324 Works

Middle Eocene terrestrial paleoweathering and climate evolution in the midlatitude Bohai Bay Basin of Eastern China

Di Chen, Xiongqi Pang, Kun Zhang, Guoyong Liu, Fujie Jiang, Liang Li, Youwei Wang, Min Li & Yang Liu
The middle Eocene is a key time period for understanding Cenozoic cooling of the global climate. In eastern Asia, this time period was marked by deposition of extensive mudstones, shales and interbedded siltstones, especially in the midlatitude Bohai Bay Basin. Still, midlatitude terrestrial records of climate evolution during the middle Eocene are rare. Here, we analyze a continuous, high-resolution record of this period using samples of the shales in the fourth submember of the third...

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Antonia Salces-Castellano, Jairo Patiño, Nadir Alvarez, Carmelo Andújar, Paula Arribas, Juan J. Braojos-Ruiz, Marcelino Del Arco-Aguilar, Víctor García-Olivares, Dirk Karger, Heriberto López, Ioanna Manolopoulou, Pedro Oromí, Antonio J. Pérez-Delgado, William W. Peterman, Kenneth F. Rijsdijk & Brent C. Emerson
Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the geographic scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance...

The impact of genetic adaptation on chimpanzee subspecies differentiation

Joshua Schmidt, Sergi Castellano, Marc De Manuel, Aida Andrés & Tomas Marques-Bonet
Chimpanzees, humans’ closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history...

Intergroup aggression in meerkats

Mark Dyble, Thomas Houslay, Marta Manser & Tim Clutton-Brock
Violent conflicts between groups have been observed among many species of group living mammals and can have important fitness consequences, with individuals being injured or killed and with losing groups surrendering territory. Here, we explore between-group conflict among meerkats (Suricata suricatta), a highly social and cooperatively breeding mongoose. We show that interactions between meerkat groups are frequently 18 aggressive and sometimes escalate to fighting and lethal violence and that these interactions have consequences for group...

Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch & Amy Litt
Background: Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also...

Data from: High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld

Jake Morris, Antonia G. P. Ford, Jarome R. Ali, Claire R. Peart, Roger Bills & Julia J. Day
Uncovering biological diversity to more accurately understand diversity patterns, and ultimately the processes driving diversification, is important not only from an evolutionary perspective but also a conservation perspective. This is particularly pertinent in Africa's rivers in which overall diversity, as well as how it arose, is poorly understood in comparison with lacustrine environments. Here we investigate population divergence in the sexually dimorphic suckermouth catfish species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in which...

Data from: The (in)effectiveness of simulated blur for depth perception in naturalistic images

Guido Maiello, Manuela Chessa, Fabio Solari & Peter J. Bex
We examine depth perception in images of real scenes with naturalistic variation in pictorial depth cues, simulated dioptric blur and binocular disparity. Light field photographs of natural scenes were taken with a Lytro plenoptic camera that simultaneously captures images at up to 12 focal planes. When accommodation at any given plane was simulated, the corresponding defocus blur at other depth planes was extracted from the stack of focal plane images. Depth information from pictorial cues,...

Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Antonia G. P. Ford, Kanchon K. Dasmahapatra, Lukas Rüber, Karim Gharbi, Timothée Cezard & Julia J. Day
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found...

Data from: Sex and genotype effects on nutrient-dependent fitness landscapes in Drosophila melanogaster

M. Florencia Camus, Kevin Fowler, Matthew W.D. Piper, Max Reuter & Matthew W. D. Piper
The sexes perform different reproductive roles and have evolved sometimes strikingly different phenotypes. One focal point of adaptive divergence occurs in the context of diet and metabolism, and males and females of a range of species have been shown to require different nutrients to maximize their fitness. Biochemical analyses in Drosophila melanogaster have confirmed that dimorphism in dietary requirements is associated with molecular sex differences in metabolite titres. In addition, they also showed significant within-sex...

