The mode of speciation during a recent radiation in open-ocean phytoplankton

Filatov, Dmitry A.; Bendif, El Mahdi; Archontikis, Odysseas A.; Hagino, K.; Rickaby, Rosalind E. M.

doi:10.1016/j.cub.2021.09.073

Cited by 28 publications

(35 citation statements)

References 92 publications

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“…Benenstan et al (2021) suggested that divergence in S. mentella was relatively recent (0.5 MYA) and driven by changes in sea level during the Pleistocene. Support for the secondary contact model found in this study is also supported by other studies of speciation history in marine organisms (Fairweather et al 2018;Filatov et al 2021;Leder et al 2021). Another aspect of our analysis is that the directionality of asymmetric gene flow, following isolation, went consistently from the deeper species to the shallower species.…”

Section: Demography Of Speciationsupporting

confidence: 90%

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences

Olivares-Zambrano

Daane

Hyde

et al. 2022

Preprint

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Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here we present exome data on two species pairs of rockfishes that are depth segregated and have different degrees of divergence: S. chlorostictus-S. rosenblatti and S. crocotulus-S. miniatus. We were able to reliably identify 'islands of divergence' in the species pair with more recent divergence (S. chlorostictus-S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.

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Section: Demography Of Speciationsupporting

confidence: 90%

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences

Olivares-Zambrano

Daane

Hyde

et al. 2022

Preprint

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“…1c), Gephyrocapsa clades are within the range of SST 18–22°C. EHB (SST 9.0–12.7°C) and EHA1 (SST 2.6–16.7°C) are distributed in temperate and even artic zones, whereas EHA2 is found in much warmer tropical regions (SST 20.9–26.4°C) similar to the ancestral state of EHUX as inferred from fossil records (Filatov et al ., 2021).…”

Section: Resultsmentioning

confidence: 99%

“…The presence of δ′ plastomes in RCC1216/RCC1217 clearly demonstrates divergent organellar haplotypes can be found within E . huxleyi , a species with extremely large population size (Filatov, 2019; Filatov et al ., 2021). While δ′ in RCC1216 could be captured from an unsampled donor lineage, an alternative explanation is the existence of ancient polymorphic haplotypes in E .…”

Section: Discussionmentioning

confidence: 99%

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Rampant nuclear–mitochondrial–plastid phylogenomic discordance in globally distributed calcifying microalgae

Kao

Wang

2022

New Phytologist

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Summary Incongruent phylogenies have been widely observed between nuclear and plastid or mitochondrial genomes in terrestrial plants and animals. However, few studies have examined these patterns in microalgae or the discordance between the two organelles. Here we investigated the nuclear–mitochondrial–plastid phylogenomic incongruence in Emiliania–Gephyrocapsa, a group of cosmopolitan calcifying phytoplankton with enormous populations and recent speciations. We assembled mitochondrial and plastid genomes of 27 strains from across global oceans and temperature regimes, and analyzed the phylogenomic histories of the three compartments using concatenation and coalescence methods. Six major clades with varying morphology and distribution are well recognized in the nuclear phylogeny, but such relationships are absent in the mitochondrial and plastid phylogenies, which also differ substantially from each other. The rampant phylogenomic discordance is due to a combination of organellar capture (introgression), organellar genome recombination, and incomplete lineage sorting of ancient polymorphic organellar genomes. Hybridization can lead to replacements of whole organellar genomes without introgression of nuclear genes and the two organelles are not inherited as a single cytoplasmic unit. This study illustrates the convoluted evolution and inheritance of organellar genomes in isogamous haplodiplontic microalgae and provides a window into the phylogenomic complexity of marine unicellular eukaryotes.

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“…Genetic and, more recently, genomic studies in marine species are shifting our understanding on diversification in the marine environment. Many morphologically conserved taxa that were taxonomized as single, widely distributed species have been recognized as multiple cryptic species (Amor et al, 2017;Duda, Kohn & Matheny, 2009), often composed by differentiated populations (Peijenburg et al, 2006), suggesting that strong barriers to gene flow can operate in marine taxa (Johannesson et al, 2018;Volk et al, 2020;Filatov et al, 2021). Genomic studies in economically important fish species revealed that effective population size varies between and within species (da Fonseca et al, 2021;Barry, Broquet & Gagnaire, 2022;Sodeland et al, 2022), suggesting that genetic drift can be a strong driver of diversification in the ocean.…”

Section: Introductionmentioning

confidence: 99%

Population genomics of a cephalopod species reflect oceanographic barriers and inbreeding patterns

Bein¹,

Lima

Lazzarotto

et al. 2022

Preprint

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Temporal variation of effective population size and gene flow determine current patterns of genetic diversity within species, and hence the genetic variation upon which natural selection can act. Although such demographic processes are well understood in terrestrial organisms, they remain largely unknown in the ocean, where species diversity is still being described. Here, we present one of the first population genomic studies in a cephalopod, Octopus insularis, which is distributed in coastal and oceanic island habitats in the Atlantic Ocean, Mexican Gulf and the Caribbean Sea. Using genomic data, we identify the South Equatorial current as the main barrier to gene flow between southern and northern parts of the range, followed by discontinuities in the habitat associated with depth. We find that genetic diversity of insular populations significantly decreases after colonization from the continental shelf, also reflecting low habitat availability. Using demographic modelling, we find signatures of a stronger population expansion for coastal relative to insular populations, consistent with estimated increases in habitat availability since the Last Glacial Maximum. The direction of gene flow is coincident with unidirectional currents and bidirectional eddies between otherwise isolated populations, suggesting that dispersal through pelagic paralarvae is determinant for population connectivity. Together, our results show that oceanic currents and habitat breaks are determinant in the diversification of marine species, shaping standing genetic variability within populations. Moreover, our results show that insular populations are particularly vulnerable to current human exploitation and selective pressures, calling the revision of their protection status.

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The mode of speciation during a recent radiation in open-ocean phytoplankton

Cited by 28 publications

References 92 publications

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences

Rampant nuclear–mitochondrial–plastid phylogenomic discordance in globally distributed calcifying microalgae

Population genomics of a cephalopod species reflect oceanographic barriers and inbreeding patterns

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