DOI: 10.5061/dryad.tb2rbp00g
title: Mitogenomics dataset for the Rasborinae of Sundaland

description: 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.
description: 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)