whale.     

<Emphasis Type="Italic">Burkholderia</Emphasis> Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis

Background  

The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei.     

Bronchoabsorption; a novel bronchoscopic technique to improve biomarker sampling of the airway

Background

Current techniques used to obtain lung samples have significant limitations and do not provide reproducible biomarkers of inflammation. We have developed a novel technique that allows multiple sampling methods from the same area (or multiple areas) of the lung under direct bronchoscopic vision. It allows collection of mucosal lining fluid and bronchial brushing from the same site; biopsy samples may also be taken. The novel technique takes the same time as standard procedures and can be conducted safely.

Methods

Eight healthy smokers aged 40–65 years were included in this study. An absorptive filter paper was applied to the bronchial mucosa under direct vision using standard bronchoscopic techniques. Further samples were obtained from the same site using bronchial brushings. Bronchoalveolar lavage (BAL) was obtained using standard techniques. Chemokine (C-C Motif) Ligand 20 (CCL20), CCL4, CCL5, Chemokine (C-X-C Motif) Ligand 1 (CXCL1), CXCL8, CXCL9, CXCL10, CXCL11, Interleukin 1 beta (IL-1β), IL-6, Vascular endothelial growth factor (VEGF), Matrix metalloproteinase 8 (MMP-8) and MMP-9 were measured in exudate and BAL. mRNA was collected from the bronchial brushings for gene expression analysis.

Results

A greater than 10 fold concentration of all the biomarkers was detected in lung exudate in comparison to BAL. High yield of good quality RNA with RNA integrity numbers (RIN) between 7.6 and 9.3 were extracted from the bronchial brushings. The subset of genes measured were reproducible across the samples and corresponded to the inflammatory markers measured in exudate and BAL.

Conclusions

The bronchoabsorption technique as described offers the ability to sample lung fluid direct from the site of interest without the dilution effects caused by BAL. Using this method we were able to successfully measure the concentrations of biomarkers present in the lungs as well as collect high yield mRNA samples for gene expression analysis from the same site. This technique demonstrates superior sensitivity to standard BAL for the measurement of biomarkers of inflammation. It could replace BAL as the method of choice for these measurements. This method provides a systems biology approach to studying the inflammatory markers of respiratory disease progression.

Trial registration

NHS Health Research Authority (13/LO/0256).     

Airway cellularity, lipid laden macrophages and microbiology of gastric juice and airways in children with reflux oesophagitis

Background and methods

Human metapneumovirus (hMPV) is a recently discovered respiratory virus associated with bronchiolitis, pneumonia, croup and exacerbations of asthma. Since respiratory viruses are frequently detected in patients with acute exacerbations of COPD (AE-COPD) it was our aim to investigate the frequency of hMPV detection in a prospective cohort of hospitalized patients with AE-COPD compared to patients with stable COPD and to smokers without by means of quantitative real-time RT-PCR.

Results

We analysed nasal lavage and induced sputum of 130 patients with AE-COPD, 65 patients with stable COPD and 34 smokers without COPD. HMPV was detected in 3/130 (2.3%) AE-COPD patients with a mean of 6.5 × 10⁵ viral copies/ml in nasal lavage and 1.88 × 10⁵ viral copies/ml in induced sputum. It was not found in patients with stable COPD or smokers without COPD.

Conclusion

HMPV is only found in a very small number of patients with AE-COPD. However it should be considered as a further possible viral trigger of AE-COPD because asymptomatic carriage is unlikely.     

Malaria and urbanization in sub-Saharan Africa

There are already 40 cities in Africa with over 1 million inhabitants and the United Nations Environmental Programme estimates that by 2025 over 800 million people will live in urban areas. Recognizing that malaria control can improve the health of the vulnerable and remove a major obstacle to their economic development, the Malaria Knowledge Programme of the Liverpool School of Tropical Medicine and the Systemwide Initiative on Malaria and Agriculture convened a multi-sectoral technical consultation on urban malaria in Pretoria, South Africa from 2nd to 4th December, 2004. The aim of the meeting was to identify strategies for the assessment and control of urban malaria. This commentary reflects the discussions held during the meeting and aims to inform researchers and policy makers of the potential for containing and reversing the emerging problem of urban malaria.     

