51 Works

Phytogeographic history of the Tea family inferred through high-resolution phylogeny and fossils

Yujing Yan, Charles Davis, Dimitar Dimitrov, Zhiheng Wang, Carsten Rahbek & Michael Borregaard
The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular...

Estimating the Net Value of Treating Hepatitis C Virus Using Newly Available Direct-Acting Antivirals in India (Supporting Datasets)

David Bloom, Alex Khoury & V. Srinivasan
Recently developed direct-acting antiviral (DAA) treatments for hepatitis C virus (HCV) have been groundbreaking for their high efficacy across disease genotypes and lack of severe side effects. This study uses a cost-of-illness (COI) approach to estimate the net value conferred by this class of drugs using the cost and efficacy of one of these novel drug combinations, sofosbuvir and velpatasvir (SOF/VEL), recently licensed for generic manufacture in India. This study considers COI of lifetime earnings...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
We report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue sections to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with...

Mirror Images: Performing a format migration of Kodak PhotoCD files

Tricia Patterson
Harvard Library’s repository holds over 3,800 still images with Kodak PhotoCD files as their preservation copy. Originally deposited in the early 2000s, when the proprietary format was still considered a sustainable option, support for PhotoCD has declined in the past two decades. Tools that can accurately render and convert the format are increasingly scarce, and the window of time for generating new high-quality preservation copies of these archival objects narrows each year. In-depth color space...

Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

Ricardo Medina, Ella Vázquez-Domínguez, Guinevere O.U. Wogan, Ke Bi, Flavia Termignoni-García, Manuel Hernando Bernal, Juan P. Jaramillo-Correa & Ian J. Wang
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioral and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the emerald-eyed treefrog, Boana platanera, distributed...

Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies

Yuttapong Thawornwattana, Fernando Seixas, Ziheng Yang & James Mallet
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer...

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe & Tereza Jezkova
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore...

Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Claudius Kratochwil, Andreas Kautt, Alexander Nater, Andreas Härer, Yipeng Liang, Frederico Henning & Axel Meyer
Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remained elusive. Here, we aimed to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic “dark morph”, about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous “gold morph”. Using a new haplotype-resolved long-read...

The AI Economist: Taxation policy design via two-level deep reinforcement learning

Stephan Zheng, Alexander Trott, Sunil Srinivasa, David Parkes & Richard Socher
This dataset contains all raw experimental data for the paper "The AI Economist: Taxation Policy Design via Two-level Deep Multi-Agent Reinforcement Learning". The accompanying simulation, reinforcement learning, and data visualization code can be found at https://github.com/salesforce/ai-economist. For the one-step economy experiments, we provide: training histories, configuration files (these experiments do not use phases), and final agent and planner models. For the Gather-Trade-Build scenario, the data covers 6 spatial layouts: two Open-Quadrant (with 4 and 10...

DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Gerard Talavera, Vladimir Lukhtanov, Naomi Pierce & Roger Vila
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts...

Exploration of marine lichenized fungi as bioindicators of coastal ocean pollution in the Boston Harbor Islands National Recreation Area

Liam Nokes, Danny Haelewaters & Donald Pfister
This preliminary exploration of marine lichenized fungi (lichens) as bioindicators of water pollution examined the distribution of intertidal lichen communities in the Boston Harbor Islands National Recreation Area with respect to recorded pollution throughout the harbor. We found significant negative associations between pollution measurements and the health of the lichen community based on cover and species richness. We also observed significant differences in species composition between areas of higher pollution and areas of lower pollution,...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution

Andrew Yegian, Yanish Tucker, Stephen Gillinov & Daniel Lieberman
This file provides the data from the manuscript "Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution" sin the American Journal of Physical Anthropology. Objectives: Brachial index is a skeletal ratio that describes the relative length of the distal forelimb. Over the course of hominin evolution, a shift towards smaller brachial indices occurred. First, Pleistocene australopiths yield values between extant chimpanzees and humans, with further evolution in Pliocene Homo to...

