Colonization history of the Canary Islands endemic Lavatera acerifolia, (Malvaceae) unveiled with genotyping‐by‐sequencing data and niche modelling

2020 ◽  
Vol 47 (4) ◽  
pp. 993-1005 ◽  
Author(s):  
Irene Villa‐Machío ◽  
Alejandro G. Fernández de Castro ◽  
Javier Fuertes‐Aguilar ◽  
Gonzalo Nieto Feliner
Keyword(s):  
Canary Islands ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Modelling ◽  
Colonization History ◽  
History Of

scholarly journals Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

2020 ◽  
Author(s):  
Rafael G Albaladejo ◽  
Sara Martín-Hernanz ◽  
J Alfredo Reyes-Betancort ◽  
Arnoldo Santos-Guerra ◽  
María Olangua-Corral ◽  
...  
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Genotyping By Sequencing ◽  
Niche Conservatism ◽  
Sequencing Data ◽  
History Of ◽  
Spatio Temporal ◽  
Dispersal Events

Abstract Background and Aims Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae). Methods We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade. Key Results Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor. Conclusions The rapid and abundant diversification (0.75–1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

scholarly journals Mastering the difficulties presented by the peculiarities of island life. A commentary on: ‘Reconstruction of the spatio-temporal diversification and ecological niche evolution ofHelianthemum(Cistaceae) in the Canary Islands using genotyping-by-sequence data’

2021 ◽  
Vol 127 (5) ◽  
pp. iii-iv
Author(s):  
Mark Carine
Keyword(s):  
Canary Islands ◽  
Ecological Niche ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Sequencing Data ◽  
Niche Evolution ◽  
Spatio Temporal

This article comments on:Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090

scholarly journals The phylogeographic history of Krascheninnikovia reflects the development of dry steppes and semi-deserts in Eurasia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna Seidl ◽  
Karin Tremetsberger ◽  
Simon Pfanzelt ◽  
Frank R. Blattner ◽  
Barbara Neuffer ◽  
...  
Keyword(s):  
North America ◽  
Central Asia ◽  
Genotyping By Sequencing ◽  
Climatic Conditions ◽  
Sequencing Data ◽  
The Caspian Sea ◽  
Dry Steppe ◽  
Steppe Belt ◽  
History Of ◽  
Suitable Habitats

AbstractConstituting one of Earth’s major biomes, steppes are characterised by naturally treeless extra-tropical vegetation. The formation of the Eurasian steppe belt, the largest steppe region in the world, began in Central Asia during the Neogene. In the glacial stages of the Pleistocene, steppe displaced forest vegetation, which in turn recolonised the area during the warmer interglacial periods, thus affecting the distribution of plants adapted to these habitats. Krascheninnikovia ceratoides (Chenopodiaceae) is a plant characteristic of dry steppe and semi-desert formations. Earlier studies showed that the ancestor of this autochthonous steppe element originated in Central Asia during the Miocene/Pliocene, i.e., in the same region and at the same time as the first appearance of steppe vegetation. However, as the extant lineages of Krascheninnikovia ceratoides diversified only 2.2 ± 0.9 Mya, it may represent a modern element of current dry steppe and semi-desert formations, rather than a component of the first steppe precursors of the Miocene. As such, it may have capitalised on the climatic conditions of the cold stages of the Quaternary to expand its range and colonise suitable habitats outside of its area of origin. To test this hypothesis, phylogeographic methods were applied to high-resolution genotyping-by-sequencing data. Our results indicate that Krascheninnikovia originated in western Central Asia and the Russian Altai, then spread to Europe in the West, and reached North America in the East. The populations of eastern Central Asia and North America belong to the same clade and are genetically clearly distinct from the Euro-Siberian populations. Among the populations west of the Altai Mountains, the European populations are genetically distinct from all others, which could be the result of the separation of populations east and west of the Urals caused by the Pleistocene transgressions of the Caspian Sea.

scholarly journals Phylogeographical and cytogeographical history of Artemisia herba-alba (Asteraceae) in the Iberian Peninsula and North Africa: mirrored intricate patterns on both sides of the Mediterranean Sea

2020 ◽  
Author(s):  
Youcef Bougoutaia ◽  
Teresa Garnatje ◽  
Joan Vallès ◽  
Meriem Kaid-Harche ◽  
Ahmed Ouhammou ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Mediterranean Sea ◽  
North Africa ◽  
Haplotype Diversity ◽  
Environmental Niche ◽  
Sequencing Data ◽  
Niche Modelling ◽  
Diversity Patterns ◽  
History Of ◽  
The Mediterranean

Abstract Artemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals Mice as stowaways? Colonization history of Danish striped field mice

2017 ◽  
Vol 13 (7) ◽  
pp. 20170064 ◽  
Author(s):  
Liselotte Wesley Andersen ◽  
Magnus Jacobsen ◽  
Christina Vedel-Smith ◽  
Thomas Secher Jensen
Keyword(s):  
Eastern Europe ◽  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Field Mouse ◽  
Colonization History ◽  
Striped Field Mouse ◽  
Steppe Region ◽  
History Of ◽  
Field Mice ◽  
Human Introduction

Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse ( Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.

scholarly journals The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

2021 ◽  
Author(s):  
Kris A. Christensen ◽  
Eric B. Rondeau ◽  
Dionne Sakhrani ◽  
Carlo A. Biagi ◽  
Hollie Johnson ◽  
...  
Keyword(s):  
Pacific Salmon ◽  
Pink Salmon ◽  
Chromosomal Polymorphism ◽  
Oncorhynchus Gorbuscha ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Temporal Isolation ◽  
History Of ◽  
Genome Assemblies ◽  
Salmon Fishery

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

scholarly journals Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

2021 ◽  
Vol 118 (34) ◽  
pp. e2104315118
Author(s):  
Pasquale Tripodi ◽  
Mark Timothy Rabanus-Wallace ◽  
Lorenzo Barchi ◽  
Sandip Kale ◽  
Salvatore Esposito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Focal Region ◽  
Nucleotide Polymorphisms ◽  
Trade Routes ◽  
Genebank Management ◽  
Capsicum Spp ◽  
History Of ◽  
Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

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