scholarly journals Coherence of Microcystis species revealed through population genomics

2019 ◽  
Author(s):  
Olga M. Pérez-Carrascal ◽  
Yves Terrat ◽  
Alessandra Giani ◽  
Nathalie Fortin ◽  
Charles W. Greer ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Geographic Location ◽  
Biological Species ◽  
Genomic Diversity ◽  
Cyanobacterial Blooms ◽  
Colony Morphology ◽  
Population Genomic

AbstractMicrocystis is a genus of freshwater cyanobacteria which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. However, colony morphology is a plastic trait which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes (of which 19 were resequenced to check for mutation in culture) mainly from Canada and Brazil. We identified eight Microcystis clusters of genomic similarity, only four of which correspond to named morphospecies and monophyletic groups. Notably, M. aeruginosa is paraphyletic, distributed across four genomic clusters, suggesting it is not a coherent species. Most monophyletic groups are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clusters further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes – including some involved in microcystin and micropeptin biosynthesis – are recombined between monophyletic groups in the same geographic location, suggesting local adaptation. Together, our results show the importance of using genomic criteria for Microcystis species delimitation and suggest the existence of locally adapted lineages and genes.ImportanceThe genus Microcystis is responsible for harmful and often toxic cyanobacterial blooms across the world, yet it is unclear how and if the genus should be divided into ecologically and genomically distinct species. To resolve the controversy and uncertainty surrounding Microcystis species, we performed a population genomic analysis of Microcystis genome from public databases, along with new isolates from Canada and Brazil. We inferred that significant genetic substructure exists within Microcystis, with several species being maintained by barriers to gene flow. Thus, Microcystis appears to be among a growing number of bacteria that adhere to a Biological Species-like Concept (BSC). Barriers to gene flow are permeable, however, and we find evidence for relatively frequent cross-species horizontal gene transfer (HGT) of genes that may be involved in local adaptation. Distinct clades of Microcystis (putative species) tend to have distinct profiles of toxin biosynthesis genes, and yet toxin genes are also subject to cross-species HGT and local adaptation. Our results thus pave the way for more informed classification, monitoring and understanding of harmful Microcystis blooms.

scholarly journals Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259124
Author(s):  
Damian C. Lettoof ◽  
Vicki A. Thomson ◽  
Jari Cornelis ◽  
Philip W. Bateman ◽  
Fabien Aubret ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Drift ◽  
Urban Areas ◽  
Population Genomics ◽  
Genomic Structure ◽  
Genomic Diversity ◽  
Effective Population ◽  
Population Genomic ◽  
Population Sizes ◽  
Urban Matrix

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

scholarly journals The Mobilome of Reptiles: Evolution, Structure, and Function

2019 ◽  
Vol 157 (1-2) ◽  
pp. 21-33 ◽  
Author(s):  
Stéphane Boissinot ◽  
Yann Bourgeois ◽  
Joseph D. Manthey ◽  
Robert P. Ruggiero
Keyword(s):  
Gene Flow ◽  
Transposable Elements ◽  
Genome Size ◽  
Local Adaptation ◽  
Size Structure ◽  
Structure And Function ◽  
Genomic Diversity ◽  
Genomic Features ◽  
And Function

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

scholarly journals Fine scale population structure and extensive gene flow within an Eastern Nearctic snake complex (Pituophis melanoleucus)

2021 ◽  
Author(s):  
Zachary L Nikolakis ◽  
Richard Orton ◽  
Brian I Crother
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Genomic Structure ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Population Genomic ◽  
Isolation By Environment ◽  
Pituophis Melanoleucus ◽  
Lineage Divergence

