Aim To understand the origin of the most isolated endemic fish fauna of the Indo‐Pacific, Easter Island (Rapa Nui), and to infer divergence times and colonization routes of the endemic coral reef fish fauna from their closest relatives. Location Easter Island, Pacific Ocean. Methods Samples of ten species were used: six small‐range species endemic to Rapa Nui and Motu Motiro Hiva (Salas y Gómez) (i.e. small‐range endemic species) and four large‐range species endemic to the southern subtropical Pacific (i.e. large‐range endemic species). We present phylogenetic reconstruction results based on mitochondrial (1 to 5) and nuclear (1 to 6) loci to place these endemic species in their respective family phylogenies (8). Using these newly calibrated phylogenetic trees, information of species distributions and geological data, we inferred the divergence times from the closest relatives of these ten endemic fishes, compared biogeographical history estimation models to reconstruct their ancestral geographic ranges, colonization routes and underlying mechanisms of speciation. Results The divergence times (i.e. divergence times from the closest relatives) of all of the small‐range endemics studied were more recent than the age of Rapa Nui and Motu Motiro Hiva; thus, these species can be considered as neoendemics. Biogeographical history estimation models indicated that speciation following a founder‐event is the most likely scenario. In contrast, the divergence estimates of the large‐range endemic species were highly variable. This being said, the divergence times of all species were more recent than the age of the oldest islands within their distributions. Main conclusions Taken together, these results demonstrate that Rapa Nui acts as a cradle of coral reef biodiversity, being responsible for the emergence of small‐range endemic fish species, but also a route of dispersion for several large‐range endemics and as a stepping stone in the diversification of the Myripristis and Pseudolabrus genera. While no common divergence time was recovered for all of the ten endemic species studied here, the common mechanism of speciation following a founder event was recovered for most of the small‐range endemic species.

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Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myr. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.

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DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA‐based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo‐Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA‐based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA‐based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo‐Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.

Aim: Sea-level changes have 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 freshwater fishes widely distributed in Southeast Asia. We specifically tested if the expansion of exposed lands and increased island connectivity during Pleistocene low sea levels (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 sea-level changes on dispersal. Temporal trends of diversification are explored through statistical selection of best-fit models. Results: The origin of Sundaland mitochondrial lineages is dated at c. 33 Ma and four major clades are identified, which diversified between c. 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.

Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.