scholarly journals Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

2015 ◽  
Author(s):  
Markus G. Stetter ◽  
Thomas Müller ◽  
Karl J. Schmid
Keyword(s):  
Gene Flow ◽  
Phenotypic Diversity ◽  
Geographic Origin ◽  
Evolutionary Relationship ◽  
South American ◽  
Seed Color ◽  
Domestication Syndrome ◽  
Amaranthus Caudatus ◽  
Grain Amaranth ◽  
Close Relatives

AbstractThe process of domestication leads to major morphological and genetic changes, which in combination are known as domestication syndrome that differentiates crops from their wild ancestors. We characterized the genomic and phenotypic diversity of the South American grain amaranthAmaranthus caudatus, which has been cultivated for thousands of years and is one of the three native grain amaranths of South and Central America. Previously, several models of domestication were proposed including a domestication from the close relatives and putative ancestorsA. hybridusorA. quitensis. To investigate the evolutionary relationship ofA. caudatusand its two close relatives, we genotyped 119 amaranth accessions of the three species from the Andean region using genotyping-by-sequencing (GBS) and compared phenotypic variation in two domestication-related traits, seed size and seed color. The analysis of 9,485 SNPs revealed a strong genetic differentiation of cultivatedA. caudatusfrom the relativesA. hybridusandA. quitensis. The two relatives did not cluster according to the species assigment but formed mixed groups according to their geographic origin in Ecuador and Peru, respectively.A. caudatushad a higher genetic diversity than its close relatives and shared a high proportion of polymorphisms with their wild relatives consistent with the absence of a strong bottleneck or a high level of recent gene flow. Genome sizes and seed sizes were not significantly different betweenA. caudatusand its relatives, although a genetically distinct group ofA. caudatusfrom Bolivia had significantly larger seeds. We conclude that despite a long history of human cultivation and selection for white grain color,A. caudatusshows a weak genomic and phenotypic domestication syndrome and is an incompletely domesticated species because of weak selection or high levels of gene flow from its sympatric close undomesticated relatives that counteracted the fixation of key domestication traits.

scholarly journals Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus )

2017 ◽  
Vol 26 (3) ◽  
pp. 871-886 ◽  
Author(s):  
Markus G. Stetter ◽  
Thomas Müller ◽  
Karl J. Schmid
Keyword(s):  
South American ◽  
Amaranthus Caudatus ◽  
Grain Amaranth

SINE-B1 Distribution and Chromosome Rearrangements in the South American Proechimys gr. goeldii (Echimyidae, Rodentia)

2021 ◽  
pp. 1-8
Author(s):  
Naiara P. Araújo ◽  
Radarane S. Sena ◽  
Cibele R. Bonvicino ◽  
Gustavo C.S. Kuhn ◽  
Marta Svartman
Keyword(s):  
Transposable Element ◽  
Genome Evolution ◽  
Significant Role ◽  
Sex Chromosomes ◽  
Chromosomal Rearrangements ◽  
Evolutionary Relationship ◽  
Chromosome Rearrangements ◽  
South American ◽  
Gross Chromosomal Rearrangements

<i>Proechimys</i> species are remarkable for their extensive chromosome rearrangements, representing a good model to understand genome evolution. Herein, we cytogenetically analyzed 3 different cytotypes of <i>Proechimys</i> gr. <i>goeldii</i> to assess their evolutionary relationship. We also mapped the transposable element SINE-B1 on the chromosomes of <i>P.</i> gr. <i>goeldii</i> in order to investigate its distribution among individuals and evaluate its possible contribution to karyotype remodeling in this species. SINE-B1 showed a dispersed distribution along chromosome arms and was also detected at the pericentromeric regions of some chromosomes, including pair 1 and the sex chromosomes, which are involved in chromosome rearrangements. In addition, we describe a new cytotype for <i>P.</i> gr. <i>goeldii</i>, reinforcing the significant role of gross chromosomal rearrangements during the evolution of the genus. The results of FISH with SINE-B1 suggest that this issue should be more deeply investigated for a better understanding of its role in the mechanisms involved in the wide variety of <i>Proechimys</i> karyotypes.

scholarly journals Multiple incursion pathways for Helicoverpa armigera in Brazil show its genetic diversity spreading in a connected world

