scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Y Miles Zhang ◽  
Jason L Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Abstract Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Author(s):  
Yuanmeng Zhang ◽  
Jason Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Targeted enrichment of ultraconserved elements (UCE) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCE in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Author(s):  
Yuanmeng Zhang ◽  
Jason Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Population Level ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Probe Selection ◽  
Wet Lab ◽  
Phylogenomic Analyses ◽  
Targeted Enrichment

Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, UCEs are underutilized in arthropod phylogenomics, and the methodology can be daunting for beginners. Our goal is to introduce UCEs phylogenomics to a wider audience by summarizing recent advances in UCE phylogenomics in arthropod research to familiarize readers with background theory and steps involved in UCEs phylogenomics. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and finally provide a roadmap of steps in the UCEs pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. The UCEs pipeline can be divided into the following steps: 1) probe selection and design 2) wet lab work and sequencing, 3) bioinformatics, and 4) phylogenomic analyses. we provide quality-control tips to ensure that best results in data collection and downstream analyses. Our hope is to encourage increased adoption of UCEs in phylogenomics studies, deepen our understanding of the function of UCEs themselves across widely divergent taxa, and toward increased understanding of the tree of life.

scholarly journals Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Jiekun He ◽  
Siliang Lin ◽  
Jiatang Li ◽  
Jiehua Yu ◽  
Haisheng Jiang
Keyword(s):  
Tibetan Plateau ◽  
Evolutionary History ◽  
The Tibetan Plateau ◽  
Change Over Time ◽  
Deep Time ◽  
Terrestrial Vertebrates ◽  
History Of ◽  
Striking Change ◽  
Time Periods ◽  
Over Time

AbstractThe Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

scholarly journals Recent advances in periodic vibrations of the middle ear with a floating mass transducer

Meccanica ◽  
2020 ◽  
Vol 55 (12) ◽  
pp. 2609-2621
Author(s):  
Rafal Rusinek ◽  
Andrzej Weremczuk
Keyword(s):  
Periodic Solutions ◽  
Time Scales ◽  
Middle Ear ◽  
Nonlinear Model ◽  
Degree Of Freedom ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Multiple Time Scales Method ◽  
Recent Advances ◽  
The Stability

AbstractThe paper investigates periodic solutions of a nonlinear model of the middle ear with a floating mass transducer. A multi degree of freedom model is used to obtain a solution near the first resonance. The model is solved analytically by means of the multiple time scales method. Next, the stability of obtained periodic solutions is analysed in order to identify the parameters of the floating mass transducer that affect the middle ear dynamics. Moreover, some parameters of the middle ear structure are investigated with respect to their impact on obtained periodic solutions.

scholarly journals Towards a Better Understanding of the Evolution of Specialized Parasites of Fungus-Growing Ant Crops

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Sze Huei Yek ◽  
Jacobus J. Boomsma ◽  
Michael Poulsen
Keyword(s):  
Evolutionary History ◽  
Recent Progress ◽  
Population Level ◽  
Future Research ◽  
Research Questions ◽  
Fungus Growing Ants

Fungus-growing ants have interacted and partly coevolved with specialised microfungal parasites of the genusEscovopsissince the origin of ant fungiculture about 50 million years ago. Here, we review the recent progress in understanding the patterns of specificity of this ant-parasite association, covering both the colony/population level and comparisons between phylogenetic clades. We use a modified version of Tinbergen's four categories of evolutionary questions to structure our review in complementary approaches addressing both proximate questions of development and mechanism, and ultimate questions of (co)adaptation and evolutionary history. Using the same scheme, we identify future research questions that are likely to be particularly illuminating for understanding the ecology and evolution ofEscovopsisparasitism of the cultivar maintained by fungus-growing ants.

Major Improvements in Survival in Hematologic Malignancies in the Early 2000s.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 632-632
Author(s):  
Dianne Pulte ◽  
Adam Gondos ◽  
Hermann Brenner
Keyword(s):  
Relative Survival ◽  
Population Level ◽  
Hematologic Malignancies ◽  
The United States ◽  
P Value ◽  
Period Analysis ◽  
Non Hodgkin Lymphoma ◽  
Percentage Points ◽  
Recent Advances ◽  
Using Data

