123 Works

Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data

Stuart C. Willis, Jason Macrander, Izeni P. Farias & Guillermo Orti
BACKGROUND: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the...

Data from: Sapwood capacitance is greater in evergreen sclerophyll species growing in high compared to low rainfall environments

Anna E. Richards, Ian J. Wright, Tanja I. Lenz & Amy E. Zanne
1. The capacitative release of water from sapwood allows photosynthesis to continue for longer into dry periods, both diurnally and seasonally. However, costs of high capacitance include increased vulnerability to xylem cavitation. The degree of reliance on stored water is predicted to differ among environments as a result of this trade off 2. Xylem water potential and sapwood capacitance were measured on 32 evergreen sclerophyll shrub and tree species in eastern Australia, sampled from four...

Data from: Assessment of disease progression in dysferlinopathy – a one year cohort study

Volker Straub, Ursula Moore, Marni Jacobs, Meredith K. James, Anna G. Mayhew, Roberto Fernandez-Torron, Jia Feng, Avital Cnaan, Michelle Eagle, Karen Bettinson, Laura E. Rufibach & Robert Muni Lofra
Objective: To assess the ability of functional measures to detect disease progression in dysferlinopathy over 6 months and 1 year. Methods: 193 patients with dysferlinopathy were recruited to the Jain Foundation’s International Clinical Outcome Study for Dysferlinopathy. Baseline, 6 months and 1 year assessments included: adapted North Star Assessment (a-NSAA), Motor Function Measure (MFM-20), timed function tests, 6 minute walk test (6MWT), Brooke Scale, Jebsen Test, manual muscle testing (MMT) and hand-held dynamometry (HHD). Patients...

Hair phenotype diversity across Indriidae lemurs

Elizabeth Tapanes, Rachel Jacobs, Ian Harryman, , Mitchell Irwin, Jason Kamilar & Brenda Bradley
Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials...

High-speed terrestrial substrate transitions: how a fleeing cursorial day gecko copes with compliance changes that are experienced in nature

Emily Naylor, Emily Naylor & Timothy Higham
1. Animal movement is often largely determined by abiotic conditions of the environment, including substrate properties. While a large body of work has improved our understanding of how different substrate properties can impact locomotor performance and behavior, few of these studies have investigated this relationship during transitions within a single locomotor event. 2. In nature, terrestrial animals frequently encounter substrate transitions, or changes in substrate level, incline, texture, and/or compliance during a single bout of...

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Matthew Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovjoy & Devin D. Bloom
Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using...

Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage

Benjamin Blanchard, Shauna Price, Scott Powell, Bonnie Blaimer & Corrie Moreau
Recent advances in phylogenomics allow for the use of large amounts of genetic information in phylogenetic inference. Ideally, the increased resolution and accuracy of such inferences facilitate improved understanding of macroevolutionary processes. Here, we integrate ultraconserved elements (UCEs) with fossil and biogeographic range data to explore diversification and geographic range evolution in the diverse turtle ant genus Cephalotes. We focus on the potential role of the uplift of the Panamanian land bridge and the putative...

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...

Nest choice in arboreal ants is an emergent consequence of network creation under spatial constraints

Matina Donaldson-Matasci, Joanna Chang, Scott Powell & Elva J. H. Robinson
Biological transportation networks must balance competing functional priorities. The self-organizing mechanisms used to generate such networks have inspired scalable algorithms to construct and maintain low-cost and efficient human-designed transport networks. The pheromone-based trail networks of ants have been especially valuable in this regard. Here, we use turtle ants as our focal system: In contrast to the ant species usually used as models for self-organized networks, these ants live in a spatially constrained arboreal environment where...

The geometry of resource constraint: an empirical study of the golden snub-nosed monkey

Rong Hou, Colin Chapman, Jessica Rothman, He Zhang, Kang Huang, Songtao Guo, Baoguo Li & David Raubenheimer
1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations. 2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (Rhinopithecus roxellana) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments. 3. We present a...

Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius

Luca Livraghi, Joseph J. Hanly, Ling Sheng Loh, Anna Ren, Ian A. Warren, Carolina Concha, Charlotte Wright, Jonah M. Walker, Jessica Foley, Henry Arenas-Castro, Arnaud Martin, William O. McMillan, Chris D. Jiggins, Steven M. Van Bellghem, Gabriela Montejo-Kovacevich, James J. Lewis, Micheal W. Perry, Zachary H. Goldberg, Laura H. Lopez, Riccardo Papa & Eva S.M. Van Der Heijden
In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions...

Data from: Systematics of the blindsnakes (Serpentes: Scolecophidia: Typhlopoidea) based on molecular and morphological evidence

Robert Alexander Pyron & Van Wallach
The blindsnake superfamily Typhlopoidea (Gerrhopilidae, Typhlopidae, and Xenotyphlopidae) is a diverse, widespread part of the global snake fauna. A recent systematic revision based on molecular phylogenetic analyses and some morphological evidence presented a preliminary solution to the non-monophyly of many previously recognized genera, but additional clarification is needed regarding the recognition of some species and genera. We rectify these problems here with a new molecular phylogenetic analysis including 95 of the 275 currently recognized, extant...

