scholarly journals Whole‐exome sequencing reveals a long‐term decline in effective population size of red spruce ( Picea rubens )

2020 ◽  
Vol 13 (9) ◽  
pp. 2190-2205 ◽  
Author(s):  
Thibaut Capblancq ◽  
John R. Butnor ◽  
Sonia Deyoung ◽  
Ethan Thibault ◽  
Helena Munson ◽  
...  
Keyword(s):  
Population Size ◽  
Exome Sequencing ◽  
Effective Population Size ◽  
Whole Exome Sequencing ◽  
Picea Rubens ◽  
Red Spruce ◽  
Effective Population ◽  
Whole Exome

scholarly journals Whole Exome Sequencing of HIV-1 long-term non-progressors identifies rare variants in genes encoding innate immune sensors and signaling molecules

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Sara Konstantin Nissen ◽  
Mette Christiansen ◽  
Marie Helleberg ◽  
Kathrine Kjær ◽  
Sofie Eg Jørgensen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variants ◽  
Signaling Molecules ◽  
Innate Immune ◽  
Whole Exome ◽  
Genes Encoding ◽  
Hiv 1

scholarly journals Whole-exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

2020 ◽  
Vol 123 (8) ◽  
pp. 1219-1222
Author(s):  
Naomi Walsh ◽  
Charlotte Andrieu ◽  
Peter O’Donovan ◽  
Cecily Quinn ◽  
Alanna Maguire ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Metastatic Breast Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Metastatic Breast ◽  
Whole Exome

High genetic variation in leopards indicates large and long-term stable effective population size

2000 ◽  
Vol 9 (11) ◽  
pp. 1773-1782 ◽  
Author(s):  
G. Spong ◽  
M. Johansson ◽  
M. Björklund
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Effective Population

scholarly journals Long-term effective population size dynamics of an intensively monitored vertebrate population

Heredity ◽  
2016 ◽  
Vol 117 (4) ◽  
pp. 290-299 ◽  
Author(s):  
A-K Mueller ◽  
N Chakarov ◽  
O Krüger ◽  
J I Hoffman
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Effective Population

scholarly journals Historical population size of the threatened New Zealand sea lion Phocarctos hookeri

2015 ◽  
Vol 97 (2) ◽  
pp. 436-443 ◽  
Author(s):  
Catherine J. Collins ◽  
B. Louise Chilvers ◽  
Matthew Taylor ◽  
Bruce C. Robertson
Keyword(s):  
New Zealand ◽  
Population Size ◽  
Effective Population Size ◽  
Carrying Capacity ◽  
Effective Population ◽  
Sea Lion ◽  
Sea Lions ◽  
Target Values ◽  
Phocarctos Hookeri

Abstract Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri . This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ~9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the population’s carrying capacity ( K ) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.

Significance of Mature Male Parr in a Small Population of Atlantic Salmon (Salmo salar)

1989 ◽  
Vol 46 (6) ◽  
pp. 928-931 ◽  
Author(s):  
Jan Hennsng L'abée-Lund
Keyword(s):  
Atlantic Salmon ◽  
Population Size ◽  
Effective Population Size ◽  
Salmo Salar ◽  
Small Population ◽  
Mature Male ◽  
Effective Population ◽  
Atlantic Salmon Salmo Salar ◽  
Mature Male Parr

The spawning population of Atlantic salmon, Salmo salar, (mature male parr and adults (anadromous salmon)) were assessed in the River Baevra, central Norway, when the river was treated with rotenone in November 1986. The spawning population of adults consisted of 15 males and 19 females. The spawning population of males consisted of 167 mature male parr per adult male. The effective population size of adults was small; Na = 33.5 individuals. The presence of mature male parr theoretically increased the effective population size to Na = 71.7 individuals. This increase indicated that mature male parr brought the effective population size above a recommended minimum (Na = 50) to ensure long term viability.

