Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding

Contrasting genetic and morphological differentiation among geographical lineages of a stenotopic miniature rasborine, Boraras maculatus, in Peninsular Malaysia

The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.

Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.

Nor SA, Lavoué S, A. Rahim M, Jamaludin NA, Mohammed Akib NA. DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia

The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.

To lump, to split or to maintain? Molecular taxonomy of the spotted barb Barbodes binotatus (Cyprinidae) and closely related species in Peninsular Malaysia

The taxonomic status of the Southeast Asian spotted barb, Barbodes binotatus (Teleostei: Cyprinidae), has puzzled researchers because of large but inconsistent geographic variation of its body melanin marking pattern. In this study, the authors appraise the differentiation of B. binotatus and two closely related species, Barbodes rhombeus and saddle barb, Barbodes banksi, in Peninsular Malaysia using mitochondrial and nuclear markers. The results of this study reveal that the Peninsular Malaysia populations of each of the three species form largely reciprocal monophyletic lineages that differ from each other by a minimum of 2.3% p-genetic distance using COI gene. Nonetheless, specimens of B. binotatus in Peninsular Malaysia are only distantly related to specimens of B. binotatus in Java (type locality). The monophyly of B. banksi is not refuted although specimens of Peninsular Malaysia are genetically distinct from those of Sarawak (type locality). The authors discuss alternative hypotheses whether each of these three valid species is a single species or each of the main five genetic lineages revealed in this study represents a distinct species. Preliminary investigations reveal a mito-nuclear discordance at one locality in Peninsular Malaysia where B. binotatus and B. banksi co-occur. Further studies should inform on the extent of reproductive porousness between these two lineages and others.

Behavioral Variation in the Pygmy Halfbeak Dermogenys collettei: Comparing Shoals With Contrasting Ecologies

Variation in biotic and abiotic factors among populations affects individual behaviors by transforming the social landscape and shaping mating systems. Consequently, describing behaviors in natural populations requires consideration of the biological and physical factors that different individuals face. Here, we examined variation in socio-sexual and locomotor behaviors in a small, livebearing, freshwater fish, the pygmy halfbeak Dermogenys collettei, across natural populations in Singapore. The pygmy halfbeak is a surface feeding fish that spends most of the time near the water surface, making it ideal for non-invasive behavioral observations. We compared behaviors between sexes among 26 shoals while simultaneously accounting for environmental variation. We demonstrated that sexual interactions and locomotor behaviors differed among shoals with varying levels of canopy cover and water flow. Specifically, in areas with greater canopy cover, sexual interactions decreased, whereas time spent in a stationary position increased. Sexual interactions were more numerous in still water, where fish spent less time swimming. Variation in the expression of socio-sexual and locomotor behaviors were not associated with differences in the amount of aquatic vegetation, water depth or halfbeak shoal size. Agonistic interactions were robust to environmental effects, showing little variation among environments. However, there were strong sex effects, with males performing more agonistic behaviors and spending less time in a stationary position compared to females, regardless of the environment. Moreover, sexual interactions, measured as actively performed by males and passively received by females, were on average more frequent in males than in females. Our findings help us explore the proximal causes of intraspecific behavioral variation and suggest that fundamental information on socio-sexual behaviors from wild populations can lead to a better understanding of how sexual selection operates when the strength of natural selection varies across environments.

Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots

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.

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes

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.

Male mate choice for large gravid spots in a livebearing fish

Male mate choice occurs in a wide range of species, and males can increase their reproductive success by distinguishing between females based on their fecundity (e.g., large body size) or their expected sperm competition risk (e.g., virgins). However, patterns of male mate choice could be mitigated by variation in female physiological receptivity, as males can benefit by directing their mating efforts toward females that are at a point in their reproductive cycle when fertilization probability is highest. Here, we perform three experiments to assess whether male mate choice is influenced by cues of female physiological receptivity, fecundity, or sperm competition risk in the pygmy halfbeak (Dermogenys collettei), a small livebearing fish. Female halfbeaks possess a "gravid spot"-an orange abdominal marking that is caused by pigmentation of the females' skin and variation in embryo development and pigmentation during pregnancy. We show that gravid spot size increases toward parturition and is largest right before giving birth, independent of abdominal width or body size. Males consistently chose females with large gravid spots over females with small gravid spots. In contrast, males did not prefer larger females over smaller females or virgin females over mated females. As female halfbeaks store sperm prior to fertilizations, we suggest that males use the size of the gravid spot as a cue to direct their mating efforts to those females where the chance of fertilization is highest.