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1. Parallel plumage colour evolution and introgressive hybridization in wheatears

Author:
Schweizer, Manuel; Warmuth, Vera; Alaei Kakhki, Niloofar; Aliabadian, Mansour; Förschler, Marc; Shirihai, Hadoram; Suh, Alexander; Burri, Reto
Source:
Journal of evolutionary biology 2019 v.32 no.1 pp. 100-110
ISSN:
1010-061X
Subject:
parallel evolution,   etc   ; Oenanthe cypriaca; ancestry; color; genetic variation; genome assembly; genomics; introgression; mitochondria; monophyly; neck; phenotype; plumage; single nucleotide polymorphism; songbirds; Cyprus;     Show all 16 Subjects
Abstract:
... Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa— ...
DOI:
10.1111/jeb.13401

2. Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

Author:
Turajlic, Samra; Xu, Hang; Litchfield, Kevin; Rowan, Andrew; Horswell, Stuart; Chambers, Tim; O’Brien, Tim; Lopez, Jose I.; Watkins, Thomas B.K.; Nicol, David; Stares, Mark; Challacombe, Ben; Hazell, Steve; Chandra, Ashish; Mitchell, Thomas J.; Au, Lewis; Eichler-Jonsson, Claudia; Jabbar, Faiz; Soultati, Aspasia; Chowdhury, Simon; Rudman, Sarah; Lynch, Joanna; Fernando, Archana; Stamp, Gordon; Nye, Emma; Stewart, Aengus; Xing, Wei; Smith, Jonathan C.; Escudero, Mickael; Huffman, Adam; Matthews, Nik; Elgar, Greg; Phillimore, Ben; Costa, Marta; Begum, Sharmin; Ward, Sophia; Salm, Max; Boeing, Stefan; Fisher, Rosalie; Spain, Lavinia; Navas, Carolina; Grönroos, Eva; Hobor, Sebastijan; Sharma, Sarkhara; Aurangzeb, Ismaeel; Lall, Sharanpreet; Polson, Alexander; Varia, Mary; Horsfield, Catherine; Fotiadis, Nicos; Pickering, Lisa; Schwarz, Roland F.; Silva, Bruno; Herrero, Javier; Luscombe, Nick M.; Jamal-Hanjani, Mariam; Rosenthal, Rachel; Birkbak, Nicolai J.; Wilson, Gareth A.; Pipek, Orsolya; Ribli, Dezso; Krzystanek, Marcin; Csabai, Istvan; Szallasi, Zoltan; Gore, Martin; McGranahan, Nicholas; Van Loo, Peter; Campbell, Peter; Larkin, James; Swanton, Charles
Source:
Cell 2018 v.173 no.3 pp. 595-610.e11
ISSN:
0092-8674
Subject:
parallel evolution,   etc   ; biomarkers; genetic variation; metastasis; monitoring; patients; prospective studies; renal cell carcinoma;     Show all 8 Subjects
Abstract:
... The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of ...
DOI:
10.1016/j.cell.2018.03.043

3. Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae)

Author:
Trucchi, Emiliano; Frajman, Božo; Haverkamp, Thomas H. A.; Schönswetter, Peter; Paun, Ovidiu
Source:
The new phytologist 2017 v.216 no.1 pp. 267-278
ISSN:
0028-646X
Subject:
parallel evolution,   etc   ; Caryophyllaceae; data collection; ecotypes; genetic variation; metagenomics; microbial communities; secondary contact; sequence analysis; Alps region;     Show all 10 Subjects
Abstract:
... The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south‐eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 i ...
DOI:
10.1111/nph.14722
PubMed:
28782803
PubMed Central:
PMC5601199

4. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana

Author:
Gould, Billie A.; Stinchcombe, John R.
Source:
Molecular ecology 2017 v.26 no.1 pp. 92-106
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Arabidopsis thaliana; flowering date; genes; genetic variation; indigenous species; introduced species; phenotype; pleiotropy; sequence analysis;     Show all 10 Subjects
Abstract:
... A long‐standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole‐genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common ...
DOI:
10.1111/mec.13643

5. Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

Author:
Irwin, Darren E.; Alcaide, Miguel; Delmore, Kira E.; Irwin, Jessica H.; Owens, Gregory L.
Source:
Molecular ecology 2016 v.25 no.18 pp. 4488-4507
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Passeriformes; gene flow; genetic variation; genome; genome assembly; genotype; models; phylogeny; recurrent selection;     Show all 10 Subjects
Abstract:
... Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 n ...
DOI:
10.1111/mec.13792

6. Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Author:
Westram, Anja M.; Panova, Marina; Galindo, Juan; Butlin, Roger K.
Source:
Molecular ecology 2016 v.25 no.13 pp. 3169-3186
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Geographical Locations; Littorina; biodiversity; ecotypes; gene flow; genetic variation; loci; phenotypic variation; predation; snails;     Show all 11 Subjects
Abstract:
... Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations – ‘outlier loci’ (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. Howe ...
DOI:
10.1111/mec.13640

7. Population and phylogenomic decomposition via genotyping‐by‐sequencing in Australian Pelargonium

Author:
Nicotra, Adrienne B.; Chong, Caroline; Bragg, Jason G.; Ong, Chong Ren; Aitken, Nicola C.; Chuah, Aaron; Lepschi, Brendan; Borevitz, Justin O.
Source:
Molecular ecology 2016 v.25 no.9 pp. 2000-2014
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Pelargonium; allopatric speciation; breeding; ecotypes; genetic variation; genomics; morphometry; taxonomy;     Show all 9 Subjects
Abstract:
... Species delimitation has seen a paradigm shift as increasing accessibility of genomic‐scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogen ...
DOI:
10.1111/mec.13584

8. The probability of parallel genetic evolution from standing genetic variation

Author:
MacPherson, A.; Nuismer, S. L.
Source:
Journal of evolutionary biology 2017 v.30 no.2 pp. 326-337
ISSN:
1010-061X
Subject:
parallel evolution,   etc   ; effective population size; evolutionary adaptation; genes; genetic drift; genetic variation; loci; mathematical models; natural selection; phenotype; phenotypic selection; probability;     Show all 12 Subjects
Abstract:
... Parallel evolution is often assumed to result from repeated adaptation to novel, yet ecologically similar, environments. Here, we develop and analyse a mathematical model that predicts the probability of parallel genetic evolution from standing genetic variation as a function of the strength of phenotypic selection and constraints imposed by genetic architecture. Our results show that the probabil ...
DOI:
10.1111/jeb.13006

9. Recurrent adaptation in a low‐dispersal trait

Author:
Raeymaekers, Joost A. M.; Backeljau, Thierry
Source:
Molecular ecology 2015 v.24 no.4 pp. 699-701
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Coleoptera; alleles; allopatry; ecotypes; genetic variation; introgression; mutation; salt marshes; screening;     Show all 10 Subjects
Abstract:
... The study of natural populations from contrasting environments has greatly enhanced our understanding of ecological‐dependent selection, adaptation and speciation. Cases of parallel evolution in particular have facilitated the study of the molecular and genetic basis of adaptive variation. This includes the type and number of genes underlying adaptive traits, as well as the extent to which these g ...
DOI:
10.1111/mec.13081

10. Evidence of gene orthology and trans‐species polymorphism, but not of parallel evolution, despite high levels of concerted evolution in the major histocompatibility complex of flamingo species

Author:
Gillingham, M. A. F.; Courtiol, A.; Teixeira, M.; Galan, M.; Bechet, A.; Cezilly, F.
Source:
Journal of evolutionary biology 2016 v.29 no.2 pp. 438-454
ISSN:
1010-061X
Subject:
parallel evolution,   etc   ; Phoenicopteridae; allopatry; amino acids; ancestry; codons; concerted evolution; exons; genetic variation; geographical distribution; loci; major histocompatibility complex; models; sequence homology; sympatry;     Show all 15 Subjects
Abstract:
... The major histocompatibility complex (MHC) is a cornerstone in the study of adaptive genetic diversity. Intriguingly, highly polymorphic MHC sequences are often not more similar within species than between closely related species. Divergent selection of gene duplicates, balancing selection maintaining trans‐species polymorphism (TSP) that predate speciation and parallel evolution of species sharin ...
DOI:
10.1111/jeb.12798

11. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

Author:
Luo, Tao; Comas, Iñaki; Luo, Dan; Lu, Bing; Wu, Jie; Wei, Lanhai; Yang, Chongguang; Liu, Qingyun; Gan, Mingyu; Sun, Gang; Shen, Xin; Liu, Feiying; Gagneux, Sebastien; Mei, Jian; Lan, Rushu; Wan, Kanglin; Gao, Qian
Source:
Proceedings of the National Academy of Sciences of the United States of America 2015 v.112 no.26 pp. 8136-8141
ISSN:
0027-8424
Subject:
parallel evolution,   etc   ; Chinese people; Mycobacterium tuberculosis; genetic variation; genotype; genotyping; humans; population density; population growth; sequence analysis; tuberculosis; China;     Show all 12 Subjects
Abstract:
... The Beijing family is the most successful genotype of Mycobacterium tuberculosis and responsible for more than a quarter of the global tuberculosis epidemic. As the predominant genotype in East Asia, the Beijing family has been emerging in various areas of the world and is often associated with disease outbreaks and antibiotic resistance. Revealing the origin and historical dissemination of this s ...
DOI:
10.1073/pnas.1424063112
PubMed:
26080405
PubMed Central:
PMC4491734

