scholarly journals Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation

2018 ◽  
Author(s):  
Alexander Esin ◽  
Tom Ellis ◽  
Tobias Warnecke
Keyword(s):  
Gene Flow ◽  
Sigma Factor ◽  
Spore Formation ◽  
Genomic Islands ◽  
Genome Architecture ◽  
Origin Of Replication ◽  
Chromosomal Organization ◽  
Metabolic Genes ◽  
Horizontal Transfers ◽  
Similar Enrichment

AbstractHorizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. These zones encompass and connect classically defined genomic islands. Analyzing topological and strand biases of recent and older transfer events, we show that restrictions on entry are rapidly enforced by selection and that restrictive and permissive zones have existed in their current locations for long periods of evolution. The largest zone, characterized by a high influx of metabolic genes, is centred on the terminus. The other two zones flank a narrow non-permissive zone around the origin of replication and extend to delimit the first third of the chromosome – the part of the chromosome that is confined to the forespore during early spore formation. Horizontal transfers into this area are biased towards functions classically controlled by the forespore-specific sigma factor σF: signal transduction, transcription, and particularly membrane biogenesis. Similar enrichment patterns are present in spore-forming but absent in non-spore-forming Bacilli. Our results suggest that the topology of HGT in Geobacillus, and Bacilli more generally, reflects constraints imposed by chromosomal organization for fast and sporulation, as asymmetric chromosomal entrapment in the forespore during early spore formation restricts where HGT-driven innovation in sporulation can occur.

scholarly journals The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis)

2020 ◽  
Vol 10 (9) ◽  
pp. 3147-3163
Author(s):  
Ashley T Sendell-Price ◽  
Kristen C Ruegg ◽  
Eric C Anderson ◽  
Claudio S Quilodrán ◽  
Benjamin M Van Doren ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
A Priori ◽  
Genomic Islands ◽  
Zosterops Lateralis ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Speciation Continuum ◽  
Genomic Patterns

Abstract Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.

scholarly journals Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

2017 ◽  
Vol 115 (2) ◽  
pp. E236-E243 ◽  
Author(s):  
Tao Ma ◽  
Kun Wang ◽  
Quanjun Hu ◽  
Zhenxiang Xi ◽  
Dongshi Wan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Populus Euphratica ◽  
Genomic Islands ◽  
Ecological Selection ◽  
Poplar Trees ◽  
Genomic Divergence ◽  
Genome Divergence ◽  
Genomic Regions ◽  
Time Of Divergence

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

scholarly journals The multiple population genetic and demographic routes to islands of genomic divergence

2019 ◽  
Author(s):  
Claudio S. Quilodrán ◽  
Kristen Ruegg ◽  
Ashley T. Sendell-Price ◽  
Eric Anderson ◽  
Tim Coulson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Drift Time ◽  
Population History ◽  
Genomic Islands ◽  
Major Question ◽  
Natural Systems ◽  
Genomic Divergence ◽  
Individual Based Simulation ◽  
Surrounding Areas ◽  
Divergence With Gene Flow

Abstract1. The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenised by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However other mechanisms related to genetic architecture and population history can also contribute to the formation of genomic islands of divergence.2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual-based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype-phenotype maps.3. Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.4. By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.

scholarly journals Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island

2019 ◽  
Author(s):  
Jae Young Choi ◽  
Michael Purugganan ◽  
Elizabeth A. Stacy
Keyword(s):  
Gene Flow ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Disruptive Selection ◽  
Metrosideros Polymorpha ◽  
Incipient Speciation ◽  
Island Endemic ◽  
Hawaii Island ◽  
Riparian Tree ◽  
Primary Gene

AbstractA long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within HawaiianMetrosideros, a hyper-variable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin ofMetrosideros polymorphavar.newellii(newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wideM. polymorphavar.glaberrima(glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 million years. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e.secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e.primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.Author summaryA long-standing question in evolution is whether or not new species can arise in the presence of gene flow, which is expected to inhibit the formation of reproductive isolating barriers. We investigated the genomics underlying the origin of a Hawaii Island-endemic riparian tree and purported case of incipient sympatric speciation due to disruptive selection across a sharp forest-riparian ecotone. We find extensive evidence of ongoing gene flow between the riparian tree and its closest relative along with local genomic regions resistant to admixture that likely formed through selection on genes for ecological adaptation and/or reproductive isolation. These results strongly suggest that where disruptive selection is strong, incipient speciation with gene flow is possible even in long-lived, highly dispersible trees.

scholarly journals Selection and gene flow shape genomic islands that control floral guides

2018 ◽  
Vol 115 (43) ◽  
pp. 11006-11011 ◽  
Author(s):  
Hugo Tavares ◽  
Annabel Whibley ◽  
David L. Field ◽  
Desmond Bradley ◽  
Matthew Couchman ◽  
...  
Keyword(s):  
Gene Flow ◽  
Sequence Divergence ◽  
Flower Color ◽  
Color Pattern ◽  
Genomic Islands ◽  
Clinal Variation ◽  
Selective Sweeps ◽  
Closely Related Species ◽  
Relative Divergence ◽  
Strong Barrier

Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightly-linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding “sea,” making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.

scholarly journals Theoretical Expression for the Evolution of Genomic Island of Speciation: From Its Birth to Preservation

2019 ◽  
Author(s):  
T. Sakamoto ◽  
H. Innan
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Divergence ◽  
Genomic Island ◽  
Evolutionary Process ◽  
Ecological Speciation ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Theoretical Expression ◽  
Locally Adaptive

AbstractEcological speciation could be driven by divergent selection that works to maintain phenotypes that are adaptive to each niche. In its early stages, genetic divergence (or FST) can be maintained around the target sites of divergent selection, while in other regions, genetic variation can be mixed by gene flow or migration. Such regions of elevated genetic divergence are called genomic islands of speciation. In this work, we theoretically consider the evolutionary process of a genomic island of speciation, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence. Our result would be useful to understand how genomes evolve through ecological speciation with gene flow.

scholarly journals Genomic islands of divergence or opportunities for introgression?

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162414 ◽  
Author(s):  
Rachael A. Bay ◽  
Kristen Ruegg
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genomic Islands ◽  
Secondary Contact ◽  
Catharus Ustulatus ◽  
Adaptive Introgression ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Isolating Mechanisms ◽  
Migratory Songbird

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush ( Catharus ustulatus ), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

scholarly journals Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island

2019 ◽  
Vol 37 (3) ◽  
pp. 695-710 ◽  
Author(s):  
Jae Young Choi ◽  
Michael Purugganan ◽  
Elizabeth A Stacy
Keyword(s):  
Gene Flow ◽  
Evolutionary Biology ◽  
Woody Species ◽  
Divergent Selection ◽  
Genomic Islands ◽  
Disruptive Selection ◽  
Metrosideros Polymorpha ◽  
Hawaii Island ◽  
Riparian Tree ◽  
Primary Gene

Abstract A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3–1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.

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