283 Works

Data from: DNA methylation mediates genetic variation for adaptive transgenerational plasticity

Jacob J. Herman & Sonia E. Sultan
Environmental stresses experienced by individual parents can influence offspring phenotypes in ways that enhance survival under similar conditions. Although such adaptive transgenerational plasticity is well documented, its transmission mechanisms are generally unknown. One possible mechanism is environmentally induced DNA methylation changes. We tested this hypothesis in the annual plant Polygonum persicaria, a species known to express adaptive transgenerational plasticity in response to parental drought stress. Replicate plants of 12 genetic lines (sampled from natural populations)...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Biodiversity and thermal ecological function: the influence of freshwater algal diversity on local thermal environments

Anouch Missirian, Eyal G. Frank, Jess T. Gersony, Jason C.Y. Wong & Shahid Naeem
The influence of temperature on diversity and ecosystem functioning is well studied; the converse however, i.e. how biodiversity influences temperature, much less so. We manipulated freshwater algal species diversity in microbial microcosms to uncover how diversity influenced primary production, which is well documented in biodiversity research. We then also explored how visible-spectrum absorbance and the local thermal environment responded to biodiversity change. Variations in the local thermal environment, that is, in the temperature of the...

Data from: Hierarchy in adaptive radiation: a case study using the Carnivora (Mammalia)

Graham J Slater & Anthony R Friscia
Simpson’s “early burst” model of adaptive radiation was intended to explain the early proliferation of morphological and functional variation in diversifying clades. Yet, despite much empirical testing, questions remain regarding its frequency across the tree of life. Here, we evaluate the support for an early burst adaptive radiation in 14 ecomorphological traits plus body mass for the extant mammalian order Carnivora and its constituent families. We find strong support for an early burst of evolution...

Data from: Phylogeography of Heliconius cydno and its closest relatives: disentangling their origin and diversification

Carlos F. Arias, Camilo Salazar, Claudia Rosales, Marcus R. Kronforst, Mauricio Linares, Eldredge Bermingham & W. Owen McMillan
The origins of phenotypic variation within mimetic Heliconius butterflies have long fascinated biologists and naturalists. However, the evolutionary processes that have generated this extraordinary diversity remain puzzling. Here we examine intraspecific variation across Heliconius cydno diversification and compare this variation to that within the closely related H. melpomene and H. timareta radiations. Our data, which consist of both mtDNA and genome scan from nearly 2250 AFLP loci, reveal a complex history of differentiation and admixture...

Data from: Complete genome sequences provide a case study for the evaluation of gene-tree thinking

Rebecca B. Dikow & William Leo Smith
Complete genome sequences from a genus of Gammaproteobacteria, Shewanella, are used to generate a genome-wide exploration of the gene-tree species-tree dichotomy. A number of datasets were constructed and analyses were attempted. Single genes were chosen from 243 regions of collinear gene homology (128 of these 243 chosen genes are from the core Shewanella genome and 162 of 243 have the complete taxon sampling) from a previous study (Dikow, 2011) and subjected to phylogenetic analysis both...

Data from: Insulin-insensitivity of male genitals maintains reproductive success in Drosophila

Austin P. Dreyer & Alexander W. Shingleton
For most arthropod species, male genital size is relatively implastic in response to variation in developmental nutrition, such that the genitals in large well-fed males are similar in size to those in small poorly-fed males. In Drosophila melanogaster, reduced nutritional plasticity of the male genitalia is a consequence of low insulin sensitivity through a tissue-specific reduction in expression of FOXO, a negative growth regulator. Despite an understanding of the proximate developmental mechanisms regulating organ size,...

Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Yifu Ding, Daniel J Vanselow, Maksim A Yakovlev, Spencer R Katz, Alex Y Lin, Darin P Clark, Phillip Vargas, Xuying Xin, Jean E Copper, Victor A Canfield, Khai C Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B Van Rossum, Patrick La Riviere & Keith Cheng
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions....

Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow

Roger K. Butlin, Maria Saura, Grégory Charrier, Benjamin Jackson, Carl André, Armando Caballero, Jerry A. Coyne, Juan Galindo, John W. Grahame, Johann Hollander, Petri Kemppainen, Mónica Martínez-Fernández, Marina Panova, Humberto Quesada, Kerstin Johannesson, Emilio Rolán-Alvarez & Johan Hollander
Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to...