12. Inter and intra island introgression in a wolf spider radiation from the Galápagos, and its implications for parallel evolution

Author:
De Busschere, Charlotte; Van Belleghem, Steven Marcel; Hendrickx, Frederik
Source:
Molecular phylogenetics and evolution 2015 v.84 pp. 73-84
ISSN:
1055-7903
Subject:
parallel evolution,   etc   ; Lycosidae; adaptive radiation; alleles; altitude; gene flow; genetic relationships; genetic variation; habitats; interspecific variation; introgression; islands; mutation; phylogeny;     Show all 14 Subjects
Abstract:
... Parallel radiations within island systems are often assumed to follow a simple scenario in which single colonization events are followed by in situ adaptive divergence. However, subsequent gene exchange after the initial colonization and during the divergence process might have important evolutionary impacts on species radiations. Gene exchange among ecologically similar species from different isl ...
DOI:
10.1016/j.ympev.2014.11.004

13. Molecular and morphological systematics of the Ellisellidae (Coelenterata: Octocorallia): Parallel evolution in a globally distributed family of octocorals

Author:
Bilewitch, Jaret P.; Ekins, Merrick; Hooper, John; Degnan, Sandie M.
Source:
Molecular phylogenetics and evolution 2014 v.73 pp. 106-118
ISSN:
1055-7903
Subject:
parallel evolution,   etc   ; Ellisellidae; biogeography; branching; genes; genetic variation; new genus; polyphyly;     Show all 8 Subjects
Abstract:
... The octocorals of the Ellisellidae constitute a diverse and widely distributed family with subdivisions into genera based on colonial growth forms. Branching patterns are repeated in several genera and congeners often display region-specific variations in a given growth form. We examined the systematic patterns of ellisellid genera and the evolution of branching form diversity using molecular phyl ...
DOI:
10.1016/j.ympev.2014.01.023

14. Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation

Author:
McElroy, Kerensa E.; Hui, Janice G. K.; Woo, Jerry K. K.; Luk, Alison W. S.; Webb, Jeremy S.; Kjelleberg, Staffan; Rice, Scott A.; Thomas, Torsten
Source:
Proceedings of the National Academy of Sciences of the United States of America 2014 v.111 no.14 pp. E1419
ISSN:
0027-8424
Subject:
parallel evolution,   etc   ; Pseudomonas aeruginosa; RNA; bacteriophages; biofilm; fimbriae; genetic variation; high-throughput nucleotide sequencing; mutation; nucleotides; regulator genes;     Show all 11 Subjects
Abstract:
... Generation of genetic diversity is a prerequisite for bacterial evolution and adaptation. Short-term diversification and selection within populations is, however, largely uncharacterised, as existing studies typically focus on fixed substitutions. Here, we use whole-genome deep-sequencing to capture the spectrum of mutations arising during biofilm development for two Pseudomonas aeruginosa strains ...
DOI:
10.1073/pnas.1314340111
PubMed:
24706926
PubMed Central:
PMC3986123

15. Phylogeography of the prickly sculpin (Cottus asper) in north‐western North America reveals parallel phenotypic evolution across multiple coastal–inland colonizations

Author:
Dennenmoser, Stefan; Nolte, Arne W.; Vamosi, Steven M.; Rogers, Sean M.
Source:
Journal of biogeography 2015 v.42 no.9 pp. 1626-1638
ISSN:
0305-0270
Subject:
parallel evolution,   etc   ; Cottus asper; coasts; fish; genetic variation; haplotypes; microsatellite repeats; mitochondrial DNA; phenotype; phylogeography; refuge habitats; rivers; Alaska; British Columbia;     Show all 14 Subjects
Abstract:
... AIM: Glacial cycles during the Pleistocene may have frequently contributed to parallel evolution of phenotypes across independently evolving genetic lineages associated with separate glacial refugia. Previous studies based on morphology suggested that the prickly sculpin (Cottus asper) survived the Last Glacial Maximum (LGM) in southern coastal and inland refugia, favouring allopatric divergence b ...
DOI:
10.1111/jbi.12527

