scholarly journals The predictability of genomic changes underlying a recent host shift in Melissa blue butterflies

2017 ◽  
Author(s):  
Samridhi Chaturvedi ◽  
Lauren K. Lucas ◽  
Chris C. Nice ◽  
James A. Fordyce ◽  
Matthew L. Forister ◽  
...  
Keyword(s):  
Host Shift ◽  
Evolutionary Change ◽  
Host Use ◽  
Genomic Changes ◽  
Genome Wide ◽  
Evolutionary Changes ◽  
Lycaeides Melissa ◽  
Repeated Evolution ◽  
Deterministic Processes ◽  
Rearing Experiment

AbstractDespite accumulating evidence that evolution can be predictable, studies quantifying the predictability of evolution remain rare. Here, we measured the predictability of genome-wide evolutionary changes associated with a recent host shift in the Melissa blue butterfly (Lycaeides melissa). We asked whether and to what extent genome-wide patterns of evolutionary change in nature could be predicted (1) by comparisons among instances of repeated evolution, and (2) from SNP × performance associations in a lab experiment. We delineated the genetic loci (SNPs) most strongly associated with host use in twoL. melissalineages that colonized alfalfa. Whereas most SNPs were strongly associated with host use in none or one of these lineages, we detected a ~two-fold excess of SNPs associated with host use in both lineages. Similarly, we found that host-associated SNPs in nature could also be partially predicted from SNP × performance (survival and weight) associations in a lab rearing experiment. But the extent of overlap, and thus degree of predictability, was somewhat reduced. Although we were able to predict (to a modest extent) the SNPs most strongly associated with host use in nature (in terms of parallelism and from the experiment), we had little to no ability to predict the direction of evolutionary change during the colonization of alfalfa. Our results show that different aspects of evolution associated with recent adaptation can be more or less predictable, and highlight how stochastic and deterministic processes interact to drive patterns of genome-wide evolutionary change.

scholarly journals Eco-evolutionary dynamics

2009 ◽  
Vol 364 (1523) ◽  
pp. 1483-1489 ◽  
Author(s):  
F. Pelletier ◽  
D. Garant ◽  
A.P. Hendry
Keyword(s):  
Time Scale ◽  
Evolutionary Dynamics ◽  
Evolutionary Change ◽  
Ecological Change ◽  
Evolutionary Changes ◽  
Microevolutionary Change ◽  
Theoretical Developments ◽  
Rapid Evolutionary Change

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.

A Reappraisal of Superficial Pleomorphic Liposarcoma

2020 ◽  
Vol 154 (3) ◽  
pp. 353-361
Author(s):  
Scott Hilliard Berg ◽  
Cathy Meade Massoud ◽  
Colleen Jackson-Cook ◽  
Sosipatros Alexander Boikos ◽  
Steven Christopher Smith ◽  
...  
Keyword(s):  
Genetic Alterations ◽  
Pleomorphic Liposarcoma ◽  
Genomic Changes ◽  
Snp Microarray ◽  
Genome Wide ◽  
Genetic Features ◽  
Atypical Cells ◽  
Microarray Studies ◽  
Gains And Losses

Abstract Objectives Superficial pleomorphic liposarcoma (PL) has a favorable prognosis compared to deeply seated PL. Given developments in the classification of lipomatous neoplasms, we reappraised a series of cases. Methods Retrospective clinicopathologic evaluation and genome-wide single-nucleotide polymorphism (SNP) microarray studies were performed for cases previously designated superficial PL. Results Four cases were identified (age, 48-70 years). Two were dermally confined, whereas two were superficial subcutaneous; no recurrences or metastases were reported. Tumors demonstrated pleomorphic spindled morphology with variable cellularity. Multivacuolated atypical lipoblasts were focal in 3 and abundant in 1. Dermal tumors demonstrated atypical cells within sclerotic collagen. Genome-wide SNP microarray studies revealed consistent gains and losses, including losses at the 13q14.2 locus encompassing RB1 and DLEU2 and deletion/disruption of the TP53 locus. Although subcutaneous examples showed genomic changes similar to deep PL, the dermal examples showed fewer genetic alterations, including changes reported in the spectrum of atypical spindle cell/pleomorphic lipomatous tumors (ASPLT). All lacked MDM2 amplification. Conclusions Careful integration of histologic and genetic features may improve classification of lipomatous neoplasms with atypia, allowing reclassification of some superficial PL as ASPLT.

scholarly journals The predictability of genomic changes underlying a recent host shift in Melissa blue butterflies

