56 Works

Data from: DNA recovery from wild chimpanzee tools

Fiona A. Stewart, Alexander K. Piel, Lydia Luncz, Joanna Osborne, Yingying Li, Beatrice H. Hahn, Michael Haslam & Joanna Osborn
Most of our knowledge of wild chimpanzee behaviour stems from fewer than 10 long-term field sites. This bias limits studies to a potentially unrepresentative set of communities known to show great behavioural diversity on small geographic scales. Here, we introduce a new genetic approach to bridge the gap between behavioural material evidence in unhabituated chimpanzees and genetic advances in the field of primatology. The use of DNA analyses has revolutionised archaeological and primatological fields, whereby...

Data from: Developmental plasticity of the stress response in female but not male guppies

Laura Chouinard-Thuly, Adam R. Reddon, Ioannis Leris, Ryan L. Earley & Simon M. Reader
To survive, animals must respond appropriately to stress. Stress responses are costly, so early-life experiences with potential stressors could adaptively tailor adult stress responses to local conditions. However, how multiple stressors influence the development of the stress response remains unclear, as is the role of sex. Trinidadian guppies (Poecilia reticulata) are small fish with extensive life history differences between the sexes and population variation in predation pressure and social density. We investigated how sex and...

Data from: Sex-specific association patterns in bonobos and chimpanzees reflect species differences in cooperation

Martin Surbeck, Cedric Girard-Buttoz, Christophe Boesch, Catherine Crockford, Barbara Fruth, Gottfried Hohmann, Kevin E. Langergraber, Klaus Zuberbühler, Roman M. Wittig & Roger Mundry
In several group-living species, individuals' social preferences are thought to be influenced by cooperation. For some societies with fission–fusion dynamics, sex-specific association patterns reflect sex differences in cooperation in within- and between-group contexts. In our study, we investigated this hypothesis further by comparing sex-specific association patterns in two closely related species, chimpanzees and bonobos, which differ in the level of between-group competition and in the degree to which sex and kinship influence dyadic cooperation. Here,...

Data from: Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome

Imran A. Rahman, Samuel Zamora, Peter L. Falkingham & Jeremy C. Phillips
Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil...

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

Rosetta Blackman, Kar Keun Sean Ling, Lynsey R Harper, Peter Shum, Bernd Hänfling & Lori Lawson-Handley
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS – particularly during the early stages of an invasion. Here, we compared the use of traditional kick-net sampling with two eDNA...

Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Owen S. Wangensteen, Judith Bakker, Stefano Mariani, Charles Baillie, Dayne Buddo, Demian D. Chapman, Austin J. Gallagher, Tristan L. Guttridge & Heidi Hertler
Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focused on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here we employed eDNA metabarcoding to compare beta...

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Charles Roseman, Terrence Capellini, Evelyn Jagoda, Scott Williams, Mark Grabowski, Christine O'Connor, John Polk & James Cheverud
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of...

Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems

Renske Onstein, Daphne Vink, Jorin Veen, Christopher Barratt, Suzette Flantua, Serge Wich & Daniel Kissling
A long-standing hypothesis in ecology and evolution is that trichromatic colour vision (the ability to distinguish red from green) in frugivorous primates has evolved as an adaptation to detect conspicuous (reddish) fruits. This could provide a competitive advantage over dichromatic frugivores which cannot distinguish reddish colours from a background of green foliage. Here, we test whether the origin, distribution and diversity of trichromatic primates is positively associated with the availability of conspicuous palm fruits, i.e....

Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

Peter Shum & Stephen Palumbi
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operation taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from...

Mammalian intestinal allometry, phylogeny, trophic level and climate

María Duque-Correa, Daryl Codron, Carlo Meloro, Amanda McGrosky, Christiann Schiffmann, Mark Edwards & Marcus Clauss
An often-stated ecomorphological assumption that has the status of ‘textbook knowledge’ is that the dimensions of the digestive tract correlate with diet, where herbivores – consuming diets of lower digestibility – have longer intestinal tracts than faunivores – consuming diets of higher digestibility. However, statistical approaches have so far failed to demonstrate this link. Here, we collated data on the length of intestinal sections and body mass of 519 mammal species, and test for various...

