Molecular Systematics and Diversification of African Zosteropidae (Aves: Passeriformes)

The hyper-diverse avian family Zosteropidae (~100 species) is renowned for its exceptional colonising ability and rapid recent diversification. The genus Zosterops dominates within the family, including over 70% of all recognised species, and is notorious for the phenotypic uniformity that has traditionally made designation of taxon boundaries within the genus difficult. While the last decade has seen an abundance of research focusing on colonisation abilities and speciation patterns of insular taxa, relationships between continental forms, specifically mainland African taxa, remain subject to great uncertainty. This thesis focuses on uncovering the relationships, origin and evolutionary history of African Zosteropidae. Chapter 1 introduces the family Zosteropidae, reviews the current literature that is based predominantly on insular systems. In introducing the African Zosteropidae complex, this chapter highlights questions associated with this group and presents the aims of the thesis. Chapter 2 focuses in on one of the most geographically complex areas within the African system, to explore the relative importance of past climatic fluctuations as a driver of diversification in Zosterops endemic to the isolated montane massifs of East Africa. Results provide the first molecular assessment of mainland African Zosteropidae and are used to examine alternative models of speciation. A dated molecular phylogeny demonstrates that divergence within African Zosteropidae is very recent (<5Ma) coinciding with periods of climatic instability during the Plio-Pleistocene. Furthermore, the non-monophyly of mainland taxa, specifically the polyphyletic nature of Z. poliogaster, leads to the rejection of a widely held assumption that the montane endemics of East Africa are relics of a previously widespread population. Instead results provide evidence for evolutionary model based on ancestrally adaptive populations. Chapter 3 attempts to further investigate relationships within the East African Zosterops and explores the usefulness of amplified fragment length polymorphism (AFLPs) in revealing inter- and intra-specific relationships. Resolution of relationships across the AFLP phylogeny is generally poor which is attributed to the low information content of the AFLP matrix generated. Bayesian hypothesis testing failed to provide support for various topological constraints tested and consequently this study was unable to confirm or reject the non-monophyly of East African montane endemics. Chapter 4 builds upon the molecular phylogeny of Chapter 2, by substantially increasing the taxonomic sampling of African species using DNA obtained from museum specimens. The use of both archive and fresh material enabled the largest genetic assessment of western Zosteropidae to date. Extensive sampling across Sub-Saharan Africa, the Indian Ocean region, the Arabian Peninsula and the Gulf of Guinea region reveals six major clades within the African Zosteropidae complex. Results confirm the widespread non-monophyly of mainland African species rendering current taxonomic arrangements invalid. GMYC (General mixed Yule-coalescent) analysis recovers 14 distinct evolutionary lineages within the African Zosteropidae system and provides a framework for further work using model-based species delimitation approaches. Finally, Chapter 5 draws together key findings from Chapters 2-4, and reviews how this work advances our understanding of the African Zosteropidae system. This chapter also highlights new gaps in our understanding of the western Zosteropidae and discusses several areas for future research

Spatial and temporal variations in plant water-use efficiency inferred from tree-ring, eddy covariance and atmospheric observations

This is the final version of the article. Available from the European Geosciences Union (EGU) via the DOI in this record.Plant water-use efficiency (WUE), which is the ratio of the uptake of carbon dioxide through photosynthesis to the loss of water through transpiration, is a very useful metric of the functioning of the land biosphere. WUE is expected to increase with atmospheric CO2, but to decline with increasing atmospheric evaporative demand &ndash; which can arise from increases in near-surface temperature or decreases in relative humidity. We have used Δ13C measurements from tree rings, along with eddy covariance measurements from Fluxnet sites, to estimate the sensitivities of WUE to changes in CO2 and atmospheric humidity deficit. This enables us to reconstruct fractional changes in WUE, based on changes in atmospheric climate and CO2, for the entire period of the instrumental global climate record. We estimate that overall WUE increased from 1900 to 2010 by 48±22%, which is more than double that simulated by the latest Earth System Models. This long-term trend is largely driven by increases in CO2, but significant inter-annual variability and regional differences are evident due to variations in temperature and relative humidity. There are several highly populated regions, such as western Europe and East Asia, where the rate of increase of WUE has declined sharply in the last 2 decades. Our data-based analysis indicates increases in WUE that typically exceed those simulated by Earth System Models-implying that these models are either underestimating increases in photosynthesis or underestimating reductions in transpiration.The contributions of M. Groenendijk, C. Huntingford, and P. M. Cox were funded by the UK Natural Environment Research Council (NERC) HYDRA project. We thank Margaret Barbour for providing tree-ring data compiled from many different sources. This work used eddy covariance data acquired by the FLUXNET community and in particular by the following networks: AmeriFlux (US Department of Energy, Biological and Environmental Research, Terrestrial Carbon Program (DE-FG02-04ER63917 and DE-FG02-04ER63911)), AfriFlux, AsiaFlux, CarboAfrica, CarboEuropeIP, CarboItaly, CarboMont, ChinaFlux, Fluxnet-Canada (supported by CFCAS, NSERC, BIOCAP, Environment Canada, and NRCan), GreenGrass, KoFlux, LBA, NECC, OzFlux, TCOS-Siberia, USCCC. We acknowledge the financial support to the eddy covariance data harmonization provided by CarboEuropeIP, FAO-GTOS-TCO, iLEAPS, Max Planck Institute for Biogeochemistry, National Science Foundation, University of Tuscia, Université Laval and Environment Canada and US Department of Energy and the database development and technical support from Berkeley Water Center, Lawrence Berkeley National Laboratory, Microsoft Research eScience, Oak Ridge National Laboratory, University of California – Berkeley, University of Virginia