2018 ◽  
Vol 27 (12) ◽  
pp. 2651-2666 ◽  
Author(s):  
Samridhi Chaturvedi ◽  
Lauren K. Lucas ◽  
Chris C. Nice ◽  
James A. Fordyce ◽  
Matthew L. Forister ◽  
...  
Keyword(s):  
Host Shift ◽  
Genomic Changes

scholarly journals Genome-Wide Characterization of Circulating Tumor Cells Identifies Novel Prognostic Genomic Alterations in Systemic Melanoma Metastasis

2014 ◽  
Vol 60 (6) ◽  
pp. 873-885 ◽  
Author(s):  
Connie G Chiu ◽  
Yoshitaka Nakamura ◽  
Kelly K Chong ◽  
Sharon K Huang ◽  
Neal P Kawas ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Stage Iiib ◽  
Melanoma Metastasis ◽  
Genomic Changes ◽  
Biomarker Panel ◽  
Regional Metastasis ◽  
Genome Wide ◽  
Systemic Metastasis

Abstract BACKGROUND Circulating tumor cells (CTC) have been found in patients with metastatic melanoma and are associated with advanced melanoma stage and poor patient outcome. We hypothesize that CTC harbor genomic changes critical in the development of distant systemic metastasis. Here, we present the first genome-wide copy-number aberration (CNA) and loss of heterozygosity (LOH)-based characterization of melanoma CTC. METHODS CTC were isolated from peripheral blood monocytes of 13 melanoma patients with regional metastasis stage IIIB/C using antibodies against melanoma-associated cell surface gangliosides. RESULTS We characterized 251 CNA in CTC. Comparative analysis demonstrated >90% concordance in single-nucleotide polymorphism profiles between paired CTC and tumor metastases. In particular, there were notable recurring CNA across patients. In exploratory studies, the presence of several top CTC-associated CNA was verified in distant metastasis (stage IV) from 27 patients, suggesting that certain genomic changes are propagated from regional metastasis to CTC and to distant systemic metastases. Lastly, an exploratory biomarker panel derived from 5 CTC-associated CNA [CSMD2 (CUB and Sushi multiple domains 2), 1p35.1; CNTNAP5 (contactin associated protein-like 5), 2q14.3; NRDE2 (NRDE-2, necessary for RNA interference, domain containing), 14q32.11; ADAM6 (ADAM metallopeptidase domain 6, pseudogene), 14q32.33; and TRPM2 (transient receptor potential cation channel, subfamily m, member 2), 21q22.3] conferred prognostic utility for melanoma recurrence [hazard ratio (HR), 1.14; CI, 1.00–1.44; P = 0.0471] and death (HR, 2.86; CI, 1.23–14.42; P = 0.0014) in 35 patients with stage IIIB/C melanoma, with a 5-year disease-free survival of 13% vs 69% (P = 0.0006) and overall survival of 28% vs 94% between high-risk and low-risk groups defined by the biomarker panel, respectively. CONCLUSIONS This study provides the first detailed CNA-based profile of melanoma CTC and illustrates how CTC may be used as a novel approach for identification of systemic metastasis.

scholarly journals Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 275
Author(s):  
Jue Wang ◽  
Chengkun Liu ◽  
Jie Chen ◽  
Ying Bai ◽  
Kejun Wang ◽  
...  
Keyword(s):  
Growth Rate ◽  
Snp Array ◽  
Glucose Absorption ◽  
Related Gene ◽  
Feed Conversion ◽  
Genomic Changes ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Show Evidence ◽  
Genomic Regions

Genetic variations introduced via introgression from Western to Chinese pigs have contributed to the performance of Chinese breeds in traits such as growth rate and feed conversion efficiency. However, little is known about the underlying genomic changes that occurred during introgression and the types of traits affected by introgression. To address these questions, 525 animals were characterized using an SNP array to detect genomic regions that had been introgressed from European to indigenous Chinese breeds. The functions of genes located in introgressed regions were also investigated. Our data show that five out of six indigenous Chinese breeds show evidence of introgression from Western pigs, and eight introgressed genome regions are shared by five of the Chinese breeds. A region located on chr13: 12.8–13.1 M was affected by both introgression and artificial selection, and this region contains the glucose absorption related gene, OXSM, and the sensory related gene, NGLY. The results provide a foundation for understanding introgression from Western to indigenous Chinese pigs.

scholarly journals Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

2020 ◽  
Vol 6 (45) ◽  
pp. eabd0079
Author(s):  
Xing-Xing Shen ◽  
Jacob L. Steenwyk ◽  
Abigail L. LaBella ◽  
Dana A. Opulente ◽  
Xiaofan Zhou ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Filamentous Fungi ◽  
Common Ancestor ◽  
Evolutionary Change ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Molecular Sequence ◽  
Genome Wide ◽  
Similarities And Differences ◽  
Genome Scale

