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Mitogenomics dataset for the Rasborinae of Sundaland

Citation

Hubert, Nicolas (2022), Mitogenomics dataset for the Rasborinae of Sundaland, Dryad, Dataset, https://doi.org/10.5061/dryad.tb2rbp00g

Abstract

Aim: Eustasy has long been put forward to explain the colonization of Southeast Asian islands by freshwater aquatic organisms. We examined the relative impact of Sundaland geology since the Oligocene and of Pleistocene Eustatic Fluctuations on the mitochondrial lineage diversification of a species-rich subfamily of Cypriniformes fishes widely distributed in Southeast Asia, the Rasborinae. We specifically tested if variations in the extent of exposed lands and island connectivity during Pleistocene eustasy (the Paleoriver hypothesis) induced bursts of diversification.

Location: Sundaland

Taxon: Rasborinae (Actinopterygii, Cypriniformes, Danionidae)

Methods: We aggregated 1,017 cytochrome oxidase I sequences and 79 mitogenomes to delineate Molecular Operational Taxonomic Units (MOTUs) and further reconstruct a time-calibrated phylogeny of Rasborinae. Ancestral area estimations were conducted using both island and paleoriver partitioning to examine the impact of island connectivity during Pleistocene eustasy on dispersal. Temporal trends of diversification are explored through a model-based approach.

Results: The origin of Sundaland mitochondrial lineages is dated at ca. 33 Ma and four major clades are identified, which diversified between ca. 31 and 22 Ma. The Island of Borneo and North Sunda paleoriver are identified as the source of Sundaland Rasborinae. Geographical patterns of lineage divergence indicate that most divergence events occurred within islands and diversification under constant birth rate models are the most likely for all clades.

Conclusions: The geographical and historical context of diversification of mitochondrial lineages in Rasborinae provides little support for the Paleoriver Hypothesis. The onset of isolation of Borneo from mainland Asia triggered the initial diversification of the group (ca. 31-22 Ma). The late colonization of Java and Sumatra occurred through several independent dispersal events, poorly explained by Pleistocene eustasy, and frequently followed by in situ diversification.

Methods

This dataset consists of five DNA alignments as follows:

(1) a 79 mitogenomes dataset including rRNA and coding regions only (13898bp), in nexus format including partitions

(2) a 286 taxa alignment for Rasborinae Clade I including 10 mitogenomes and 276 DNA barcodes

(3) a 133 taxa alignment for Rasborinae Clade II including 13 mitogenomes and 120 DNA barcodes

(4) a 140 taxa alignment for Rasborinae Clade III including 8 mitogenomes and 132 DNA barcodes

(5) a 524 taxa alignment for Rasborinae Clade III including 34 mitogenomes and 490 DNA barcodes

 

This dataset consists of 15 phylogenetic reconstructions as follows:

(6) BEAST phylogenetic reconstruction based on DNA sequence alignment 1 (79 mitogenomes, 13898bp), yule model as tree prior

(7) RAxML phylogenetic reconstruction based on DNA sequence alignment 1 (79 mitogenomes, 13898bp)

(8) BEAST phylogenetic reconstruction based on DNA sequence alignment 1 (79 mitogenomes, 13898bp), birth-death model as tree prior

(9) StarBEAST gene tree for Clade I based on DNA sequence alignment 2 (10 mitogenomes, 276 DNA barcodes)

(10) RAxML gene tree for Clade I based on DNA sequence alignment 2 (10 mitogenomes, 276 DNA barcodes)

(11) StarBEAST species tree for Clade I based on DNA sequence alignment 2 (10 mitogenomes, 276 DNA barcodes)

(12) StarBEAST gene tree for Clade II based on DNA sequence alignment 3 (13 mitogenomes, 120 DNA barcodes)

(13) RAxML gene tree for Clade II based on DNA sequence alignment 3 (13 mitogenomes, 120 DNA barcodes)

(14) StarBEAST species tree for Clade II based on DNA sequence alignment 3 (13 mitogenomes, 120 DNA barcodes)

(15) StarBEAST gene tree for Clade III based on DNA sequence alignment 4 (8 mitogenomes, 132 DNA barcodes)

(16) RAxML gene tree for Clade III based on DNA sequence alignment 4 (8 mitogenomes, 132 DNA barcodes)

(17) StarBEAST species tree for Clade III based on DNA sequence alignment 4 (8 mitogenomes, 132 DNA barcodes)

(18) StarBEAST gene tree for Clade IV based on DNA sequence alignment 5 (34 mitogenomes, 490 DNA barcodes)

(19) RAxML gene tree for Clade IV based on DNA sequence alignment 5 (34 mitogenomes, 490 DNA barcodes)

(20) StarBEAST species tree for Clade IV based on DNA sequence alignment 5 (34 mitogenomes, 490 DNA barcodes)