270 Works

Data from: Infant feeding and risk of developing celiac disease: a systematic review

Marco Silano, Carlo Agostoni, Yolanda Sanz & Stefano Guandalini
Objective: To review the evidence for the association of breast feeding, breastfeeding duration or the timing of gluten introduction and the later development of celiac disease (CD). Design: Systematic review. Methods: We searched MEDLINE, via PubMed, EMBASE and Web of Science, for studies published up to 31 August 2015 investigating the association of breastfeeding duration, breast feeding at the moment of gluten introduction or the timing of gluten introduction and the later development of CD....

Data from: Convergent evolution in social swallows (Aves: Hirundinidae)

Allison E. Johnson, Jonathan S. Mitchell & Mary Bomberger Brown
Behavioral shifts can initiate morphological evolution by pushing lineages into new adaptive zones. This has primarily been examined in ecological behaviors, such as foraging, but social behaviors may also alter morphology. Swallows and martins (Hirundinidae) are aerial insectivores that exhibit a range of social behaviors, from solitary to colonial breeding and foraging. Using a well-resolved phylogenetic tree, a database of social behaviors, and morphological measurements, we ask how shifts from solitary to social breeding and...

Data from: Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids

Daniel R. Matute & Jackie Gavin-Smyth
Sex chromosomes have a large effect on reproductive isolation and play an important role in hybrid inviability. In Drosophila hybrids, X-linked genes have pronounced deleterious effects on fitness in male hybrids, which have only one X chromosome. Several studies have succeeded at locating and identifying recessive X-linked alleles involved in hybrid inviability. Nonetheless, the density of dominant X-linked alleles involved in interspecific hybrid viability remains largely unknown. In this report, we study the effects of...

Data from: The magnitude of behavioral isolation is affected by characteristics of the mating community

Daniel R. Matute
Gene exchange between species occurs in areas of secondary contact, where two species have the opportunity to hybridize. If heterospecific males are more common than conspecific males, females will experience more encounters with males of other species. These encounters might increase the likelihood of heterospecific matings, and lead to the production of hybrid progeny. I studied the mating behavior of two pairs of sibling species endemic to Africa: Drosophila yakuba/D. santomea and D. simulans/D. sechellia....

Data from: Mate preference for a phenotypically plastic trait is learned, and may facilitate preference-phenotype matching

Erica L. Westerman, Napon Chirathivat, Elizabeth Schyling & Antónia Monteiro
Fixed, genetically determined, mate preferences for species whose adult phenotype varies with rearing environment may be maladaptive, as the phenotype that is most fit in the parental environment may be absent in the offspring environment. Mate preference in species with polyphenisms (environmentally dependent alternative phenotypes) should therefore either not focus on polyphenic traits, be polyphenic themselves, or learned each generation. Here we test these alternative hypotheses by first describing a female-limited seasonal polyphenism in a...

Data from: A fish and tetrapod fauna from Romer’s gap preserved in Scottish Tournaisian floodplain deposits

Benjamin K. A. Otoo, Jennifer A. Clack, Timothy R. Smithson, Carys E. Bennett, Timothy J. Kearsey & Michael I. Coates
The end‐Devonian mass extinction has been framed as a turning point in vertebrate evolution, enabling the radiation of tetrapods, chondrichthyans and actinopterygians. Until very recently ‘Romer's Gap’ rendered the Early Carboniferous a black box standing between the Devonian and the later Carboniferous, but now new Tournaisian localities are filling this interval. Recent work has recovered unexpected tetrapod and lungfish diversity. However, the composition of Tournaisian faunas remains poorly understood. Here we report on a Tournaisian...

Data from: Testing for differences in rates of speciation, extinction, and morphological evolution in four tribes of cichlids endemic to Lake Tanganyika, East Africa

Marie E. Hoerner
Patterns of morphological disparity yield important insight into the causes of diversification and adaptive radiation in East African cichlids. However, comparisons of cichlid disparity have often failed to consider the effects that differing clade ages or stochasticity may have on disparity before making interpretations. Here, a model of branching morphological evolution allows assessment of the relative contributions of differing turnover and morphological change rates, clade ages, and stochastic variation to the observed patterns of disparity...

Reconstructing Ecological Niche Evolution via Ancestral State Reconstruction with Uncertainty Incorporated

Hannah Owens, Vivian Ribiero, Erin Saupe, Marlon E. Cobos, Peter Hosner, Jacob Cooper, Abdallah Samy, Vijay Barve, Narayani Barve, Carlos Muñoz & A. Townsend Peterson
Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods can infer the history of ecological niche evolution inaccurately because (1) species’ niches are often poorly characterized; and (2) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species’ environmental tolerances. Here we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty...

Life history predicts flight muscle phenotype and function in birds

Shane DuBay, Yongjie Wu, Graham Scott, Yanhua Qu, Qiao Liu, Joel Smith, Chao Xin, Andrew Hart Reeve, Chen Juncheng, Dylan Meyer, Jing Wang, Jacob Johnson, Zachary Cheviron, Fumin Lei & John Bates
1. Functional traits are the essential phenotypes that underlie an organism’s life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. 2. We asked how age- and sex-dependent demands on...