On the number of New World founders: a population genetic portrait of the peopling of the Americas

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.     

Increased immortalization‐upregulated protein 2 (IMUP‐2) by hypoxia induces apoptosis of the trophoblast and pre‐eclampsia

In regulation of the developmental process, the balance between cellular proliferation and cell death is critical. Placental development tightly controls this mechanism, and increased apoptosis of placental trophoblasts can cause a variety of gynecological diseases. Members of the immortalization‐upregulated protein (IMUP) family are nuclear proteins implicated in SV40‐mediated immortalization and cellular proliferation; however, the mechanisms by which their expression is regulated in placental development are still unknown. We compared IMUP‐2 expression in normal and pre‐eclamptic placental tissues and evaluated the function of IMUP‐2 in HTR‐8/SVneo trophoblast cells under hypoxic conditions. IMUP‐2 was expressed in syncytiotrophoblasts and syncytial knots of the placental villi. IMUP‐2 expression was significantly higher in preterm pre‐eclampsia patients than in patients who went to term (P < 0.001); however, we observed no differences in IMUP‐2 expression between normal term patients with and without pre‐eclampsia. Hypoxic conditions increased apoptosis of HTR8/SVneo trophoblast cells and induced IMUP‐2 expression. Also, apoptosis of HTR‐8/SVneo trophoblast cells was increased after IMUP‐2 gene transfection. These results suggest that IMUP‐2 expression is specifically elevated in preterm pre‐eclampsia and under hypoxic conditions, and that IMUP‐2 induces apoptosis of the trophoblast. Therefore, IMUP‐2 might have functional involvement in placental development and gynecological diseases such as pre‐eclampsia. J. Cell. Biochem. 110: 522–530, 2010. © 2010 Wiley‐Liss, Inc.     

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such data can be useful for inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind of sampling scheme, one that may be more suited to studying relatively ancient divergence. Data sets extracted from whole-genome alignments may represent very few individuals but contain a very large number of loci. To take advantage of such data we developed a new maximum-likelihood method for genomic data under the isolation-with-migration model. Unlike many coalescent-based likelihood methods, our method does not rely on Monte Carlo sampling of genealogies, but rather provides a precise calculation of the likelihood by numerical integration over all genealogies. We demonstrate that the method works well on simulated data sets. We also consider two models for accommodating mutation rate variation among loci and find that the model that treats mutation rates as random variables leads to better estimates. We applied the method to the divergence of Drosophila melanogaster and D. simulans and detected a low, but statistically significant, signal of gene flow from D. simulans to D. melanogaster.IN the study of speciation researchers often inquire of the extent that populations have exchanged genes as they diverged and on the time since populations began to diverge. Answers to questions about historical divergence and gene flow potentially lie in patterns of genetic variation that are found in present day populations. To bridge the gap between population history and current genetic data, population geneticists can make use of a gene genealogy, G, a bifurcating tree that represents the history of ancestry of sampled gene copies. The probability of a particular value of G can be calculated for a particular parameter set using coalescent models. Then given a particular genealogy, genetic variation can be examined using a mutation model that is appropriate for the kind of data being used. Finally by considering multiple values of G, the connection can be made between the population evolution history and the data. A mathematical representation that treats G as a key interstitial variable was given by Felsenstein (1988),(1)where X represents the sequence data, G represents gene genealogy, Ψ represents the set of all possible genealogies, and Θ represents the vector of population parameters included in the model.Unless sample sizes are very small, (1) cannot be solved analytically, and so considerable effort has gone into finding approximate solutions (Kuhner et al. 1995; Griffiths and Marjoram 1996; Wilson and Balding 1998). One general approach is to sample genealogies using a Markov chain Monte Carlo (MCMC) simulation. This is the approach developed by Kuhner and colleagues (Kuhner et al. 1995) and that has since been extended to models with migration (Beerli and Felsenstein 1999, 2001; Nielsen and Wakeley 2001). A general problem for these methods is that they usually require long running times to generate sufficiently large and independent samples, especially when the MCMC simulation is mixing slowly.With fast-improving DNA sequencing techniques, more and more genome sequences are becoming available, and alignments of these whole-genome sequences are a very useful source of information for the study of divergence. However, traditional MCMC methods are likely to be slow on genome-scale data because running times are proportional to the number of loci. To overcome this difficulty Yang developed a likelihood method (Yang 2002) for data sets containing one sample from each of the three populations at every locus. This method uses numerical integration to calculate the likelihood function in Equation 1. By using a very large number of loci, the method can make up for using a very small number of individuals (i.e., genomes).Yang''s method is based on a divergence model that assumes no gene flow between separated populations. However, there are many situations where gene flow may have been occurring and where it is preferable to include it within the divergence model. One model that has been used a lot in this context is the isolation-with-migration (IM) model, which incorporates both population separation and migration (Nielsen and Wakeley 2001). Under an IM model the genealogies include not only some fixed number of coalescent events and speciation events, but also any possible number of migration events. The potential for very large numbers of migration events complicates the sample space of G and makes the numerical integration seemingly impossible. Innan and Watanabe (2006) circumvent this problem by using a recursion method to estimate the coalescent rates on a series of time points. In their recursion, the accuracy in calculating coalescent rate at one time point depends on the accuracy of calculations at previous time points, and this may impair the precision of the overall likelihood calculation. Therefore we developed a method that relies on numerical integration to calculate the likelihood under an IM model. We tested the accuracy of this method on simulated data sets of various sample sizes and applied it to a genome alignment of Drosophila melanogaster and D. simulans (with D. yakuba as an outgroup).     