Data from: Defensive traits exhibit an evolutionary trade-off and drive diversification in ants

Benjamin D. Blanchard & Corrie S. Moreau
Evolutionary biologists have long predicted that evolutionary trade-offs among traits should constrain morphological divergence and species diversification. However, this prediction has yet to be tested in a broad evolutionary context in many diverse clades, including ants. Here, we reconstruct an expanded ant phylogeny representing 82% of ant genera, compile a new family-wide trait database, and conduct various trait-based analyses to show that defensive traits in ants do exhibit an evolutionary trade-off. In particular, the use...

Data from: SK2 channels in cerebellar Purkinje cells contribute to excitability modulation in motor learning-specific memory traces

Giorgio Grasselli, Henk-Jan Boele, Heather K. Titley, Nora Bradford, Lisa Van Beers, Lindsey Jay, Chris I. De Zeeuw, Martijn Schonewille, Christian Hansel, Gerco Beekhof & Silas Busch
Neurons store information by changing synaptic input weights. In addition, they can adjust their membrane excitability to alter spike output. Here, we demonstrate a role of such ‘intrinsic plasticity’ in behavioral learning in a mouse model that allows us to detect consequences of absent excitability modulation, without alterations in synaptic plasticity. SK2-type, calcium-dependent K+ conductances are involved in excitability control as they contribute to the afterhyperpolarization (AHP) following spike bursts. SK2 channels are downregulated in...

Data from: Postcrania of Borealestes (Mammaliformes: Docodonta) and the emergence of ecomorphological diversity in early mammals

Elsa Panciroli, Roger Benson, Vincent Fernandez, Matthew Humpage, Alberto Martin-Serra, Stig Walsh, Zhe-Xi Luo & Nick Fraser
The Middle Jurassic witnessed the early diversification of mammal groups, including the stem-mammalian clade, Docodonta. Recent discoveries in China indicate docodontans exhibited ecomorphological diversity akin to small-bodied mammals living >100 million years later, in the Cenozoic. Our understanding of the emergence of this ecological diversity is hindered by a lack of Middle Jurassic fossil material from other parts of the world. The two partial postcranial skeletons of Borealestes described here come from the Kilmaluag Formation,...

De novo genome assembly of Leptodactylus fuscus

Lu Yang, Peter Andolfatto, Andrew Crawford, Santiago Herrera-Álvarez, Maríadel Pilar Rodríguez-Ordoñez, Julie Peng, Shabnam Mohammadi, Jay Storz, Arbel Harpak & Susanne Dobler
This presents a de novo genome assembly of Leptodactylus fuscus. High molecular weight DNA was extracted from a L. fuscus embryo which had been preserved in ethanol upon collection in Garzón, Huila, Colombia. The library was prepared and sequenced with 10X Genomics Chromium. Linked reads were processed by Long Ranger basic v2.2.2 and assembled with Supernova v2.1.1. The assembled genome is 2.42 Gb with 16,530 scaffolds >=10 kb, and scaffold N50 = 363 kb. The...

Temporal pole responds to subtle changes in local thyroid hormone signaling

Antonio Bianco, Marcelino Cicera, McAninch Elizabeth, Gustavo Fernandes, Barbara Bocco & Miriam Ribeiro
To study thyroid hormone (TH) signaling in the human brain, we analyzed published microarray data sets of the temporal pole (Brodmann area 38) of 19 deceased donors. An index of TH signaling built on the expression of 19 well known TH-responsive genes in mouse brains (T3S+) varied from 0.92 to 1.1. After Factor analysis, T3S+ correlated independently with the expression of TH transporters (MCT8, LAT2), TH receptor (TR) beta and TR coregulators (CARM1, MED1, KAT2B,...

Neural population dynamics in motor cortex are different for reach and grasp

Aneesha Suresh, James Goodman, Elizaveta Okorokova, Matthew Kaufman, Nicholas Hatsopoulos & Sliman Bensmaia
Low-dimensional linear dynamics are observed in neuronal population activity in primary motor cortex (M1) when monkeys make reaching movements. This population-level behavior is consistent with a role for M1 as an autonomous pattern generator that drives muscles to give rise to movement. In the present study, we examine whether similar dynamics are also observed during grasping movements, which involve fundamentally different patterns of kinematics and muscle activations. Using a variety of analytical approaches, we show...

