23 Works

DEPP: Deep learning enables extending species trees using single genes

Yueyu Jiang, Metin Balaban, Qiyun Zhu & Siavash Mirarab
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. However, existing placement methods have a fundamental limitation: they assume that query sequences have evolved using specific models directly on the reference phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA amplicons) onto their own gene tree. This practice is a proxy for a more ambitious goal: extending a (genome-wide) species tree given data from individual genes. No algorithm...

Associated data files and scripts for 'Ancestry-inclusive dog genomics challenges popular breed stereotypes'

Kathleen Morrill, Jessica Hekman, Xue Li, Jesse McClure, Brittney Logan, Mingshi Gao, Yinan Dong, Marjie Alonso, Elena Carmichael, Noah Snyder-Mackler, Jacob Alonso, Hyun Ji Noh, Jeremy Johnson, Michele Koltookian, Charlie Lieu, Kate Megquier, Ross Swofford, Jason Turner-Maier, Michelle White, Zhiping Weng, Andrés Colubri, Diane Genereux, Kathryn Lord & Elinor Karlsson
Behavioral genetics in dogs has focused on modern breeds, isolated subgroups <200 years old with distinctive physical, and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,371 purebred and mixed-breed dogs, and densely genotyping (~45 million markers) a subset of 2,155 dogs. Most behavioral traits are heritable (h2>25%), and admixture patterns in mixed-breed dogs can reveal breed propensities. However, breed poorly predicts an individual purebred dog’s behavioral phenotype, explaining just 9% of...

Evolutionary causes and consequences of ungulate migration

Joel Abraham, Nathan Upham, Alejandro Damian-Serrano & Brett Jesmer
Ungulate migrations are crucial for maintaining abundant populations and functional ecosystems. However, little is known about how or why migratory behavior evolved in ungulates. To investigate the evolutionary origins of ungulate migration, we employed phylogenetic path analysis using a comprehensive species-level phylogeny of mammals. We found that 95 of 207 extant ungulate species are at least partially migratory, with migratory behavior originating independently in 17 lineages. The evolution of migratory behavior is associated with reliance...

The global distribution of known and undiscovered ant biodiversity

Jamie Kass, Benoit Guénard, Kenneth Dudley, Clinton Jenkins, Fumika Azuma, Brian Fisher, Catherine Parr, Heloise Gibb, John Longino, Philip Ward, Anne Chao, David Lubertazzi, Michael Weiser, Walter Jetz, Robert Guralnick, Rumsaïs Blatrix, James Des Lauriers, David Donoso, Christos Georgiadis, Kiko Gomez, Peter Hawkes, Robert Johnson, John Lattke, Joe MacGown, William Mackay … & Evan Economo
Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their...

Mobility Transition Model - excerpt from 2018 Decision Theatre scenario data

Andreas Geiges, Steffen Fürst, Gesine Steudle, Sarah Wolf & Carlo Jaeger

Individual and collective encoding of risk in animal groups

Matthew M.G. Sosna, Colin R. Twomey, Joseph Bak-Coleman, Winnie Poel, Bryan C. Daniels, Pawel Romanczuk & Iain D. Couzin
The need to make fast decisions under risky and uncertain conditions is a widespread problem in the natural world. While there has been extensive work on how individual organisms dynamically modify their behavior to respond appropriately to changing environmental conditions (and how this is encoded in the brain), we know remarkably little about the corresponding aspects of collective information processing in animal groups. For example, many groups appear to show increased “sensitivity” in the presence...

Data from: Environmental controls on African herbivore responses to landscapes of fear

Andrew Davies, Joris Cromsigt, Craig Tambling, Elizabeth Le Roux, Nicholas Vaughn, Dave Druce, David Marneweck & Gregory Asner
Herbivores balance forage acquisition with the need to avoid predation, often leading to tradeoffs between forgoing resources to avoid areas of high predation risk, or tolerating increased risk in exchange for improved forage. The outcome of these decisions is likely to change with varying resource levels, with herbivores altering their response to predation risk across heterogeneous landscapes. Such contrasting responses will alter the strength of non-consumptive predation effects, but are poorly understood in multiple- predator/multiple-prey...

Data from: Habitat isolation reduces intra- and interspecific biodiversity and stability

Christopher Steiner & Mitra Asgari
Fragmentation is predicted to reduce biodiversity and stability by increasing habitat isolation and impeding dispersal among patches. These effects may manifest at both the interspecific and intraspecific levels, yet few studies have simultaneously explored dispersal effects across levels of organization. We used field mesocosm experiments to examine how habitat isolation (in the form of dispersal rate) alters inter- and intraspecific stability and diversity in local zooplankton communities. We observed effects of increasing dispersal rate at...

