scholarly journals Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change

2017 ◽  
Author(s):  
Amir Szitenberg ◽  
Laura Salazar-Jaramillo ◽  
Vivian C. Blok ◽  
Dominik R. Laetsch ◽  
Soumi Joseph ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
Root Knot Nematodes ◽  
Geographic Origins ◽  
Dynamic Genome ◽  
History Of ◽  
Global Agriculture ◽  
Variable Success ◽  
Ploidy Changes ◽  
Genomic Basis

AbstractThe Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes pose challenges due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the MIG apomicts are hypotriploids, with a proportion of one genome present in a second copy, and this proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.

Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

2013 ◽  
Vol 23 (2) ◽  
pp. 343-359 ◽  
Author(s):  
Yongshuai Sun ◽  
Richard J. Abbott ◽  
Lili Li ◽  
Long Li ◽  
Jiabin Zou ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
Tibet Plateau ◽  
History Of ◽  
Homoploid Hybrid ◽  
Qinghai Tibet Plateau

scholarly journals Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

2018 ◽  
Author(s):  
Yuuhiko Tanabe ◽  
Haruyo Yamaguchi
Keyword(s):  
Evolutionary History ◽  
Core Genome ◽  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Green Light ◽  
Water Bloom ◽  
Phylogenetic Groups ◽  
Genome Phylogeny ◽  
History Of ◽  
Genomic Basis

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.

scholarly journals THE EVOLUTIONARY HISTORY OF PARTHENOGENETICCNEMIDOPHORUS LEMNISCATUS(SAURIA, TEIIDAE). I. EVIDENCE FOR A HYBRID ORIGIN

Evolution ◽  
1990 ◽  
Vol 44 (4) ◽  
pp. 906-921 ◽  
Author(s):  
Jack W. Sites ◽  
Denise M. Peccinini-Seale ◽  
Craig Moritz ◽  
John W. Wright ◽  
Wesley M. Brown
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
History Of

scholarly journals A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241231
Author(s):  
Joel H. Nitta ◽  
Atsushi Ebihara ◽  
Alan R. Smith
Keyword(s):  
Costa Rica ◽  
Evolutionary History ◽  
Cloud Forest ◽  
Dna Barcode ◽  
Hybrid Origin ◽  
Forest Reserve ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Ferns And Lycophytes

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

scholarly journals The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes

2020 ◽  
Vol 70 (1) ◽  
pp. 1-13
Author(s):  
Dawson M White ◽  
Jen-Pan Huang ◽  
Orlando Adolfo Jara-Muñoz ◽  
Santiago MadriñáN ◽  
Richard H Ree ◽  
...  
Keyword(s):  
South America ◽  
Evolutionary History ◽  
Amazon Basin ◽  
Plant Domestication ◽  
Target Sequence ◽  
South American ◽  
Sequence Capture ◽  
Domestication Event ◽  
Geographic Origins ◽  
History Of

Abstract Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]

scholarly journals The Aquilegia genome reveals a hybrid origin of core eudicots

2018 ◽  
Author(s):  
Gökçe Aköz ◽  
Magnus Nordborg
Keyword(s):  
Evolutionary History ◽  
Genetic Material ◽  
Diploid Species ◽  
Hybrid Origin ◽  
The Core ◽  
Whole Genome Duplications ◽  
Core Eudicots ◽  
Eventual Return ◽  
Genome Duplications ◽  
History Of

AbstractBackgroundWhole-genome duplications (WGD) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots.ResultsWithin-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization, and that core eudicots thus have a hybrid origin.ConclusionsNovel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

scholarly journals An African origin for Mycobacterium bovis

2019 ◽  
Author(s):  
Chloé Loiseau ◽  
Fabrizio Menardo ◽  
Abraham Aseffa ◽  
Elena Hailu ◽  
Balako Gumi ◽  
...  
Keyword(s):  
Population Structure ◽  
Mycobacterium Bovis ◽  
Evolutionary History ◽  
Whole Genome ◽  
African Origin ◽  
Genome Sequences ◽  
Geographic Origins ◽  
History Of ◽  
Global Population ◽  
Different Parts

ABSTRACTBackground and objectivesMycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis (TB) in livestock and the most important causes of zoonotic TB in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens.MethodologyWe compiled a global collection of 3364 whole-genome sequences from M. bovis and M. caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age.ResultsOur results resolved the phylogenetic relationship among the four previously defined clonal complexes of M. bovis, and another eight newly described here. Our phylogeographic analysis showed that M. bovis likely originated in East Africa. While some groups remained restricted to East- and West Africa, others have subsequently dispersed to different parts of the world.Conclusions and implicationsOur results allow a better understanding of the global population structure of M. bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M. bovis in settings where whole genome sequencing cannot easily be implemented.

scholarly journals Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

2021 ◽  
Author(s):  
Weizhao Yang ◽  
Nathalie Feiner ◽  
Daniele Salvi ◽  
Hanna Laakkonen ◽  
Daniel Jablonski ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mediterranean Basin ◽  
Evolutionary History ◽  
Central Italy ◽  
Hybrid Origin ◽  
Recent Common Ancestor ◽  
Extant Species ◽  
History Of ◽  
The Mediterranean ◽  
The Mediterranean Basin

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an Out-of-Italy expansion following the Messinian salinity crisis (~5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flow have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.

scholarly journals The Evolutionary History of Parthenogenetic Cnemidophorus lemniscatus (Sauria, Teiidae). I. Evidence for a Hybrid Origin

Evolution ◽  
1990 ◽  
Vol 44 (4) ◽  
pp. 906 ◽  
Author(s):  
Jack W. Sites ◽  
Denise M. Peccinnini-Seale ◽  
Craig Moritz ◽  
John W. Wright ◽  
Wesley M. Brown
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
History Of

scholarly journals Phylogenetic Diversity of Sequences of Cyanophage Photosynthetic Gene psbA in Marine and Freshwaters

2008 ◽  
Vol 74 (17) ◽  
pp. 5317-5324 ◽  
Author(s):  
C. Chénard ◽  
C. A. Suttle
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
D1 Protein ◽  
The Arctic ◽  
Aquatic Environments ◽  
Single Family ◽  
Aquatic Communities ◽  
Widespread Occurrence ◽  
Geographic Origins ◽  
History Of

ABSTRACT Many cyanophage isolates which infect the marine cyanobacteria Synechococcus spp. and Prochlorococcus spp. contain a gene homologous to psbA, which codes for the D1 protein involved in photosynthesis. In the present study, cyanophage psbA gene fragments were readily amplified from freshwater and marine samples, confirming their widespread occurrence in aquatic communities. Phylogenetic analyses demonstrated that sequences from freshwaters have an evolutionary history that is distinct from that of their marine counterparts. Similarly, sequences from cyanophages infecting Prochlorococcus and Synechococcus spp. were readily discriminated, as were sequences from podoviruses and myoviruses. Viral psbA sequences from the same geographic origins clustered within different clades. For example, cyanophage psbA sequences from the Arctic Ocean fell within the Synechococcus as well as Prochlorococcus phage groups. Moreover, as psbA sequences are not confined to a single family of phages, they provide an additional genetic marker that can be used to explore the diversity and evolutionary history of cyanophages in aquatic environments.

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