Evaluation of Copper Supplementation to Control <Emphasis Type="Italic">Haemonchus contortus</Emphasis>Infections of Sheep in Sweden

A pen study was conducted to assess the effect of providing daily copper mineral supplement, or copper wire particle (COWP) capsules, on established or incoming mixed nematode infections in young sheep. For lambs with established (6 week old) infections, COWP resulted in 97% and 56% reduction of the adult and early L4 stages of H. contortus, respectively, compared with controls (p < 0.001). Additionally there was a 74% reduction in Teladorsagia circumcincta infections in the COWP lambs compared with controls (p < 0.01). However, no effect was observed when COWP were given at the commencement of a larval dosing period of 6 weeks. There was no significant effect of copper mineral supplement (given at the recommended rate to prevent Cu deficiency) on either established, or developing parasite infections. In addition, a field trial was conducted on a commercial farm to assess the effects of COWP in the management of recurrent H. contortus infections, but lack of parasites during the grazing season prevented an adequate assessment from being made. These results indicate that there is little, if any, benefit from a parasite control standpoint in recommending copper therapy, specifically to control parasites in Swedish sheep flocks.     

Mitochondrial and nuclear genes present conflicting portraits of human origins

Human mitochondrial DNA (mtDNA) sequences reveal an abundance of polymorphic sites in which the frequencies of the segregating bases are very different. A typical polymorphism involves one base at low frequency and the other base at high frequency. In contrast, nuclear gene data sets tend to show an excess of polymorphisms in which both segregating bases are at intermediate frequencies. A new statistical test of this difference finds significant differences between mtDNA and nuclear gene data sets reported in the literature. However, differences in the polymorphism patterns could be caused by different sample origins for the different data sets. To examine the mtDNA-nuclear difference more closely, DNA sequences were generated from a portion of the X-linked pyruvate dehydrogenase E1 alpha subunit (PDHA1) locus and from a portion of mitochondrial control region I (CRI) from each of eight individuals, four from sub-Saharan Africa. The two genes revealed a significant difference in the site frequency distribution of polymorphic sites. PDHA1 revealed an excess of intermediate-frequency polymorphisms, while CRI showed an excess of sites with the low-high frequency pattern. The discrepancy suggests that mitochondrial variation has been shaped by natural selection, and may not be ideal for some questions on human origins.