DOI: 10.5061/dryad.3xsj3txrf
title: Aquatic biotas of Sundaland and fragmented but not refugial

description: 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. Species delimitation methods, applied to 1,062 sequences
 belonging to 37 species from 188 sites, detected 95 Molecular Operational
 Taxonomic Units (MOTUs). Among the nine most widespread species, the
 number of MOTUs ranged from 1 to 11 and correlated with time to the most
 recent common ancestor. Extended Bayesian Skyline Plots applied to
 mitogenomes and cytochrome c oxidase I sequence detected no variation in
 past effective population size within MOTUs, while hierarchical
 Approximate Bayesian Computation provided no evidence of congruent changes
 in effective population sizes. Fragmentation of an ancestral range is the
 most likely explanation for the rampant cryptic diversity observed, but
 demographic inferences do not support MOTUs as being refugial from an
 evolutionary perspective.
description: <strong><em>Sequencing</em></strong> 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 <em>c</em> 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®<sup>TM</sup> (USB Corporation, Cleveland, OH, USA) and sequenced in both directions. Sequencing reactions were performed using “BigDye® Terminator v3.1 Cycle Sequencing Ready Reaction” reagents, and sequencing was performed on an ABI 3130 DNA Analyzer or an ABI 3730XL DNA Analyzer (Applied Biosystems, Waltham, MA, USA). Sequences and related information (photographs, voucher collections number, and collections data) were deposited in BOLD [2] and the National Center for Biotechnology Information’s GenBank database. Genomic libraries for mitogenome skimming [3,4] were prepared for 94 individuals belonging to the nine nominal species selected for investigation following the protocol developed by Tilak et al. (2015). Genomic DNA was physically fragmented using ultrasound (35 kHz) for a duration varying between 10 and 20 min. We followed the Illumina library preparation procedure with blunt-end repair, adapter ligation, adapter fill-in, and indexing PCR steps (13 cycles) developed by Meyer and Kircher (2010). Each step was followed by a purification using SPRI bead suspensions (Agencourt® AMpure® XP), adding 1.7 volume of Agencourt® AMpure® XP reagent per volume of sample, and eluted in 25µl of ultra-pure water. The DNA libraries were quantified with a Nanodrop ND-800 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). Montpellier Genomix platform (MGX, Montpellier, France) performed sequencing. In brief, indexed libraries were pooled using their relative concentrations to ensure equimolarity and a single pool was subjected to single-read sequencing (150-bp long reads) on an Illumina HiSeq 2500 lane. Mitogenomes were assembled using reference mitogenomes of each species when available in GenBank (KJ808811 for <em>Anabas testudineus</em>, NC_034755 for <em>Barbodes binotatus</em>, NC_032037 <em>Channa striata</em>, NC_012711 for <em>Chitala lopis</em>, KF670818 for <em>Hampala macrolepidota</em>, KP100265 for <em>Trichopodus trichopterus)</em> or close relative (<em>Monopterus albus </em>(NC_003192) for <em>M. javanensis</em> and a <em>Metzia longinasus</em> (KF955011) for <em>Parachela hypophtalmus</em>) using Geneious Mapper tool with default parameters of Geneious 9.0.5 [7] and annotated using the online MitoAnnotator tool [8] available at https://mitofish.aori.u-tokyo.ac.jp. <strong><em>Genetic species delimitations and phylogenetic reconstructions</em></strong> The inventory of MOTUs, defined as diagnosable mitochondrial lineages, was conducted by applying six methods of species delimitation to the COI data set (1,062 fish specimens corresponding to 37 nominal species). The following algorithms were used: (1) Refined Single Linkage (RESL), implemented in BOLD to produce Barcode Index Numbers (BINs; Ratnasingham and Hebert 2013); (2) Automatic Barcode Gap Discovery (ABGD; Puillandre et al. 2012) available at https://bioinfo.mnhn.fr/abi/public/abgd/; (3) Poisson Tree Process (PTP, Zhang et al. 2013) in its single-threshold (sPTP), (4) multiple-threshold versions (mPTP) available at https://mptp.h-its.org/; and (5) the Generalized Mixed Yule-Coalescent (GMYC) in its single (sGMYC) and (6) multiple rate version (mGMYC) as implemented in the R package Splits v 1.0-19 [12] in R v 4.2.1 [13]. The final delimitation scheme used to delineate MOTUs was established following a majority-rule consensus among the six methods [14,15]. Both RESL and ABGD use DNA alignments as input. For PTP analyses, a maximum likelihood (ML) tree was generated using IQ‐TREE v 1.6.12 [16] while using the most-likely substitution model (TPM2 + I+ Γ) according to ModelFinder [17] based on the Bayesian Information Criterion (BIC), as available at http://iqtree.cibiv.univie.ac.at [18]. Finally, the ultrametric and fully resolved tree required by GMYC analyses was reconstructed using the Bayesian approach implemented in BEAST 2.4.8 [19]. We ran BEAST with two Markov chains, each with a chain length of 50 million