Perspective piece: Comparison of eastern and western North American monarch butterflies

Micah Freedman
Monarch butterflies are a species of conservation priority due to declining overwintering populations in both eastern and western North America. Declines in western overwintering monarchs—more than 99.9% since monitoring began—are especially acute. However, the degree to which western monarchs are a distinct biological entity is uncertain. In this review, we focus on phenotypic and genetic differentiation between eastern and western monarchs, with the goal of informing researchers and policy-makers who are interested in monarch conservation....

Sound velocities and P-V-T data of phase A obtained at GSECARS beamline 13-ID-D

Nao Cai, Xintong Qi, Ting Chen, Siheng Wang, Tony Yu, Yanbing Wang, Toru Inoue, Duojun Wang & Baosheng Li
The sound velocities and lattice parameters for sample in the under review paper, "Enhanced visibility of subduction slabs by the formation of dense hydrous phase A", submitted to the journal 'Geophysical Research Letters', are published. The high pressure and high-temperature experiment was conducted in the 1000-ton Kawai type large volume apparatus (T-25) installed at the GSECARS beamline 13-ID-D of Advanced Photon Source, Argonne National Laboratory. The datasets were obtained at conditions up to 11 GPa...

Data from: Genomic evidence for panmixia of eastern and western North American migratory monarch butterflies

V Talla, AA Pierce, KL Adams, TJB De Man, S Nallu, FX Villablanca, MR Kronforst & JC De Roode
Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 kilometers to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. Monarch numbers have recently dwindled, and monarch migration may be on the brink of extinction. It is often assumed that eastern and western monarchs form distinct evolutionary units...

Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset

Arjun Biddanda, Daniel Rice & John Novembre
A key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing rela tionships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic...

Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)

Dahiana Arcila, Lily C. Hughes, Fernando Meléndez-Vazquez, Carole C. Baldwin, William T. White, Kent E. Carpenter, Jeffrey T. Williams, Mudjekeewis D. Santos, John J. Pogonoski, Masaki Miya, Guillermo Ortí & Ricardo Betancur-R.
The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to...

Code and data from: Evolution of sexual cooperation from sexual conflict

Maria R Servedio, John M Powers, Russell Lande & Trevor D Price
This C code conducts deterministic iterations of the exact recursion equations presented in the Model section of "Evolution of sexual cooperation from sexual conflict" by Servedio, Powers, Lande and Price. The code produces a two-dimensional grid with any parameters of choice on the x and y axis. Examples can be found in Figures 2c, 3c and 4 of the main text as well as many similar figures in the Supplementary Material. A sample parameter file...

Adult facilitation becomes competition as juvenile soapberry bugs age

Meredith Cenzer
Intraspecific interactions can change from facilitative to competitive depending on the organism’s ontogeny. In plant-feeding insects, host plant defenses can be strengthened or weakened by insect feeding, and can therefore be important for determining whether two insects feeding on the same plant help or harm each other’s fitness. Here I conducted two experiments looking at the direct effect of a physical seed defense and the role of intraspecific facilitation in reducing the effects of that...

Slower environmental cycles maintain greater life-history variation within populations

John Park & Tim Wootton
Populations in nature are comprised of individual life histories, whose variation underpins ecological and evolutionary processes. Yet the forces of environmental selection that shape intrapopulation life-history variation are still not well understood, and efforts have largely focused on random (stochastic) fluctuations of the environment. However, a ubiquitous mode of environmental fluctuation in nature is cyclical, whose periodicities can change independently of stochasticity. Here we test theoretically-based hypotheses for whether shortened (‘Fast’) or lengthened (‘Slow’) environmental...

Data for Manuscript: A desert songbird with no confamilials in the Western Hemisphere (Verdin, Auriparus flaviceps) investigates divergent conspecific songs

Emma Greig, Eva Kinnebrew, Max Witynski & Eric Larsen
This is the dataset that accompanies the manuscript: A desert songbird with no confamilials in the Western Hemisphere (Verdin, Auriparus flaviceps) investigates divergent conspecific songs, published in the journal Ornithology (2021). One spreadsheet is a dataset for analysis of Verdin song acoustic structure (“Supplementary Material Acoustic Data.xls”), one spreadsheet is a dataset for analysis of Verdin response to playbacks (“Supplementary Material Playback Data.xls”), and one spreadsheet is metadata about all the recordings used in the...

Phylogeny, biogeography, and classification of the elms (Ulmus)

Andrew Hipp, Alan Whittemore, Ryan S. Fuller, Bethany H. Brown, Marlene Hahn, Linus Gog & Jaime A. Weber
A RAD-seq phylogeny is presented for the genus Ulmus, and a revised infrageneric classification is given, with keys, descriptions, and range maps for the subgenera and sections. The previously accepted classification was based on a cpDNA phylogeny, but several well-marked clades in the chloroplast phylogeny are not recovered in the RAD-seq phylogeny and do not seem to represent valid clades in the organismal phylogeny. Ordination and STRUCTURE analysis support a broad species concept in Ulmus...

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Nicholas Crouch, Stewart Edie, Katie Collins, Rüdiger Bieler & David Jablonski
Analyses of evolutionary dynamics can be profoundly affected by age calibrations of phylogenetic nodes under different models of lineage branching. Most time-calibrated molecular phylogenies of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. Lineages can also split via budding, in which a parent lineage persists following the origin of a daughter lineage, and nodes are calibrated using the age...

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