scholarly journals The genomics of ecological vicariance in threespine stickleback fish

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Marius Roesti ◽  
Benjamin Kueng ◽  
Dario Moser ◽  
Daniel Berner
Keyword(s):  
Molecular Level ◽  
Parallel Evolution ◽  
Threespine Stickleback ◽  
Ancestral Population ◽  
Selective Sweeps ◽  
Population Genomic ◽  
Genomic Analyses ◽  
The Face ◽  
Freshwater Stickleback ◽  
Different Populations

Abstract Populations occurring in similar habitats and displaying similar phenotypes are increasingly used to explore parallel evolution at the molecular level. This generally ignores the possibility that parallel evolution can be mimicked by the fragmentation of an ancestral population followed by genetic exchange with ecologically different populations. Here we demonstrate such an ecological vicariance scenario in multiple stream populations of threespine stickleback fish divergent from a single adjacent lake population. On the basis of demographic and population genomic analyses, we infer the initial spread of a stream-adapted ancestor followed by the emergence of a lake-adapted population, that selective sweeps have occurred mainly in the lake population, that adaptive lake–stream divergence is maintained in the face of gene flow from the lake into the streams, and that this divergence involves major inversion polymorphisms also important to marine-freshwater stickleback divergence. Overall, our study highlights the need for a robust understanding of the demographic and selective history in evolutionary investigations.

scholarly journals Evidence of multiple origins of glyphosate resistance evolution in Lolium multiflorum

2021 ◽  
Author(s):  
Caio Brunharo ◽  
Matthew Streisfeld
Keyword(s):  
Lolium Multiflorum ◽  
Glyphosate Resistance ◽  
Genetic Alterations ◽  
Resistance Evolution ◽  
Multiple Origins ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Resistance Patterns ◽  
Different Populations ◽  
Or Genes

The multitude of herbicide resistance patterns in the weed Lolium multiflorum L. is a remarkable example of the rapid adaptation to anthropogenic-driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of L. multiflorum in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine if known mechanisms were responsible for glyphosate resistance, if resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance. We found no evidence of genetic alterations or expression changes at known target and non-target sites of glyphosate resistance. Population genomic analyses indicated that resistant populations tended to have largely distinct ancestry from one another, with little evidence of admixture, suggesting that glyphosate resistance did not spread among populations via gene flow. Rather, resistance appears to have evolved independently on different genetic backgrounds. We also detected potential loci associated with the resistance phenotype, some of which encode proteins with potential effects on herbicide metabolism. Our results suggest that Oregon populations of L. multiflorum evolved resistance to glyphosate due to a novel mechanism. Future studies that characterize the gene or genes involved in resistance will be necessary to confirm this conclusion.

scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

scholarly journals Parallel evolution and ecological selection: replicated character displacement in spadefoot toads

2009 ◽  
Vol 276 (1676) ◽  
pp. 4189-4196 ◽  
Author(s):  
Amber M. Rice ◽  
Aaron R. Leichty ◽  
David W. Pfennig
Keyword(s):  
Resource Competition ◽  
Parallel Evolution ◽  
Character Displacement ◽  
Population History ◽  
Ancestral Population ◽  
Sympatric Populations ◽  
Trait Evolution ◽  
Ecological Selection ◽  
Spadefoot Toads ◽  
Repeated Evolution

Ecological character displacement—trait evolution stemming from selection to lessen resource competition between species—is most often inferred from a pattern in which species differ in resource-use traits in sympatry but not in allopatry, and in which sympatric populations within each species differ from conspecific allopatric populations. Yet, without information on population history, the presence of a divergent phenotype in multiple sympatric populations does not necessarily imply that there has been repeated evolution of character displacement. Instead, such a pattern may arise if there has been character displacement in a single ancestral population, followed by gene flow carrying the divergent phenotype into multiple, derived, sympatric populations. Here, we evaluate the likelihood of such historical events versus ongoing ecological selection in generating divergence in trophic morphology between multiple populations of spadefoot toad ( Spea multiplicata ) tadpoles that are in sympatry with a heterospecific and those that are in allopatry. We present both phylogenetic and population genetic evidence indicating that the same divergent trait, which minimizes resource competition with the heterospecific, has arisen independently in multiple sympatric populations. These data, therefore, provide strong indirect support for competition's role in divergent trait evolution.

scholarly journals Salinity-induced phenotypic plasticity in threespine stickleback sperm activation

2017 ◽  
Vol 13 (10) ◽  
pp. 20170516 ◽  
Author(s):  
Annette Taugbøl ◽  
Anna B. Mazzarella ◽  
Emily R. A. Cramer ◽  
Terje Laskemoen
Keyword(s):  
Phenotypic Plasticity ◽  
Freshwater Fish ◽  
Osmotic Shock ◽  
Phenotypic Expression ◽  
Regulatory System ◽  
Threespine Stickleback ◽  
Sperm Activation ◽  
Freshwater Population ◽  
Freshwater Stickleback ◽  
Sperm Mobility

Phenotypic expression may be and often is influenced by an organism's developmental environment, referred to as phenotypic plasticity. The sperm cells of teleosts have been found to be inactive in the seminal plasma and are activated by osmotic shock for most fish species, through release in either hypertonic (for marine fish) or hypotonic (for freshwater fish) water. If this is the case, the regulatory system of sperm mobility should be reversed in salt- and freshwater fish. We tested this hypothesis by first activating sperm of salt- and freshwater populations of threespine stickleback in salt- and freshwater. The sperm from saltwater stickleback could be activated in either salinity, which matches the freshwater colonization history of the species, whereas the sperm from the freshwater population acted as predicted by the osmotic shock theory and was activated in freshwater only. As the freshwater population used here was calculated to be thousands of years old, we went on to test whether the trait(s) were plastic and sperm from freshwater males still could be activated in saltwater after individuals were exposed to saltwater. After raising freshwater stickleback in saltwater, we found the mature males to have active sperm in both saltwater and freshwater. Further, we also found the sperm of wild-caught freshwater stickleback to be active in saltwater after exposing those mature males to saltwater for only 2 days. This illustrates that the ability for stickleback sperm to be activated in a range of water qualities is an environmentally induced plastic trait.

