270 Works

Phylogenomics of bonytongue fishes (Osteoglossomorpha) shed light on the craniofacial evolution and biogeography of the weakly electric clade (Mormyridae)

Rose Peterson, John Sullivan, Carl Hopkins, Aintzane Santaquiteria, Casey Dillman, Stacy Pirro, Ricardo Betancur, Dahiana Arcila, Lily C. Hughes & Guillermo Ortí
Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrosensory capabilities (Notopteridae and Mormyroidea) have attracted interest by many, yet a comprehensive phylogenetic framework for comparative analysis is missing. We provide a phylogenomic analysis of 179 species (out of 260), 28 out of...

Key roles for the freezing line and disturbance in driving the low plant species richness of temperate regions

Suresh K Rana, Alexander E White & Trevor D Price
Aim: At the macroscale, climate strongly correlates with species richness gradients, resulting from differences in in-situ diversification and dispersal. One historical explanation for the pattern is that regions spanning temperate climates contain few species because past disturbances have generated high extinction rates, and species from tropical regions are unable to easily colonize temperate regions. We test these postulates for Himalayan plants, which span subtropical to temperate climates over steep elevational gradients. Location: Himalaya Time period:...

Multiscale models for the SARS-CoV-2 Virion

Yu Alvin & Gregory Voth
This repository contains coarse-grained (CG) models for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to G.A.V. in response to the COVID-19 pandemic.

Preface: SCiL 2020 Editor's Note

Allyson Ettinger, Gaja Jarosz & Max Nelson

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...

Data from: What can interaction webs tell us about species roles?

J. Timothy Wootton, Elizabeth L. Sander & Stefano Allesina
The group model is a useful tool to understand broad-scale patterns of interaction in a network, but it has previously been limited in use to food webs, which contain only predator-prey interactions. Natural populations interact with each other in a variety of ways and, although most published ecological networks only include information about a single interaction type (e.g., feeding, pollination), ecologists are beginning to consider networks which combine multiple interaction types. Here we extend the...

Data from: Hotspots of soil N2O emission enhanced through water absorption by plant residue

Alexandra N. Kravchenko, Ehsan R. Toosi, Andrey K. Guber, Nathaniel E. Ostrom, J. Yu, K. Azeem, Mark L. Rivers & G. Philip Robertson
N2O is a highly potent greenhouse gas and arable soils represent its major anthropogenic source. Field-scale assessments and predictions of soil N2O emission remain uncertain and imprecise due to the episodic and microscale nature of microbial N2O production, most of which occurs within very small discrete soil volumes. Such hotspots of N2O production are often associated with decomposing plant residue. Here we quantify physical and hydrological soil characteristics that lead to strikingly accelerated N2O emissions...

Data from: Testing for human impacts in the mismatch of living and dead ostracode assemblages at nested spatial scales in subtropical lakes from the Bahamian archipelago

Andrew V. Michelson, Susan M. Kidwell, Lisa E. Park Boush & Jeanine L. Ash
Naturally time-averaged accumulations of skeletal remains – death assemblages – provide reliable, albeit temporally coarse, information on the species composition and structure of communities in diverse settings, and their mismatch with local living communities usually signals recent human-driven ecological change. Here, we present the first test of live-dead mismatch as an indicator of human stress using ostracodes. On three islands along a gradient of human population density in the Bahamas, we compared the similarity of...

Data from: Song recognition and heterospecific associations between two fairy-wren species (Maluridae)

Allison E. Johnson, Christina Masco & Stephen Pruett-Jones
Although heterospecific associations beneficial to one or both species involved (e.g. commensalisms or mutualisms) are common, it is generally assumed that interactions between species are transient and not particular to individuals. However, long-term interactions between individuals of different species do occur. In such heterospecific social groups, discrimination between heterospecific individuals may be beneficial, allowing individuals to direct beneficial or aggressive behaviors towards appropriate targets. Here we describe heterospecific groups composed of splendid and variegated fairy-wrens...

Data from: Ecological limits on diversification of the Himalayan core Corvoidea

Jonathan David Kennedy, Jason T. Weir, Daniel Marc Hooper, D. Thomas Tietze, Jochen Martens & Trevor Douglas Price
Within regions, differences in the number of species among clades must be explained by clade age, net diversification rate, or immigration. We examine these alternatives by assessing historical causes of the low diversity of a bird parvorder in the Himalayas (the core Corvoidea, 57 species present) relative to its more species rich sister clade. The core Corvoidea contain ecologically diverse species spanning a large range of body sizes and elevations. Despite this diversity, on the...