Improving landscape-scale productivity estimates by integrating trait-based models and remotely-sensed foliar-trait and canopy-structural data

Daniel Wieczynski, Sandra Diaz, Sandra Duran, Nikolaos Fyllas, Norma Salinas, Roberta Martin, Alexander Shenkin, Miles Silman, Gregory Asner, Lisa Bentley, Yadvinder Malhi, Brian Enquist & Van Savage
Assessing the impacts of anthropogenic degradation and climate change on global carbon cycling is hindered by a lack of clear, flexible, and easy-to-use productivity models along with scarce trait and productivity data for parameterizing and testing those models. We provide a simple solution: a mechanistic framework (RS-CFM) that combines remotely-sensed foliar-trait and canopy-structural data with trait-based metabolic theory to efficiently map productivity at large spatial scales. We test this framework by quantifying net primary productivity...

A new genus of treeshrew and other micromammals from the middle Miocene hominoid locality of Ramnagar, Udhampur District, Jammu & Kashmir, India

Ramesh Sehgal, Abhishek Singh, Christopher Gilbert, Biren Patel, Christopher Campisano, Keegan Selig, Rajeev Patnaik & Ningthoujam Premjit Singh
The fossil record of treeshrews, hedgehogs, and other micromammals from the Lower Siwaliks of India is sparse. Here, we report on a new genus and species of fossil treeshrew, specimens of the hedgehog Galerix, and other micromammals from the middle Miocene (Lower Siwalik) deposits surrounding Ramnagar (Udhampur District, Jammu & Kashmir), at a fossil locality known as Dehari. The treeshrew from Dehari (Sivatupaia ramnagarensis gen. nov. et sp. nov.) currently represents the oldest record of...

Data to accompany: Seedling responses to soil moisture amount versus pulse frequency in a dominant semi-arid shrub

Ashley Davis, Kevin Hultine, Osvaldo Sala & Heather Throop
The timing, frequency and quantity of rainfall is rapidly changing in dryland regions, leading to profound alterations to dryland plant communities. Understanding dryland plant responses to future rainfall scenarios is crucial for implementing proactive management strategies, particularly in light of intensive changes to land cover concurrent with climate change. One such change is woody plant encroachment, an increasing abundance of woody plant species in areas formerly dominated by grasslands or savannas. The continued encroachment of...

Physiological status is a stronger predictor of nutrient selection than ambient plant nutrient content for a wild herbivore

Marion Le Gall
There is generally a close relationship between a consumer's food and its optimal nutrients. When there is a mismatch, it is hypothesized that mobile herbivores switch between food items to balance nutrients, however, there are limited data for field populations. In this study, we measured ambient plant nutrient content at two time points and contrasted our results with the nutrient ratio selected by wild female and male grasshoppers (Oedaleus senegalensis). Few plants were near O....

Hemotological and morphometric measurements from geladas

Kenneth L. Chiou, Mareike C. Janiak, India A. Schneider-Crease, Sharmi Sen, Ferehiwot Ayele, Idrissa S. Chuma, Sascha Knauf, Alemayehu Lemma, Anthony V. Signore, Anthony M. D’Ippolito, Belayneh Abebe, Abebaw Azanaw Haile, Fanuel Kebede, Peter J. Fashing, Nga Nguyen, Colleen McCann, Marlys L. Houck, Jeffrey D. Wall, Andrew S. Burrell, Christina M. Bergey, Jeffrey Rogers, Jane E. Phillips-Conroy, Clifford J. Jolly, Amanda D. Melin, Jay F. Storz … & Noah Snyder-Mackler
Primates have adapted to numerous environments and lifestyles but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of haematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers...

Highly resolved papilionoid legume phylogeny based on plastid phylogenomics

In-Su Choi, Domingos Cardoso, Luciano Queiroz, Haroldo Lima, Chaehee Lee, Tracey Ruhlman, Robert Jansen & Martin Wojciechowski
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae,...

Species-level tree crown maps improve predictions of tree recruit abundance in a tropical landscape

Cristina Barber, Sarah Graves, Jefferson Hall, Pieter Zuidema, Jodi Brandt, Stephanie Bohlman, Gregory Asner, Mario Bailón & T. Trevor Caughlin
Predicting forest recovery at landscape scales will aid forest restoration efforts. The first step in successful forest recovery is tree recruitment. Forecasts of tree recruit abundance, derived from the landscape-scale distribution of seed sources (i.e. adult trees), could assist efforts to identify sites with high potential for natural regeneration. However, previous work has revealed wide variation in the effect of seed sources on seedling abundance, from positive to no effect. We quantified the relationship between...

