Results 21 to 30 of about 14,913 (198)

Strong plastid degradation is consistent within section Chondrophyllae, the most speciose lineage of Gentiana

Ecology and Evolution, 2022
Recovering phylogenetic relationships in lineages experiencing intense diversification has always been a persistent challenge in evolutionary studies, including in Gentiana section Chondrophyllae sensu lato (s.l.).
Peng‐Cheng Fu, Shi‐Long Chen, Shan‐Shan Sun, Adrien Favre   +3 more
doaj   +1 more source

Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae) [PDF]

BMC Evolutionary Biology, 2018
Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish
Max R. Bangs, Marlis R. Douglas, Steven M. Mussmann, Michael E. Douglas   +3 more
openaire   +3 more sources

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes

BMC Plant Biology, 2020
Background Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus ...
Xu Zhang, Yanxia Sun, Jacob B. Landis, Zhenyu Lv, Jun Shen, Huajie Zhang, Nan Lin, Lijuan Li, Jiao Sun, Tao Deng, Hang Sun, Hengchang Wang   +11 more
doaj   +1 more source

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal [PDF]

Proceedings of the Royal Society B: Biological Sciences, 2015
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree ...
Prashant P, Sharma, Rosa, Fernández, Lauren A, Esposito, Edmundo, González-Santillán, Lionel, Monod   +4 more
openaire   +2 more sources

Effects of discordance between species and gene trees on phylogenetic diversity conservation

Journal of Mathematical Biology, 2022
Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying ...
Kristina Wicke, Mareike Fischer, Laura Kubatko   +2 more
openaire   +3 more sources

Phylogenetic analysis of the full‐length SARS‐CoV sequences: Evidence for phylogenetic discordance in three genomic regions [PDF]

Journal of Medical Virology, 2004
AbstractThe origin of the severe acute respiratory syndrome‐coronavirus (SARS‐CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS‐CoV, for the largest part of the genome (∼80%), is more closely related to Group II coronaviruses sequences ...
Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Vandamme, A.-M., Van Ranst, M., Moulton, V., Hatzakiu, A.   +6 more
openaire   +4 more sources

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. [PDF]

PLoS ONE, 2017
Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications.
Uyen Mai, Erfan Sayyari, Siavash Mirarab
doaj   +1 more source

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment [PDF]

, 2012
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in ...
A Löytynoja, A Löytynoja, B Sipos, BG Hall, BG Hall, BP Blackburne, C Chothia, C Dessimoz, C Kemena, C Kemena, C Notredame, CB Do, CL Strope, DA Dalquen, DA Morrison, DH Mathews, ER Mardis, G Blackshields, G Jordan, G Landan, GP Raghava, I Walle Van, J Kim, J Stoye, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JH Havgaard, JP Huelsenbeck, K Mizuguchi, LA Stebbings, M Anisimova, M Pop, MR Aniba, P Gardner, RA Cartwright, RB Russell, RC Edgar, RC Edgar, SA Berger, SF Altschul, T Golubchik, T Koestler, T Lassmann, T Lassmann, T Lassmann, W Fletcher   +49 more
core   +2 more sources

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence [PDF]

, 2007
Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years.
(Max) Zong-Ming Cheng, Gerald Tuskan, Timothy Tschaplinski, Xiaohan Yang, Xiaohan Yang   +4 more
core   +2 more sources

Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis

BMC Plant Biology, 2022
Background Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic ...
Jian Liu, Anders J. Lindstrom, Xun Gong
doaj   +1 more source