Article
Evolutionary Biology
Sophia Lambert, Jakub Voznica, Helene Morlon
Summary: In this paper, the authors propose a deep learning approach for inference of birth-death models and their extensions to include trait data. The approach demonstrates high accuracy and time efficiency in various models, and its application to the phylogeny of primates showcases its potential in the field.
SYSTEMATIC BIOLOGY
(2023)
Article
Evolutionary Biology
Xiao-Xu Pang, Da-Yong Zhang
Summary: This study examines the impact of ghost introgression on species tree estimations and found that many results obtained for introgression between extant species can be extended to ghost introgression. The performance of summary species tree method (ASTRAL) and full-likelihood method (*BEAST) varies under different introgression scenarios. When an outgroup ghost acts as the donor of introgressed genes, the time of root divergence is generally overestimated, while ingroup introgression leads to underestimation. The accuracy of root divergence estimation is higher with stronger incomplete lineage sorting (ILS), although the topology of the species tree is more prone to be biased by introgression.
SYSTEMATIC BIOLOGY
(2023)
Article
Business
Lee Roberts, Monomita Nandy, Abeer Hassan, Suman Lodh, Ahmed A. Elamer
Summary: This study contributes to the literature by examining the relationship between corporate accountability in species protection and factors affecting such accountability. Results show positive relations between ecologically conscious companies and external assurance, environmental performance, partnerships with socially responsible organizations, and awards for sustainable activities. The findings are robust and can guide policymakers and stakeholders in making better decisions in responding to environmental challenges.
JOURNAL OF BUSINESS ETHICS
(2022)
Article
Genetics & Heredity
Ivana Matera, Domenico Bordo, Marco Di Duca, Margherita Lerone, Giuseppe Santamaria, Marta Pongiglione, Antonella Lezo, Antonella Diamanti, Maria Immacolata Spagnuolo, Alessio Pini Prato, Daniele Alberti, Girolamo Mattioli, Paolo Gandullia, Isabella Ceccherini
Summary: This study identified variants in the ACTG2 gene in 11 patients, with four carrying novel missense variants and four carrying variants affecting arginine residues, with de novo occurrence confirmed in six families.
The 3D molecular modeling of ACTG2 variants in patients provides further insights into the effects on enteric muscle contraction, improving understanding of visceral myopathies and implications for genetic counseling in severe disorders related to intestinal pseudo-obstruction.
Article
Multidisciplinary Sciences
Md Amdadul Haque, Jonaira Rashid, Md Lipon Mia, Md Khaled Rahman, Md Azhar Ali, Anuradha Bhadra, Yahia Mahmud
Summary: This study confirms the presence of a new species of Mahseer, called Tor barakae, in the Sangu River basin in Bangladesh through DNA identification techniques.
Article
Astronomy & Astrophysics
Janis Fluri, Tomasz Kacprzak, Alexandre Refregier, Aurelien Lucchi, Thomas Hofmann
Summary: The paper proposes a novel approach to construct parameter estimators using deep summary statistics and demonstrates its effectiveness in cosmological parameter inference.
Article
Biochemistry & Molecular Biology
William R. Conner, Emily K. Delaney, Michael J. Bronski, Paul S. Ginsberg, Timothy B. Wheeler, Kelly M. Richardson, Brooke Peckenpaugh, Kevin J. Kim, Masayoshi Watada, Ary A. Hoffmann, Michael B. Eisen, Artyom Kopp, Brandon S. Cooper, Michael Turelli
Summary: The Drosophila montium species group consists of 94 named species closely related to D. melanogaster, distributed widely across Asia, Africa, and Australasia. Genomic data from 42 species were used to estimate phylogeny, relative divergence times, and support monophyly within the group. However, age estimates for the montium crown group compared to D. melanogaster remain uncertain.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Shuran Liao, Yishu Wang, Duting Jin, Rong Chen, Zongqing Wang, Yanli Che
Summary: This study constructed phylogenetic trees using gene sequences to infer the relationship between Homalosilpha and Mimosilpha, revealing a close relationship and describing four new species.
Article
Multidisciplinary Sciences
Ahlam H. Tolba, Tahani A. Abushal, Dina A. Ramadan
Summary: In this study, point and interval estimations for the power Rayleigh distribution are obtained using the joint progressive type-II censoring technique. The maximum likelihood and Bayes methods are utilized for parameter estimation. The study also provides approximate credible intervals and confidence intervals for the estimators. The findings of the Bayes estimators are obtained using the Markov chain Monte Carlo method, with the Metropolis-Hasting technique and Gibbs sampling.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Mahim Mahbub, Zahin Wahab, Rezwana Reaz, M. Saifur Rahman, Md Shamsuzzoha Bayzid
Summary: Estimating species trees from genes sampled from the whole genome is challenging due to gene tree-species tree discordance, with incomplete lineage sorting being a common cause. Quartet-based weighted methods offer a statistically consistent way for accurate species tree estimation in such cases. The proposed wQFM method extends the quartet FM algorithm to a weighted setting, providing highly accurate species tree estimation results on simulated and real biological datasets.
Article
Biochemistry & Molecular Biology
Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A. Williams, Gergely J. Szollosi, Alexandros Stamatakis
Summary: SpeciesRax is a maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. It leverages the phylogenetic rooting signal in gene trees and infers species tree branch lengths and support values through paralogy-aware quartets extracted from the gene family trees. It is faster and at least as accurate as the best competing methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Medicine, Legal
Soyeon Bae, Sohyoung Won, Heebal Kim
Summary: This study identified 160 SNPs with high allele frequencies for paternity testing in Koreans by filtering candidate SNPs from the Ansan-Ansung cohort data and calculating likelihood ratios. Validation using Twin-Family cohort data showed accurate distinction between paternity and non-paternity when using the selected 160 SNPs for calculation.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Wei Wang, Chunyan Ma, Longling Ouyang, Wei Chen, Ming Zhao, Fengying Zhang, Yin Fu, Keji Jiang, Zhiqiang Liu, Heng Zhang, Lingbo Ma
Summary: Genetic diversity and population structure of Lateolabrax maculatus populations in coastal regions of China were analyzed, revealing distinct genetic clustering into Northern and Southern groups, likely due to geographic separation and divergent environmental conditions. The study also suggested potential anthropogenic transportation events from northern populations to southern aquaculture areas as a primary cause for genetic relationships observed. High genetic diversity and limited genetic exchange were observed in some populations, indicating better conservation efforts in those regions, with all populations showing signs of bottleneck events in history.
SCIENTIFIC REPORTS
(2021)
Article
Evolutionary Biology
Odile Maliet, Helene Morlon
Summary: Diversification rates vary across species due to environmental conditions and species-specific features. A new inference technique is presented here that reduces computation time by using data augmentation, allowing for the estimation of posterior distribution of tree with extinct and unsampled lineages as well as associated diversification rates. Simulation results demonstrate the statistical performance of this approach, which is applied to the study of bird radiation.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Maria Florencia Nadal, Alda Gonzalez, Gilberto Avalos
Summary: The study proposed a methodology to detect and exclude habitat-tourist species, revealing that common estimators overestimate species richness when including these species, resulting in erroneous conclusions. Additionally, the research found that including juveniles (such as spiders) may enhance analysis outcomes by allowing the detection of more habitat-tourist species.
ECOLOGICAL PROCESSES
(2022)