Aquatic biotas of Sundaland and fragmented but not refugial
Creators: name: Delrieu-Trottin, Erwan
name: Ben Chehida, Selim
name: Sukmono, Tedjo
name: Dahrrudin, Hadi
name: Sholihah, Arni
name: Kustiati, Kustiati
name: Fitriana, Yuli
name: Muchlisin, Zainal Abidin
name: Elvyra, Roza
name: Wibowo, Arif
name: Utama, Ilham Vemandra
name: Nurhaman, Ujang
name: Sauri, Sopian
name: Risdawati, Renny
name: Zein, Muhammad Syamsul Arifin
name: Pouzadoux, Juliette
name: Agnèse, Jean-François
name: Tilak, Marie-Ka
name: Page, Lawrence M.
name: von Rintelen, Thomas
name: Wowor, Daisy
name: Steinke, Dirk
name: Mona, Stefano
name: Rüber, Lukas
name: Hebert, Paul D.
name: Hubert, Nicolas
Publisher: name: Zenodo
Year: 2025
Subjects: coalescent analysis
Past effective population size
Mitochondrial genomes
simulations
Geneological trees

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: Funding provided by: Federal Ministry of Education and ResearchROR ID: https://ror.org/04pz7b180Award Number: 01DQ18005
Funding provided by: Natural Environment Research CouncilROR ID: https://ror.org/02b5d8509Award Number: NE/F003749/1
description: 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 (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 Anabas testudineus, NC_034755 for Barbodes binotatus, NC_032037 Channa striata, NC_012711 for Chitala lopis, KF670818 for Hampala macrolepidota, KP100265 for Trichopodus trichopterus) or close relative (Monopterus albus (NC_003192) for M. javanensis and a Metzia longinasus (KF955011) for Parachela hypophtalmus) 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.

Genetic species delimitations and phylogenetic reconstructions

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 km2 was adopted. Finally, comparisons were also performed between the TMCA of each MOTU and the number of islands where it occurs.

Genetic diversity and species demographic inferences

Haplotype diversity (h), nucleotide diversity (p), number of segregating sites (s), and Tajima's D were calculated in R [31] using the packages pegas (h, p and Tajima's D Paradis 2010) and popgenome (s, 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 (Ne) through time without specifying any prior hypothesis on the tempo and mode of demographic changes. Reductions in Ne 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 Ne. 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.

Community demographic inferences

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 < n, then species followed a one-step population size change. This model was characterized by three demographic parameters: an ancestral population of size Nanc changing instantaneously to Nmod at a given time t. 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 (θΠ), Watterson's estimator of theta (θs), and Tajima's D 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. Three substitution rates were used: (1) 1.2% per Myr following the calibration derived from the study of fish species pairs separated by closure of the Isthmus of Panama [20], (2) 2.4% per Myr, corresponding to the lower bound of an accelerated rate of substitution in recent time for fishes [48], (3) 7.2% per Myr, corresponding to the upper bound of an accelerated rate of substitution in recent time for fishes [48].

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