Aquatic biotas of Sundaland and fragmented but not refugial

Tropical insular systems have long attracted biologists, stimulating some important controversies in ecology and evolution. Eustatic fluctuations during the Pleistocene have been invoked to explain species dispersal and proliferation in these fragmented systems by controlling the extent of landmasses and their temporary connections. In ancient archipelagos, the Pleistocene represents only a small slice of their history so long-standing configurations might better explain insular diversity patterns. With a geological history of ca. 30 million years, the Sunda Shelf is old. Upon entering the Pleistocene, islands of the Sunda Shelf repeatedly separated and merged; however, recent reappraisals of its paleoenvironments and evolutionary dynamics have questioned their biogeographic significance. Based on the molecular inventory of six common freshwater fish families, we explored population fragmentation and demographic history of the most common species using mitochondrial DNA sequences. Speci..., Sequencing
Total genomic DNA was extracted from each specimen using QIAGEN DNeasy 96 tissue extraction kits while following the manufacturer's protocol. For the 1,062 fish specimens corresponding to 37 species, a 652-bp segment from the 5′ region of the cytochrome c oxidase I gene was amplified using C_FishF1t1/C_FishR1t1 primers including M13 tails [1]. PCR amplifications were performed using an ABI Veriti 96-well Fast thermocycler (Applied Biosystems) in a final reaction volume of 10.0 μl containing 5.0 μl Buffer 2X, 3.3 μl of ultrapure water, 1.0 μl of each primer (10μM), 0.2 μl of Phire® Hot Start II DNA polymerase enzyme (5U), and 0.5 μl of DNA template (~50 ng). Amplifications employed the following thermocycling regime: initial denaturation at 98 °C for 5 min followed by 30 cycles of denaturation at 98 °C for 5 s, annealing at 56 °C for 20 s and extension at 72 °C for 30 s, followed by a final extension step at 72 °C for 5 min. The PCR products were purified with ExoSap-IT®TM (US..., , # Aquatic biotas of Sundaland are fragmented but not refugial

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Combined use of mitogenome and cytochrome c oxidase I (COI) to explore the phylogeographic structure and past population demography of Sundaland freshwater fishes.

## Description of the Data and file structure

Data are included as follows:

* 1: (in Related Works section) Excel spreadsheet including specimens colateral information (Systematic, sample ID, GenBank accession number, and geographic origin) and results of the species delimitation analyses (including species partitioning obtained with BIN, sPTP, mPTP, sGMYC, mGMYC, ABGD, and majority-rule consensus)
* 2: fasta file with the 1,062 COI sequences used for species delimitation analyses
* 3: alignment of COI sequences and mitogenomes of Anabantidae species used to reconstruct SpeciesTreeUCLN gene and species trees
* 4: alignment of COI sequences and mitogenomes of *Barbodes* species and allied used to reconstruct SpeciesTreeUCLN gene and species trees
* 5: align...