Data from: The impact of HCV infection duration on HIV disease progression and response to cART amongst HIV seroconverters in the UK

Jamie Inshaw, Clifford Leen, Martin Fisher, Richard Gilson, David Hawkins, Simon Collins, Julie Fox, Ken McLean, Sarah Fidler, Andrew Phillips, Sam Lattimore, Abdel Babiker & Kholoud Porter
Introduction: The effect of HCV infection on HIV disease progression remains unclear; the effect of HCV infection duration on HIV disease progression is unknown. Methods: We used data from a cohort of HIV seroconverters to investigate the effect of HCV infection duration on time from HIV seroconversion to CD4 <350cells/mm3, AIDS or death, censoring at the earlier of cART initiation or last clinic visit, adjusting for confounders and splitting data into follow up periods from...

Data from: Cardiovascular disease risk factors in Ghana during the rural-to-urban transition: a cross-sectional study

Nuri Kodaman, Melinda C. Aldrich, Rafal Sobota, Folkert Asselbergs, Kwabena Poku, Nancy J. Brown, Jason H. Moore, Scott M. Williams, Folkert W. Asselbergs & Kwabena A. Poku
Populations in sub-Saharan Africa are shifting from rural to increasingly urban. Although the burden of cardiovascular disease is expected to increase with this changing landscape, few large studies have assessed a wide range of risk factors in urban and rural populations, particularly in West Africa. We conducted a cross-sectional, population-based survey of 3317 participants from Ghana (≥18 years old), of whom 2265 (57% female) were from a mid-sized city (Sunyani, population ~250,000) and 1052 (55%...

Data from: Sporadic sampling not climatic forcing drives observed early hominin diversity

Simon J. Maxwell, Philip J. Hopley, Paul Upchurch & Christophe Soligo
The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both...

Data from: Dietary choices are influenced by genotype, mating status, and sex in Drosophila melanogaster

M. Florencia Camus, Chun-Chen Huang, Max Reuter, Kevin Fowler & Chun-Cheng Huang
Mating causes many changes in physiology, behaviour and gene expression in a wide range of organisms. These changes are predicted to be sex-specific, influenced by the divergent reproductive roles of the sexes. In female insects, mating is associated with an increase in egg production which requires high levels of nutritional input with direct consequences for the physiological needs of individual females. Consequently, females alter their nutritional acquisition in line with the physiological demands imposed by...

Data from: Autocorrelation structure at rest predicts value correlates of single neurons during reward-guided choice

Sean E. Cavanagh, Joni D. Wallis, Steven W. Kennerley & Laurence T. Hunt
Correlates of value are routinely observed in the prefrontal cortex (PFC) during reward-guided decision making. In previous work (Hunt et al., 2015), we argued that PFC correlates of chosen value are a consequence of varying rates of a dynamical evidence accumulation process. Yet within PFC, there is substantial variability in chosen value correlates across individual neurons. Here we show that this variability is explained by neurons having different temporal receptive fields of integration, indexed by...

Data from: Environmental enrichment normalizes hippocampal timing coding in a malformed hippocampus

Amanda E. Hernan, J. Matthew Mahoney, Willie Curry, Greg Richard, Marcella M. Lucas, Andrew Massey, Gregory L. Holmes, Rodney C. Scott & Rod C. Scott
Neurodevelopmental insults leading to malformations of cortical development (MCD) are a common cause of psychiatric disorders, learning impairments and epilepsy. In the methylazoxymethanol (MAM) model of MCDs, animals have impairments in spatial cognition that, remarkably, are improved by post-weaning environmental enrichment (EE). To establish how EE impacts network-level mechanisms of spatial cognition, hippocampal in vivo single unit recordings were performed in freely moving animals in an open arena. We took a generalized linear modeling approach...

Data from: Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Claire R. Peart, Kanchon K. Dasmahapatra & Julia J. Day
Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa’s Great lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non-cichlid littoral taxa from these systems. To begin to address this we generated restriction-site associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika in two...

Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case

Mario Dos Reis, Gregg F. Gunnell, Jose Barba-Montoya, Alex Wilkins, Ziheng Yang & Anne D. Yoder
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size

Monika Böhm, Rhiannon Williams, Huw R. Bramhall, Kirsten M. McMillan, Ana D. Davidson, Andrés Garcia, Lucie M. Bland, Jon Bielby & Ben Collen
Aim Evaluating the relative roles of biological traits and environmental factors that predispose species to an elevated risk of extinction is of fundamental importance to macroecology. Identifying species that possess extinction-promoting traits allows targeted conservation action before precipitous declines occur. Such analyses have been carried out for several vertebrate groups, with the notable exception of reptiles. We identify traits correlating with high extinction risk in squamate reptiles, assess whether these differ with geography, taxonomy and...

Data from: Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition

Jonathan P. Tennant, Philip D. Mannion & Paul Upchurch
Crocodyliforms have a much richer evolutionary history than represented by their extant descendants, including several independent marine and terrestrial radiations during the Mesozoic. However, heterogeneous sampling of their fossil record has obscured their macroevolutionary dynamics, and obfuscated attempts to reconcile external drivers of these patterns. Here, we present a comprehensive analysis of crocodyliform biodiversity through the Jurassic/Cretaceous (J/K) transition using subsampling and phylogenetic approaches and apply maximum-likelihood methods to fit models of extrinsic variables to...

Data from: Eutherian morphological disparity across the end-Cretaceous mass extinction

Thomas John Dixon Halliday & Anjali Goswami
In the aftermaths of mass extinction events, during radiations of clades, and in several other evolutionary scenarios, there is often a decoupling of taxonomic diversity and morphological disparity. The placental mammal radiation after the end-Cretaceous mass extinction is one of the archetypal adaptive radiations, but the change in morphological disparity of the entire skeleton has never been quantified across this important boundary. We reconstruct ancestral morphologies of 680 discrete morphological characters onto dated phylogenies of...

Data from: Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

Thomas W. Davies, Mark A. Bell, Anjali Goswami & Thomas J.D. Halliday
There is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, whilst no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated in order to assess the suggestion that a poor fossil record is largely responsible for the difference...

Data from: The complexity of mating decisions in stalk-eyed flies

Nadine C. Chapman, Penthai Siriwat, James Howie, Aaron Towlson, Lawrence Bellamy, Kevin Fowler & Andrew Pomiankowski
All too often, studies of sexual selection focus exclusively on the responses in one sex, on single traits, typically those that are exaggerated and strongly sexually dimorphic. They ignore a range of less obvious traits and behavior, in both sexes, involved in the interactions leading to mate choice. To remedy this imbalance, we analyze a textbook example of sexual selection in the stalk-eyed fly (Diasemopsis meigenii). We studied several traits in a novel, insightful, and...

Data from: Response repetition biases in human perceptual decisions are explained by activity decay in competitive attractor models

James J. Bonaiuto, Archy O. De Berker, Sven Bestmann & Archy De Berker
Animals and humans have a tendency to repeat recent choices, a phenomenon known as choice hysteresis. The mechanism for this choice bias remains unclear. Using an established, biophysically informed model of a competitive attractor network for decision making, we found that decaying tail activity from the previous trial caused choice hysteresis, especially during difficult trials, and accurately predicted human perceptual choices. In the model, choice variability could be directionally altered through amplification or dampening of...

Data from: Smart wing rotation and trailing-edge vortices enable high frequency mosquito flight

Richard J. Bomphrey, Toshiyuki Nakata, Nathan Phillips & Simon M. Walker
Mosquitoes exhibit unusual wing kinematics; their long, slender wings flap at remarkably high frequencies for their size (>800 Hz)and with lower stroke amplitudes than any other insect group1. This shifts weight support away from the translation-dominated, aerodynamic mechanisms used by most insects2, as well as by helicopters and aeroplanes, towards poorly understood rotational mechanisms that occur when pitching at the end of each half-stroke. Here we report free-flight mosquito wing kinematics, solve the full Navier–Stokes...

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