The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for designing new approaches in crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

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Brassicales to Brassica : integrating phylogenomics and population genomics

10.32469/10355/86505 ◽

2020 ◽

Author(s):

◽

Makenzie Elizabeth Mabry

Keyword(s):

Brassica Oleracea ◽

Population Genomics ◽

Animal Feed ◽

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Phenotypic Traits ◽

Crop Species ◽

Brussels Sprouts ◽

Feral Populations ◽

The Family

The Brassicales are an economically important order of flowering plants. Many crop species such as kale, broccoli, cabbage, cauliflower, canola oil, capers, and papaya, as well as the model plant organism, Arabidopsis thaliana, all belong to this diverse order. The focus of my dissertation has been to use phylogenomics and population genomics to understand the evolution of the Brassicales, as well as the important crop species Brassica oleracea. Within the Brassicales, the family Brassicaceae is notable for many whole-genome duplication (WGD) events, including one at the base of the family. The sister family to the Brassicaceae, the Cleomaceae, is also known to have a WGD event; however, it has never been placed within the family. Previous studies assessing the relationships between and within these families have either used a few genes or a few taxa. Phylo-transcriptomics, a quickly evolving field that uses RNA-seq data to make phylogenomic inferences from many more nuclear genes than traditional PCR, is a great method to no longer have to choose between too few genes or taxa. For my second chapter, I used phylotranscriptiomics to estimate relationships in the Brassicales and used the resulting phylogeny as a framework for inferring WGD events. These analyses recovered the known At-[beta] and At-[alpha] events, as well as multiple independent WGD events in the Cleomaceae, Capparaceae, and Resedaceae. The horticultural crop Brassica oleracea is a notable member of the Brassicales, playing an important role in global food systems. Brassica oleracea is unique in that it has been domesticated into several morphotypes (cultivars), including broccoli, Brussels sprouts, cabbage, cauliflower, kale, kohlrabi, and several lesser well known morphotypes, such as walking stick kale and marrow cabbage. These crops are widely used as leaf and root vegetables, as well as for animal feed. There are several hypotheses on the origin of these crops. However, after resolving the relationships between wild relatives and domesticated types, I have determined that cultivation likely originated in the Eastern Mediterranean region, with additional domestications occurring around the world. I also identified feral populations that had previously been mistaken as progenitor populations. Using this system of diversity within domesticated B. oleracea, I examined patterns of relationships among morphotypes, including signals of hybridization and introgression. Brassica oleracea vegetable crops are frequently regarded as superfoods (e.g., kale) and are an important diet source for key minerals and elements. Ionomics, the measurement of the total elemental composition of an organism, allows for high throughput characterization of the levels of these elements at the same time, including those important to diet such as iron and zinc. Using association mapping techniques, I have identified genes underlying quantitative phenotypic traits of economic importance such as iron, as well as total element composition. This knowledge can then allow for further decisions of the best accessions to target for human health, as well as provide an excellent resource for future studies wanting to enhance specific elements in different crops. To conclude, I discuss the unique opportunity that feral populations provide for the study of natural selection and how this information can be leveraged for improvement of crops in breeding them to be more locally adapted.

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Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary

BMC Evolutionary Biology ◽

10.1186/s12862-019-1426-z ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Brawin Kumar ◽

Jilong Cheng ◽

Deyan Ge ◽

Lin Xia ◽

Qisen Yang

Keyword(s):

Ecological Niche ◽

Evolutionary History ◽

Ecological Niche Modeling ◽

Niche Modeling ◽

History Of

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Taxonomic notes on the snakes of Northern Cyprus, with observations on their morphologies and ecologies

Animal Biology ◽

10.1163/157075609x417062 ◽

2009 ◽

Vol 59 (1) ◽

pp. 1-30 ◽

Cited By ~ 4

Author(s):

Abidin Budak ◽

Bayram Göçmen ◽

Nuren Alpagut-Keskin ◽

Hasan Bahar ◽

Mehmet Zülfü Yildiz ◽

...