African apes data set

Joana Silva Carvalho
Aim: Modelling African great ape distribution has until now focused on current or past conditions, whilst future scenarios remain scarcely explored. Using an ensemble forecasting approach, we predicted changes in taxon-specific distribution under future scenarios of climate, land-use and human populations for 1) areas outside protected areas (PAs) only (assuming complete management effectiveness of PAs), 2) the entire study region, and 3) interspecies range overlap. Location: Tropical Africa Methods: We compiled occurrence data (n=5,203) on...

Data from: Microplastics disrupt hermit crab shell selection

Andrew Crump, Charlotte Mullens, Emily Bethell, Eoghan Cunningham & Gareth Arnott
Microplastics (plastics < 5 mm) are a potential threat to marine biodiversity. However, the effects of microplastic pollution on animal behaviour and cognition are poorly understood. We used shell selection in common European hermit crabs (Pagurus bernhardus) as a model to test whether microplastic exposure impacts the essential survival behaviours of contacting, investigating, and entering an optimal shell. We kept 64 female hermit crabs in tanks containing either polyethylene spheres (n = 35) or no...

Environmental DNA effectively captures functional diversity of coastal fish communities

Giorgio Aglieri, Charles Baillie, Stefano Mariani, Carlo Cattano, Antonio Calò, Gabriele Turco, Davide Spatafora, Antonio Di Franco, Manfredi Di Lorenzo, Paolo Guidetti & Marco Milazzo
Robust assessments of taxonomic and functional diversity are essential components of research programs aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies [Underwater Visual Census strip transects (UVCt), Baited Underwater Videos (BUVs) and Small Scale Fishery catches (SSFc)], and one novel molecular technique...

Dataset from: Ardipithecus hand provides evidence that humans and chimpanzees evolved from an ancestor with suspensory adaptations

Thomas Cody Prang, Kristen Ramirez, Mark Grabowski & Scott Williams
The morphology and positional behavior of the last common ancestor of humans and chimpanzees are critical for understanding the evolution of bipedalism. Early 20th century anatomical research supported the view that humans evolved from a suspensory ancestor bearing some resemblance to apes. However, the hand of the 4.4 million-year-old hominin Ardipithecus ramidus, purportedly provides evidence that the hominin hand was derived from a more generalized form. Here we use morphometric and phylogenetic comparative methods to...

Evolutionary versatility of the avian neck

Ryan Marek, Peter Falkingham, Roger Benson, James Gardiner, Thomas Maddox & Karl Bates
Bird necks display unparalleled levels of morphological diversity compared to other vertebrates, yet it is unclear what factors have structured this variation. Using 3D geometric morphometrics and multivariate statistics we show that the avian cervical column is a hierarchical morpho-functional appendage, with varying magnitudes of ecologically-driven morphological variation at different scales of organisation. Contrary to expectations given the widely-varying ecological functions of necks in different species, we find that regional modularity of the avian neck...

Data from: Downsizing a giant: re-evaluating Dreadnoughtus body mass

Karl T. Bates, Peter L. Falkingham, Sophie Macaulay, Charlotte Brassey & Susannah C. R. Maidment
Estimates of body mass often represent the founding assumption on which biomechanical and macroevolutionary hypotheses are based. Recently, a scaling equation was applied to a newly discovered titanosaurian sauropod dinosaur (Dreadnoughtus), yielding a 59 300 kg body mass estimate for this animal. Herein, we use a modelling approach to examine the plausibility of this mass estimate for Dreadnoughtus. We find that 59 300 kg for Dreadnoughtus is highly implausible and demonstrate that masses above 40...

Data from: The effect of roads on spider monkeys’ home range and mobility in a heterogeneous regenerating forest

Norberto Asensio, Elvin Murillo-Chacon, Colleen M. Schaffner & Filippo Aureli
Arboreal fauna living in tropical ecosystems may be particularly affected by roads given their dependency on forest cover and the high vulnerability of such ecosystems to changes. Over a period of four years, we followed subgroups of spider monkeys living in a regenerating dry tropical forest with 8.2 km of roads within their home range. We aimed to understand whether roads shaped the home range of spider monkeys and which road features affected their movement....

Data from: A high quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal

David A. Wells, Michael A. Cant, Hazel J. Nichols, Joe I. Hoffman & Joseph I. Hoffman
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical...

Data from: Ecological divergence combined with ancient allopatry in lizard populations from a small volcanic island

Nicolas M. Suárez, Jose Pestano & Richard P. Brown
Population divergence and speciation are often explained by geographical isolation, but may also be possible under high gene flow due to strong ecology-related differences in selection pressures. This study combines coalescent analyses of genetic data (11 microsatellite loci and 1 Kbp of mtDNA) and ecological modelling to examine the relative contributions of isolation and ecology to incipient speciation in the scincid lizard Chalcides sexlineatus within the volcanic island of Gran Canaria. Bayesian multispecies coalescent dating...