Abstract Background: Recent advances in the treatment of hematologic malignancies have led to improvements in response and survival in clinical trials for several conditions. Translation of these improvements to better survival on the population level should be monitored in as timely as possible a manner. Methods: We estimated trends in relative survival in patients with common hematologic malignancies in the United States between the years 2000 and 2004 using data from the Surveillance, Epidemiology, and End Results (SEER) program, employing the recently introduced technique of modeled period analysis to provide the most up-to-date and precise estimates of survival1. We calculated survival according to gender and age group as well as overall survival for each malignancy. Results: Major improvements in 5-year relative survivals were observed for nodal and extra-nodal non-Hodgkin lymphoma (NHL) (+8.3 and +7.1 percentage points, respectively, p<0.0001), acute myeloblastic leukemia (AML) (+4.8 percentage points, p=0.005), and chronic myelocytic leukemia (CML) (+15.9 percentage points, p<0.0001). Improvement in 10-year survivals were observed in nodal and extra-nodal (EN) NHL (+8.7 and +7.8 percentage points, p<0.0001), AML (+4.3 percentage points, p=0.009), CML (+16.2 percentage points, p<0.0001), and myeloma (+3.4 percentage points, p=0.01). Statistically significant improvements in 10-year survival were seen in both genders for NHL and CML, but were limited to women for MM and AML, although a trend towards improved survival was seen in men with these conditions as well. Improvements in prognosis were largely restricted to patients aged less than 65, except for NHL and CML. Patients over 65 with EN NHL actually had a greater improvement than younger patients, with increases of 6.0 and 8.5 percentage points, respectively for patients over and under 65. The single greatest improvement observed was in patients less than 65 with CML, who had a 25.2 percentage point improvement in 10-year relative survival between 2000 and 2004. Conclusions: Application of modeled period analysis to an examination of hematologic malignancies revealed profound improvements in survival in the 5 years between 2000 and 2004. Survival in CML has improved dramatically, and major improvements were also seen for survival in NHL, AML, and MM. A combination of new therapeutic options, improved supportive care, and wider application of recent advances is likely to be responsible for the improvements observed. Our results emphasize the importance of timely information about translation of therapeutic advances into clinical practice, such as can be provided by modeled period analysis. 1. Brenner H, Hakulinen T. Up-to-date and precise estimates of cancer patient survival: model-based period analysis. Am J Epidemiol.2006;164:689–696. 10-year survival in hematologic malignanices in 2000 and 2004 Malignancy Number 10-year survival (SE)-2000 10-yr survival (SE)-2004 Difference P-value HD 9989 78.3 (1.2) 81.8 (1.1) +3.5 0.12 NHL-nodal 40,121 45.4 (0.9) 54.1 (0.9) +8.7 <0.0001 NHL-EN 19,447 60.1 (1.4) 67.9 (1.3) +7.8 0.00015 MM 17,330 14.3 (0.9) 17.7 (1.0) +3.4 0.01 ALL 2222 26.5 (2.8) 33.2 (2.9) +6.7 0.14 CLL 12,881 54.2 (2.0) 56.6 (2.0) +2.4 0.45 AML 10,153 15.0 (1.0) 19.3 (1.2) +4.3 0.0085 CML 5308 22.4 (2.0) 38.6 (2.4) +16.2 <0.0001

EMERGING PROPERTIES IN POPULATION DYNAMICS WITH DIFFERENT TIME SCALES

1995 ◽  
Vol 03 (02) ◽  
pp. 591-602 ◽  
Author(s):  
PIERRE AUGER ◽  
JEAN-CHRISTOPHE POGGIALE
Keyword(s):  
Differential Equations ◽  
Time Scales ◽  
Time Scale ◽  
Population Level ◽  
Nonlinear Process ◽  
Linear Process ◽  
Fast Time ◽  
Slow Part ◽  
Spatial Patches ◽  
Different Time Scales

The aim of this work is to show that at the population level, emerging properties may occur as a result of the coupling between the fast micro-dynamics and the slow macrodynamics. We studied a prey-predator system with different time scales in a heterogeneous environment. A fast time scale is associated to the migration process on spatial patches and a slow time scale is associated to the growth and the interactions between the species. Preys go on the spatial patches on which some resources are located and can be caught by the predators on them. The efficiency of the predators to catch preys is patch-dependent. Preys can be more easily caught on some spatial patches than others. Perturbation theory is used in order to aggregate the initial system of ordinary differential equations for the patch sub-populations into a macro-system of two differential equations governing the total populations. Firstly, we study the case of a linear process of migration for which the aggregated system is formally identical to the slow part of the full system. Then, we study an example of a nonlinear process of migration. We show that under these conditions emerging properties appear at the population level.

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