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 for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Orality and Literacy. Unmarked and Marked Elements in Verbal Communication

Gregory Nagy

Zebrafish larvae exploration and aversive chemotaxis dataset

Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat & Claire Wyart
This dataset contains recordings of larval zebrafish behavior. The full details are described in the paper "A lexical approach for identifying behavioral action sequences". The experiment investigates zebrafish larvae behavior in free swimming and aversive chemotaxis conditions. In each experiment, 12 larvae (7 dpf) are placed in 12 rectangular wells. Ten min-long videos were recorded at 160 Hz with an exposure time of 1 ms, and a pixel size of 70 µm using a ViewWorks...

Investigating sources of conflict in deep phylogenomics of vetigastropod snails

Tauana Cunha, James Reimer & Gonzalo Giribet
Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 million years ago, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity...

Supplementary results for: Visit-to-visit blood pressure variability, neuropathology and cognitive function

Yuan Ma
Objective Large systolic blood pressure (SBP) variability has been proposed as a novel risk factor for dementia above and beyond SBP levels, but the underlying neuropathology is largely unknown. We investigated the relationship among visit-to-visit SBP variability, cognitive deterioration and underlying neuropathological changes. Methods We used longitudinal data (between 2005 and 2019) from the National Alzheimer’s Coordinating Center. 13,284 dementia-free participants aged≥50 years were followed over a median of 5.0 (interquartile range: 3.1-7.6) years. Neuropathology...

Convergence of undulatory swimming kinematics across a diversity of fishes

Elsa Goerig, Valentina Di Santo, Dylan K. Wainwright, Theodore Castro-Santos, James Liao, Otar Akanyeti & George Lauder
Fishes exhibit an astounding diversity of locomotor behaviors, from classic swimming with their body and fins to jumping, flying, walking, and burrowing. Fishes that use their body and caudal fin (BCF) during undulatory swimming have been traditionally divided into modes based on the length of the propulsive body wave and the ratio of head:tail oscillation amplitude: anguilliform, sub-carangiform, carangiform and thunniform. This classification was first proposed based on key morphological traits, such as body stiffness...

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

Andrew Ontano, Guilherme Gainett, Shlomi Aharon, Jesús Balesteros, Ligia Benavides, Kevin Corbett, Efrat Gavish-Regev, Mark Harvey, Scott Monsma, Carlos Santibáñez-López, Emily Setton, Jakob Zehms, Jeanne Zeh, David Zeh & Prashant Sharma
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch...

Data: Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere

Aaron A. Comeault, Andreas F. Kautt & Daniel R. Matute
Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced ranges of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales....

Long-term dietary flavonoid intake and subjective cognitive decline in US men and women

Tian-Shin Yeh, Changzheng Yuan, Alberto Ascherio, Bernard Rosner, Walter Willett & Deborah Blacker
Objective: To prospectively examine the associations between long-term dietary flavonoids and subjective cognitive decline (SCD). Methods: We followed 49,493 women from the Nurses’ Health Study (NHS) (1984-2006) and 27,842 men from the Health Professionals Follow-up Study (HPFS) (1986-2002). Poisson regression was used to evaluate the associations between dietary flavonoids (flavonols, flavones, flavanones, flavan-3-ols, anthocyanins, polymeric flavonoids, and proanthocyanidins) and subsequent SCD. For the NHS, long-term average dietary intake was calculated from seven repeated food frequency...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Data from: Developmental origins of the crocodylian skull table and platyrostral face

Zachary S. Morris, Kent A. Vliet, Arhat Abzhanov & Stephanie E. Pierce
The dorsoventrally flattened skull typifies extant Crocodylia perhaps more than any other anatomical feature and is generally considered an adaptation for semi-aquatic feeding. Although the evolutionary origins have been extensively studied, the developmental origins of craniofacial flattening have yet to be explored. To understand how the skull table and platyrostral snout develop, we quantified embryonic development and post-hatching growth (ontogeny) of the crocodylian skull in lateral view using geometric morphometrics. Our dataset (n=103) includes all...

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Affiliations

  • Harvard University
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  • Yale University
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  • Zhejiang University
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  • University of Washington
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  • Stanford University
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  • Botanical Institute of Barcelona
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  • University of California, San Diego
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  • University of Nevada Reno
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  • National Autonomous University of Mexico
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