Data from: Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

João Filipe Riva Tonini, Karen H. Beard, Rodrigo Barbosa Ferreira, Walter Jetz & R. Alexander Pyron
Macroevolutionary rates of diversification and anthropogenic extinction risk differ vastly throughout the Tree of Life. This results in a highly heterogeneous distribution of Evolutionary distinctiveness (ED) and threat status among species. We examine the phylogenetic distribution of ED and threat status for squamates (amphisbaenians, lizards, and snakes) using fully-sampled phylogenies containing 9574 species and expert-based estimates of threat status for ~ 4000 species. We ask whether threatened species are more closely related than would be...

Data from: A quantitative method for inferring locomotory shifts in amniotes during ontogeny, its application to dinosaurs, and its bearing on the evolution of posture

Kimberley E. J. Chapelle, Roger B. J. Benson, Josef Stiegler, Alejandro Otero, Qi Zhao & Jonah N. Choiniere
Evolutionary transitions between quadrupedal and bipedal postures are pivotal to the diversification of amniotes on land, including in our own lineage (Hominini). Heterochrony is suggested as a macroevolutionary mechanism for postural transitions, but understanding postural evolution in deep time is hindered by a lack of methods for inferring posture in extinct species. Dinosaurs are an excellent natural laboratory for understanding postural transitions, because their lineage contains at least four instances of quadrupedality evolving from bipedality,...

Data from: Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

R. Alexander Pyron, Catriona R. Hendry, Vincent M. Chou, Emily M. Lemmon, Alan R. Lemmon & Frank T. Burbrink
Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, M. Islam & Z. C. Hou
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: Does increased heat resistance result in higher susceptibility to predation? A test using (Drosophila melanogaster) selection and hardening

Sandra Hangartner, Ian Dworkin, Michael DeNieu & Ary A. Hoffmann
Heat resistance of ectotherms can be increased both by plasticity and evolution, but these effects may have trade-offs resulting from biotic interactions. Here we test for predation costs in Drosophila melanogaster populations with altered heat resistance produced by adult hardening and directional selection for increased heat resistance. In addition, we also tested for genetic trade-offs by testing heat resistance in lines that have evolved under increased predation risk. We show that while 35/37°C hardening increases...

Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: Ecological fidelity of functional traits based on species presence-absence in a modern mammalian bone assemblage (Amboseli, Kenya)

Joshua H. Miller, Anna Kay Behrensmeyer, Andrew Du, S. Kathleen Lyons, David Patterson, Anikó Tóth, Amelia Villaseñor, Erustus Kanga & Denné Reed
Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for...

Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years

Yi Hu, Catherine D’Amelio, Benoît Béchade, Christian Cabuslay, Piotr Lukasik, Jon Sanders, Shauna Price, Emily Fanwick, Scott Powell, Corrie Moreau & Jacob Russell
Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus Cephalotes. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that Cephalotes...

Speciation hypotheses from phylogeographic delimitation yield an integrative taxonomy for Seal Salamanders (Desmognathus monticola)

Robert Pyron, Kyle O'Connell, Sophie Duncan, Frank Burbrink & David Beamer
Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases; a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly...

Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)

Robert Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon & David A. Beamer
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 “candidate species” presenting a complex history of...

Detection of prey odors underpins dietary specialization in a Neotropical top-predator: how army ants find their ant prey

John Manubay & Scott Powell
1. Deciphering the mechanisms that underpin dietary specialization and niche partitioning is crucial to understanding the maintenance of biodiversity. New world army ants live in species-rich assemblages throughout the Neotropics and are voracious predators of other arthropods. They are therefore an important and potentially informative group for addressing how diverse predator assemblages partition available prey resources. 2. New World army ants are largely specialist predators of other ants, with each species specializing on different ant...

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Rebecca Prescott, Tatyana Zamkovaya, Stuart Donachie, Diana Northup, Joseph Mendley, Natalia Monsalve, Jimmy Saw, Alan Decho, Patrick Chain & Penelope Boston
Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing...

Data from: When are adaptive radiations replicated in areas? Ecological opportunity and unexceptional diversification in West Indian dipsadine snakes (Colubridae: Alsophiini)

Frank T. Burbrink, Sara Ruane & Robert Alexander Pyron
AIM: We examine diversification in Caribbean alsophiine snakes and hypothesize that, given ecological opportunity presented by colonizing the West Indies, alsophiines should show the signature of an early burst of diversification and associated low-within clade ecological and morphological disparification. We also test if changes in morphology or ecology are associated with changes in diversification rate, as trait-dependent diversification is hypothesized to affect historical inferences of diversification and disparification. Finally, as replicated radiations are found across...

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