scholarly journals On the independent loci assumption in phylogenomic studies

2016 ◽  
Author(s):  
W. Bryan Jennings
Keyword(s):  
Homologous Recombination ◽  
Population Size ◽  
Effective Population Size ◽  
Gene Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Long Term Effects ◽  
Effective Population ◽  
Independent Assortment

AbstractStudies using multi-locus coalescent methods to infer species trees or historical demographic parameters usually require the assumption that the gene tree for each locus (or SNP) is genealogically independent from the gene trees of other sampled loci. In practice, however, researchers have used two different criteria to delimit independent loci in phylogenomic studies. The first criterion, which directly addresses the condition of genealogical independence of sampled loci, considers the long-term effects of homologous recombination and effective population size on linkage between two loci. In contrast, the second criterion, which only considers the single-generation effects of recombination in the meioses of individuals, identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment. Methods that use these criteria to estimate the number of independent loci per genome as well as intra-chromosomal “distance thresholds” that can be used to delimit independent loci in phylogenomic datasets are reviewed. To compare the efficacy of each criterion, they are applied to two species (an invertebrate and vertebrate) for which relevant genetic and genomic data are available. Although the independent assortment criterion is relatively easy to apply, the results of this study show that it is overly conservative and therefore its use would unfairly restrict the sizes of phylogenomic datasets. It is therefore recommended that researchers only refer to genealogically independent loci when discussing the independent loci assumption in phylogenomics and avoid using terms that may conflate this assumption with independent assortment. Moreover, whenever feasible, researchers should use methods for delimiting putatively independent loci that take into account both homologous recombination and effective population size (i.e., long-term effective recombination).

Global changes explain the long-term demographic trend of the Eurasian common lizard (Squamata: Lacertidae)

2021 ◽  
Author(s):  
Jose L Horreo ◽  
Patrick S Fitze
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Climatic Changes ◽  
Vegetation Changes ◽  
Effective Population ◽  
Short Term ◽  
Demographic Trend ◽  
Common Lizard

Abstract The demographic trend of a species depends on the dynamics of its local populations, which can be compromised by local or by global phenomena. However, the relevance of local and global phenomena has rarely been investigated simultaneously. Here we tested whether local phenomena compromised a species’ demographic trend using the Eurasian common lizard Zootoca vivipara, the terrestrial reptile exhibiting the widest geographic distribution, as a model species. We analysed the species’ ancient demographic trend using genetic data from its six allopatric genetic clades and tested whether its demographic trend mainly depended on single clades or on global phenomena. Zootoca vivipara’s effective population size increased since 2.3 million years ago and started to increase steeply and continuously from 0.531 Mya. Population growth rate exhibited two maxima, both occurring during global climatic changes and important vegetation changes on the northern hemisphere. Effective population size and growth rate were negatively correlated with global surface temperatures, in line with global parameters driving long-term demographic trends. Zootoca vivipara’s ancient demography was not driven by a single clade, nor by the two clades that colonized huge geographic areas after the last glaciation. The low importance of local phenomena, suggests that the experimentally demonstrated high sensitivity of this species to short-term ecological changes is a response in order to cope with short-term and local changes. This suggests that what affected its long-term demographic trend the most, were not these local changes/responses, but rather the important and prolonged global climatic changes and important vegetation changes on the northern hemisphere, including the opening up of the forest by humans.

Familial AML With Germline CEBPA Mutations: Extended Clinical Outcomes and Analysis Of Secondary Mutations Using Whole Exome Sequencing

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 740-740
Author(s):  
Kiran Tawana ◽  
Aline Renneville ◽  
Jun Wang ◽  
Panayiotis Georgiades ◽  
Xavier Thomas ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Clinical Outcomes ◽  
Whole Exome Sequencing ◽  
Germline Mutations ◽  
Whole Exome ◽  
Disease Episode ◽  
Cebpa Mutations ◽  
Tumor Dna

