The spatial scale of immune gene variation within and among bottlenecked populations

The general aim of this thesis is to explore different spatial scales at which pathogen-mediated selection drives the evolution of immune genes across and within populations of Berthelot’s pipit (Anthus berthelotii), a historically bottlenecked passerine endemic to the oceanic islands of the Canary, Selvagens and Madeira archipelagos. I first investigated the evolution of key innate immune genes among the populations that the pipits inhabit. I found that while demographic history has played the major role in shaping patterns of among population variation at toll-like receptor loci, balancing selection (possibly pathogen-mediated) appears to have helped maintain functional variation at some specific loci. Second, I assessed the contribution of environmental factors to pathogen distribution and their subsequent effects on the major histocompatibility complex (MHC) class I genes of the acquired immune system within the population on Tenerife. I found a high prevalence of malaria in this population, the presence of which was correlated with climatic and anthropogenic variables: temperature, distance to poultry farms and distance to artificial water sources. Within the MHC I found evidence of trans-species polymorphism and gene conversion, and signatures of positive selection. Using landscape genetic analysis methods I found no evidence for overall within population patterns of structure at either neutral markers or the MHC. However, one MHC allele was associated to malaria infection risk and its distribution was (more strongly) associated with distance to poultry farms. These results suggest that demographic processes are the most important evolutionary force shaping variation at functional loci in isolated, bottlenecked populations. Nevertheless, selection can also shape patterns of variation at immunity loci, both at the coarser and the finer landscape scale, apparently in response to pathogens. This study therefore highlights the importance of considering different spatial scales when studying the evolutionary processes that shape functional genetic variation within populations

454 screening of individual MHC variation in an endemic island passerine

Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot’s pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot’s pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot’s pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot’s pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC

Landscape-scale variation in an anthropogenic factor shapes immune gene variation within a wild population

Understanding the spatial scale at which selection acts upon adaptive genetic variation in natural populations is fundamental to our understanding of evolutionary ecology, and has important ramifications for conservation. The environmental factors to which individuals of a population are exposed can vary at fine spatial scales, potentially generating localized patterns of adaptation. Here, we compared patterns of neutral and major histocompatibility complex (MHC) variation within an island population of Berthelot's pipit (Anthus berthelotii) to assess whether landscape-level differences in pathogen-mediated selection generate fine-scale spatial structuring in these immune genes. Specifically, we tested for spatial associations between the distribution of avian malaria, and the factors previously shown to influence that distribution, and MHC variation within resident individuals. Although we found no overall genetic structure across the population for either neutral or MHC loci, we did find localized associations between environmental factors and MHC variation. One MHC class I allele (ANBE48) was directly associated with malaria infection risk, while the presence of the ANBE48 and ANBE38 alleles within individuals correlated (positively and negatively, respectively) with distance to the nearest poultry farm, an anthropogenic factor previously shown to be an important determinant of disease distribution in the study population. Our findings highlight the importance of considering small spatial scales when studying the patterns and processes involved in evolution at adaptive loci

Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India

Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

MHC genotypes by zone

This file contains the MHC genotypes for 310 Berthelot's pipits divided by zone. There are four zones. The first part of the table shows the frquency of each MHC allele in each of the four geographical zones

Phylogenetic relationships and biogeography of the ancient genus Onychorhynchus (Aves: Onychorhynchidae) suggest cryptic Amazonian diversity

We examined phylogeographic patterns and cryptic diversity within the royal flycatcher, Onychorhynchus coronatus (Aves: Onychorhynchidae), a widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of the six recognized subspecies was constructed from mtDNA sequence data of the NADH dehydrogenase subunit two gene, using Bayesian Inference and Maximum Likelihood methods. Phylogenetic analyses revealed high levels of intraspecific divergence within O. coronatus, supporting the existence of at least six independent lineages. The phylogenetic results uncovered the following relationships: (O. c. swainsoni [Southern Atlantic Forest], (O. c. coronatus [western Amazonia], (O. c. castelnaui [eastern Amazonia], (O. c. mexicanus [Central America], (O. c. occidentalis [Tumbesian], O. c. fraterculus [extreme northwestern South America])))). Biogeographic and dating analyses suggest that vicariant and dispersal events acted across approximately six million years to influence lineage diversification within this genus. Some of those events include the formation of the Amazon River and its tributaries, Andean uplift, and climatically induced vegetational shifts. Phylogenetic and biogeographic analyses of O. coronatus lineages support a hypothesis of area relationships in which the first divergence event isolated the Southern Atlantic Forest from Amazonia during the Late Miocene/Early Pliocene. This event was followed by the split of western and eastern Amazonia at the Early/Late Pliocene, the divergence of cis‐ and trans‐Andean lowland regions also at the Early/Late Pliocene, the split between Central America and the extreme northwestern South America/Tumbes at the Early/Middle Pleistocene, and the split between extreme northwestern South America and Tumbes at Middle/Late Pleistocene. Subsequent divergence of the southern and northern populations in the western and eastern Onychorhynchus lineages took place during the Pleistocene. Comparison of phylogenetic trees and patterns in Onychorhynchus with those from published work suggests that across large New World radiations such as the Suboscines, some co‐distributed lineages began to diverge long before others, which exemplifies the complexity of their evolutionary history

Sample Sizes and Geographic Origins of Samples

<p>The latitudes and longitudes used for the various groups are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-st002" target="_blank">Table S2</a>.</p

Mean <i>F_st</i> Values for Each Indian Group across Comparisons with 18 Populations from East Asia, 12 Populations from Europe and the Middle East, and the Other 14 Groups from India

<div><p>(A) 715 microsatellites.</p><p>(B) 207 indels.</p><p>Error bars denote standard deviations across comparisons.</p></div