263 Works

Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest

Cooper Rosin, Kendall Beals, Michael Belovitch, Ruby Harrison, Megan Pendred, Megan Sullivan, Nicolas Yao & John Poulsen
African forest elephants (Loxodonta cyclotis) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of...

Tree functional traits as predictors of microburst-associated treefalls in tropical wet forests

Alana Rader, Amy Cotrell, Anna Kudla, Tiffany Lum, David Henderson & Harshad Karandikar
On 19 May 2018 a microburst caused 600 isolated forest gaps in a Costa Rican tropical forest. We surveyed fallen and standing trees within gaps to determine if certain variables are associated with treefalls. Our results highlight considerations for future research to understand the impacts of microbursts in tropical forests. Our results show that at the scale and locality of our study, treefall vulnerability to microbursts and characteristics of fall events are independent of the...

Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution

Kate Ostevik, Kieran Samuk & Loren Rieseberg
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic...

Social relationships, social status, and survival in wild baboons: A tale of two sexes

Fernando Campos, Francisco Villavicencio, Elizabeth Archie, Fernando Colchero & Susan Alberts
People who are more socially integrated or have higher social status live longer, and recent studies on aging and social environments in mammals show some striking convergences with this human pattern. Nonhuman primates are especially valuable models of aging, and studies of several populations of wild primates have shown parallel results to human studies. Specifically, greater numbers and strength of social bonds and/or higher social dominance rank predict longer lifespan in females of several nonhuman...

A molecular phylogenetic evaluation of the Ramalina siliquosa complex, with notes on species circumscription and relationships within Ramalina

Scott LaGreca
Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and Southeast Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS RPB1 and RPB2)...

Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons

Shuxi Zeng
Code scripts for "Social bonds fail to mediate the connection between early adversity and fecal glucocorticoids in wild baboons ".

Sounds of senescence: Male swamp sparrows respond less aggressively to the song of older individuals

Matthew Zipple, Susan Peters, William Searcy & Stephen Nowicki
Age-related changes in assessment signals occur in a diverse array of animals, including humans. Age-related decline in vocal quality in humans is known to affect perceived attractiveness by potential mates and voters, but whether such changes have functional implications for non-human animals is poorly understood. Most studies of age-related change in animal signals focus on increases in signal quality that occur soon after the age of first breeding (“delayed maturation”), but a few have shown...

Data from: High fat diet induces microbiota-dependent silencing of enteroendocrine cells

John Rawls, Lihua Ye, Olaf Mueller, Jennifer Bagwell, Michel Bagnat & Rodger Liddle
Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here, we established a new experimental system to directly investigate EEC activity in vivo using a zebrafish reporter of EEC calcium signaling. Our results reveal that high fat feeding alters EEC morphology and converts them into a nutrient insensitive state that...

Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

William Morris
Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate...

Integrating climate adaptation and biodiversity conservation in the global ocean

Derek Tittensor, Maria Beger, Kristina Boerder, Daniel Boyce, Rachel Cavanagh, Aurelie Cosandey-Godin, Guillermo Crespo, Daniel Dunn, Wildan Ghiffary, Susie Grant, Lee Hannah, Pat Halpin, Mike Harfoot, Susan Heaslip, Nicholas Jeffery, Naomi Kingston, Heike Lotze, Jennifer McGowan, Elizabeth McLeod, Chris McOwen, Bethan O'Leary, Laurenne Schiller, Ryan Stanley, Maxine Westhead, Kristen Wilson … & Boris Worm
The impacts of climate change and the socioecological challenges they present are ubiquitous and increasingly severe. Practical efforts to operationalize climate-responsive design and management in the global network of marine protected areas (MPAs) are required to ensure long-term effectiveness for safeguarding marine biodiversity and ecosystem services. Here, we review progress in integrating climate change adaptation into MPA design and management and provide eight recommendations to expedite this process. Climate-smart management objectives should become the default...

Comparative skeletal anatomy of neonatal ursids and the extreme altriciality of the giant panda

Peishu Li & Kathleen Smith
Vertebrate neonates are born with a wide range of maturity at birth. Altricial newborns are born with limited sensory agency and require significant parental care, while precocial neonates are relatively mature physically and often capable of independent function. In extant mammals, placental newborns span this range, while marsupials and monotremes are all extremely altricial at birth. Bears (family Ursidae) have one of the lowest neonatal-maternal mass ratios in placental mammals and are considered to have...

Convergent evolution in lemur environmental niches

James Herrera
Aim: To test the hypothesis that adaptive convergent evolution of climate niches occurred in multiple independent lemur lineages. Location: Madagascar Taxon: Lemurs Methods: I collected climate and altitude data from WorldClim and summarized the niches of almost all living lemurs (83 species) into phylogenetically-controlled principal components. To test for convergent evolution, I searched for multiple, similar climate optima using multi-peak Ornstein-Uhlenbeck models (surface, l1-ou, bayou). I compared the observed level of climate convergence to that...