Keyword(s):

Mediterranean Region ◽

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Field Studies ◽

Geological History ◽

Snake Species ◽

Ecological Information ◽

Northern Cyprus ◽

History Of ◽

Points Of View

AbstractA total of 66 specimens belonging to eleven snake species, some of which were collected during the field studies of 17-31 July and 3-25 September 2003, and some others which have been previously collected and all have been deposited into the collection of ZDEU (Zoology Dept. Ege University), were evaluated taxonomically. 25 of the specimens belonged to Typhlopidae, 37 to Colubridae, three to Viperidae and one to Boidae. These specimens were evaluated from the points of view of pholidosis, pattern and coloration and morphological measurements. Some biological and ecological information were also given with the brief geological history of eastern Mediterranean region.

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WHEAT EVOLUTION

Israel Journal of Plant Sciences ◽

10.1080/07929978.1995.10676595 ◽

1995 ◽

Vol 43 (2) ◽

pp. 85-98 ◽

Cited By ~ 44

Author(s):

Adina Breiman ◽

Dan Graur

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Wild Relatives ◽

Wheat Species ◽

Polyploid Species ◽

Wheat Evolution ◽

History Of ◽

Nuclear Genomes ◽

Evolutionary Consequences ◽

Independent Evolutionary History

Many wild and cultivated wheat species are amphidiploid, i.e., they are polyploid species containing two or more distinct nuclear genomes, each with its own independent evolutionary history, but whose genetic behavior resembles that of diploids. Amphidiploidy has important evolutionary consequences in wheat. Since the beginning of this century different methods have been employed to identify the diploid donors of the coexisting genomes in the polyploids. To date, several of the genomic donors have been identified, and the search for the others has been narrowed down considerably. Molecular methodologies that are being increasingly used in studies aimed at reconstructing the evolutionary history of wheat species and their wild relatives have resolved many of the phylogenetic relationships among the various taxa.

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Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

Biology Letters ◽

10.1098/rsbl.2006.0467 ◽

2006 ◽

Vol 2 (3) ◽

pp. 451-454 ◽

Cited By ~ 23

Author(s):

Nikos Poulakakis ◽

Aris Parmakelis ◽

Petros Lymberakis ◽

Moysis Mylonas ◽

Eleftherios Zouros ◽

...

Keyword(s):

Dna Sequence ◽

Ancient Dna ◽

Evolutionary History ◽

Eastern Mediterranean ◽

Multiple Displacement Amplification ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Mediterranean Islands ◽

Amplification Method ◽

History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

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Expanding the RNA Virosphere by Unbiased Metagenomics

Annual Review of Virology ◽

10.1146/annurev-virology-092818-015851 ◽

2019 ◽

Vol 6 (1) ◽

pp. 119-139 ◽

Cited By ~ 26

Author(s):

Yong-Zhen Zhang ◽

Yan-Mei Chen ◽

Wen Wang ◽

Xin-Chen Qin ◽

Edward C. Holmes

Keyword(s):

Evolutionary History ◽

Genetic Material ◽

Virus Species ◽

Future Directions ◽

Important Species ◽

Virus Diversity ◽

Limited Perspective ◽

Etiologic Agents ◽

History Of ◽

Overt Disease

Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.

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Progress towards elimination of lymphatic filariasis in the Eastern Mediterranean Region

International Health ◽

10.1093/inthealth/ihaa037 ◽

2020 ◽

Vol 13 (Supplement_1) ◽

pp. S28-S32

Author(s):

Reda M R Ramzy ◽

Abdul Samid Al Kubati

Keyword(s):

Lymphatic Filariasis ◽

Mediterranean Region ◽

Disease Burden ◽

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Public Health Problem ◽

World Health ◽

Prevention Measures ◽

Control And Prevention ◽

History Of

Abstract Lymphatic filariasis (LF), a neglected tropical disease, is targeted for global elimination as a public health problem. This article reviews the history of LF control and elimination activities in the countries of the World Health Organization's (WHO) Eastern Mediterranean Region (EMR) over the last 2 decades. In 2000, the estimated at-risk population in EMR countries was 12.6 million people, accounting for approximately 1% of the global disease burden. Of the 22 EMR countries, 3 countries (Egypt, Sudan and Yemen) were LF endemic and the disease was suspected in 4 other countries (Djibouti, Oman, Somalia and Saudi Arabia). After almost 2 decades of implementing sustained control and prevention measures, Egypt and Yemen were successfully validated by the WHO as having achieved the elimination criteria in 2017 and 2019, respectively. In 2018, Sudan completed mapping of LF, reaching 26.2% geographical coverage where mass drug administration (MDA) is required and is scaling-up MDA. Extensive epidemiological assessment indicated the absence of LF transmission in the four suspected countries and no MDA required. Challenges faced during the elimination and post-elimination phases are described and discussed.

