CONSERVATION GENETICS OF THE ENDANGERED HAWAIIAN PETREL (PTERODROMA SANDWICHENSIS) ACROSS SPACE AND TIME

The endemic Hawaiian Petrel (Pterodroma sandwichensis) is a long-lived pelagic seabird. Although endangered, subfossil evidence indicates that it was formerly more abundant in the past. In addition to a wider distribution on islands where the petrel currently breeds, two colonies, one on Oahu and one on Molokai, have been extirpated since humans colonized the Islands. Despite this, little is known about this species. Here I use conservation genetic and ancient DNA techniques to investigate the taxonomic status and population dynamics of the Hawaiian petrel. Investigation of the timing and magnitude of divergence between the Hawaiian petrel and its sister species, the Galapagos petrel (P. phaeopygia), revealed that these taxa diverged approximately 550,000 years ago. In a phylogenetic tree constructed from mitochondrial data Galapagos and Hawaiian petrels were reciprocally monophyletic, however, trees from the nuclear data set were unresolved. Low estimates of gene flow between taxa indicate that incomplete lineage sorting is causing the difference in resolution between data sets and that Galapagos and Hawaiian petrels are likely separate species. In addition to the mitochondrial and nuclear intron data sets, I developed a suite of 20 polymorphic microsatellite loci: I developed 10 specifically for the Hawaiian petrel, and characterized an 10 additional previously reported loci in this species. Using these three data sets I investigated the pattern of gene flow and divergence between modern, historical, and ancient populations of the Hawaiian petrel. The mitochondrial data set showed strong levels of differentiation between modern populations. The two nuclear data sets also revealed significant population structure, although it was weaker. Mitochondrial DNA sequences obtained from subfossil bones indicate that populations were significantly differentiated in the past, although there was low divergence between the extirpated Oahu and Molokai populations and modern birds from Lanai, suggesting that perhaps as colonies dwindled individuals dispersed to that island. Investigation of the effective population size indicates that no significant change has occurred on Hawaii or Maui. It appears that the long generation time of this species may have allowed it to escape a genetic bottleneck after the arrival of humans in the Hawaiian Islands

Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to resolve Recent Radiations of Pelagic Seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales

Fewer pests and more ecosystem service‐providing arthropods in shady African cocoa farms: Insights from a data integration study

Agricultural intensification is leading to conversion of cocoa agroforestry towards monocultures across the tropics. In the context of cocoa agriculture, arthropods provide a range of ecosystem services and dis‐services. Arthropod pests (e.g., mirids and mealybugs) can cause major damage to crops, whilst pollinators and natural enemies (e.g., predatory insects and parasitoids) have the potential to enhance agricultural yields. Understanding how intensification of cocoa farming affects different arthropod groups is therefore important in maximising the abundance of beneficial arthropod taxa and reducing pest burdens. However, little is known about the influences of agricultural intensification on tropical arthropod communities, especially in Africa, where ~70% of the world's cocoa is produced. Most research on arthropod communities considers data from different sampling methods separately, as proxies of abundance; whilst these proxies can be informative, estimating true abundance enables direct comparison between arthropod taxa, and therefore the study of community dynamics. Here, we develop a Bayesian hierarchical model that integrates data from three common arthropod survey techniques to estimate population size of arthropod orders and to investigate how arthropod community composition responds to farm shade cover (an indicator of management intensity). Our results show that eight of 11 arthropod taxa responded to farm shade cover; importantly, brown capsids (the primary pest of cocoa in Africa), Coleoptera pests and Hemiptera pests decreased with increasing farm shade cover, whilst Araneae (natural enemies) and Diptera (potential pollinators) were more abundant in shady farms. Synthesis and applications. To achieve lower pest burdens and higher abundances of potential pollinators and natural enemies, African cocoa farms should maintain a dense canopy of shade trees. The current shift towards high‐intensity cocoa farming in Africa could result in long‐term losses due to pest infestations and loss of arthropod‐mediated ecosystem services

Not all farms are created equal: Shady African cocoa farms promote a richer bat fauna

Bats provide important pest suppression services with economic value to cocoa farmers, yet the impact of cocoa farm management on bat diversity metrics is still poorly understood. This is especially important if we consider that Afrotropical cocoa farms supply 68 % of the world's chocolate market, with expected increases in production in the forthcoming decades. In this study, we investigated for the first time how bat abundance, richness and diversity varied between African cocoa farms with different levels of shade tree cover, shade tree communities and cocoa characteristics. We found that shade tree cover and shade tree height were the main drivers associated with an increase of Shannon diversity, and abundance and richness of insectivores. Frugivorous and nectarivorous bats were positively associated with the presence of planted shade trees, but richness varied with the size of shade trees. The insectivorous Hipposideros fuliginosus was only present in high shade farms, being captured 51 times only in this shade system, while the frugivorous Myonycteris angolensis was associated with low shade farms. Our findings show that indeed not all farms are created equal, with high shade farms with large, tall forest shade trees (i.e., containing key plant resources) having richer bat communities. Therefore, policymakers seeking to conserve wildlife within cocoa farming systems should adopt cocoa management systems like those mentioned above and promote a combination of forest and planted shade trees to be able support a rich community of insectivorous, frugivorous and nectarivorous bats and maintain their associated ecosystems services

Palaeoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

Aim: Palaeoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well-resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of palaeoceanographic changes on shearwaters' diversification and speciation. We investigate shearwater biogeography and the evolution of a key phenotypic trait, body size, and we assess the validity of their current taxonomy

Keystone Individuals - Linking Predator Traits to Community Ecology

Individual behavioral plasticity enables animals to adjust to different scenarios. Yet, personality traits limit this flexibility, leading to consistent inter-individual differences in behavior. These individual behavioral traits have the potential to govern community interactions, although testing this is difficult in complex natural systems. For large predators who often exert strong effects on ecosystem functioning, this behavioral diversity may be especially important and lead to individualized ecosystem roles. We present a framework for quantifying individual behavioral plasticity and personality traits of large wild predators, revealing the extent to which certain natural behaviors are governed by these latent traits. The outcomes will reveal how the innate characteristics of wildlife can scale up to affect community interactions

Carotenoid skin ornaments as flexible indicators of male foraging behavior in a marine predator: Variation among Mexican colonies of brown booby ( Sula leucogaster )

Carotenoid-dependent ornaments can reflect animals’ diet and foraging behaviors. However, this association should be spatially flexible and variable among populations to account for geographic variation in optimal foraging behaviors. We tested this hypothesis using populations of a marine predator (the brown booby, Sula leucogaster) that forage across a gradient in ocean depth in and near the Gulf of California. Specifically, we quantified green chroma for two skin traits (foot and gular color) and their relationship to foraging location and diet of males, as measured via global positioning system tracking and stable carbon isotope analysis of blood plasma. Our three focal colonies varied in which foraging attributes were linked to carotenoid-rich ornaments. For gular skin, our data showed a shift from a benthic prey-green skin association in the shallow waters in the north to a pelagic prey-green skin association in the deepest waters to the south. Mean foraging trip duration and distance of foraging site from coast also predicted skin coloration in some colonies. Finally, brown booby colonies varied in which trait (foot versus gular skin color) was associated with foraging metrics. Overall, our results indicate that male ornaments reflect quality of diet and foraging–information that may help females select mates who are adapted to local foraging conditions and therefore, are likely to provide better parental care. More broadly, our results stress that diet-dependent ornaments are closely linked to animals’ environments and that we cannot assume ornaments or ornament signal content are ubiquitous within species, even when ornaments appear similar among populations

Bird communities in African cocoa agroforestry are diverse but lack specialised insectivores

Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities. Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities. Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores. Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms. Synthesis and applications. Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity

Bird communities in African cocoa agroforestry are diverse but lack specialised insectivores

Forests are being converted to agriculture throughout the Afrotropics, driving declines in sensitive rainforest taxa such as understorey birds. The ongoing expansion of cocoa agriculture, a common small‐scale farming commodity, has contributed to the loss of 80% rainforest cover in some African countries. African cocoa farms may provide habitat for biodiversity, yet little is known about their suitability for vertebrate fauna, or the effect of farm management on animal communities. Here, we report the first in‐depth investigation into avian diversity and community composition in African cocoa, by assembling a dataset of 9,566 individual birds caught across 83 sites over 30 years in Southern Cameroon. We compared bird diversity in mature forest and cocoa using measures of alpha, beta and gamma diversity, and we investigated the effect of cocoa farm shade and forest cover on bird communities. Gamma diversity was higher in cocoa than forest, though alpha diversity was similar, indicating a higher dissimilarity (beta diversity) between cocoa farms. Cocoa farms differed from forest in community composition, with a distinctive decrease in relative abundance of insectivores, forest specialists and ant‐followers and an increase in frugivores. Within cocoa farms, we found that farms with high shade cover in forested landscapes resulted in higher relative abundance and richness of sensitive forest species; shady farms contained up to five times the proportion of forest specialists than sunny farms. Synthesis and applications. Sunny African cocoa farms were less able to support sensitive bird guilds compared with shaded farms in forested landscapes. Our findings support the notion that certain ecological and dietary guilds, such as ant‐followers and forest specialists are disproportionately affected by land‐use change. In light of the current push to increase cocoa production in sub‐Saharan Africa, our results provide policymakers opportunities for more wildlife‐friendly cocoa schemes that maximize avian diversity

Evolutionary history of polar and brown bears

Taxonomists have long recognised polar and brown bears as separate species with distinct ecological niches and largely nonoverlapping ranges. Surprisingly, phylogenetic studies of maternally inherited mitochondrial DNA (mtDNA) found polar bears nested within brown bears, with an estimated divergence time of 300 000 to 4–5 million years. These studies confirm uniqueness of the polar bear lineage, provide more time for speciation and adaptation, and have uncovered numerous candidate genes for evolutionary adaptations. Several instances of introgressive hybridisation between polar and brown bears have been inferred, revealing trans-species transmission of mtDNA and some nuclear loci