Understanding the processes and mechanisms that promote lineage divergence is a central goal in evolutionary biology. For instance, studies investigating the spatial distribution of genomic variation often highlight biogeographic barriers underpinning geographic isolation, as well as patterns of isolation by environment and isolation by distance that can also lead to lineage divergence. However, the patterns and processes that shape genomic variation and drive lineage divergence may be taxa-specific, even across closely related taxa co-occurring within the same biogeographic region. Here, we use molecular data in the form of ultra-conserved elements (UCEs) to infer the evolutionary relationships and population genomic structure of the Eastern Pinesnake complex (Pituophis melanoleucus) – a polytypic wide-ranging species that occupies much of the Eastern Nearctic. In addition to inferring evolutionary relationships, population genomic structure, and gene flow, we also test relationships between genomic diversity and putative barriers to dispersal, environmental variation, and geographic distance. We present results that reveal shallow population genomic structure and ongoing gene flow, despite an extensive geographic range that transcends geographic features found to reduce gene flow among many taxa, including other squamate reptiles within the Eastern Nearctic. Further, our results indicate that the observed genomic diversity is spatially distributed as a pattern of isolation by distance and suggest that the current subspecific taxonomy do not adhere to independent lineages, but rather, show a significant amount of admixture across the entire P. melanoleucus range.

scholarly journals A Few Stickleback Suffice for the Transport of Alleles to New Lakes

2019 ◽  
Vol 10 (2) ◽  
pp. 505-514 ◽  
Author(s):  
Jared Galloway ◽  
William A. Cresko ◽  
Peter Ralph
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
De Novo ◽  
Empirical Studies ◽  
Low Frequency ◽  
Small Fish ◽  
Marine Population ◽  
Standing Variation ◽  
Population Genomic ◽  
Genomic Studies

Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established “de novo” from marine colonists. Independently evolved freshwater populations exhibit similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels of gene flow leads to significant mutation load – but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.

scholarly journals Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation

2010 ◽  
Vol 63 (4) ◽  
pp. 623-635 ◽  
Author(s):  
Maren L. Friesen ◽  
Matilde A. Cordeiro ◽  
R. Varma Penmetsa ◽  
Mounawer Badri ◽  
Thierry Huguet ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Medicago Truncatula ◽  
Genomic Analysis ◽  
Population Genomic

scholarly journals The population genomics of adaptive loss of function

Heredity ◽  
2021 ◽  
Author(s):  
J. Grey Monroe ◽  
John K. McKay ◽  
Detlef Weigel ◽  
Pádraic J. Flood
Keyword(s):  
Population Genetics ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Loss Of Function ◽  
Population Genomic ◽  
Genomic Tools ◽  
Challenges And Opportunities ◽  
Early View

AbstractDiscoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

scholarly journals The Drosophila Genome Nexus: a population genomic resource of 605 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population

2014 ◽  
Author(s):  
Justin Lack ◽  
Charis Cardeno ◽  
Marc Crepeau ◽  
William Taylor ◽  
Russ Corbett-Detig ◽  
...  
Keyword(s):  
Population Genomics ◽  
Demographic History ◽  
Genetic Research ◽  
Genomic Analysis ◽  
Data Sets ◽  
Large Sample Size ◽  
Drosophila Genome ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Variant Detection

Hundreds of wild-derived D. melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach, and settled on an assembly strategy that utilizes two alignment programs and incorporates both SNPs and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets (previous DPGP releases and the DGRP freeze 2.0), and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 605 consistently aligned genomes, and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.

scholarly journals Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana

2018 ◽  
Vol 115 (19) ◽  
pp. 5028-5033 ◽  
Author(s):  
Nicholas Price ◽  
Brook T. Moyers ◽  
Lua Lopez ◽  
Jesse R. Lasky ◽  
J. Grey Monroe ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Local Adaptation ◽  
Genetic Basis ◽  
Population Genomics ◽  
Frequency Spectra ◽  
Population Genomic ◽  
Trade Offs ◽  
Trait Locus ◽  
Genomic Regions ◽  
Transplant Experiments

Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077–21082]. We find that genomic regions enriched in high FST SNPs colocalize with GT QTL peaks. Many of these high FST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.

scholarly journals Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 223-232 ◽  
Author(s):  
Fanna Maina ◽  
Sophie Bouchet ◽  
Sandeep R. Marla ◽  
Zhenbin Hu ◽  
Jianan Wang ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Local Adaptation ◽  
Population Genomics ◽  
Geographic Origin ◽  
Genome Scan ◽  
Genomic Diversity ◽  
Chromosome 9 ◽  
Local Varieties ◽  
A Genome ◽  
Agroclimatic Zones

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.

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