Štrbac, Ljuba Dedović, Nebojša Trivunović, Snežana Janković, Dobrila Šaran, Momčilo Stanojević, Dragan Đedović, Radica Pracner, Doni
Published in
Contemporary Agriculture
This research aims to estimate heritability and repeatability based on the data on milk production traits (MY – milk yield; FY – milk fat yield; FC – milk fat content; PY – milk protein yield and PC – milk protein content) as well as pedigree and genomic information. A total of 6,041 animals were included in the research, while 2,565 of them had da...
Di Lecce, Irene Perrier, Charles Szulkin, Marta Sudyka, Joanna
Most of what is known about extra-pair paternity in hole-nesting birds derives from studies using artificial nesting sites, such as nestboxes. However, it has rarely been investigated whether inference drawn from breeding events taking place in nestboxes matches what would be observed under natural conditions, that is, in natural cavities. We here ...
Suetsugu, Kenji Hirota, Shun K. Hayakawa, Hiroshi Fujimori, Shohei Ishibashi, Masayuki Hsu, Tian-Chuan Suyama, Yoshihisa
Published in
Journal of Plant Research
The systematics of the Old World Spiranthes sinensis (Pers.) Ames species complex (Orchidaceae) has been complicated by its wide distribution and morphological variations. Within the species complex, S. australis Lindl. has been generally accepted as the only Spiranthes Rich. species distributed on the Japanese mainland. The present study provides ...
Sanchez, Théophile Bray, Erik Madison Jobic, Pierre Guez, Jérémy Letournel, Anne-Catherine Charpiat, Guillaume Cury, Jean Jay, Flora
Published in
Bioinformatics
Motivation We present dnadna , a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural networks designed for population genetic data. Results dnadna defines multiple user-friendly workflows. First, use...
Suetsugu, Kenji Hirota, Shun K. Hsu, Tian-Chuan Kurogi, Shuichi Imamura, Akio Suyama, Yoshihisa
Published in
Journal of Plant Research
Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum , with the monotypic species M. humile , has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrativ...
Tian, Xiao-Ling Ma, Yong-Peng
Published in
Frontiers in Genetics
Barrett, Craig F Santee, Mathilda V Fama, Nicole M Freudenstein, John V Simon, Sandra J Sinn, Brandon T
Published in
Molecular ecology
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts p...
Nußberger, Jens Boesel, Frederic Lenz, Stefan Binder, Harald Hess, Moritz
Published in
Briefings in bioinformatics
Deep generative models can be trained to represent the joint distribution of data, such as measurements of single nucleotide polymorphisms (SNPs) from several individuals. Subsequently, synthetic observations are obtained by drawing from this distribution. This has been shown to be useful for several tasks, such as removal of noise, imputation, for...
de Jong, Menno J. de Jong, Joost F. Hoelzel, A.R. Janke, Axel
SNP data sets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time-consuming and challenging process, not in the least because at present many different software packages are needed to...
López, María Eugenia Linderoth, Tyler Norris, Ashie Lhorente, Jean Paul Neira, Roberto Yáñez, José Manuel
Published in
Frontiers in Genetics
Domestication of Atlantic salmon started approximately 40 years ago, using artificial selection through genetic improvement programs. Selection is likely to have imposed distinctive signatures on the salmon genome, which are often characterized by high genetic differentiation across population and/or reduction in genetic diversity in regions associ...