generations while using a Yule pure birth model tree prior, a strict-clock model with a substitution rate of 1.2% genetic distance per million years (Myr; Bermingham et al. 1997), and a TPM2 + I + Γ substitution model. Trees were sampled every 10,000 states after an initial burn-in period of 10 million generations. The results of the two runs were combined using LogCombiner 2.4.8, and the maximum credibility tree with Common Ancestor heights was established using TreeAnnotator 2.4.7 [19]. Sequences were collapsed into haplotypes prior to Bayesian inference analyses. Once MOTUs were delimited, DNA barcodes and mitogenomes were used to reconstruct phylogenetic trees with the StarBEAST2 package [21] in BEAST 2.4.8. As StarBEAST2 jointly reconstructs gene trees and MOTU trees, we designated MOTUs in StarBEAST2 based on the majority-rule consensus of the lineage delimitation analyses. Analyses were conducted using a single partition including protein-coding regions, a GTR + I + Γ substitution model, an Uncorrelated Log-Normal (UCLN) species tree model, a relaxed lognormal molecular clock to account for varying rates among lineages, and an MCMC chain length of 50 million steps. A substitution rate of 1.2 % per Myr was applied for the final reconstructions [20], as it provided age estimates consistent with the geology of the area in other freshwater fish groups [22–27]. Independent runs were combined using LogCombiner 1.10.4 (Bouckaert et al. 2014). Gene and MOTUs maximum clade credibility trees, age estimates, and 95% highest posterior density (HPD) intervals were summarized using TreeAnnotator 1.10.4 [19]. We examined the relationship (strength and direction) between the TMRCA of each MOTU and its geographic range by first performing a Kendall’s nonparametric τ test between TMRCA and the area of geographic range of MOTUs; then by performing a Wilcoxon – Mann – Whitney test to assess if MOTUs that diverged during the Pleistocene possess greater geographic ranges than MOTUs that diverged before the Pleistocene. The area of the geographic range occupied by each MOTU was estimated using convex hulls, which are the smallest convex envelopes that contain all occurrences of a given MOTU. Convex hulls were computed using the ‘CHullAreaEarth’ function of the GeoRange R package v 0.1.0 [28] and visualized using ggplot2 v 3.5.1 [29] and ggConvexHull v 0.1.0 [30] in R v 4.2.1 [13]. When a MOTU was only observed at a single site, a conservative range area of 500 km<sup>2</sup> was adopted. Finally, comparisons were also performed between the TMCA of each MOTU and the number of islands where it occurs. <strong><em>Genetic diversity and species demographic inferences</em></strong> Haplotype diversity (<em>h</em>), nucleotide diversity (<em>p</em>), number of segregating sites (<em>s</em>), and Tajima’s <em>D</em> were calculated in R [31] using the packages pegas (<em>h</em>, <em>p</em> and Tajima’s <em>D</em> Paradis 2010) and popgenome (<em>s</em>, Pfeifer et al. 2014). We investigated potential drivers of genetic diversity by performing multiple correlation tests using Kendall’s ranked correlation between diversity indices (number of MOTUs, h, and p) and species maximum standard length, as a proxy of dispersal ability [34, 35], generation time, and time to the most recent common ancestors (TMRCAs) in R. Generation time and maximum standard length were extracted from Fishbase [36]. Past population demography was explored using the EBSP method in BEAST v 2.4.8 [37]. The EBSP is a non-parametric model that estimates changes in effective population size (<em>N</em><sub>e</sub>) through time without specifying any prior hypothesis on the tempo and mode of demographic changes. Reductions in <em>N</em>e may happen as a consequence of fragmentation and genetic structuring, reducing the combination of possible breeding events, or a reduction in census population size [38–42]. Because the demographic signature of fragmentation is more likely to be observed at the scale of species range, while fluctuating population size is expected to impact panmictic subpopulations, we performed EBSP for species and MOTUs to disentangle the relative impact of fragmentation and potential reduction in population size on <em>N</em>e. EBSP was performed with mitochondrial genomes and COI sequences, but we also performed Bayesian Skyline Plots (BSPs) [43] on COI sequences for each species to evaluate the potential effect of missing data on EBSP analyses. Because all mitochondrial genes are linked, we applied the same genealogy and molecular clock rate to the 13 protein-coding genes. However, the EBSP framework allowed us to set different substitution models for each gene. We applied the best model of the evolution of each gene retrieved with ModelFinder available on the IQ-TREE web server (http://iqtree.cibiv.univie.ac.at) using the BIC in BEAST v 2.4.8. A rate of 1.2 % sequence divergence per million years was used to set a relaxed lognormal clock for each analysis. <strong><em>Community demographic inferences</em></strong> We performed a hierarchical