Parallel adaptations to an altitudinal gradient persist in tetraploid snowtrout (Cyprinidae: Schizothorax), despite extensive genomic exchange within adjacent Himalayan rivers

Replicated evolutionary patterns are often attributed to recurrent emergence following parallel selective pressures. However, similar genetic patterns (e.g., 'genomic islands') can also emerge following extensive homogenization in secondary contact, as a by-product of heterogeneous introgression. For example, within Himalayan tributaries of the Ganges/Brahmaputra rivers, drainage-specific mtDNA clades of polyploid snowtrout (Cyprinidae: Schizothorax) are partitioned as co-occurring morphological 'ecotypes,' hypothesized to represent parallel divergence among adjacent streams. To evaluate this scenario, we utilized a reduced-representation genomic approach (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs) applied to high-altitude Nepali/Bhutanese snowtrout (N=48 each). We unambiguously quantified ploidy levels by first deriving genome-wide allelic depths followed by ploidy-aware Bayesian models that produced genotypes statistically consistent with diploid/tetraploid expectations. When genotyped SNPs were clustering within drainages, the convergence of eco-phenotypes was sustained. However, subsequent partitioned analyses of phylogeny and population admixture instead identified subsets of loci under selection which retained genealogical concordance with morphology, with apparent patterns of parallel ecotype emergence instead driven by widespread genomic homogenization. Here, prior isolation is effectively masked by admixture occurring in secondary contact. We note two salient factors:1) Polyploidy has promoted homogenization in tetraploid Himalayan snowtrout; and 2) Homogenization varies across Himalayan tributaries, presumably in lockstep with extent of anthropogenic modification.

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Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout

Royal Society Open Science ◽

10.1098/rsos.210727 ◽

2021 ◽

Vol 8 (10) ◽

Author(s):

Tyler K. Chafin ◽

Binod Regmi ◽

Marlis R. Douglas ◽

David R. Edds ◽

Karma Wangchuk ◽

...

Keyword(s):

De Novo ◽

Alternative Hypothesis ◽

Anthropogenic Factors ◽

Secondary Contact ◽

Evolutionary Patterns ◽

Geometric Morphometric ◽

Morphological Adaptations ◽

Genome Wide ◽

Genealogical Concordance ◽

Phylogenetic Discordance

The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ‘ecotypes’ observed in polyploid snowtrout (Cyprinidae: Schizothorax ). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq ( N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples ( N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ‘ecotypes’ were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively ‘masks’ previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

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Genome-wide methylation sequencing identifies progression-related epigenetic drivers in myelodysplastic syndromes

Cell Death and Disease ◽

10.1038/s41419-020-03213-2 ◽

2020 ◽

Vol 11 (11) ◽

Author(s):

Jing-dong Zhou ◽

Ting-juan Zhang ◽

Zi-jun Xu ◽

Zhao-qun Deng ◽

Yu Gu ◽

...

Keyword(s):

Cancer Progression ◽

Myelodysplastic Syndromes ◽

Bisulfite Sequencing ◽

De Novo ◽

Dna Hypermethylation ◽

Reduced Representation ◽

Targeted Bisulfite Sequencing ◽

Specific Pcr ◽

Genome Wide ◽

Potential Biomarker

AbstractThe potential mechanism of myelodysplastic syndromes (MDS) progressing to acute myeloid leukemia (AML) remains poorly elucidated. It has been proved that epigenetic alterations play crucial roles in the pathogenesis of cancer progression including MDS. However, fewer studies explored the whole-genome methylation alterations during MDS progression. Reduced representation bisulfite sequencing was conducted in four paired MDS/secondary AML (MDS/sAML) patients and intended to explore the underlying methylation-associated epigenetic drivers in MDS progression. In four paired MDS/sAML patients, cases at sAML stage exhibited significantly increased methylation level as compared with the matched MDS stage. A total of 1090 differentially methylated fragments (DMFs) (441 hypermethylated and 649 hypomethylated) were identified involving in MDS pathogenesis, whereas 103 DMFs (96 hypermethylated and 7 hypomethylated) were involved in MDS progression. Targeted bisulfite sequencing further identified that aberrant GFRA1, IRX1, NPY, and ZNF300 methylation were frequent events in an additional group of de novo MDS and AML patients, of which only ZNF300 methylation was associated with ZNF300 expression. Subsequently, ZNF300 hypermethylation in larger cohorts of de novo MDS and AML patients was confirmed by real-time quantitative methylation-specific PCR. It was illustrated that ZNF300 methylation could act as a potential biomarker for the diagnosis and prognosis in MDS and AML patients. Functional experiments demonstrated the anti-proliferative and pro-apoptotic role of ZNF300 overexpression in MDS-derived AML cell-line SKM-1. Collectively, genome-wide DNA hypermethylation were frequent events during MDS progression. Among these changes, ZNF300 methylation, a regulator of ZNF300 expression, acted as an epigenetic driver in MDS progression. These findings provided a theoretical basis for the usage of demethylation drugs in MDS patients against disease progression.

