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Significance The process by which new complex traits evolve has been a persistent conundrum throughout the history of evolutionary inquiry. How multiple physiological changes at the organism level and genetic changes at the molecular level combine is still unclear for many traits. Here, we studied the displays of manakins, who beat their wings toge...
Hybridization often occurs at the parapatric range interface between closely related species, but fitness outcomes vary: hybrid offspring exhibit diverse rates of viability and reproduction compared with their parental species. The mobile hybrid zone between two chickadee congeners (Poecile atricapillus × Poecile carolinensis) has been well studied...
English common names are widely used in ornithological research, birding, media and by the general public and, unlike other taxa, often receive considerably greater use than scientific names. Across the world, many of these names were coined from 18th and 19th century European perspectives and are symbolic of a time when this was the only worldview...
Synopsis Third-generation (long-read–based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upward of thousands of...
The Hardy-Weinberg principle (HWP) is an application of the binomial expansion theorem that is foundational to the field of population genetics. Because of the important history of the HWP in answering how variation is preserved during evolution, and the ability of Hardy-Weinberg equilibrium (HWE) to detect natural and sexual selection acting on a...
How does a naive, young animal decide from which adults to learn behavior? Obligate brood parasitic birds, including brown-headed cowbirds (Molothrus ater), face a particular challenge in learning species-specific behaviors; they lay their eggs in the nest of another species, and juveniles are raised without exposure to adult conspecifics. Neverthe...
Eciton burchellii is a Neotropical army ant that influences the ecology of many associated animal species, including their prey and species that attend the ant's foraging raids. At least 29 bird species are obligate specialists on foraging at army ant raid fronts, and additional species across diverse avian orders follow army ant raids in a faculta...
Yellow-shafted Flickers (Colaptes auratus auratus subspecies group of the Northern Flicker) occasionally have orange to red flight feathers in eastern North America far from the hybrid zone with the Red-shafted Flicker (C. a. cafer subspecies group). Blocks of feathers of anomalous color tend to show bilateral symmetry and may differ from one year...
Sleep homeostasis, which refers to the maintenance of sleep amount or depth following sleep deprivation, indicates that sleep and sleep-like states serve fundamental functions that cannot be bypassed [1 • Cirelli C. • Tononi G. Is sleep essential?.PLoS Biol. 2008; 6: e216 • Crossref • PubMed • Scopus (323) • Google Scholar ]. Homeostasis of sleep...
The Academy of Natural Sciences of Philadelphia (ANSP) is the oldest continuously operating natural history museum in North America. Founded in 1812 by a small group of Philadelphians with a shared interest in natural history, the Academy has, over the last two centuries, grown into a premier institution for systematic and environmental research th...
I'm running r8s as part of the CAFE manual to create an ultrametric tree for CAFE input.
I need to run r8s using a Unix operating system, but the download only comes with an OS X executable file.
After adding to the path, when I run the r8s command, my error is
"cannot execute binary file"
I have added executable permission of the file, which is a potential source of this error.
Additionally, the manual says that after I untar the file, "This sets up a subdirectory called dist which has four subdirectories, bin, sample, doc, and src." In the 1.8 version of r8s, the dist directory opens up but the four subdirectories are not present. I have found answers online for solving this problem, but they rely on the subdirectories, which just flat out aren't there.
The manual speaks on the issue here as well,
"If you are working on another UNIX operating system (so the OS X executable is
obviously useless!), or if you are on OS X but wish to compile the program from its
source code, a makefile is included that works on Linux machines and OS X (assuming
you have installed FORTRAN correctly). There are known incompatibilities with some
other compiler's libraries or headers, most of which are easy to resolve. You should own
a copy of Numerical Recipes in C (Press et al. 1992 or more recent versions) to compile
and run from source."
The manual is attached.
But I am having difficulty deciphering this.