scholarly journals Stochastic delay models for molecular clocks and somite formation

2007 ◽  
Author(s):  
Kevin Burrage ◽  
Pamela Burrage ◽  
André Leier ◽  
Tatiana T. Marquez-Lago
Keyword(s):  
Molecular Clocks ◽  
Stochastic Delay ◽  
Delay Models ◽  
Somite Formation

Arithmetic Asian Options under Stochastic Delay Models

2011 ◽  
Vol 18 (5) ◽  
pp. 423-446 ◽  
Author(s):  
Nairn McWilliams ◽  
Sotirios Sabanis
Keyword(s):  
Asian Options ◽  
Stochastic Delay ◽  
Delay Models

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

scholarly journals Survival analysis of a stochastic delay single-species system in polluted environment with psychological effect and pulse toxicant input

2020 ◽  
Vol 2020 (1) ◽  
Author(s):  
Xiangjun Dai ◽  
Suli Wang ◽  
Weizhi Xiong ◽  
Ni Li
Keyword(s):  
Sufficient Conditions ◽  
Single Species ◽  
Threshold Value ◽  
Psychological Effect ◽  
Polluted Environment ◽  
Population System ◽  
Stochastic Delay ◽  
Species Population ◽  
The Mean ◽  
Single Species Population

Abstract We propose and study a stochastic delay single-species population system in polluted environment with psychological effect and pulse toxicant input. We establish sufficient conditions for the extinction, nonpersistence in the mean, weak persistence, and strong persistence of the single-species population and obtain the threshold value between extinction and weak persistence. Finally, we confirm the efficiency of the main results by numerical simulations.

scholarly journals Molecular clocks in ancient proteins: Do they reflect the age at death even after millennia?

2021 ◽  
Author(s):  
Nina Sophia Mahlke ◽  
Silvia Renhart ◽  
Dorothea Talaa ◽  
Alexandra Reckert ◽  
Stefanie Ritz-Timme
Keyword(s):  
Protein Degradation ◽  
Forensic Medicine ◽  
Molecular Clocks ◽  
Post Mortem ◽  
Age At Death ◽  
Morphological Examination ◽  
Dental Tissues ◽  
Ancient Proteins ◽  
Age Estimates ◽  
Age At Death Estimation

AbstractAge at death estimation in cases of human skeletal finds is an important task in forensic medicine as well as in anthropology. In forensic medicine, methods based on “molecular clocks” in dental tissues and bone play an increasing role. The question, whether these methods are applicable also in cases with post-depositional intervals far beyond the forensically relevant period, was investigated for two “protein clocks”, the accumulation of D-aspartic acid (D-Asp) and the accumulation of pentosidine (Pen) in dentine. Eight teeth of skeletons from different burial sites in Austria and with post-depositional intervals between c. 1216 and c. 8775 years were analysed. The results of age at death estimation based on D-Asp and Pen in dentine were compared to that derived from a classical morphological examination. Age at death estimation based on D-Asp resulted consistently in false high values. This finding can be explained by a post-mortem accumulation of D-Asp that may be enhanced by protein degradation. In contrast, the Pen-based age estimates fitted well with the morphological age diagnoses. The described effect of post-mortem protein degradation is negligible in forensically relevant time horizons, but not for post-depositional intervals of thousands of years. That means that the “D-Asp clock” loses its functionality with increasing post-depositional intervals, whereas Pen seems to be very stable. The “Pen-clock” may have the potential to become an interesting supplement to the existing repertoire of methods even in cases with extremely long post-depositional intervals. Further investigations have to test this hypothesis.

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