Data from: A cost for high levels of sperm competition in rodents: increased sperm DNA fragmentation

Javier DelBarco-Trillo, Olga García-Álvarez, Ana Soler, Maximiliano Tourmente, Julian Garde & Eduardo R. S. Roldan
Sperm competition, a prevalent evolutionary process in which the spermatozoa of two or more males compete for the fertilization of the same ovum, leads to morphological and physiological adaptations, including increases in energetic metabolism that may serve to propel sperm faster but that may have negative effects on DNA integrity. Sperm DNA damage is associated with reduced rates of fertilization, embryo and foetal loss, offspring mortality, and mutations leading to genetic disease. We tested whether...

Data from: Thrifty phenotype vs cold adaptation: trade-offs in upper limb proportions of Himalayan populations of Nepal

Stephanie Payne, Rajendra B.C. Kumar, Emma Pomeroy, Alison Macintosh, Jay Stock & Rajendra Kumar BC
The multi-stress environment of high altitude has been associated with growth deficits in humans, particularly in zeugopod elements (forearm, lower leg). This is consistent with the thrifty phenotype hypothesis, which has been observed in Andeans, but has yet to be tested in other high altitude populations. In Himalayan populations, other factors, such as cold stress, may shape limb proportions. The current study investigated whether relative upper limb proportions of Himalayan adults (n=254) differ between highland...

Data from: Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys

Kei Tsutsui, Masahiro Otoh, Kodama Sakurai, Nami Suzuki-Hashido, Takashi Hayakawa, Takumi Misaka, Yoshiro Ishimaru, Filippo Aureli, Amanda D. Melin, Shoji Kawamura & Hiroo Imai
Background: New World monkeys (NWMs) are unique in that they exhibit remarkable interspecific variation in color vision and feeding behavior, making them an excellent model for studying sensory ecology. However, it is largely unknown whether non-visual senses co-vary with feeding ecology, especially gustation, which is expected to be indispensable in food selection. Bitter taste, which is mediated by bitter taste receptors (TAS2Rs) in the tongue, helps organisms avoid ingesting potentially toxic substances in food. In...

Data from: Temporal and phylogenetic evolution of the sauropod dinosaur body plan

Karl T. Bates, Philip D. Mannion, Peter L. Falkingham, Stephen L. Brusatte, John R. Hutchinson, Alexandros Otero, William I. Sellers, Corwin Sullivan, Kent A. Stevens & Vivian Allen
The colossal size and body plan of sauropod dinosaurs are unparalleled in terrestrial vertebrates. However, to date, there have been only limited attempts to examine temporal and phylogenetic patterns in the sauropod bauplan. Here, we combine three-dimensional computational models with phylogenetic reconstructions to quantify the evolution of whole-body shape and body segment properties across the sauropod radiation. Limitations associated with the absence of soft tissue preservation in fossils result in large error bars about mean...

Data from: Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

Anna Mattout, Yair Aaronson, Badi Sri Sailaja, Edupuganti V. Raghu Ram, Arigela Harikumar, Jan-Philipp Mallm, Kae Hwan Sim, Malka Nissim-Rafinia, Emmanuelle Supper, Prim B. Singh, Siu Kwan Sze, Susan M. Gasser, Karsten Rippe & Eran Meshorer
Background: Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results: Here we identify Heterochromatin Protein 1β (HP1β) as...

Data from: Genetic diversity and historical biogeography of the Maltese wall lizard, Podarcis filfolensis (Squamata: Lacertidae)

Virginia Rodríguez, Richard P. Brown, Bàrbara Terrasa, Valentín Pérez-Mellado, Antònia Picornell, José A. Castro & Cori Ramon
Podarcis filfolensis is an endemic lizard from the Maltese archipelago. There is evidence of human-mediated decline and even extirpation of some insular populations of this species. However, information about the intraspecific genetic diversity and phylogeographic patterns of this species is limited. Here we analyze genetic markers from a multi-locus dataset (mtDNA, 2,533 bp; nuclear c-mos gene, 353 bp; 11 microsatellites) for individuals from extant populations of P. filfolensis. Despite generally low genetic variability, two main...

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