16. The origin and genetic divergence of “black” kokanee, a novel reproductive ecotype of Oncorhynchus nerka

Author:
Moreira, Amanda L.; Taylor, Eric B.
Source:
Canadian journal of fisheries and aquatic sciences 2015 v.72 no.10 pp. 1584-1595
ISSN:
1205-7533
Subject:
parallel evolution,   etc   ; Oncorhynchus nerka; anadromous fish; basins; biodiversity; color; ecotypes; genetic variation; lakes; loci; microsatellite repeats; mitochondrial DNA; spawning; spring; streams; sympatry; winter; British Columbia; Japan;     Show all 19 Subjects
Abstract:
... Kokanee and sockeye salmon are the freshwater-resident and anadromous forms, respectively, of Oncorhynchus nerka. Unique populations of “black” kokanee are found in Lake Saiko, Japan, and in Anderson and Seton lakes in the southwestern interior of British Columbia. They are distinct from other populations of O. nerka in that black kokanee display black nuptial colouration and they spawn between 20 ...
DOI:
10.1139/cjfas-2015-0145

17. Evolved resistance to PCB- and PAH-induced cardiac teratogenesis, and reduced CYP1A activity in Gulf killifish (Fundulus grandis) populations from the Houston Ship Channel, Texas

Author:
Oziolor, Elias M.; Bigorgne, Emilie; Aguilar, Lissette; Usenko, Sascha; Matson, Cole W.
Source:
Aquatic toxicology 2014 v.150 pp. 210-219
ISSN:
0166-445X
Subject:
parallel evolution,   etc   ; Fundulus grandis; Fundulus heteroclitus; dioxins; divergent evolution; estuaries; furans; genetic variation; mercury; pollution; polychlorinated biphenyls; polycyclic aromatic hydrocarbons; reciprocal crosses; toxicity; Gulf of Mexico; Texas;     Show all 16 Subjects
Abstract:
... The Houston Ship Channel (HSC), connecting Houston, Texas to Galveston Bay and ultimately the Gulf of Mexico, is heavily industrialized and includes several areas that have historically been identified as containing significant levels of mercury, dioxins, furans, polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs). Gulf killifish, Fundulus grandis, inhabit this entire est ...
DOI:
10.1016/j.aquatox.2014.03.012

18. Reduce, reuse, and recycle: Developmental evolution of trait diversification

Author:
Preston, Jill C.; Hileman, Lena C.; Cubas, Pilar
Source:
American journal of botany 2011 v.98 no.3 pp. 397-403
ISSN:
0002-9122
Subject:
parallel evolution,   etc   ; Magnoliophyta; genes; genetic variation; growth and development; phenotypic variation;     Show all 6 Subjects
Abstract:
... A major focus of evolutionary developmental (evo-devo) studies is to determine the genetic basis of variation in organismal form and function, both of which are fundamental to biological diversification. Pioneering work on metazoan and flowering plant systems has revealed conserved sets of genes that underlie the bauplan of organisms derived from a common ancestor. However, the extent to which var ...
DOI:
10.3732/ajb.1000279
PubMed:
21613133

19. More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms

Author:
Qi, Xinshuai; Liu, Yan; Vigueira, Cynthia C.; Young, Nelson D.; Caicedo, Ana L.; Jia, Yulin; Gealy, David R.; Olsen, Kenneth M.
Source:
Molecular ecology 2015 v.24 no.13 pp. 3329-3344
ISSN:
0962-1083
Subject:
parallel evolution,   etc   ; Oryza sativa; chromosome mapping; crops; crossing; cultivars; domestication; genes; genetic variation; heading; hulls; inbred lines; inflorescences; loci; paddies; pericarp; pigmentation; quantitative trait loci; quantitative traits; rice; seed shattering; weeds; United States;     Show all 23 Subjects
Abstract:
... Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this proc ...
DOI:
10.1111/mec.13256

20. Evidence for the persistence of the land planarian species Microplana terrestris (Müller, 1774) (Platyhelminthes, Tricladida) in microrefugia during the Last Glacial Maximum in the northern section of the Iberian Peninsula

Author:
Álvarez-Presas, Marta; Mateos, Eduardo; Vila-Farré, Miquel; Sluys, Ronald; Riutort, Marta
Source:
Molecular phylogenetics and evolution 2012 v.64 no.3 pp. 491-499
ISSN:
1055-7903
Subject:
parallel evolution,   etc   ; Tricladida; biogeography; cytochrome-c oxidase; demography; forests; genes; genetic variation; habitats; internal transcribed spacers; Iberian Peninsula;     Show all 11 Subjects
Abstract:
... The land planarian species Microplana terrestris (Müller, 1774), shows a wide distribution in the north of the Iberian Peninsula, where mature humid forests can be found. Since most terrestrial planarians require the presence and good condition of wet forests to survive, a parallel evolution of the taxon and its habitat might be expected. Performing molecular analyses (mitochondrial cytochrome oxi ...
DOI:
10.1016/j.ympev.2012.05.001
PubMed:
22587911