Evolutionary & ecological genetics of African wild dogs

Loss of adaptive variation arising from population declines and fragmentation is a primary concern in conservation. However, many conservation programmes assess only neutral genetic variation. Whilst assessments of neutral variation are informative about demographic history, inbreeding and genetic structure, they do not provide information on adaptive variation. The Major Histocompatibility Complex (MHC) is a group of genes that has been extensively studied and are known to be important in effective immune responses. Given the threat posed by infectious diseases to wildlife, the MHC is increasingly being assessed in endangered species. African wild dogs (Lycaon pictus, hereafter wild dog) are an endangered canid that has suffered extensive declines in the wild and now persist as small and fragmented populations totalling less than 8,000 individuals. The purpose of this study was to assess how neutral and MHC marker data genetic data can be used to assist conservation of this species. As such, I assessed sequence diversity across ~300bp of mitochondrial DNA, patterns of polymorphism and heterozygosity at 10 neutral microsatellite loci, compared to sequence variation and haplotype diversity at the MHC. Wild dogs were found to be genetically depauperate at the MHC compared to other canids. Patterns of variation indicate a historical loss of variation, followed by more recent diversification. However, it was also shown that evolutionary history contributes to differences in diversity between species. The spatial and temporal structure of MHC diversity was found to be largely correlated with neutral markers, which may suggest that selection is unable to counter strong genetic drift in such small populations. Overall, genetic diversity of both neutral and MHC markers appeared to be largely determined by demographic stability and size of populations. Habitat fragmentation and loss were associated with genetic isolation of wild dog populations, which showed strong structuring. However, the barriers to, or corridors for, dispersal of wild dogs were not always clear. The European captive breeding population was found to have comparable diversity metrics to wild populations, and was found to contain a large proportion of the MHC variation from the Southern African populations from which they were originally sourced. Careful genetic management is now required to correct the severe over- and underrepresentation of some founder lineages in this captive population to reduce inbreeding and loss of genetic variation

Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector anopheles arabiensis

Association mapping is a widely applied method for elucidating the genetic basis of phenotypic traits. However, factors such as linkage disequilibrium and levels of genetic diversity influence the power and resolution of this approach. Moreover, the presence of population subdivision among samples can result in spurious associations if not accounted for. As such, it is useful to have a detailed understanding of these factors before conducting association mapping experiments. Here we conducted whole-genome sequencing on 24 specimens of the malaria mosquito vector, Anopheles arabiensis, to further understanding of patterns of genetic diversity, population subdivision and linkage disequilibrium in this species. We found high levels of genetic diversity within the An. arabiensis genome, with ~800,000 high-confidence, single- nucleotide polymorphisms detected. However, levels of nucleotide diversity varied significantly both within and between chromosomes. We observed lower diversity on the X chromosome, within some inversions, and near centromeres. Population structure was absent at the local scale (Kilombero Valley, Tanzania) but detected between distant populations (Cameroon vs. Tanzania) where differentiation was largely restricted to certain autosomal chromosomal inversions such as 2Rb. Overall, linkage disequilibrium within An. arabiensis decayed very rapidly (within 200 bp) across all chromosomes. However, elevated linkage disequilibrium was observed within some inversions, suggesting that recombination is reduced in those regions. The overall low levels of linkage disequilibrium suggests that association studies in this taxon will be very challenging for all but variants of large effect, and will require large sample sizes

Cytomegalovirus-Specific IL-10-Producing CD4+ T Cells Are Governed by Type-I IFN-Induced IL-27 and Promote Virus Persistence

CD4+ T cells support host defence against herpesviruses and other viral pathogens. We identified that CD4+ T cells from systemic and mucosal tissues of hosts infected with the β-herpesviridae human cytomegalovirus (HCMV) or murine cytomegalovirus (MCMV) express the regulatory cytokine interleukin (IL)-10. IL-10+CD4+ T cells co-expressed TH1-associated transcription factors and chemokine receptors. Mice lacking T cell-derived IL-10 elicited enhanced antiviral T cell responses and restricted MCMV persistence in salivary glands and secretion in saliva. Thus, IL-10+CD4+ T cells suppress antiviral immune responses against CMV. Expansion of this T-cell population in the periphery was promoted by IL-27 whereas mucosal IL-10+ T cell responses were ICOS-dependent. Infected Il27rα-deficient mice with reduced peripheral IL-10+CD4+ T cell accumulation displayed robust T cell responses and restricted MCMV persistence and shedding. Temporal inhibition experiments revealed that IL-27R signaling during initial infection was required for the suppression of T cell immunity and control of virus shedding during MCMV persistence. IL-27 production was promoted by type-I IFN, suggesting that β-herpesviridae exploit the immune-regulatory properties of this antiviral pathway to establish chronicity. Further, our data reveal that cytokine signaling events during initial infection profoundly influence virus chronicity

IL-27 promotes splenic CD4⁺IL-10⁺ T cell development whereas ICOS is required for salivary gland CD4⁺IL-10⁺ T cell accumulation.

<p><i>Il-27r</i>α^-/- or WT (C57BL/6) mice were infected with MCMV and spleen and salivary gland CD4⁺/IL-10⁺ (A) responses were quantified and expressed at mean + SEM of 11 mice/group. (B) Representative bivariant FACS plots of IFNγ versus IL-10 expression by splenic CD4⁺CD3⁺ T cells. (C&D) gp130 and (E) ICOS expression by IL-10⁺ (Thy1.1⁺) and IL-10^- (Thy1.1^-) CD4⁺CD3⁺ T cells was assessed in 10-Bit mice and shown as representative FACS plots (C) and histogram overlays (E) with mean + SEM of 5–6 mice/group (D). Gating was determined using Thy1.1⁺ CD4⁺CD3⁺ cells derived from fluorescent minus one-stained samples from mice infected for 14 days. (F&G) WT (C57BL/6) mice were infected with MCMV and at d6 and d10 pi αICOS or Isotype antibody was added. At d14 pi (F) salivary glands and (G) spleen CD4⁺/IL-10⁺ responses were quantified and expressed as mean + SEM of 6 mice/group.</p

IL-27 promotes CD4⁺IL-10⁺ development and impairs anti-MCMV T_H1 immunity and control of MCMV persistence.

<p><i>Il-27r</i>α^-/- or WT (C57BL/6) mice were infected with MCMV and spleen and salivary gland CD4⁺/IFNγ⁺ (A) responses were quantified and expressed as mean + SEM of 11 mice/group. (B) Replicating virus in salivary gland homogenates of <i>Il-27r</i>α^-/- and WT mice is shown as individual mice + median. Data is representative of 2 experiments. (C) MCMV genomes in saliva were quantified by qPCR. Data is shown as mean ± SEM from 11 mice per group from 2 replicative experiments.</p