486 Works

Stars and Galaxies: The chemical abundance breakthrough

Kathryn Grasha
Measuring the chemical history of galaxies is critical to understand how galaxies form and evolve. This program aims to address shortcomings in current methods used to measure elements in a novel approach that combines observations and state-of-the-art modelling. Expected outcomes include a model for the history of the elements as the theoretical basis to derive new, robust galaxy diagnostics. There are tremendous benefits as this research topic is a major science driver for the next...

Genomic and phenomic analysis of island ant community assembly

Clive Darwell, Georg Fischer, Eli Sarnat, Nicholas Friedman, Cong Liu, Guilherme Baiao, Alexander Mikheyev & Evan Economo
Island biodiversity has long fascinated biologists as it typically presents tractable systems for unpicking the eco-evolutionary processes driving community assembly. In general, two recurring themes are of central theoretical interest. First, immigration, diversification, and extinction typically depend on island geographical properties (e.g. area, isolation, and age). Second, predictable ecological and evolutionary trajectories readily occur after colonization, such as the evolution of adaptive trait syndromes, trends toward specialization, adaptive radiation, and eventual ecological decline. Hypotheses such...

Genetic barcoding of museum eggshell improves data integrity of avian biological collections

Alicia Grealy, Naomi Langmore, Leo Joseph & Clare Holleley
Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we...

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Helen Bothwell, Luke Evans, Erika Hersch-Green, Scott Woolbright, Gerard Allan & Thomas Whitham
Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate...

Stress in the city: meta-analysis indicates no overall evidence for stress in urban vertebrates

Maider Iglesias-Carrasco
As cities continue to grow it is increasingly important to understand the long-term responses of wildlife to urban environments. There have been increased efforts to determine whether urbanization imposes chronic stress on wild animals, but empirical evidence is mixed. Here we conduct a meta-analysis to test whether there is, on average, a detrimental effect of urbanisation based on baseline and stress-induced glucocorticoid levels of wild vertebrates. We found no effect of urbanisation on glucocorticoid levels,...

Combined effects of rearing and testing temperatures on sperm traits

Megan Head, Maider Iglesias-Carrasco, Lauren Harrison & Michael Jennions
Temperature experienced during early development can affect a range of adult life history traits. Animals often show seemingly adaptive developmental plasticity – with animals reared at certain temperatures performing better as adults at those temperatures. The extent to which this type of adaptive response occurs in gonadal tissue that affect sperm traits is, however, poorly studied. We initially reared male mosquitofish (Gambusia holbrooki) at either 18oC or 30oC, and then measured their sperm reserves as...

Geographic locations of presence points and the size of 14 skull measurements

Rasoul Khosravi, Mahmoud-Reza Hemami, Colin Groves & Mohsen Ahmadi
The phylogeny and species boundaries of Gazella subgutturosa and G. marica have been long debated. The achievements of past conservation efforts have been compromised by a lack of knowledge about the phylogeny and taxonomic status of different populations. We integrated the recent genetic findings by previous studies with morphometric analyses and ecological niche modelling (ENM) to assess discreteness among populations of these gazelle species in Asia. Taxonomic diversity of gazelles was investigated by using principal...

Survival and home ranges of woodland birds in restoration plantings

Donna Belder, David Lindenmayer, Jennifer Pierson & Ashwin Rudder
Woodland birds are a species assemblage of conservation concern, and their persistence in fragmented agricultural landscapes is dependent on both the preservation of existing woodland remnants and the implementation of restoration plantings. However, little is known about the habitat-use and persistence of birds in fragmented agricultural landscapes. We present a detailed, population-oriented study of woodland birds in temperate eucalypt woodland restoration plantings and remnant woodland patches in the South-west Slopes bioregion of New South Wales,...

Can evolutionary theories of dispersal and senescence predict postrelease survival, dispersal, and body condition of a reintroduced threatened mammal?

