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

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.

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Lack of specialization in trophic morphology between genetically differentiated dwarf and normal forms of lake whitefish (Coregonus clupeaformis Mitchill) in Lac de l'Est, Quebec

Canadian Journal of Zoology ◽

10.1139/z96-226 ◽

1996 ◽

Vol 74 (11) ◽

pp. 1989-1998 ◽

Cited By ~ 31

Author(s):

Angelo Chouinard ◽

Dany Pigeon ◽

Louis Bernatchez

Keyword(s):

Gene Flow ◽

Trophic Ecology ◽

Early Stage ◽

Population Divergence ◽

Gene Pools ◽

Coregonus Clupeaformis ◽

Lake Whitefish ◽

Apparent Lack ◽

Enzyme Loci ◽

Trophic Niches

We recently observed a bimodal distribution in size of sexually maturing lake whitefish (Coregonus clupeaformis Mitchill) in Lac de L'Est, Quebec. The objective of this study was to test the hypothesis that these two spawning size classes represent genetically distinct ecotypes, potentially adapted in morphology for occupying different trophic niches. This was accomplished by quantifying the extent of genetic (mitochondrial DNA (mtDNA) and enzyme loci) and morphological differences. Significant differences in haplotype and allele frequency distributions confirmed the hypothesis that whitefish maturing at small (dwarf) and normal sizes are structured into two distinct gene pools. However, low Fst values at mtDNA and enzyme loci, coupled with the apparent lack of spatial and temporal spawning segregation, suggest that reproductive isolation is incomplete and that gene flow is still occurring between the two forms. Patterns of mtDNA diversity favoured the origin of genetically distinct dwarf and normal-size lake whitefish forms in Lac de l'Est through sympatric divergence. However, a lack of differences in morphological traits potentially related to trophic ecology did not support the hypothesis that the two forms represent ecotypes which are morphologically specialized in trophic niches. This study established that sympatric dwarf and normal-size spawning groups of lake whitefish in Lac de l'Est represent two genetically distinct populations despite the potential for gene flow between them. This, coupled with their low level of morphological diversification, suggests that they represent an early stage of population divergence, and therefore makes them of particular interest for understanding the gene–environment processes involved in the early steps of speciation events.

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Dynamics of an Exploited Population of Lake Whitefish (Coregonus clupeaformis)

Journal of the Fisheries Research Board of Canada ◽

10.1139/f77-147 ◽

1977 ◽

Vol 34 (7) ◽

pp. 942-953 ◽

Cited By ~ 14

Author(s):

Graham Bell ◽

Paul Handford ◽

Carl Dietz

Keyword(s):

Life History ◽

Sex Ratio ◽

Age Structure ◽

Annual Rate ◽

Multiple Regression Equation ◽

Coregonus Clupeaformis ◽

Lake Whitefish ◽

History Of ◽

Almost All ◽

Key Words Population Dynamics

The life history of the exploited lake whitefish (Coregonus clupeaformis) population of Lesser Slave Lake, Alberta, is described. Mean age is high, having increased under continued exploitation during the last 30 yr. A method of estimating the population age structure is described. The apparent annual rate of survival of adult fish has fluctuated markedly, but on average seems to lie in the interval 0.40–0.50; the annual rate of natural survival is estimated to be 0.53. Juveniles survive better than adults. Rate of survival during the 1st yr of life was estimated to be about 0.0002. Maturity was late, the median age at first reproduction being 6–61/2 yr. The regressions of fecundity on age and length are described; length now contributes almost all the attributable variance to maturity and fecundity. The sex ratio fluctuates in time; this is caused by the fluctuations in age structure, since sex ratio varies with age. The relationship between sex ratio and age is used to calculate the relative rates of survival of male and female fish.These data are used to construct a life table and to compute population parameters. It is inferred that the ability of the population to respond to exploitation has been eroded during the last 30 yr. In some respects, the life history of the Lesser Slave Lake stock appears to be unusual.After about 30 yr of large-amplitude oscillation the whitefish population collapsed in 1965. This does not seem to have been caused by chronic overfishing. In the first place, the rate of fishing mortality is no more than moderate. Secondly, a multiple regression equation describing whitefish catch in 48 other Alberta lakes in which there has been no overall decline in catch successfully predicts the observed mean catch at Lesser Slave Lake. The oscillations in catch are claimed to reflect a limit cycle in the abundance of the whitefish, driven by a lagged relationship between a predator (the fishermen) and its prey (the whitefish). Whether or not this cycle was deterministically stable, such behavior will inevitably put the population in risk of extinction during troughs in the cycle. We suggest that current management policies may encourage the destabilization of whitefish populations, and we propose a remedy. Key words: population dynamics, population regulation, life history, exploitation, survival, fecundity, Coregonus clupeaformis