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

Evolution at All Scales in the Vertebrate Fossil Record

2002 ◽  
Vol 11 ◽  
pp. 165-178
Author(s):  
John P. Hunter
Keyword(s):  
Fossil Record ◽  
Large Scale ◽  
Large Time ◽  
Evolutionary Change ◽  
Theory Of Evolution ◽  
Evolutionary Forces ◽  
The Past ◽  
Evolutionary Changes ◽  
Abundant Evidence ◽  
Transitional Forms

The fossil record of vertebrates provides abundant evidence for both the fact and the theory of evolution (Carroll, 1997; Prothero and Schoch, 1994). In support of the fact that evolution has indeed occurred, the vertebrate fossil record clearly documents evolutionary change along lineages, that is, along direct lines of ancestors and descendents. The fossil record also shows step-wise evolutionary changes resulting in the emergence of new kinds of vertebrates from pre-existing kinds—for example, the origin of mammals from the “mammal-like” reptiles. In support of the theory that natural selection, in particular, has been largely responsible for evolutionary change, the fossil record shows that the numerous “transitional” forms that lived in the past—far from being nonviable “monsters”—were functionally integrated organisms that were well adapted to their ecological roles. Finally, the vertebrate fossil record preserves certain large-scale phenomena, such as radiations and trends, which show that evolutionary forces can act over very large time scales.

scholarly journals A homeotic shift late in development drives mimetic color variation in a bumble bee

2019 ◽  
pp. 201900365 ◽  
Author(s):  
Li Tian ◽  
Sarthok Rasique Rahman ◽  
Briana D. Ezray ◽  
Luca Franzini ◽  
James P. Strange ◽  
...  
Keyword(s):  
Gene Expression Analysis ◽  
Color Pattern ◽  
Color Variation ◽  
Genomic Changes ◽  
Adult Transition ◽  
Genome Wide ◽  
Genomic Tools ◽  
Multiple Species ◽  
Genomic Basis ◽  
Black Color

Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally nonmodel systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns through parallel shifts of midabdominal segments from red to black. Using genome-wide association, we establish that a cis-regulatory locus between the abdominal fate-determining Hox genes, abd-A and Abd-B, controls the red–black color switch in a western species, Bombus melanopygus. Gene expression analysis reveals distinct shifts in Abd-B aligned with the duration of setal pigmentation at the pupal–adult transition. This results in atypical anterior Abd-B expression, a late developmental homeotic shift. Changing expression of Hox genes can have widespread effects, given their important role across segmental phenotypes; however, the late timing reduces this pleiotropy, making Hox genes suitable targets. Analysis of this locus across mimics and relatives reveals that other species follow independent genetic routes to obtain the same phenotypes.

Genome-wide copy number analysis of Hodgkin Reed-Sternberg cells identifies recurrent imbalances with correlations to treatment outcome

Blood ◽  
2010 ◽  
Vol 116 (3) ◽  
pp. 418-427 ◽  
Author(s):  
Christian Steidl ◽  
Adele Telenius ◽  
Sohrab P. Shah ◽  
Pedro Farinha ◽  
Lorena Barclay ◽  
...  
Keyword(s):  
Copy Number ◽  
Nuclear Factor Κb ◽  
Primary Treatment ◽  
Comparative Genomic ◽  
Multidrug Resistance Gene ◽  
Genomic Changes ◽  
Genome Wide ◽  
Doxorubicin Toxicity ◽  
Toxicity In Vitro

Abstract In classical Hodgkin lymphoma (cHL) the mechanisms underlying primary refractory disease and relapse remain unknown. To gain further insight into cHL pathogenesis and genomic changes linked to treatment response, we studied 53 cHL patients by array comparative genomic hybridization, including 23 patients whose primary treatment failed, using DNA from microdissected HRS cells. Copy number alterations found in more than 20% of cases included gains of 2p, 9p, 16p, 17q, 19q, 20q, and losses of 6q, 11q, and 13q. We identified at high resolution recurrent changes defining minimally gained and lost regions harboring genes involved in nuclear factor κB signaling, such as REL, IKBKB, CD40, and MAP3K14. Gains of chromosome 16p11.2-13.3 were significantly more frequent in pretreatment and relapse biopsies of unresponsive patients and were associated with shortened disease-specific survival (P = .028). In the therapy-resistant HL cell line KMH2, we found genomic gains and overexpression of the multidrug resistance gene ABCC1 mapping to cytoband 16p13.11. We show that doxorubicin exposure to KMH2 induces ABCC1 expression and that siRNA silencing of ABCC1 sensitizes KMH2 cells to doxorubicin toxicity in vitro, suggesting that overexpression of ABCC1 contributes to the drug resistance phenotype found in KMH2.

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