Natasha M. Robinson
Theories of dispersal and senescence (or ageing) predict that dispersal, and ongoing survival and body condition, are influenced by evolutionary drivers, along with intrinsic and extrinsic factors. Such theories are relevant to translocations of animals where high mortality, loss of body condition, and dispersal beyond the area of release are commonly reported. However, these theories have rarely been tested using data from translocations. We explore whether theories of dispersal and senescence, together with biological knowledge...

Distribution and habitat attributes associated with the Himalayan red panda in the westernmost distribution range

Saroj Shrestha, Arjun Thapa, Damber Bista, Natasha Robinson, Ang Sherpa, Krishna Acharya, Shant Jnawali, Sonam Lama & Sony Lama
The Himalayan red panda (Ailurus fulgens), a recently confirmed distinct species in the red panda genus, is distributed in Nepal, India, Bhutan and south Tibet. Nepal represents the western most distribution of the Himalayan red panda. This study aim to determine important habitat features influencing the distribution of red panda and recommend possible habitat corridors. This manuscript described current potential habitat of 3,222 km2 with the relative abundance of 3.34 signs/km in Nepal. Aspect, canopy...

Regarding the F-word: the effects of data Filtering on inferred genotype-environment associations

Collin Ahrens, Rebecca Jordan, Jason Bragg, Peter Harrison, Tara Hopley, Helen Bothwell, Kevin Murray, Dorothy Steane, John Whale, Margaret Byrne, Rose Andrew & Paul Rymer
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results. These effects could be amplified in downstream predictions, including management strategies. Here, we investigate the effects of filtering on...

Temporal patterns of forest seedling emergence across different disturbance histories data

Elle Bowd
Forest ecosystems experience a myriad of natural and anthropogenic disturbances that shape ecological communities. Seedling emergence is a critical, preliminary stage in the recovery of forests post-disturbance and is triggered by a series of abiotic and biotic changes. However, the long-term influence of different disturbance histories on patterns of seedling emergence is poorly understood. Here, we address this research gap by using an 11-year dataset gathered between 2009 and 2020 to quantify the influence of...

Quantity discrimination in a lizard

Birgit Szabo, Daniel W. A. Noble, Martin J. Whiting, Marco E. S. Monteiro & Kaitlin J. McCloghry
While foraging or during social interactions, animals may benefit from judging relative quantity. Individuals may select larger prey or a patch with more food and likewise, it may pay to track the number and type of individuals and social interactions. We tested for spontaneous quantity discrimination in the gidgee skink (Egernia stokesii), a family-living lizard. Lizards were presented with food quantities differing in number or size and selected the larger quantity of food items when...

Can an introduced predator select for adaptive sex allocation?

Rob Heinsohn
Most species produce equal numbers of sons and daughters, and sex differences in survival after parental care do not usually affect this pattern. Temporary overproduction of the scarcer sex can be adaptive when generations overlap, the sexes differ in life history expectations, and parents can anticipate future mating opportunities. However an alternative strategy of maximising the competitiveness of the more abundant sex in these circumstances remains unexplored. We develop theory showing how mothers can maximise...

Additional data: Submillimetre mechanistic designs of termite-built structures

Sebastian Oberst, Richard Martin, Benjamin Halkon, Joseph Lai, Theodore Evans & Mohammed Saadatfar
Termites inhabit complex underground mounds of intricate stigmergic labyrinthine designs with multiple functions as nursery, food storage, and refuge, while maintaining a homeostatic microclimate. Past research studied termite building activities rather than the actual material structure. Yet, prior to understanding how multi-functionality shaped termite building, a thorough grasp of submillimetre mechanistic architecture of mounds is required. Here, we identify for Nasutitermes exitiosus via granulometry and Fourier transform infrared spectroscopy analysis, preferential particle sizes related to...

Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)

Lucy Peters, Jisca Huisman, Loeske Kruuk, Josephine Pemberton & Susan Jonston
Sexually-selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually-selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer. On the island of Rum, Scotland, males with larger antlers have increased breeding success,...

Data from: Inbreeding, inbreeding depression and infidelity in a cooperatively-breeding bird

Gabriela Karolina Hajduk, Andrew Cockburn, Nicolas Margraf, Helen L. Osmond, Craig A. Walling, Loeske E.B. Kruuk & Loeske E. B. Kruuk
Inbreeding depression plays a major role in shaping mating systems: in particular, inbreeding avoidance is often proposed as a mechanism explaining extra-pair reproduction in socially-monogamous species. This suggestion relies on assumptions which are rarely comprehensively tested: that inbreeding depression is present, that higher kinship between social partners increases infidelity, and that infidelity reduces the frequency of inbreeding. Here, we test these assumptions using 26 years of data for a cooperatively-breeding, socially-monogamous bird with high female...

Data from: Social effects on foraging behaviour and success depend on local environmental conditions

Harry H. Marshall, Alecia J. Carter, Alexandra Ashford, J. Marcus Rowcliffe & Guy Cowlishaw
In social groups, individuals' dominance rank, social bonds, and kinship with other group members have been shown to influence their foraging behavior. However, there is growing evidence that the particular effects of these social traits may also depend on local environmental conditions. We investigated this by comparing the foraging behavior of wild chacma baboons, Papio ursinus, under natural conditions and in a field experiment where food was spatially clumped. Data were collected from 55 animals...

Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird

Alexandra Pavlova, J. Nevil Amos, Leo Joseph, Kate Loynes, Jeremy J. Austin, J. Scott Keogh, Graham N. Stone, James Allan Nicholls & Paul Sunnucks
Relationships among multi-locus genetic variation, geography and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic...

Data from: Evolutionary relationships among pollinators and repeated pollinator sharing in sexually deceptive orchids

Ryan D. Phillips, Graham R. Brown, Kingsley W. Dixon, Christine Hayes, Celeste C. Linde & Rod Peakall
The mechanism of pollinator attraction is predicted to strongly influence both plant diversification and the extent of pollinator sharing between species. Sexually deceptive orchids rely on mimicry of species-specific sex pheromones to attract their insect pollinators. Given that sex pheromones tend to be conserved among related species, we predicted that in sexually deceptive orchids, (i) pollinator sharing is rare, (ii) closely related orchids use closely related pollinators and (iii) there is strong bias in the...

Data from: How mountains shape biodiversity: the role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae)

Damien Esquerre, Ian G. Brennan, Renee A. Catullo, Fernando Torres-Perez, J.Scott Keogh & J. Scott Keogh
Testing hypotheses on the drivers of clade evolution and trait diversification provides insight into many aspects of evolutionary biology. Often, studies investigate only the intrinsic biological properties of organisms as the causes of diversity, however extrinsic properties of a clade’s environment, particularly geological history, may also offer compelling explanations. The Andes are a young mountain chain known to have shaped many aspects of climate and diversity of South America. The Liolaemidae are a radiation of...

Data from: Capture enrichment of aquatic environmental DNA: a first proof of concept

Taylor M. Wilcox, Katherine E. Zarn, Maxine P. Piggott, Michael K. Young, Kevin S. McKelvey & Michael K. Schwartz
Environmental DNA (eDNA) sampling – the detection of genetic material in the environment to infer species presence – has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from...

Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture

Luisa C. Teasdale, Frank Köhler, Kevin D. Murray, Tim O'Hara & Adnan Moussalli
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Statistical comparison of trait-dependent biogeographical models indicates that Podocarpaceae dispersal is influenced by both seed cone traits and geographical distance

Kristina Vanessa Klaus & Nicholas Joseph Matzke
The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer sister families Podocarpaceae and Araucariaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared to other predictors of dispersal such as the geographic distance between...

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