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

Evolution ◽

10.1111/evo.12075 ◽

2013 ◽

Vol 67 (9) ◽

pp. 2483-2497 ◽

Cited By ~ 150

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

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Vital Activity Parameters as Related to the Early Life History of Larval and Post-Larval Lake Whitefish (Coregonus clupeaformis)

The Early Life History of Fish ◽

10.1007/978-3-642-65852-5_44 ◽

1974 ◽

pp. 547-558 ◽

Cited By ~ 10

Author(s):

W. J. Hoagman

Keyword(s):

Life History ◽

Early Life ◽

Early Life History ◽

Coregonus Clupeaformis ◽

Lake Whitefish ◽

Vital Activity ◽

History Of

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Stocks are Chameleons: Plasticity in Gill Rakers of Coregonid Fishes

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f81-202 ◽

1981 ◽

Vol 38 (12) ◽

pp. 1497-1506 ◽

Cited By ~ 107

Author(s):

C. C. Lindsey

Keyword(s):

Gene Flow ◽

Northern Hemisphere ◽

Phenotypic Variation ◽

Morphological Characters ◽

Yukon Territory ◽

Coregonus Clupeaformis ◽

Lake Whitefish ◽

Gill Rakers ◽

Gill Raker ◽

Coregonid Fishes

The characters that apparently render a stock of fish distinctive may in reality be a reflection of the presence or absence of other fish species with which the stock shares its environment. Over the northern hemisphere, the whitefish genera Coregonus, "Leucichthys," and Prosopium offer striking examples of morphological characters being displaced because of coinhabiting species. Whenever one of the groups is missing, another tends to shift its gill rakers so as to fill in the vacant part of the spectrum in gill-raker counts. Plankton-feeding lake whitefish (Coregonus clupeaformis) having many long gill rakers exist in several lakes sympatrically with bottom-feeding lake whitefish having fewer and shorter gill rakers, but only if the even more specialized plankton-feeding species of ciscoes are absent. Lake whitefish in Yukon Territory have on the average fewer rakers in those lakes that contain ciscoes than in those that do not. Artificial transplants demonstrate that gill-raker characteristics can change quickly in a new environment. Gill-raker count is less subject to phenotypically induced variation from environmental influences than are most morphological characters, but it is not immune. Partial hybridization, where bimodal populations are maintained by a balance between gene flow and selection, also poses special problems for the stock concept. When employing even relatively stable characters such as gill-raker counts, one should beware that the "stocks" may be chameleons which shift their appearance in response to the biological color of their surroundings.Key words: coregonids, whitefish, gill rakers, phenotypic variation, hybridization, selection, transplants, stocks

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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

G3 Genes|Genome|Genetics ◽

10.1534/g3.115.019067 ◽

2015 ◽

Vol 5 (7) ◽

pp. 1481-1491 ◽

Cited By ~ 39

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

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Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

10.1101/2020.05.05.079467 ◽

2020 ◽

Author(s):

Frank T. Burbrink ◽

Marcelo Gehara ◽

Edward A. Myers

Keyword(s):

Gene Flow ◽

Spatial Information ◽

Hybrid Zones ◽

Gray Zone ◽

Population Genomic ◽

Species Pairs ◽

History Of ◽

Flow Changes ◽

Network Approaches ◽

Obsoletus Complex

AbstractInferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the gray zone of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates gene flow often ignore spatial information, for example the formation and shape of hybrid zones. Using population genomic data from the eastern ratsnake complex (Pantherophis obsoletus), we infer phylogeographic groups, gene flow, changes in demography, the timing of divergence, and hybrid zone widths. We examine the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches are applied to understand how landscape features and past climate have influenced population genetic structure among these lineages prior to hybridization. Rates of migration between lineages are associated with the width and shape of hybrid zones. Timing of divergence is not related to migration rate across species pairs and is therefore a poor proxy for inferring position in the gray zone. However, timing of divergence is related to the number of loci weakly introgressing through hybrid zones.

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