scholarly journals Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2019 ◽  
Vol 51 (7) ◽  
pp. 1187-1189
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Population Genomic ◽  
Genomic Analyses

scholarly journals Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River

2020 ◽  
Vol 8 (6) ◽  
pp. 471
Author(s):  
Nguyen Thanh Vu ◽  
Tran Thi Thuy Ha ◽  
Vo Thi Bich Thuy ◽  
Vu Thi Trang ◽  
Nguyen Hong Nguyen
Keyword(s):  
Genetic Diversity ◽  
Mekong River ◽  
Effective Population ◽  
Wild Stock ◽  
Pangasianodon Hypophthalmus ◽  
Population Genomic ◽  
Diversity Assessment ◽  
Genomic Analyses ◽  
In The Wild ◽  
Striped Catfish

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

scholarly journals Use of DNA Markers for Grape Phylloxera Population and Evolutionary Genetics: From RAPDs to SSRs and Beyond

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 317 ◽  
Author(s):  
Javier Tello ◽  
Astrid Forneck
Keyword(s):  
Molecular Level ◽  
Evolutionary Genetics ◽  
Reproductive Mode ◽  
Native Range ◽  
Daktulosphaira Vitifoliae ◽  
Grape Phylloxera ◽  
The World ◽  
Major Pest ◽  
Different Populations ◽  
Adequate Management

Grape phylloxera (Daktulosphaira vitifoliae Fitch) is a major pest of cultivated grapevines (Vitis spp.), occurring in virtually all viticultural regions around the world. Different grape phylloxera strains can be found at varying levels on leaves and roots on both own-rooted plants and in plants grafted onto partially resistant rootstocks. Considering its relevance for the adequate management of the pest in infested vineyards, the analysis of its genetic diversity has received considerable attention from the scientific community in the last decades. Here, we review 25 years of DNA-based molecular markers applied to the analysis of the genetic structure and the reproductive mode of grape phylloxera in its native range and in different introduced regions. The use given to RAPD, AFLP, mtDNA sequencing and microsatellite (SSR) genetic markers for the analysis of grape phylloxera diversity is discussed, and an overview of the main findings obtained after their application to different populations collected in diverse regions all around the world is shown. Lastly, we explore how recent advancements in molecular biology and in modern high throughput genotyping technologies may be applied to better understand grape phylloxera natural diversity at a molecular level.

scholarly journals Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 400 ◽  
Author(s):  
Alexandre Rêgo ◽  
Samridhi Chaturvedi ◽  
Amy Springer ◽  
Alexandra M. Lish ◽  
Caroline L. Barton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Allele Frequency ◽  
Development Time ◽  
Callosobruchus Maculatus ◽  
Parallel Evolution ◽  
Frequency Change ◽  
Multiple Traits ◽  
Population Genomic ◽  
Performance Traits ◽  
Frequency Changes

Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

Postglacial evolution in lateral plate morphs in Norwegian freshwater populations of the threespine stickleback (Gasterosteus aculeatus)

1995 ◽  
Vol 73 (5) ◽  
pp. 898-906 ◽  
Author(s):  
Tom Klepaker
Keyword(s):  
Gasterosteus Aculeatus ◽  
Alternative Hypothesis ◽  
Morphological Variability ◽  
Threespine Stickleback ◽  
Evolutionary Stage ◽  
Lateral Plate ◽  
Land Uplift ◽  
Founding Population ◽  
Freshwater Stickleback ◽  
Age Range

Norwegian freshwater stickleback populations were founded after the last glacial period, and the progressive uplift of the land has produced an age range (1000 – 13 000 years) of the stickleback habitats. Most of the freshwater populations of today have probably been formed by isolation of marine sticklebacks in the process of land uplift. The freshwater threespine stickleback is known for its great morphological variability. Three distinct morphs ("low," "partial," and "complete") are recognized on the basis of variation in the lateral row of plates. Among the Norwegian populations, all three morphs were found, but the low morph was by far the most common and occurred mostly in monomorphic populations. The presence of the complete and partial morphs was mostly restricted to young lakes near the sea. It is likely that the plate polymorphism in this region is a transitionary evolutionary stage from a founding population dominated by complete to a monomorphic low population. The hypothesis of a polytypic origin of the low morph is discussed, and an alternative hypothesis is proposed. Within each plate morph, the number of plates also varied, and populations with exceptionally low plate numbers were mostly confined to three different areas. Within these areas, populations with plateless specimens also occurred. These plateless specimens tended to inhabit old lakes. The low plate number and plateless populations were found in parts of Norway that were deglaciated early. The advanced plate reduction can therefore be a result of a longer period of isolation and freshwater evolution. Other populations may be on their way towards extreme plate reduction, but have not yet reached the level of platelessness.

scholarly journals PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

2014 ◽  
Vol 31 (7) ◽  
pp. 1929-1936 ◽  
Author(s):  
Bastian Pfeifer ◽  
Ulrich Wittelsbürger ◽  
Sebastian E. Ramos-Onsins ◽  
Martin J. Lercher
Keyword(s):  
Population Genomic ◽  
Genomic Analyses
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