Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers

Tariel, Juliette; Longo, Gary C.; Bernardi, Giacomo

doi:10.1016/j.ympev.2016.01.010

Cited by 20 publications

(21 citation statements)

References 35 publications

(48 reference statements)

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“…; Rougemont et al . ), or phylogenetic relationships are being explored between species (Combosch & Vollmer ; Tariel, Longo & Bernardi ), then a higher value of n may be required to detect these fixed polymorphisms. This being said, it may be difficult to derive a biological judgement of the known amount of differentiation between individuals – for example, if cryptic population structure exists.…”

Section: Discussionmentioning

confidence: 99%

Lost in parameter space: a road map for stacks

2017

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Summary Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. Using three empirical RAD‐seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. Visualisation of the metrics plotted for the three RAD‐seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. Our methods will help the community in honing the analytical skills necessary to accurately assemble a RAD‐seq dataset.

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Section: Discussionmentioning

confidence: 99%

Lost in parameter space: a road map for stacks

2017

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“…In marine fishes, sympatric speciation has been suggested in cases such as angelfishes (Holacanthus spp. ; Tariel, Longo, & Bernardi, 2016) and reef fishes of the genus Hexagrammos (Crow, Munehara, & Bernardi, 2010). In contrast, studies of divergent lineages within the European sea bass Dicentrarchus labrax (Tine et al, 2014) and European anchovy Engraulis encrasicolus (Le Moan, Gagnaire, & Bonhomme, 2016) employing genomic data and analysis of JAFS have found strong support for scenarios involving isolation followed by secondary contact implying allopatric divergence.…”

Section: Speciation In Oceanic Environmentsmentioning

confidence: 99%

Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analysed using genomic data

Nikolic¹,

Liu

Jacobsen

et al. 2020

Molecular Ecology

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Speciation in the ocean could differ from terrestrial environments due to fewer barriers to gene flow. Hence, sympatric speciation might be common, with American and European eel being candidates for exemplifying this. They show disjunct continental distributions on both sides of the Atlantic, but spawn in overlapping regions of the Sargasso Sea from where juveniles are advected to North American, European and North African coasts. Hybridization and introgression are known to occur, with hybrids almost exclusively observed in Iceland. Different speciation scenarios have been suggested, involving either vicariance or sympatric ecological speciation. Using RAD sequencing and whole‐genome sequencing data from parental species and F1 hybrids, we analysed speciation history based on the joint allele frequency spectrum (JAFS) and pairwise sequentially Markovian coalescent (PSMC) plots. JAFS supported a model involving a split without gene flow 150,000–160,000 generations ago, followed by secondary contact 87,000–92,000 generations ago, with 64% of the genome experiencing restricted gene flow. This supports vicariance rather than sympatric speciation, likely associated with Pleistocene glaciation cycles and ocean current changes. Whole‐genome PSMC analysis of F1 hybrids from Iceland suggested divergence 200,000 generations ago and indicated subsequent gene flow rather than strict isolation. Finally, simulations showed that results from both approaches (JAFS and PSMC) were congruent. Hence, there is strong evidence against sympatric speciation in North Atlantic eels. These results reiterate the need for careful consideration of cases of possible sympatric speciation, as even in seemingly barrier‐free oceanic environments palaeoceanographic factors may have promoted vicariance and allopatric speciation.

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“…We observed striking genetic structure among the seven marine lake populations, indicating limitations to gene flow, even on small spatial (<200 km) and temporal (~6,000 years) scales. Compared to other studies using RADseq in marine organisms, mussels from marine lakes show moderate-to-high pairwise F ST values, and clear structure in admixure analyses (Lal, Southgate, Jerry, & Zenger, 2016;Tariel, Longo, & Bernardi, 2016;Van Wyngaarden et al, 2016). There is not a complete barrier to the sea, as the vector of water that can carry propagules in and out of the lakes is ongoing.…”

Section: Rapid Population Differentiationmentioning

confidence: 74%

Rapid divergence of mussel populations despite incomplete barriers to dispersal

Maas

Prost

et al. 2018

Molecular Ecology

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Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence.

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Tempo and mode of speciation in Holacanthus angelfishes based on RADseq markers

Cited by 20 publications

References 35 publications

Lost in parameter space: a road map for stacks

Lost in parameter space: a road map for stacks

Speciation history of European (Anguilla anguilla) and American eel (A. rostrata), analysed using genomic data

Rapid divergence of mussel populations despite incomplete barriers to dispersal

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