Selection in males purges the mutation load on female fitness

Karl Grieshop, Paul Maurizio, Göran Arnqvist & David Berger
Theory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, in part because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of the many rare and partially recessive deleterious alleles that make up the main part of a population’s mutation load. Here, we...

Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia

Stewart Edie, Safia Khouja, Katie Collins, Nicholas Crouch & David Jablonski
Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via the stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channeling morphological evolution along lines of least resistance—a process that may be particularly important in the accumulation of disparity among organisms with accretionary growth, as in many invertebrate systems. We use a time-calibrated phylogenetic hypothesis and high-density, 3D...

Data from: Twist and chew: three dimensional tongue kinematics during chewing in macaque primates

Kara Feilich, J.D. Laurence-Chasen, Courtney Orsbon, Nicholas Gidmark & Callum Ross
Three-dimensional (3D) tongue movements are central to performance of feeding functions by mammals and other tetrapods, but 3D tongue kinematics during feeding are poorly understood. Tongue kinematics were recorded during grape chewing by macaque primates using biplanar videoradiography. Complex shape changes in the tongue during chewing are dominated by a combination of flexion in the tongue’s sagittal planes and roll about its long axis. As hypothesized for humans, in macaques during tongue retraction the middle...

Hinge and ecomorphology of Legumen Conrad, 1858 (Bivalvia, Veneridae), and the contraction of venerid morphospace following the end-Cretaceous extinction

Katie S. Collins, Stewart M. Edie & David Jablonski
The Veneridae are the most speciose modern family of bivalves, and one of the most morphologically conservative and homoplastic, making subfamilial and sometimes even genus-level classification difficult. The widespread Cretaceous genus Legumen Conrad, 1858 is currently placed in the subfamily Tapetinae of the Veneridae although it more closely resembles the Solenoida (razor clams, Pharidae and Solenidae) in general shell form. Here we provide high-resolution images of the Legumen hinge for the first time. We confirm...

Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades

David Cerny, Daniel Madzia & Graham Slater
Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM,...

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

Mark Bitter, Lydia Kapsenberg, Katherine Silliman, Jean-Pierre Gattuso & Catherine Pfister
Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus...

Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

Anna Wisniewski, Graeme T. Lloyd & Graham J. Slater
A clade’s evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated...

A dataset of ovariole number from more than 2,000 insect species

Samuel H. Church, Bruno A. S. De Medeiros, Seth Donoughe, Nicole L. Márquez Reyes & Cassandra G. Extavour
The number of offspring an organism can produce is a key component of its evolutionary fitness and life-history. This number differs widely between organisms, and its variation is the foundation for several hypotheses about life-history evolution, including the prediction that there is an evolutionary trade off between the number of offspring and their size. In insects, the number of egg-producing compartments in the ovary, called ovarioles, has been used as a proxy for potential offspring...

Data from: Concerted evolution reveals co-adapted amino acid substitutions in Na+K+ ATPase of frogs that prey on toxic toads

Shabnam Mohammadi, Lu Yang, Arbel Harpak, Santiago Herrera-Álvarez, María Del Pilar Rodríguez-Ordoñez, Julie Peng, Karen Zhang, Jay Storz, Susanne Dobler, Andrew Crawford & Peter Andolfatto
Gene duplication is an important source of evolutionary innovation, but the functional distinction between duplicates can be opposed by ongoing gene conversion between them. Here we document a tandem duplication of Na+,K+-ATPase subunit α1 (ATP1A1) sharedby frogs in the genus Leptodactylus,a group of species that feeds on toxic toads. One ATP1A1 paralog evolved resistance to toad toxins while the other paralog retained ancestral susceptibility. Frequent non-allelic gene conversion homogenized most of the paralog sequences,yet the...

mRNA editing analysis of Doryteuthis pealeii

Sofia Medina Ruiz, Caroline Albertin, Therese Mitros, Hannah Schmidbaur, Gustavo Sanchez, Z.Y. Wang, Jane Grimwood, Joshua Rosenthal, Clifton Ragsdale, Oleg Simakov & Daniel Rokhsar
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid Doryteuthis (Loligo) pealeii and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring....

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