THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

Evolution ◽  
2013 ◽  
Vol 67 (9) ◽  
pp. 2483-2497 ◽  
Author(s):  
Pierre-Alexandre Gagnaire ◽  
Scott A. Pavey ◽  
Eric Normandeau ◽  
Louis Bernatchez
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genetic Architecture ◽  
Rad Sequencing ◽  
Lake Whitefish ◽  
Species Pairs

scholarly journals Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

2022 ◽  
Author(s):  
Claire M&eacuterot ◽  
Kristina S R Stenl&oslashkk ◽  
Clare Venney ◽  
Martin Laporte ◽  
Michel Moser ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genetic Architecture ◽  
Large Fraction ◽  
Sympatric Species ◽  
Secondary Contact ◽  
Species Differentiation ◽  
Lake Whitefish ◽  
Structural Variants ◽  
Species Pairs ◽  
Long Read

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

scholarly journals Genome-wide patterns of divergence during speciation: the lake whitefish case study

2012 ◽  
Vol 367 (1587) ◽  
pp. 354-363 ◽  
Author(s):  
S. Renaut ◽  
N. Maillet ◽  
E. Normandeau ◽  
C. Sauvage ◽  
N. Derome ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Genomic Islands ◽  
Next Generation Sequencing Data ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Lake Whitefish ◽  
Sequencing Data ◽  
Species Pairs ◽  
Selective Forces ◽  
Genomic Regions

The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish ( Coregonus clupeaformis ) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F ST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.

scholarly journals Modeling the Multiple Facets of Speciation-with-Gene-Flow Towards Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus Clupeaformis)

2016 ◽  
Author(s):  
Clément Rougeux ◽  
Louis Bernatchez ◽  
Pierre-Alexandre Gagnaire
Keyword(s):  
Gene Flow ◽  
Genomic Variation ◽  
Secondary Contact ◽  
Lake Whitefish ◽  
Lineage Sorting ◽  
Effective Population ◽  
Modeling Framework ◽  
Species Pairs ◽  
History Of ◽  
And Migration

AbstractParallel divergence patterns across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate. We investigate the divergence history of five sympatric Lake Whitefish limnetic (dwarf) and benthic (normal) species pairs characterized by variable degrees of ecological divergence and reproductive isolation. Genome-wide SNPs were used to document the extent of genetic differentiation in each species pair, and 26 divergence models were fitted and compared to the unfolded joint allele frequency spectrum of each pair. We found evidence that a recent (circa 3000-4000 generations) asymmetrical secondary contact between expanding post-glacial populations has accompanied Whitefish diversification. Our results suggest that heterogeneous genomic differentiation patterns have emerged through the combined effects of linked selection generating variable rates of lineage sorting across the genome during geographical isolation, and heterogeneous introgression eroding divergence at different rates across the genome upon secondary contact. This study thus provides a new retrospective insight into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation.

scholarly journals Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

2017 ◽  
Vol 9 (8) ◽  
pp. 2057-2074 ◽  
Author(s):  
Clément Rougeux ◽  
Louis Bernatchez ◽  
Pierre-Alexandre Gagnaire
Keyword(s):  
Gene Flow ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Species Pairs ◽  
History Of

scholarly journals Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids

2020 ◽  
Vol 287 (1924) ◽  
pp. 20200270
Author(s):  
Anna F. Feller ◽  
Marcel P. Haesler ◽  
Catherine L. Peichel ◽  
Ole Seehausen
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Related Species ◽  
Genetic Architecture ◽  
Lake Victoria ◽  
Sympatric Species ◽  
Sister Species ◽  
Species Pair ◽  
Closely Related Species ◽  
Nuptial Coloration

One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.

scholarly journals The importance of intrinsic postzygotic barriers throughout the speciation process

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190533 ◽  
Author(s):  
Jenn M. Coughlan ◽  
Daniel R. Matute
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Rapid Evolution ◽  
Theoretical Work ◽  
Sympatric Species ◽  
Species Boundaries ◽  
Biological Models ◽  
Speciation Process ◽  
Species Pairs ◽  
Postzygotic Barriers

Intrinsic postzygotic barriers can play an important and multifaceted role in speciation, but their contribution is often thought to be reserved to the final stages of the speciation process. Here, we review how intrinsic postzygotic barriers can contribute to speciation, and how this role may change through time. We outline three major contributions of intrinsic postzygotic barriers to speciation. (i) reduction of gene flow : intrinsic postzygotic barriers can effectively reduce gene exchange between sympatric species pairs. We discuss the factors that influence how effective incompatibilities are in limiting gene flow. (ii) early onset of species boundaries via rapid evolution : intrinsic postzygotic barriers can evolve between recently diverged populations or incipient species, thereby influencing speciation relatively early in the process. We discuss why the early origination of incompatibilities is expected under some biological models, and detail how other (and often less obvious) incompatibilities may also serve as important barriers early on in speciation. (iii) reinforcement : intrinsic postzygotic barriers can promote the evolution of subsequent reproductive isolation through processes such as reinforcement, even between relatively recently diverged species pairs. We incorporate classic and recent empirical and theoretical work to explore these three facets of intrinsic postzygotic barriers, and provide our thoughts on recent challenges and areas in the field in which progress can be made. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Evidence for Initiation of Post-Zygotic Reproductive Isolation between Drosophila ananassae and D. pallidosa as Indicated by Reduction in the Fertility of Hybrid Males

2020 ◽  
Vol 12 (2) ◽  
pp. 41
Author(s):  
Roshni Singh ◽  
Bashisth Narayan Singh
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sibling Species ◽  
Hybrid Sterility ◽  
Divergence Time ◽  
Sexual Isolation ◽  
Drosophila Ananassae ◽  
Species Pair ◽  
Hybrid Fertility ◽  
Species Pairs

There are several barriers to preclude the gene flow between diverging populations. On the basis of their temporal nature, these can be broadly categorized into two forms: pre- and post-zygotic. Post-zygotic reproductive isolation can manifest in the form of reductions in hybrid fertility. Keeping this fact in view, in the present study, we studied sterility in hybrids of D. ananassae and D. pallidosa. Surprisingly a distinguishable pattern of infertility was found in the hybrids. This pattern, referred to as Haldane’s rule, is often observed in hybrids of recently diverged populations or species. Reduction in the fertility of hybrids provides the clue of incipient kind of post-zygotic reproductive isolation in these two sibling species. This is the first report of hybrid sterility in this species pair. However, hybrid sterility is not very prominent especially when compared to that of other species pairs with the similar divergence time. Thus, on the basis of our results, we conclude that either sexual isolation between these sibling species is sufficient and does not require the aid of post-zygotic isolation to preclude gene flow or rate of divergence between D. ananassae and D. pallidosa is very slow in comparison to other species pair or even races of some species.

scholarly journals RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs

2015 ◽  
Vol 5 (7) ◽  
pp. 1481-1491 ◽  
Author(s):  
Martin Laporte ◽  
Sean M. Rogers ◽  
Anne-Marie Dion-Côté ◽  
Eric Normandeau ◽  
Pierre-Alexandre Gagnaire ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Architecture ◽  
Body Shape ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Species Pairs ◽  
Genome Level ◽  
Level Parallelism
Sign in / Sign up

Export Citation Format

Share Document