AIMC Topic: Phylogeny

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De novo transcriptome assembly of pummelo and molecular marker development.

PloS one
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...

Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.

Interdisciplinary sciences, computational life sciences
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...

Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.

PloS one
Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-le...

A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps.

Bioinformatics (Oxford, England)
MOTIVATION: Self-organizing maps (SOMs) are readily available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To inc...

phyddle: Software for Exploring Phylogenetic Models with Deep Learning.

Systematic biology
Phylogenies contain a wealth of information about the evolutionary history and process that gave rise to the diversity of life. This information can be extracted by fitting phylogenetic models to trees. However, many realistic phylogenetic models lac...

Divergent Clonal Evolution and Early Dissemination Promote Genetic Heterogeneity of Metastases in Castration-Resistant Prostate Cancer.

Cancer research
UNLABELLED: Lethal prostate cancer has passed through at least two evolutionary bottlenecks: acquisition of metastatic potential and development of castration resistance. A better understanding of how this affects genetic heterogeneity across metasta...

Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification.

Briefings in bioinformatics
With the rapid development of genomic sequencing technologies, there is an increasing demand for efficient and accurate sequence analysis methods. However, existing methods face challenges in handling long, variable-length sequences and large-scale d...

Towards the next generation of species delimitation methods: an overview of machine learning applications.

Molecular phylogenetics and evolution
Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, whether based on morphological, molecular, or o...

Premolar Ecomorphology in Anthropoid Primates: A Machine Learning Approach.

Journal of morphology
Reconstructing the diets of extinct taxa is essential for understanding their ecologies and evolutionary histories, yet traditional methods and proxies such as molar morphology have limited resolution. The potential of premolar morphology as a dietar...

Ultraviolet in swallowtail butterflies: contrasted dorso-ventral evolution highlights a trade-off between natural and sexual selection on visual cues.

Evolution; international journal of organic evolution
The evolutionary dynamics of color pattern diversification in animals is strongly influenced by visual interactions within and among species. While much attention has been given to color pattern variation in the human-visible range, perception outsid...