scholarly journals Long-term molecular evolutionary rate determines intraspecific genetic diversity

2019 ◽  
Author(s):  
Jiaqi Wu ◽  
Takahiro Yonezawa ◽  
Hirohisa Kishino
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
Early Stage ◽  
Morphological Evolution ◽  
Biological Traits ◽  
Gene Trees ◽  
Intraspecific Genetic Diversity ◽  
Molecular Evolutionary Rates ◽  
Species Specific

AbstractWhat determines genetic diversity and how it connects to the various biological traits is unknown. In this work, we offer answers to these questions. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual genomes of human, chimpanzee, gorilla, mouse and dog/wolf, we found that intraspecific genetic diversity is determined by long-term molecular evolutionary rates, rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Expanding this new finding, we developed a method to detect fluctuations of species-specific selection on genes as the deviations of intra-species genetic diversity predicted from long-term rates. We show that the evolution of epithelial cells, rather than of connective tissue, mainly contributes to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps subjected by infectious diseases are most representative of adaptive evolution.

scholarly journals Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 306
Author(s):  
Maurizio Rossetto ◽  
Peter D. Wilson ◽  
Jason Bragg ◽  
Joel Cohen ◽  
Monica Fahey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
A Priori ◽  
Genetic Data ◽  
Environmental Data ◽  
Specific Data ◽  
Acacia Species ◽  
Simple Observation ◽  
Source Plant ◽  
Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

Long-term outcomes of patients with advanced-stage cutaneous T-cell lymphoma and large cell transformation

Blood ◽  
2008 ◽  
Vol 112 (8) ◽  
pp. 3082-3087 ◽  
Author(s):  
Suzanne O. Arulogun ◽  
H. Miles Prince ◽  
Jonathan Ng ◽  
Stephen Lade ◽  
Gail F. Ryan ◽  
...  
Keyword(s):  
De Novo ◽  
Cell Transformation ◽  
Early Stage ◽  
Large Cell ◽  
Tumor Stage ◽  
Advanced Stage ◽  
Long Term Outcomes ◽  
Stage Disease ◽  
Large Cell Transformation

Abstract Although mycosis fungoides (MF) is typically an indolent disease, patients with advanced-stage disease (stages IIB-IVB), including Sézary syndrome (SS), often have a poor outcome. A 31-year, retrospective analysis of our cutaneous lymphoma database, of 297 patients with MF and SS, was undertaken to study long-term outcomes and identify clinical predictors of outcome in patients with advanced-stage disease (ASD, n = 92) and large cell transformation (LCT, n = 22). Two-thirds of patients with ASD presented with de novo ASD. The median overall survival (OS) for ASD was 5 years with a 10-year predicted OS of 32%. Age at initial diagnosis (P = .01), tumor stage (P = .01), and clinical stage (P = .001) were found to be significant predictors of outcome. Patients who presented with de novo ASD demonstrated better outcomes that were not statistically significant than those with a prior diagnosis of early-stage MF (P = .25). Transformation developed in 22 of the 297 MF/SS patients (7.4%), with a transformation rate of only 1.4% in patients with early-stage disease, compared with stage IIB (27%) and stage IV (56%-67%) disease. The median OS from diagnosis of LCT was 2 years. We confirm that the incidence of LCT is strongly dependent on tumor stage at diagnosis, and we demonstrate a much lower overall risk of LCT than previously reported.

scholarly journals P.015 Long-term progression and prognosis in different subtypes of Parkinson’s disease: validation of a new multi-domain subtyping method

2019 ◽  
Vol 46 (s1) ◽  
pp. S17
Author(s):  
S Fereshtehnejad ◽  
Y Zeighami ◽  
A Dagher ◽  
RB Postuma
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
De Novo ◽  
Early Stage ◽  
Real Life ◽  
Clinical Manifestations ◽  
Personalized Care ◽  
Autonomic Disturbance ◽  
Progression Markers

