Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers.

  title={Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers.},
  author={Andr{\'e} E. Moura and Kypher Shreves and Małgorzata Pilot and Kimberly R. Andrews and Daniel M. Moore and Takushi Kishida and Luciana M. M{\"o}ller and Ada Natoli and Stefania Gaspari and Michael R. McGowen and Ing Chen and Howard W. I. Gray and Mauvis Gore and Ross M. Culloch and Muhammad Shoaib Kiani and Maia Sarrouf Willson and Asma Al Bulushi and Tim Collins and Robert F. Baldwin and Andrew Willson and Gianna Minton and Louisa Shobhini Ponnampalam and A. Rus Hoelzel},
  journal={Molecular phylogenetics and evolution},

Figures and Tables from this paper

Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

This study performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella, finding that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity.

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

It is found that spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene, suggesting similar mechanisms are driving species diversification in northern and southern species.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea

This study reveals the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggests that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species’ gene pools.

There and Back Again: Reticulate Evolution in Ceratopteris

This work constructed a split network analysis using thousands of single nucleotide polymorphisms from samples collected throughout the pan-tropical range of Ceratopteris to better understand the patterns of hybridization and reticulate evolution in the genus.

Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean

It is demonstrated that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.

Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea

This work uses publicly available genomes from nine species, representing all three Delphinoidea families, to investigate signs of post-divergence gene flow across their genomes, and to address the speciation processes that led to the diversity seen today within the superfamily.

Reticulated evolution marks the rapid diversification of the Delphinoidae

  • M. Fontaine
  • Biology
    Peer Community In Evolutionary Biology
  • 2022
The conclusion drawn, that 'Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea' still largely hangs on the author's interpretation of the hPSMC method, is recommended to be more conservative in the PSMC plots of unphased pseudo-diploid genome generated by mapping short-reads to a distant relative as gene flow events that occurred millions of years ago.

Current status and future perspectives of Neotropical freshwater stingrays (Potamotrygoninae, Myliobatiformes) genetics

The genetic studies of Potamotrygoninae were grouped in thematic areas, and the advances and challenges of each topic comprising evolution, taxonomy, phylogeography, hybridization, cytogenetics, and transcriptomes were discussed.

A cautionary note on the use of haplotype callers in Phylogenomics

This work shows how the haplotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level, and quantified the level at which the accuracy of heterozygote calls declines with increasing distance to the reference genome.



Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the resolution of a strongly supported, bifurcating phylogeny, and a chronology of the divergences within the Delphinidae family.

Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

By collecting and analyzing seven new mitochondrial genomes, this work provides strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.

How to contend with paraphyly in the taxonomy of the delphinine cetaceans

Until molecular and/or morphological analyses adequately sort out relationships in this very recently radiated group, one possible solution indeed would be to merge all the delphinine genera with Delphinus, and implications of such a move and alternatives are discussed.

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

An important role for geographic isolation in the emergence of species barriers is suggested, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.

Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

Phylogenetic discordance at the species boundary: comparative gene genealogies among rapidly radiating Heliconius butterflies.

The finding of discordant genealogies between genes is consistent with models of adaptive speciation with ongoing gene flow and highlights the need for multiple locus comparisons to resolve phylogeny among closely related species.

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae)

For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.