2019 ◽  
Author(s):  
Jonas A. Arnemann ◽  
Stephen H. Roxburgh ◽  
Tom Walsh ◽  
Jerson V.C. Guedes ◽  
Karl H.J. Gordon ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Gene Flow ◽  
South America ◽  
New World ◽  
Flow Patterns ◽  
South American ◽  
Southern Brazil ◽  
American Continent ◽  
Central Brazil ◽  
South American Continent

AbstractThe Old World cotton bollworm Helicoverpa armigera was first detected in Brazil with subsequent reports from Paraguay, Argentina, Bolivia, and Uruguay. This pattern suggests that the H. armigera spread across the South American continent following incursions into northern/central Brazil, however, this hypothesis has not been tested. Here we compare northern and central Brazilian H. armigera mtDNA COI haplotypes with those from southern Brazil, Uruguay, Argentina, and Paraguay. We infer spatial genetic and gene flow patterns of this dispersive pest in the agricultural landscape of South America. We show that the spatial distribution of H. armigera mtDNA haplotypes and its inferred gene flow patterns in the southwestern region of South America exhibited signatures inconsistent with a single incursion hypothesis. Simulations on spatial distribution patterns show that the detection of rare and/or the absence of dominant mtDNA haplotypes in southern H. armigera populations are inconsistent with genetic signatures observed in northern and central Brazil. Incursions of H. armigera into the New World are therefore likely to have involved independent events in northern/central Brazil, and southern Brazil/Uruguay-Argentina-Paraguay. This study demonstrates the significant biosecurity challenges facing the South American continent, and highlights alternate pathways for introductions of alien species into the New World.

scholarly journals Multiple incursion pathways for Helicoverpa armigera in Brazil show its genetic diversity spreading in a connected world

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jonas Andre Arnemann ◽  
Stephen Roxburgh ◽  
Tom Walsh ◽  
Jerson Guedes ◽  
Karl Gordon ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Gene Flow ◽  
South America ◽  
New World ◽  
Flow Patterns ◽  
South American ◽  
Southern Brazil ◽  
American Continent ◽  
Central Brazil ◽  
South American Continent

AbstractThe Old World cotton bollworm Helicoverpa armigera was first detected in Brazil with subsequent reports from Paraguay, Argentina, Bolivia, and Uruguay. This pattern suggests that the H. armigera spread across the South American continent following incursions into northern/central Brazil, however, this hypothesis has not been tested. Here we compare northern and central Brazilian H. armigera mtDNA COI haplotypes with those from southern Brazil, Uruguay, Argentina, and Paraguay. We infer spatial genetic and gene flow patterns of this dispersive pest in the agricultural landscape of South America. We show that the spatial distribution of H. armigera mtDNA haplotypes and its inferred gene flow patterns in the southwestern region of South America exhibited signatures inconsistent with a single incursion hypothesis. Simulations on spatial distribution patterns show that the detection of rare and/or the absence of dominant mtDNA haplotypes in southern H. armigera populations are inconsistent with genetic signatures observed in northern and central Brazil. Incursions of H. armigera into the New World are therefore likely to have involved independent events in northern/central Brazil, and southern Brazil/Uruguay-Argentina-Paraguay. This study demonstrates the significant biosecurity challenges facing the South American continent, and highlights alternate pathways for introductions of alien species into the New World.

scholarly journals The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 258 ◽  
Author(s):  
Dominique L. Chaput ◽  
David Bass ◽  
Md. Mehedi Alam ◽  
Neaz Al Hasan ◽  
Grant D. Stentiford ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Geographical Origin ◽  
Rna Virus ◽  
Geographic Origin ◽  
South American ◽  
Reassortment Event ◽  
Coding Regions ◽  
Whole Genomes ◽  
History Of ◽  
Negative Sense

Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.

scholarly journals Patterns of Genome-Wide Variation, Population Differentiation and SNP Discovery of the Red Banded Stink Bug (Piezodorus guildinii)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Maria I. Zucchi ◽  
Erick M. G. Cordeiro ◽  
Clint Allen ◽  
Mariana Novello ◽  
João Paulo Gomes Viana ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Structure ◽  
Insect Pests ◽  
Geographic Origin ◽  
The United States ◽  
Basic Knowledge ◽  
Stink Bug ◽  
Mixed Ancestry ◽  
Significant Genetic Structure