A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history

White-eyes (Zosterops) are a hyper-diverse genus of passerine birds that have rapidly radiated across the Afrotropics and Southeast Asia. Despite their broad range, a disproportionately large number of species are currently recognised from islands compared to the mainland. Described species-level diversity of this ‘great speciator’ from continental Africa-Arabia is strikingly low, despite the vast size and environmental complexity of this region. However, efforts to identify natural groups using traditional approaches have been hindered by the remarkably uniform morphology and plumage of these birds. Here, we investigated the phylogenetic relationships and systematics of Afrotropical Zosterops, including the Gulf of Guinea and western Indian Ocean islands. We included exceptional sampling (∼160 individuals) from all except one subspecies of the 54 taxa (31 species, plus 22 additional named sub-species) currently recognized throughout the region, in addition to a subset of extra-Afrotropical taxa, by exploiting blood and archival samples. Employing a multi-locus phylogenetic approach and applying quantitative species delimitation we tested: 1) if there has been a single colonisation event of the Afrotropical realm; 2) if constituent mainland and island birds are monophyletic; and 3) if mainland diversity has been underestimated. Our comprehensive regional phylogeny revealed a single recent colonisation of the Afrotropical realm c.1.30 Ma from Asia, but a subsequent complex colonisation history between constituent island and mainland lineages during their radiation across this vast area. Our findings suggest a significant previous underestimation of continental species diversity and, based on this, we propose a revised taxonomy. Our study highlights the need to densely sample species diversity across ranges, providing key findings for future conservation assessments and establishing a robust framework for evolutionary studies

A question of scale: Human migrations writ large and small

Several recent papers illustrate the importance of migration and gene flow in molding the patterns of genetic variation observed in humans today. We place the varied demographic processes covered by these terms into a more general framework, and discuss some of the challenges facing attempts to reconstruct past human mobility and determine its influence on our genetic heritage

Seabird diving behaviour reveals the functional significance of shelf-sea fronts as foraging hotspots

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Oceanic fronts are key habitats for a diverse range of marine predators, yet how they influence fine-scale foraging behaviour is poorly understood. Here, we investigated the dive behaviour of northern gannets Morus bassanus in relation to shelf-sea fronts. We GPS tracked 53 breeding birds and examined the relationship between 1901 foraging dives (from time-depth recorders) and thermal fronts (identified via Earth Observation composite front mapping) in the Celtic Sea, North-East Atlantic. We (1) used a habitat use-availability analysis to determine whether gannets preferentially dived at fronts, and (2) compared dive characteristics in relation to fronts to investigate the functional significance of these oceanographic features. We found that relationships between gannet dive probabilities and fronts varied by frontal metric and sex. Whilst both sexes were more likely to dive in the presence of seasonally persistent fronts, links to more ephemeral features were less clear. Here, males were positively correlated with distance to front and cross-front gradient strength, with the reverse for females. Both sexes performed two dive strategies: shallow V-shaped plunge dives with little or no active swim phase (92% of dives), and deeper U-shaped dives with an active pursuit phase of at least three seconds (8% of dives). When foraging around fronts, gannets were half as likely to engage in U-shaped dives compared with V-shaped dives, independent of sex. Moreover, V-shaped dive durations were significantly shortened around fronts. These behavioural responses support the assertion that fronts are important foraging habitats for marine predators, and suggest a possible mechanistic link between the two in terms of dive behaviour. This research also emphasises the importance of cross-disciplinary research when attempting to understand marine ecosystems.This work was funded by a PhD studentship to SLC by the Natural Environment Research Council (NERC; NE/J500380/1), Natural Resources Wales (Seabirds Cymru) and a NERC grant (NE/H007466/1)