Background: Parkinson’s disease (PD) varies in clinical manifestations and course of progression from person to person. Identification of distinct PD subtypes is of great priority to develop personalized care approaches. We aimed to compare long-term progression and prognosis between different PD subtypes. Methods: Data on 421 individuals with de novo early-onset PD was retrieved from Parkinson’s Progression Markers Initiative (PPMI). Using a newly developed multi-domain subtyping method (based on motor phenotype, RBD, autonomic disturbance, early cognitive deficit), we divided PD population into three subtypes at baseline: “mild motor-predominant”, “Diffuse malignant” and “Intermediate”. Rate of global progression (mixed motor and non-motor features) and developing dementia were compared between the subtypes. Results: Patients with “diffuse malignant” PD experienced 0.5 z-score further worsening of global composite outcome (p=0.017) and 2.2 further decline in MOCA score (p=0.001) after 6-years of follow-up. Hazard for MCI/dementia was significantly higher in “diffuse malignant” (HR=3.2, p<0.001) and “intermediate” (HR=1.8, p<0.001) subtypes. Individuals with “diffuse malignant” PD had the lowest level of CSF amyloid-beta (p=0.006) and SPECT striatal binding ratio (p=0.001). Conclusions: This multi-domain subtyping is a valid method to predict subgroups of PD with distinct patterns of long-term progression at drug-naïve early-stage with potential application in real-life clinical practice.

scholarly journals Inferring past demographic changes in a critically endangered marine fish after fishery collapse

2014 ◽  
Vol 71 (7) ◽  
pp. 1619-1628 ◽  
Author(s):  
Fausto Valenzuela-Quiñonez ◽  
John Carlos Garza ◽  
Juan A. De-Anda-Montañez ◽  
Francisco J. García-de-León
Keyword(s):  
Genetic Diversity ◽  
Marine Fish ◽  
Extinction Risk ◽  
Substantial Reduction ◽  
Critically Endangered ◽  
Biological Traits ◽  
Genetic Level ◽  
Loss Of Genetic Diversity ◽  
Fishery Collapse

Several worldwide marine fish stocks need to recover from collapse or overexploitation. However, the effects of a fishery collapse at the genetic level are still largely unknown, as is the extent of reduction in genetic diversity caused by fisheries and the consequences for extinction risk. Here we present a case study of totoaba, the first marine fish considered as critically endangered. We assessed 16 microsatellite loci to determine whether the demographic collapse of the species resulted in a loss of genetic diversity. Our data indicate that genetic diversity of totoaba is in the range of values observed for fish with similar biological traits without a documented fishery collapse. Contemporary demographic analysis indicated no loss of genetic diversity. Long-term genealogical analysis showed a substantial reduction in effective population size. However, the time and causal effects for population decline cannot be inferred because of the large uncertainty in estimates. Our results indicate that the totoaba in the Gulf of California has not suffered a measurable contemporary reduction in genetic diversity, and that genetic diversity is driven by long-term climatic events. Estimates of current effective size indicate that it is large enough that genetic factors may not be a major problem for conservation. We conclude that the recent fishery collapse of totoaba did not have sufficient consequences at the genetic level to increase the risk of extinction from genetic drift. However, selective effects of fishing on the adaptive potential in totoaba remain unclear.

scholarly journals Clinicopathological study of lepromatous leprosy and histoid leprosy in a tertiary care institute

2021 ◽  
Vol 11 (1) ◽  
pp. 1818-1824
Author(s):  
SindhuShree N
Keyword(s):  
De Novo ◽  
Clinical Course ◽  
Early Stage ◽  
Tertiary Care ◽  
Clinicopathological Characteristics ◽  
Lepromatous Leprosy ◽  
Medical Sciences ◽  
Inadequate Therapy ◽  
History Of

Background: Lepromatous leprosy is a clinical course seen in patients with inefficient cellular immunity against Mycobacterium leprae, resulting in anergy. A highly bacilliferrous type of lepromatous leprosy is histoid leprosy. Histoid leprosy was initially reported to manifest after the failure of long-term dapsone monotherapy, irregular therapy, or inadequate therapy. However, it is now well known that histoid leprosy develops de-novo as well. This study was undertaken to know the incidence and clinicopathological characteristics of lepromatous leprosy and histoid leprosy.Materials and Methods: This was a combined (both retrospective and prospective) study of lepromatous and histoid Leprosy, undertaken in the Department of Pathology, Karnataka Institute of Medical Sciences, Hubballi, over 42 months from January 2013 to June 2016.Results: Out of the 16 clinically diagnosed lepromatous leprosy cases, only 5 were histologically proven to be the same. Of the seven clinically diagnosed histoid leprosy cases, 4 were histoid leprosy on histopathology and the remaining 3 were lepromatous leprosy. All 4 patients of histoid leprosy were cases of De- Novo histoid leprosy. The commonest skin lesion encountered were erythematous patches (9/16) in lepromatous leprosy and nodules (5/7) in histoid leprosy.Conclusions: Lepromatous leprosy when diagnosed in an early stage, interrupts the epidemiological chain and avoids the associated disabilities and psychological effects for the patient and family. Histoid leprosy is a rare entity that can also present with no history of prior anti-leprosy treatment, the diagnosis of “de-novo histoid leprosy” should be kept in mind.