Data for: The correlated evolution of foraging mode and reproductive output in lizards

Dylan Padilla, Dale DeNardo & Michael Angilletta
Life-history theory suggests that the optimal reproductive output of an organism is affected by factors such as energy acquisition and predation risk. The observation that some organisms actively search for their prey and others ambush them creates the expectation of different energy needs and predation risk associated with each foraging behavior, the so-called “foraging-mode paradigm”. Although this paradigm has been around for decades, the empirical evidence consists of conflicting results derived from competing models based...

The thermal performance curve for aerobic metabolism of a flying endotherm

Jordan Glass & Jon Harrison
Performance benefits of stable, warm muscles are believed to be important for the evolution of endothermy in mammals, birds, and flying insects. However, thermal performance curves have never been measured for a free-flying endotherm, as it is challenging to vary body temperatures of these animals, and maximal flight performance is difficult to elicit. We varied air temperatures and gas densities to manipulate thoracic temperatures of flying honey bees from 29-44°C, with low air densities used...

Body and wing morphology, flight metabolic rates, and wingbeat frequencies for 13 stingless bee species

Jon Harrison, Meghan Duell, David Roubik & C. Jaco Klok
Understanding the effect of body size on flight costs is critical for development of models of aerodynamics and animal energetics. Prior scaling studies that have shown that flight costs scale hypometrically have focused primarily on larger (> 100 mg) insects and birds, but most flying species are smaller. We studied the flight physiology of thirteen stingless bee species over a large range of body sizes (1-115 mg). Metabolic rate during hovering scaled hypermetrically (scaling slope...

Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq

Jessica Warren
Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in Sileneae species and Arabidopsis thaliana. We investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage Sileneae that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as...

Data and code from: Correlates of individual participation in boundary patrols by male chimpanzees

Anthony Massaro, Ian Gilby, Nisarg Desai, Alexander Weiss, Joseph Feldblum, Anne Pusey & Michael Wilson
Group territory defense poses a collective action problem: individuals can free-ride, benefiting without paying the costs. Individual heterogeneity has been proposed to solve such problems, as individuals high in reproductive success, rank, fighting ability, or motivation may benefit from defending territories even if others free-ride. To test this hypothesis, we analyzed 30 years of data from chimpanzees (Pan troglodytes) in the Kasekela community, Gombe National Park, Tanzania (1978-2007). We examined the extent to which individual...

Generational variation in nutrient regulation for an outbreaking herbivore

Marion Le Gall
Multivoltine insects can produce multiple generations in one year. Favorable conditions support more generations, leading to serious outbreaks. For herbivores, plant nutrient availability is a major environmental factor affecting fitness and it can shift substantially throughout seasons. In a stochastic environment, organisms can adopt several strategies to regulate their nutrient intake and maximize performance. However, data regarding nutrient regulation of wild herbivores are scarce, and even more so regarding potential intergenerational plasticity. To bridge this...

Supplementary materials: Return of the pika: American pikas re-occupy long-extirpated, warm locations

Constance Millar & Andrew Smith
To accompany: Return of the pika: American pikas re-occupy long-extirpated, warm locations by Constance I. Millar and Andrew T. Smith, Nature Notes. American pika re-colonization sites identified in this study Bodie State Historic Park – Noonday Mine 38.004 N; -119.1005 W; 2,615 m Site also clearly identified in maps in Smith (1974a), Smith & Gilpin (1997), Smith & Nagy (2015). North Mono Craters Site 37.9116 N; -118.9985 W; 2,145-2,250 m

Macroclimatic and maternal effects on the evolution of reproductive traits in lizards

Dylan Padilla & Michael Angilletta
Much of life-history theory rests on fundamental assumptions about constraints on the acquisition and allocation of energy to growth and reproduction. In general, the allocation of energy to reproduction depends on maternal size, which in turn depends on environmental factors experienced throughout the life of the mother. Here, we used phylogenetic path analyses to evaluate competing hypotheses about the environmental and maternal drivers of reproductive traits in lizards. In doing so, we discovered that precipitation,...

Registration Year

  • 2022

Resource Types

  • Dataset


  • Arizona State University
  • University of Michigan–Ann Arbor
  • Duke University
  • Princeton University
  • University of Florida
  • Smithsonian Tropical Research Institute
  • Harvard University
  • Pontifical Catholic University of Peru
  • Instituto Geofísico de la Escuela Politécnica Nacional
  • City University of New York