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Article
Open AccessBifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools
Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-end...
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Article
Federated learning and Indigenous genomic data sovereignty
Indigenous peoples are under-represented in genomic datasets, which can lead to limited accuracy and utility of machine learning models in precision health. While open data sharing undermines rights of Indigen...
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Open AccessThe gut microbiome of exudivorous marmosets in the wild and captivity
Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild...
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Article
Open AccessGenie: an interactive real-time simulation for teaching genetic drift
Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is especially challenging. Here we present Genie, a browser-based educational tool that demo...
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Article
Open AccessGenomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates
The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few gene...
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Open AccessMitogenomic phylogeny of Callithrix with special focus on human transferred taxa
Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have b...
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Open AccessThe importance of selection in the evolution of blindness in cavefish
Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation...
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Article
Open AccessA composite genome approach to identify phylogenetically informative data from next-generation sequencing
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homolo...
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DeNovoGear: de novo indel and point mutation discovery and phasing
The DeNovoGear software detects de novo point mutations and indels with high specificity in familial and somatic tissue sequence data.
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Comparative population genomics of maize domestication and improvement
Jeff Ross-Ibarra and colleagues report a population genomic analysis of maize evolution. They analyze genome-wide evidence for selection during the initial domestication of wild maize and during the improvemen...
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Bards, Poets, and Cliques: Frequency-Dependent Selection and the Evolution of Language Genes
The ability of humans to communicate via language is a complex, adapted phenotype, which undoubtedly has a recently evolved genetic component. However, the evolutionary dynamics of language-associated alleles ...
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Open AccessThe multiple personalities of Watson and Crick strands
In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two ter...
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Article
Open AccessPICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination
We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence i...
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Open AccessLogarithmic gap costs decrease alignment accuracy
Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologic...