scholarly journals Development of Polymorphic Microsatellite Loci for Potato Wart from Next-Generation Sequence Data

2016 ◽  
Vol 106 (6) ◽  
pp. 636-644 ◽  
Author(s):  
Marie-Claude Gagnon ◽  
Theo A. J. van der Lee ◽  
Peter J. M. Bonants ◽  
Donna S. Smith ◽  
Xiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Geographic Origin ◽  
Whole Genome Sequence ◽  
Specific Detection ◽  
Potato Wart ◽  
Intraspecific Genetic Diversity ◽  
Polymorphic Microsatellite ◽  
Genetic Clustering ◽  
Species Specific

Synchytrium endobioticum is the fungal agent causing potato wart disease. Because of its severity and persistence, quarantine measures are enforced worldwide to avoid the spread of this disease. Molecular markers exist for species-specific detection of this pathogen, yet markers to study the intraspecific genetic diversity of S. endobioticum were not available. Whole-genome sequence data from Dutch pathotype 1 isolate MB42 of S. endobioticum were mined for perfect microsatellite motifs. Of the 62 selected microsatellites, 21 could be amplified successfully and displayed moderate levels of polymorphism in 22 S. endobioticum isolates from different countries. Nineteen multilocus genotypes were observed, with only three isolates from Canada displaying identical profiles. The majority of isolates from Canada clustered genetically. In contrast, most isolates collected in Europe show no genetic clustering associated with their geographic origin. S. endobioticum isolates with the same pathotype displayed highly variable genotypes and none of the microsatellite markers correlated with a specific pathotype. The markers developed in this study can be used to assess intraspecific genetic diversity of S. endobioticum and allow track and trace of genotypes that will generate a better understanding of the migration and spread of this important fungal pathogen and support management of this disease.

Association of the Non-Motor Burden with Patterns of Striatal Dopamine Loss in de novo Parkinson’s Disease

2020 ◽  
Vol 10 (4) ◽  
pp. 1541-1549
Author(s):  
Seok Jong Chung ◽  
Sangwon Lee ◽  
Han Soo Yoo ◽  
Yang Hyun Lee ◽  
Hye Sun Lee ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
De Novo ◽  
Early Stage ◽  
Striatal Dopamine ◽  
Motor Deficits ◽  
Dopamine Depletion ◽  
Severe Motor ◽  
Severe Group ◽  
Striatal Dopamine Depletion

Background: Striatal dopamine deficits play a key role in the pathogenesis of Parkinson’s disease (PD), and several non-motor symptoms (NMSs) have a dopaminergic component. Objective: To investigate the association between early NMS burden and the patterns of striatal dopamine depletion in patients with de novo PD. Methods: We consecutively recruited 255 patients with drug-naïve early-stage PD who underwent 18F-FP-CIT PET scans. The NMS burden of each patient was assessed using the NMS Questionnaire (NMSQuest), and patients were divided into the mild NMS burden (PDNMS-mild) (NMSQuest score <6; n = 91) and severe NMS burden groups (PDNMS-severe) (NMSQuest score >9; n = 90). We compared the striatal dopamine transporter (DAT) activity between the groups. Results: Patients in the PDNMS-severe group had more severe parkinsonian motor signs than those in the PDNMS-mild group, despite comparable DAT activity in the posterior putamen. DAT activity was more severely depleted in the PDNMS-severe group in the caudate and anterior putamen compared to that in the PDMNS-mild group. The inter-sub-regional ratio of the associative/limbic striatum to the sensorimotor striatum was lower in the PDNMS-severe group, although this value itself lacked fair accuracy for distinguishing between the patients with different NMS burdens. Conclusion: This study demonstrated that PD patients with severe NMS burden exhibited severe motor deficits and relatively diffuse dopamine depletion throughout the striatum. These findings suggest that the level of NMS burden could be associated with distinct patterns of striatal dopamine depletion, which could possibly indicate the overall pathological burden in PD.

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