Point-of-care screening for a current Hepatitis C virus infection: influence on uptake of a concomitant offer of HIV screening

Eliminating hepatitis C as a public health threat requires an improved understanding of how to increase testing uptake. We piloted point-of-care testing (POCT) for a current HCV infection in an inner-city Emergency Department (ED) and assessed the influence on uptake of offering concomitant screening for HIV. Over four months, all adults attending ED with minor injuries were first invited to complete an anonymous questionnaire then invited to test in alternating cycles offering HCV POCT or HCV+HIV POCT. Viral RNA was detected in finger-prick blood by GeneXpert. 814/859 (94.8%) questionnaires were returned and 324/814 (39.8%) tests were accepted, comprising 211 HCV tests and 113 HCV+HIV tests. Offering concomitant HIV screening reduced uptake after adjusting for age and previous HCV testing (odds ratio 0.51; 95% confidence interval [CI] 0.38–0.68; p < 0.001). HCV prevalence was 1/324 (0.31%; 95% CI 0.05–1.73); no participant tested positive for HIV. 167/297 (56.2%) POCT participants lived in the most deprived neighbourhoods in England. HCV RNA testing using finger-prick blood was technically feasible. Uptake was moderate and the offer of concomitant HIV screening showed a detrimental impact on acceptability in this low prevalence population. The findings should be confirmed in a variety of other community settings

Elevated CO₂ does not increase eucalypt forest productivity on a low-phosphorus soil

Rising atmospheric CO2 stimulates photosynthesis and productivity of forests, offsetting CO2 emissions. Elevated CO2 experiments in temperate planted forests yielded ~23% increases in productivity over the initial years. Whether similar CO2 stimulation occurs in mature evergreen broadleaved forests on low-phosphorus (P) soils is unknown, largely due to lack of experimental evidence. This knowledge gap creates major uncertainties in future climate projections as a large part of the tropics is P-limited. Here,we increased atmospheric CO2 concentration in a mature broadleaved evergreen eucalypt forest for three years, in the first large-scale experiment on a P-limited site. We show that tree growth and other aboveground productivity components did not significantly increase in response to elevated CO2 in three years, despite a sustained 19% increase in leaf photosynthesis. Moreover, tree growth in ambient CO2 was strongly P-limited and increased by ~35% with added phosphorus. The findings suggest that P availability may potentially constrain CO2-enhanced productivity in P-limited forests; hence, future atmospheric CO2 trajectories may be higher than predicted by some models. As a result, coupled climate-carbon models should incorporate both nitrogen and phosphorus limitations to vegetation productivity in estimating future carbon sinks

A bird's eye view of discard reforms: bird-borne cameras reveal seabird/fishery interactions.

notes: PMCID: PMC3590202types: Journal Article; Research Support, Non-U.S. Gov'tCopyright: © 2013 Votier et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Commercial capture fisheries produce huge quantities of offal, as well as undersized and unwanted catch in the form of discards. Declines in global catches and legislation to ban discarding will significantly reduce discards, but this subsidy supports a large scavenger community. Understanding the potential impact of declining discards for scavengers should feature in an eco-system based approach to fisheries management, but requires greater knowledge of scavenger/fishery interactions. Here we use bird-borne cameras, in tandem with GPS loggers, to provide a unique view of seabird/fishery interactions. 20,643 digital images (one min(-1)) from ten bird-borne cameras deployed on central place northern gannets Morus bassanus revealed that all birds photographed fishing vessels. These were large (>15 m) boats, with no small-scale vessels. Virtually all vessels were trawlers, and gannets were almost always accompanied by other scavenging birds. All individuals exhibited an Area-Restricted Search (ARS) during foraging, but only 42% of ARS were associated with fishing vessels, indicating much 'natural' foraging. The proportion of ARS behaviours associated with fishing boats were higher for males (81%) than females (30%), although the reasons for this are currently unclear. Our study illustrates that fisheries form a very important component of the prey-landscape for foraging gannets and that a discard ban, such as that proposed under reforms of the EU Common Fisheries Policy, may have a significant impact on gannet behaviour, particularly males. However, a continued reliance on 'natural' foraging suggests the ability to switch away from scavenging, but only if there is sufficient food to meet their needs in the absence of a discard subsidy.EU INTERREG project CHARM-IIINatural Environment Research CouncilAssociation for the Study of Animal Behaviour research gran