approximate Bayesian computation (hABC) analysis with the goal of detecting potential concerted demographic changes across MOTUs [44]. This method makes it possible to combine datasets from different species to estimate if and when changes in population size occurred, whether they were synchronous or not, and the timing of such congruent demographic changes [44–46]. The hABC approach assumes that if different species responded similarly to environmental perturbations, the true demographic history should be more easily detected by exploiting comparative data rather than by considering each species independently. Contrary to previous approaches which focused on the detection of the co-expansion of a group of species [44,46], here we built our null hypotheses on the basis of previous results which suggested that most of the MOTUs under investigation have been stable through time. In other words, we tested whether a group of MOTUs is best described by a constant-size demographic model, allowing the other MOTUs to vary in size according to a simple two-phase population model. Briefly, we first extracted the number of MOTUs ζ with constant effective population size from a uniform prior distribution bounded between one and n (total number of MOTUs). Each of these MOTUs was characterized by its own effective population size extracted from an independent prior distribution. If ζ &lt; n, then species followed a one-step population size change. This model was characterized by three demographic parameters: an ancestral population of size N<sub>anc</sub> changing instantaneously to N<sub>mod</sub> at a given time<em> t</em>. The prior distribution for the hierarchical and MOTU-specific parameters is shown in Table S2. We performed 1,000,000 coalescent simulations with fastsimcoal [47] and computed the mean, variance, skewness, and kurtosis of the distribution of mean pairwise differences (<em>θ</em><sub>Π</sub>), Watterson’s estimator of theta (<em>θ</em><sub>s</sub>), and Tajima’s <em>D</em> computed over simulated species. Local linear regressions were then applied to the best 5,000 simulations to estimate the posterior distribution of each parameter. We adopted a cross-validation strategy to test the power of our approach to detect groups of MOTUs with constant population size. To this end, we randomly simulated 1,000 datasets generated from prior distributions and re-analyzed them under the same hABC conditions. Finally, we performed a cross-validation experiment on a simulated dataset of 5000 loci, each with the same characteristics as the observed data. This is a power analysis that helps to understand the amount of genetic data that would be needed to correctly estimate the number ζ of species with constant population size through time. The hABC and cross-validation analyses were run with three substitution rates to explore the sensitivity of our hABC inferences to the pace of molecular evolution. As information about mitochondrial mutation rates for our focal study species is lacking, estimates were derived from known substitution rates per million years and approximated by the product of generation time and substitution rates converted to years. 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description: # Aquatic biotas of Sundaland are fragmented but not refugial --- 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: alignment of COI
 sequences and mitogenomes of *Channa* species used to reconstruct
 SpeciesTreeUCLN gene and species trees * 6: alignment of COI sequences and
 mitogenomes of *Chitala* species used to reconstruct SpeciesTreeUCLN gene
 and species trees * 7: alignment of COI sequences and mitogenomes of
 *Hampala* species used to reconstruct SpeciesTreeUCLN gene and species
 trees * 8: alignment of COI sequences and mitogenomes of *Monopterus*
 species used to reconstruct SpeciesTreeUCLN gene and species trees * 9:
 alignment of COI sequences and mitogenomes of *Parachela* species and
 allied used to reconstruct SpeciesTreeUCLN gene and species trees * 10:
 alignment of COI sequences and mitogenomes of *Trigonopoma* species used
 to reconstruct SpeciesTreeUCLN gene and species trees * 11: BEAST xml file
 used to reconstruct SpeciesTreeUCLN gene and species trees of Anabantidae
 species with COI sequences and mitogenomes * 12: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Barbodes* species
 and allied with COI sequences and mitogenomes * 13: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Channa* species
 with COI sequences and mitogenomes * 14: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Chitala* species
 with COI sequences and mitogenomes * 15: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Hampala* species
 with COI sequences and mitogenomes * 16: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Monopterus* species
 with COI sequences and mitogenomes * 17: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Parachela* species
 with COI sequences and mitogenomes * 18: BEAST xml file used to
 reconstruct SpeciesTreeUCLN gene and species trees of *Trigonopoma*