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The origin and remolding of genomic islands of differentiation in the European sea bass

10.1101/223750 ◽

2017 ◽

Cited By ~ 4

Author(s):

Maud Duranton ◽

François Allal ◽

Christelle Fraïsse ◽

Nicolas Bierne ◽

François Bonhomme ◽

...

Keyword(s):

Reproductive Isolation ◽

Sea Bass ◽

Genomic Islands ◽

Secondary Contact ◽

European Sea Bass ◽

Closely Related Species ◽

Fitness Effects ◽

Genome Wide ◽

Complex Process ◽

Linked Selection

AbstractSpeciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unlinked to speciation can interfere. Here, we used haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. We show that genomic islands first emerged in allopatry through the effect of linked selection acting on a heterogeneous recombination landscape. Upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we found that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.

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Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets

10.1101/2020.08.06.236307 ◽

2020 ◽

Author(s):

Pascal Giehr ◽

Charalampos Kyriakopoulos ◽

Karl Nordström ◽

Abduhlrahman Salhab ◽

Fabian Müller ◽

...

Keyword(s):

Dna Methylation ◽

Molecular Mechanisms ◽

De Novo ◽

Epigenetic Modification ◽

Embryonic Stem ◽

Regulatory Elements ◽

Sequencing Data ◽

Reduced Representation ◽

Genome Wide ◽

Global And Local

AbstractBackgroundDNA methylation is an essential epigenetic modification which is set and maintained by DNA methyl transferases (Dnmts) and removed via active and passive mechanisms involving Tet mediated oxidation. While the molecular mechanisms of these enzymes are well studied, their interplay on shaping cell specific methylomes remains less well understood. In our work we model the activities of Tets and Dnmts at single CpGs across the genome using a novel type of high resolution sequencing data.ResultsTo accurately measure 5mC and 5hmC levels at single CpGs we developed RRHPoxBS, a reduced representation hairpin oxidative bisulfite sequencing approach. Using this method we mapped the methylomes and hydroxymethylomes of wild type and Tet triple knockout mouse embryonic stem cells. These comprehensive datasets were then used to develop an extended Hidden Markov model allowing us i) to determine the symmetrical methylation and hydroxymethylation state at millions of individual CpGs, ii) infer the maintenance and de novo methylation efficiencies of Dnmts and the hydroxylation efficiencies of Tets at individual CpG positions. We find that Tets exhibit their highest activity around unmethylated regulatory elements, i.e. active promoters and enhancers. Furthermore, we find that Tets’ presence has a profound effect on the global and local maintenance and de novo methylation activities by the Dnmts, not only substantially contributing to a universal demethylation of the genome but also shaping the overall methylation landscape.ConclusionsOur analysis demonstrates that a fine tuned and locally controlled interplay between Tets and Dnmts is important to modulate de novo and maintenance activities of Dnmts across the genome. Tet activities contribute to DNA methylation patterning in the following ways: They oxidize 5mC, they locally shield DNA from accidental de novo methylation and at the same time modulate maintenance and de novo methylation efficiencies of Dnmts across the genome.

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Genomic islands of divergence or opportunities for introgression?

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.2414 ◽

2017 ◽

Vol 284 (1850) ◽

pp. 20162414 ◽

Cited By ~ 15

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.

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Demographic histories and genome-wide patterns of divergence in incipient species of shorebirds

10.1101/559633 ◽

2019 ◽

Cited By ~ 1

Author(s):

Xuejing Wang ◽

Kathryn H. Maher ◽

Nan Zhang ◽

Pingjia Que ◽

Chenqing Zheng ◽

...

Keyword(s):

Gene Flow ◽

Evolutionary Biology ◽

De Novo ◽

Secondary Contact ◽

Z Chromosome ◽

Phenotypic Traits ◽

Incipient Species ◽

Genome Wide ◽

Genomic Regions ◽

Kentish Plover

AbstractUnderstanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behaviour, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.

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Faculty Opinions recommendation of Genome-wide profiling of heritable and de novo STR variations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727556430.793546826 ◽

2018 ◽

Author(s):

Melanie Bahlo

Keyword(s):

De Novo ◽

Genome Wide

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Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Forests ◽

10.3390/f12020222 ◽

2021 ◽

Vol 12 (2) ◽

pp. 222

Author(s):

Bartosz Ulaszewski ◽

Joanna Meger ◽

Jaroslaw Burczyk

Keyword(s):

Population Genomics ◽

De Novo ◽

Genetic Studies ◽

Genomic Libraries ◽

Reduced Representation ◽

Large Numbers ◽

Broadleaved Tree Species ◽

Fagus Sylvatica L ◽

Reference Genomes ◽

Future Population

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

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