89 Works

Data from: Environmentally induced development costs underlie fitness tradeoffs

Gregory M. Walter, Melanie J. Wilkinson, J. David Aguirre, Mark W. Blows, Daniel Ortiz-Barrientos & Greg M. Walter
Local adaptation can lead to genotype‐by‐environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of biodiversity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly...

Data from: The effects of life history and sexual selection on male and female plumage colouration

James Dale, Cody J. Dey, Kaspar Delhey, Bart Kempenaers & Mihai Valcu
Classical sexual selection theory provides a well-supported conceptual framework for understanding the evolution and signalling function of male ornaments. It predicts that males obtain greater fitness benefits than females through multiple mating because sperm are cheaper to produce than eggs. Sexual selection should therefore lead to the evolution of male-biased secondary sexual characters. However, females of many species are also highly ornamented. The view that this is due to a correlated genetic response to selection...

Data from: Competition both drives and impedes diversification in a model adaptive radiation

Susan F. Bailey, Jeremy R. Dettman, Paul B. Rainey & Rees Kassen
Competitors are known to be important in governing the outcome of evolutionary diversification during an adaptive radiation, but the precise mechanisms by which they exert their effects remain elusive. Using the model adaptive radiation of Pseudomonas fluorescens, we show experimentally that the effect of competition on diversification of a focal lineage depends on both the strength of competition and the ability of the competitors to diversify. We provide evidence that the extent of diversification in...

Data from: The genetic architecture of constitutive and induced trichome density in two new RIL populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response

Rebecca H. Bloomer, Alan M. Lloyd & V. Vaughan Symonds
Background: Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has...

Data from: Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan & Hendrik N. Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within...

Data from: Biotic and abiotic variables influencing plant litter breakdown in streams: a global study

Luz Boyero, Richard Pearson, Cang Hui, Mark Gessner, Javier Perez, Markos Alexandrou, Manuel Graça, Bradley Cardinale, Ricardo Albariño, M. Arunachalam, Leon Barmuta, Andrew Boulton, Andreas Bruder, Marcos Callisto, Eric Chauvet, Russell Death, David Dudgeon, Andrea Encalada, Veronica Ferreira, Ricardo Figueroa, Alex Flecker, , Julie Helson, Tomoya Iwata, Tajang Jinggut … & Catherine Yule
Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, have high rates of carbon dioxide evasion and they contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and...

Data from: Diversification across a heterogeneous landscape

Gregory M. Walter, Melanie J. Wilkinson, Maddie E. James, Thomas J. Richards, J. David Aguirre, Daniel Ortiz-Barrientos & Greg M. Walter
Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the...

Data from: Not the time or the place: the missing spatio-temporal link in publicly available genetic data

Lisa C. Pope, Libby Liggins, Jude Keyse, Silvia B. Carvalho & Cynthia Riginos
Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be ‘repurposed’ to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy,...

Data from: Closing the gap: avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response

Steven A. Trewick, Stephen Pilkington, Lara D. Shepherd, Gillian C. Gibb, Mary Morgan-Richards & Steve A. Trewick
The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and...

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Kathryn Tiplady, Thomas Lopdell, Edwardo Reynolds, Richard Sherlock, Michael Keehan, Thomas Johnson, Jennie Pryce, Stephen Davis, Richard Spelman, Bevin Harris, Dorian Garrick & Mathew Littlejohn
Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each...

Functional beta diversity of New Zealand fishes: characterising morphological turnover along depth and latitude gradients, with derivation of functional bioregions

Elisabeth Myers, David Eme, Libby Liggins, Euan Harvey, Clive Roberts & Marti Anderson
Changes in the functional structures of communities are rarely examined along multiple large-scale environmental gradients. Here, we describe patterns in functional beta diversity for New Zealand marine fishes vs depth and latitude, including broad-scale delineation of functional bioregions. We derived eight functional traits related to food acquisition and locomotion and calculated complementary indices of functional beta diversity for 144 species of marine ray-finned fishes occurring along large-scale depth (50 - 1200 m) and latitudinal gradients...

The influence of nutrient enrichment on riverine food web function and stability

Adam Canning & Russell Death
Nutrient enrichment of rivers and lakes has been increasing rapidly over the past few decades, primarily because of agricultural intensification. Although nutrient enrichment is known to drive excessive algal and microbial growth, which can directly and indirectly change the ecological community composition, the resulting changes in food web emergent properties are poorly understood. We used ecological network analysis (ENA) to examine the emergent properties of 12 riverine food webs across a nutrient enrichment gradient in...

Data from: Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model

Gang He, Kang Huang, SongTao Guo, WeiHong Ji, Yi Ren, XueLin Jin & BaoGuo Li
Molecular studies using trace DNA, such as from museum specimens, ancient or forensic samples and samples obtained noninvasively, often have a common problem of low quality of DNA templates. Amplification errors, such as allelic dropout and false allele, may arise during polymerase chain reaction (PCR) using such samples. A mathematical model which treats homozygotes and heterozygotes discriminately has been developed to measure sample quality and compute the confidence level of using multiple-tube approaches. We use...

Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

Peter J. Waddell, Michael D. Hendy, David Penny & Masami Hasegawa
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts...

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