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Multivariate analysis of recombination between wild and cultivated genomes within the primary gene pool of pearl millet (Pennisetum typhoides)

Genome ◽

10.1139/g92-032 ◽

1992 ◽

Vol 35 (2) ◽

pp. 208-219 ◽

Cited By ~ 7

Author(s):

T. Robert ◽

A. Sarr

Keyword(s):

Multivariate Analysis ◽

Pearl Millet ◽

Evolutionary History ◽

Wild Relatives ◽

Genome Recombination ◽

History Of ◽

Morphological And Physiological Traits ◽

Primary Gene Pool ◽

Different Levels ◽

Primary Gene

Recombination between wild and cultivated genomes of pearl millet were studied by multivariate analysis on morphological and physiological traits in backcross progenies from four cultivated × wild crosses. The cultivated genotypes, Souna and Thiotandé, have evolved in sympatric and allopatric situations, respectively, with wild forms. The distinct evolutionary history of the cultivated genotypes seems to have an incidence on the segregation pattern of their progenies with the wild relatives. Segregation distortions favouring the recovery of "wild-like" phenotypes were observed in progenies with Thiotandé as the cultivated parent. They are probably a consequence of the genetic divergence between this genotype and wild forms already shown at different levels of observation (histological, physiological, and genetic). On the other hand, when Souna is the cultivated parent, the recovery of "cultivated-like" phenotypes was shown to be easier with Souna as the female. This could be due to preferential homogametic fertilization favouring "Souna-type" gametes on Souna pistils owing to intergametophytic competition through a pollen–pistil interaction, already evidenced on the genotypes used here.Key words: pearl millet, multivariate analysis, segregation distortion, wild/cultivated genome recombination, genetic resources.

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Reassessing the age of Karpathos ophiolite (Dodecanese, Greece): consequences for Aegean correlations and Neotethys evolution

Geological Magazine ◽

10.1017/s0016756819000657 ◽

2019 ◽

Vol 157 (2) ◽

pp. 263-274

Author(s):

Fabrice Cordey ◽

Frédéric Quillévéré

Keyword(s):

Late Cretaceous ◽

Mediterranean Basin ◽

Mediterranean Region ◽

Eastern Mediterranean ◽

Eastern Mediterranean Region ◽

Aegean Islands ◽

History Of ◽

Eastern Mediterranean Basin ◽

Of Greece ◽

Radiolarian Assemblages

AbstractWhile the Neogene history of the Eastern Mediterranean region is now fairly well understood, our knowledge of older regional palaeogeographies is less accurate, especially the positions of blocks and nappes constituting the Aegean Islands prior to the Cenozoic. Our study focuses on the ophiolite exposed on the island of Karpathos (Dodecanese), which is located in the Aegean fore-arc at a pivotal position between the ‘western’ and ‘eastern’ ophiolites of the Mediterranean region and where conflicting Late Jurassic and Late Cretaceous ages have led to diverging tectonic and palaeogeographic interpretations. To test these ages, we targeted the radiolarian cherts that depositionally overlie the ophiolite and extracted diagnostic radiolarian assemblages of Aptian (∼125−113 Ma), early–middle Albian (∼113−105 Ma) and Turonian (∼93.9−89.8 Ma) ages. These results suggest that previous Late Cretaceous K–Ar isotopic ages (from 95.3 ± 4.2 Ma to 81.2 ± 1.6 Ma) may have been reset by Late Cretaceous metamorphism or affected by argon loss. Overall, the new Early Cretaceous ages show that the Karpathos ophiolite should not be correlated with the Pindos Nappes of Greece or the ophiolites of Cyprus or Syria but rather with the Lycian Nappes of Turkey and their root located in the Izmir–Ankara–Erzincan Suture Zone. Therefore, the Karpathos ophiolite represents a remnant of the Northern Neotethys, not the Pindos Ocean or the proto-Eastern Mediterranean Basin.

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