Abstract Background Germline mutations in the N-terminal of CCAAT/enhancer binding protein α (CEBPA) are a feature of autosomal dominant AML. Despite the strong penetrance of these mutations, the age of disease onset varies considerably and is usually precipitated by acquiring a C-terminal mutation. Although biallelic CEBPA-mutations in sporadic AML are associated with favorable clinical outcomes, little is known about long-term survival or the secondary molecular events linked with familial cases. Aims We sought to establish the long term clinical outcomes in familial CEBPA-mutated AML and to examine the patterns of secondary mutations associated with leukemic transformation. Methods and Results Disease specific and follow up information was collected in 16 affected patients, from 7 pedigrees, published between 2004 and 2011. In 94% of patients (n=15), at least 3 years follow up was achieved. All pedigrees had a germline N-terminal CEBPA mutation and 17 of 18 documented disease episodes had an acquired C-terminal mutation. The age at AML diagnosis varied from 2-39 years (median 24.5 yrs) with a single asymptomatic carrier detected (now 23 yrs). With the exception of 1 patient diagnosed in 1963, all cases received combination chemotherapy at diagnosis. Additional consolidation comprised autologous stem cell transplantation (SCT, n=3) and allogeneic SCT in 1 patient failing to achieve CR post induction therapy. Ten patients had at least 1 further disease episode, the first recurrence presenting after a median of 2.1 years (range 0.5-14 yrs), 5 continued in CR and 1 patient was lost to follow up. In 3 out of 4 patients, where CEBPA was screened at recurrence, the acquired C-terminal mutations differed from diagnosis, signifying new episodes of AML. The median overall survival (OS) for the entire cohort was 20 years (1.1-46 yrs, n=16) and 17.3 years for patients with multiple disease episodes, reflecting durable responses to second line therapies. To identify potential co-operating mutations in CEBPA pedigrees, whole exome sequencing (WES) was performed in 7 tumor samples from 5 patients across 3 pedigrees, all with the germline mutation p.P23fs (Figure 1). All tumor DNA samples were sequenced with matched remission or skin DNA as a germline control. The number of acquired mutations in familial tumors was similar to sporadic disease, with 10-22 (median=14) non-synonymous tier 1 mutations per sample. In addition to the acquired C-terminal CEBPA mutation, these included established AML loci such as EZH2, TET2, WT1, GATA2, NRAS, CSF3R and the recently identified cohesin complex gene, SMC3. Of note, FLT3-ITD, NPM1 and DNMT3A mutations were absent in all tumors. A minimum of 2 established mutations were identified in each tumor and, at present, we can only speculate on which additional mutations are ‘driver' or ‘passenger' events. Reflecting findings in sporadic AML, biallelic CEBPA and GATA2 mutations co-occurred in both siblings from Pedigree 1 and were subsequently identified by Sanger sequencing in the child III.2 (Figure 1). All 3 patients continue in long term remission following chemotherapy. We were able to trace the clonal evolution in patient I.2 (Pedigree 3) by WES of 3 consecutive tumor samples which arose over a 17 year period. At diagnosis (Dx) the patient received induction and consolidation chemotherapy and remained disease free for 14 years. The second disease episode (R1) was treated with chemotherapy followed by autologous SCT and the third presentation (R2) was chemo-refractory. Tumor DNA from R2 was clonally related to Dx, sharing 7 identical mutations, including the original C-terminal CEBPA deletion. In contrast, R1 appeared molecularly distinct from Dx and R2, most likely representing a new clone which was subsequently eradicated with treatment. Conclusion This is the first report of long term clinical outcomes in familial CEBPA-mutated AML. Although many patients experienced disease recurrence, our extended follow up showed that OS remained favorable despite multiple episodes of disease. Assessment of C-terminal CEBPA mutations provided a unique insight into the recurrence of AML, with some patients appearing to develop completely new leukemic episodes. Although the penetrance of germline mutations is high, healthy carriers and late onset disease are noted, emphasizing the need for clinical vigilance and screening of all related potential SCT donors. Disclosures: No relevant conflicts of interest to declare.

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