Abstract Unravelling the details of range expansion and ecological dominance shifts of insect pests has been challenging due to the lack of basic knowledge about population structure, gene flow, and most importantly, how natural selection is affecting the adaptive process. Piezodous guildinii is an emerging pest of soybean in the southern region of the United States, and increasingly important in Brazil in recent years. However, the reasons P. guildinii is gradually becoming more of a problem are questions still mostly unanswered. Here, we have genotyped P. guildinii samples and discovered 1,337 loci containing 4,083 variant sites SNPs that were used to estimate genetic structure and to identify gene candidates under natural selection. Our results revealed the existence of a significant genetic structure separating populations according to their broad geographic origin, i.e., U.S. and Brazil, supported by AMOVA (FGT = 0.26), STRUCTURE, PCA, and FST analyses. High levels of gene flow or coancestry within groups (i.e., within countries) can be inferred from the data, and no spatial pattern was apparent at the finer scale in Brazil. Samples from different seasons show more heterogeneous compositions suggesting mixed ancestry and a more complex dynamic. Lastly, we were able to detect and successfully annotated 123 GBS loci (10.5%) under positive selection. The gene ontology (GO) analysis implicated candidate genes under selection with genome reorganization, neuropeptides, and energy mobilization. We discuss how these findings could be related to recent outbreaks and suggest how new efforts directed to better understand P. guildinii population dynamics.

scholarly journals Parallel Seed Color Adaptation during Multiple Domestication Attempts of an Ancient New World Grain

2019 ◽  
Vol 37 (5) ◽  
pp. 1407-1419 ◽  
Author(s):  
Markus G Stetter ◽  
Mireia Vidal-Villarejo ◽  
Karl J Schmid
Keyword(s):  
Genomic Region ◽  
Color Variation ◽  
Chromosome 9 ◽  
Seed Color ◽  
Color Adaptation ◽  
Crop Species ◽  
Grain Amaranth ◽  
Amaranth Species ◽  
Genomic Regions ◽  
Selection Of

Abstract Thousands of plants have been selected as crops; yet, only a few are fully domesticated. The lack of adaptation to agroecological environments of many crop plants with few characteristic domestication traits potentially has genetic causes. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. Although three grain amaranth species have been cultivated as crop for millennia, all three lack key domestication traits. We sequenced 121 crop and wild individuals to investigate the genomic signature of repeated incomplete adaptation. Our analysis shows that grain amaranth has been domesticated three times from a single wild ancestor. One trait that has been selected during domestication in all three grain species is the seed color, which changed from dark seeds to white seeds. We were able to map the genetic control of the seed color adaptation to two genomic regions on chromosomes 3 and 9, employing three independent mapping populations. Within the locus on chromosome 9, we identify an MYB-like transcription factor gene, a known regulator for seed color variation in other plant species. We identify a soft selective sweep in this genomic region in one of the crop species but not in the other two species. The demographic analysis of wild and domesticated amaranths revealed a population bottleneck predating the domestication of grain amaranth. Our results indicate that a reduced level of ancestral genetic variation did not prevent the selection of traits with a simple genetic architecture but may have limited the adaptation of complex domestication traits.

Galaxias maculatus: An explanation of its biogeography

1996 ◽  
Vol 47 (6) ◽  
pp. 845 ◽  
Author(s):  
TM Berra ◽  
LELM Crowley ◽  
W Ivantsoff ◽  
PA Fuerst
Keyword(s):  
Gene Flow ◽  
New Zealand ◽  
Oceanic Islands ◽  
Western Pacific ◽  
Disjunct Distribution ◽  
South American ◽  
Salt Tolerant ◽  
Galaxias Maculatus ◽  
Break Up ◽  
The Western Pacific

Galaxias maculatus is a small diadromous fish found in Australia, New Zealand, South America and on some oceanic islands. Two hypotheses have been advanced to explain this widespread, disjunct distribution. McDowall promoted dispersal through the sea of salt-tolerant juveniles but Rosen and others claimed that the distribution reflected the break-up of Gondwana and subsequent drift of the southern continents. Allozyrne electrophoresis of muscle extracts of specimens of Galaxias maculatus from eastern and western Australia, New Zealand and Chile was used to test the hypothesis that populations of G. maculatus from the western Pacific and the eastern Pacific do not differ genetically. FST based on allele frequencies and genotypes was 0.14, suggesting only minor differentiation between eastern and western Pacific populations. Minor differentiation in allele frequency existed at some loci, but no fixation of alternative alleles has occurred. The populations examined appear to be part of the same gene pool, indicating that gene flow via dispersal through the sea occurs today. It is unlikely that South American and Australasian populations would be conspecific if they have exchanged no migrants since the break-up of Gondwana at the end of the Mesozoic.

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