 species with COI sequences and mitogenomes * 19: Anabantidae gene tree
 reconstructed with SpeciesTreeUCLN based on COI sequences and mitogenomes
 * 20: *Barbodes* species and allied gene tree reconstructed with
 SpeciesTreeUCLN based on COI sequences and mitogenomes * 21: *Channa* gene
 tree reconstructed with SpeciesTreeUCLN based on COI sequences and
 mitogenomes * 22: *Chitala* gene tree reconstructed with SpeciesTreeUCLN
 based on COI sequences and mitogenomes * 23: *Hampala* gene tree
 reconstructed with SpeciesTreeUCLN based on COI sequences and mitogenomes
 * 24: *Monopterus* gene tree reconstructed with SpeciesTreeUCLN based on
 COI sequences and mitogenomes * 25: *Parachela* gene tree reconstructed
 with SpeciesTreeUCLN based on COI sequences and mitogenomes * 26:
 *Trigonopoma* gene tree reconstructed with SpeciesTreeUCLN based on COI
 sequences and mitogenomes * 27: Anabantidae species tree reconstructed
 with SpeciesTreeUCLN based on COI sequences and mitogenomes, and MOTUs
 according to the majority rule consensus of the species delimitation
 analyses * 28: *Barbodes* species and allied species tree reconstructed
 with SpeciesTreeUCLN based on COI sequences and mitogenomes, and MOTUs
 according to the majority rule consensus of the species delimitation
 analyses * 29: *Channa* species tree reconstructed with SpeciesTreeUCLN
 based on COI sequences and mitogenomes, and MOTUs according to the
 majority rule consensus of the species delimitation analyses * 30:
 *Chitala* species tree reconstructed with SpeciesTreeUCLN based on COI
 sequences and mitogenomes, and MOTUs according to the majority rule
 consensus of the species delimitation analyses * 31: *Hampala* species
 tree reconstructed with SpeciesTreeUCLN based on COI sequences and
 mitogenomes, and MOTUs according to the majority rule consensus of the
 species delimitation analyses * 32: *Monopterus* species tree
 reconstructed with SpeciesTreeUCLN based on COI sequences and mitogenomes,
 and MOTUs according to the majority rule consensus of the species
 delimitation analyses * 33: *Parachela* species tree reconstructed with
 SpeciesTreeUCLN based on COI sequences and mitogenomes, and MOTUs
 according to the majority rule consensus of the species delimitation
 analyses * 34: *Trigonopoma* species tree reconstructed with
 SpeciesTreeUCLN based on COI sequences and mitogenomes, and MOTUs
 according to the majority rule consensus of the species delimitation
 analyses * 35: alignment of COI sequences and mitogenomes of *Anabas
 testudineus* used to perform EBSP analysis * 36: alignment of COI
 sequences and mitogenomes of *Barbodes binotatus* used to perform EBSP
 analysis * 37: alignment of COI sequences and mitogenomes of *Channa
 striata* used to perform EBSP analysis * 38: alignment of COI sequences
 and mitogenomes of *Chitala lopis* used to perform EBSP analysis * 39:
 alignment of COI sequences and mitogenomes of *Hampala macrolepidota* used
 to perform EBSP analysis * 40: alignment of COI sequences and mitogenomes
 of *Monopterus albus* used to perform EBSP analysis * 41: alignment of COI
 sequences and mitogenomes of *Parachela hypophthalmus* used to perform
 EBSP analysis * 42: alignment of COI sequences and mitogenomes of
 *Trichopodus trichopterus* used to perform EBSP analysis * 43: alignment
 of COI sequences and mitogenomes of *Trigonopoma pauciperforatum* used to
 perform EBSP analysis * 44: BEAST xml file used to perform EBSP analysis
 for *Anabas testudineus* with COI sequences and mitogenomes * 45: BEAST
 xml file used to perform EBSP analysis for *Barbodes binotatus* with COI
 sequences and mitogenomes * 46: BEAST xml file used to perform EBSP
 analysis for *Channa striata* with COI sequences and mitogenomes * 47:
 BEAST xml file used to perform EBSP analysis for *Chitala lopis* with COI
 sequences and mitogenomes * 48: BEAST xml file used to perform EBSP
 analysis for *Hampala macrolepidota* with COI sequences and mitogenomes *
 49: BEAST xml file used to perform EBSP analysis for *Monopterus albus*
 with COI sequences and mitogenomes * 50: BEAST xml file used to perform
 EBSP analysis for *Parachela hypophthalmus* with COI sequences and
 mitogenomes * 51: BEAST xml file used to perform EBSP analysis for
 *Trichopodus trichopterus* with COI sequences and mitogenomes * 52: BEAST
 xml file used to perform EBSP analysis for *Trigonopoma pauciperforatum*
 with COI sequences and mitogenomes * 53: Input file of hABC analysis
 including MOTU label (dataset), corresponding nominal species, number of
 individuals (n.ind), number of base pairs analyzed (n.sites), nucleotide
 diversity, genetic diversity (theta.s), Tajima D score (Tajima D pegas),
 species generation time, mutation rate (substitution_rate * gen) and
 number of segregating sites (n.segregating.sites) * 54: (in Related Works
 section) Supplementary material cited in the manuscript ## Sharing/Access
 Information Links to other publicly accessible locations of the data: in
 BOLD as
 **[dx.doi.org/10.5883/DS-BIFCOPY](http://dx.doi.org/10.5883/DS-BIFCOPY)**