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: Constraints on mammalian forelimb development: insights from developmental disparity

Darcy L. Ross, Jonathan D. Marcot, Keith J. Betteridge, Nanette Nasone-Yoder, C. Scott Bailey, Karen E. Sears, Darcy Ross & Nanette Nascone-Yoder
Tetrapod limb development has been studied extensively for decades, yet the strength and role of developmental constraints in this process remains unresolved. Mammals exhibit a particularly wide array of limb morphologies associated with various locomotion modes and behaviors, providing a useful system for identifying periods of developmental constraint and conserved developmental mechanisms or morphologies. In this study, landmark-based geometric morphometrics are used to investigate levels and patterns of morphological diversity (disparity) among the developing forelimbs...

Data from: Rearing temperature influences adult response to changes in mating status

Erica L. Westerman, Antónia Monteiro & Erica Westerman
Rearing environment can have an impact on adult behavior, but it is less clear how rearing environment influences adult behavior plasticity. Here we explore the effect of rearing temperature on adult mating behavior plasticity in the butterfly Bicyclus anynana, a species that has evolved two seasonal forms in response to seasonal changes in temperature. These seasonal forms differ in both morphology and behavior. Females are the choosy sex in cohorts reared at warm temperatures (WS...

Data from: Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms

Benjamin E. R. Rubin & Corrie S. Moreau
Symbiosis—the close and often long-term interaction of species—is predicted to drive genome evolution in a variety of ways. For example, parasitic interactions have been shown to increase rates of molecular evolution, a trend generally attributed to the Red Queen Hypothesis. However, it is much less clear how mutualisms impact the genome, as both increased and reduced rates of change have been predicted. Here we sequence the genomes of seven species of ants, three that have...

Data from: Stable recombination hotspots in birds

Sonal Singhal, Ellen M. Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel M. Hooper, Alva I. Strand, Qiye Li, Brian Raney, Christopher N. Balakrishnan, Simon C. Griffith, Gil McVean & Molly Przeworski
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have...

Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians

Brandon L. Pierce, Lin Tong, Lin S. Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A. Baron, Muhammad G. Kibriya & Habibul Ahsan
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis-...

Data from: A framework phylogeny of the American oak clade based on sequenced RAD data

Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender-Bares, Elisabeth Fitzek, Rick Nipper & Paul S. Manos
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters....

Data from: When can clades be potentially resolved with morphology?

David W. Bapst
Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of...

Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago

Daniel R. Matute & Julien F. Ayroles
Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands...

Data from: Early and dynamic colonization of Central America drives speciation in Neotropical army ants

Max E. Winston, Daniel J. C. Kronauer & Corrie S. Moreau
The emergence of the Isthmus of Panama is one of the most important events in recent geological history, yet its timing and role in fundamental evolutionary processes remain controversial. While the formation of the isthmus was complete around 3 million years ago (Ma), recent studies have suggested prior intercontinental biotic exchange. In particular, the possibility of early intermittent land bridges facilitating colonization constitutes a potential mechanism for speciation and colonization before full closure of the...

Data from: Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), an early ray-finned fish

Sam Giles, Michael I. Coates, Russell J. Garwood, Martin D. Brazeau, Robert Atwood, Zerina Johanson & Matt Friedman
As the sister lineage of all other actinopterygians, the Middle to Late Devonian (Eifelian–Frasnian) Cheirolepis occupies a pivotal position in vertebrate phylogeny. Although the dermal skeleton of this taxon has been exhaustively described, very little of its endoskeleton is known, leaving questions of neurocranial and fin evolution in early ray-finned fishes unresolved. The model for early actinopterygian anatomy has instead been based largely on the Late Devonian (Frasnian) Mimipiscis, preserved in stunning detail from the...

Data from: Oldest known multituberculate stapes suggests an asymmetric bicrural pattern as ancestral for Multituberculata

Julia A. Schultz, Irina Ruf & Thomas Martin
Middle ear ossicles (malleus, incus, stapes) are known only for few multituberculate taxa, and three different stapedial morphotypes have been suggested: (1) slender, columelliform and microperforate, (2) robust and rod-like, and (3) bicrural. Reinvestigation of Upper Jurassic (Kimmeridgian) mammalian petrosals from the Guimarota coal mine in central Portugal (Western Europe) revealed an asymmetric bicrural stapes (ABS) in the paulchoffatiid Pseudobolodon oreas. The middle ear bones displaced inside the osseous vestibule were detected by a microCT...

Data from: Geographic patterns of song variation in four species of Malurus fairy-wrens

David D. Yandell, Wesley M. Hochachka, Stephen Pruett-Jones, Michael S. Webster & Emma I. Greig
Geographic variation in song is widespread among birds, particularly in species that learn vocalizations. The relationship between geographic distance and song variation is likely related to the degree of isolation between populations. To assess this effect of geographic isolation on song divergence, we examined patterns of geographic song variation in four species of Australian fairy-wrens (Malurus), two with suspected histories of geographic isolation and two without. Song variation in all four species was consistent with...

Data from: Reconstructing ecological niche evolution when niches are incompletely characterized

Erin E. Saupe, Narayani Barve, Hannah L. Owens, Jacob C. Cooper, Peter A. Hosner & A. Townsend Peterson
Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches...

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