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Kelsie E Hunnicutt, George P Tiley, Rachel C Williams, Peter A Larsen, Marina B Blanco, Rodin M Rasoloarison, Christopher Ryan Campbell, Kevin Zhu, David W Weisrock, Hiroaki Matsunami & Anne D Yoder
Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within...

Data from: Multi-scale predictors of parasite risk in wild male savanna baboons (Papio cynocephalus)

Bobby Habig, David A.W.A.M. Jansen, Mercy Y. Akinyi, Laurence R. Gesquiere, Susan C. Alberts & Elizabeth A. Archie
Several factors are thought to shape male parasite risk in polygynous and polygynandrous mammals, including male-male competition, investment in potentially immunosuppressive hormones, and dispersal. Parasitism is also driven by processes occurring at larger scales, including host social groups and populations. To date, studies that test parasite-related costs of male behavior at all three scales—individual hosts, social groups, and the host population—remain rare. To fill this gap, we investigated multi-scale predictors of helminth parasitism in 97...

Data from: Eulerian videography technology improves classification of sleep architecture in primates

Emilie M. Melvin, David R. Samson & Charles L. Nunn
Sleep is a critically important dimension of primate behavior, ecology, and evolution, yet primate sleep is under-studied because current methods of analyzing sleep are expensive, invasive, and time-consuming. In contrast to electroencephalography (EEG) and actigraphy, videography is a cost-effective and non-invasive method to study sleep architecture in animals. With video data, however, it is challenging to score subtle changes that occur in different sleep states, and technology has lagged behind innovations in EEG and actigraphy....

Data from: A logical model of homology for comparative biology

Paula Mabee, James Balhoff, Wasila Dahdul, Hilmar Lapp, Christopher Mungall & Todd Vision
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry)...

Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).

Laurence R. Gesquiere, Toni E. Ziegler, Patricia A. Chen, Katherine A. Epstein, Susan C. Alberts & Jeanne Altmann
The development of non-invasive methods, particularly fecal determination, has made possible the assessment of hormone concentrations in wild animal populations. However, measuring fecal metabolites needs careful validation for each species and for each sex. We investigated whether radioimmunoassays (RIAs) previously used to measure fecal testosterone (fT) in male baboons and fecal estrogens (fE) in female baboons were well suited to measure these hormones in the opposite sex. We compared fE and fT concentrations determined by...

Data from: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, E. A. Archie, Laura E Grieneisen, Elizabeth A Archie, Susan C Alberts, Jeanne Altmann, Luis B Barreiro, Jean-Christophe Grenier, Michael B Burns & Ran Blekhman
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship,...

Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection

Carl J. Rothfels & Eric Schuettpelz
Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary...

Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Maggie R. Wagner, Derek S. Lundberg, Devin Coleman-Derr, Susannah G. Tringe, Jeffery L. Dangl & Thomas Mitchell-Olds
Plant phenology is known to depend on many different environmental variables, but soil microbial communities have rarely been acknowledged as possible drivers of flowering time. Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. Flowering time was sensitive to both microbes and the abiotic properties of different soils; varying soil microbiota also altered...

Data from: Long-term data reveal patterns and controls on streamwater chemistry in a forested stream: Walker Branch, Tennessee

Brian D. Lutz, Patrick J. Mulholland & Emily S. Bernhardt
We present 20 years of weekly streamwater chemistry, hydrology, and climate data for the Walker Branch watershed in eastern Tennessee, USA. Since 1989, the watershed has experienced a ~1.0˚C increase in mean annual temperature, a ~20% decline in precipitation, and a ~30% increase in forest evapotranspiration rates. As a result, runoff has declined by ~34%. We evaluate long-term trends in streamwater concentrations and fluxes for 9 solutes and use wet deposition data to calculate approximate...

Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony

Mira V. Han & Matthew W. Hahn
Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that...

Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen, Susanne Schulmeister, Debra L. Murray & Alexandr P. Rasnitsyn
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically,...

Data from: Self-organizing dominance hierarchies in a wild primate population

Mathias Franz, Emily McLean, Jenny Tung, Jeanne Altmann & Susan C. Alberts
Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The ‘prior attributes hypothesis’ posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the ‘social dynamics hypothesis’ posits that dominance ranks emerge from...

Data from: A framework for detecting natural selection on traits above the species level

Kenneth B. Hoehn, Paul G. Harnik & V. Louise Roth
To what extent can natural selection act on groupings above the species level? Despite extensive theoretical discussion and growing practical concerns over increased rates of global ecological turnover, the question has largely evaded empirical resolution. A flexible and robust hypothesis-testing framework for detecting the phenomenon could facilitate significant progress in resolving this issue. We introduce a permutation-based approach, implemented in the R package perspectev, which provides an explicit test of whether empirical patterns of correlation...

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