Contrasting life histories contribute to divergent patterns of genetic diversity and population connectivity in freshwater sculpin fishes

Population genetics analysis based on mitochondrial cytochrome c oxidase subunit I (CO1) gene sequences of Cottus koreanus in South Korea

BACKGROUND

The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species.

OBJECTIVE

To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis.

METHODS

We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea.

RESULTS

In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak.

CONCLUSIONS

C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately.

Low Genetic Diversity and Complex Population Structure in Black Piranha (Serrasalmus rhombeus), a Key Amazonian Predator

The black piranha (Serrasalmus rhombeus), a widely spread species in the rivers of the Amazon basin, plays a vital role as both key predator and important prey. Despite its essential contribution to ecosystem stability, there is a lack of information regarding its genetic diversity and population dynamics in the central Amazon region. As the Amazon continues to undergo environmental changes in the context of growing anthropogenic threats, such knowledge is fundamental for assist in the conservation of this species. This study is the first to analyze the genetic diversity and population structure of S. rhombeus in the central Amazon region using high-resolution genomic data. We employed a Genotyping-by-Sequencing approach with 248 samples across 14 study sites from various tributaries, encompassing diverse water types (black, white, and clear water) and characterized by 34 physiochemical parameters. The data reveals low diversity accompanied by pronounced signs of inbreeding in half of the sites and robust genetic differentiation and variation among sites and within-sites. Surprisingly, we also found evidence of higher dispersal capacity than previously recognized. Our analysis exposed a complex and high population structure with genetic groups exclusive to some sites. Gene flow was low and some groups presented ambiguous genealogical divergence index (gdi) signals, suggesting the occurrence of potential cryptic species. Moreover, our results suggest that the population structure of black piranha appears more influenced by historical events than contemporary factors. These results underscore the need to give greater attention to this keystone species, for which no regulatory framework or conservation strategies is presently in effect.

Phylogeography of the Korean endemic Coreoleuciscus (Cypriniformes: Gobionidae): the genetic evidence of colonization through Eurasian continent to the Korean Peninsula during Late Plio-Pleistocene

Background

Freshwater endemism is thought to have been formed through the vicariance of connected water systems or the process by which ancestral populations colonized specific areas. The Korean Peninsula is well recognized for its high level of freshwater endemism with about 40% of freshwater fish species being endemic.

Objective

In this study, we attempted to reconstruct the process of speciation and phylogenetic dispersal of Coreoleuciscus species, which is endemic in the Korean Peninsula.

Methods

We used fossil-calibrated divergence time estimation and ancestral distributional reconstruction to infer phylogeographic reconstruction of Coreoleuciscus based on mitochondrial cytochrome c oxidate subunit I (COI) sequences (1551 bp).

Results

Our phylogeographic analysis based on a total of 626 individuals revealed that the two Coreoleuciscus species have originated from the independent colonization of different lineages in the ancestral populations, probably during the Late Plio-Pleistocene. The full-scale expansion of Coreoleuciscus populations appears to have taken place after major river structures were completed on the Korean Peninsula. We also provided evidence that the common ancestors of Coreoleuciscus was distributed in Eastern Eurasian continent and subsequently dispersed into the tip of East Asia. High genetic diversity was mainly concentrated in large drainage populations, while small populations showed an monomorphism, which could give important implications for planning the conservation and management of Coreoleuciscus.

Conclusions

The phylogenetic background of the rheophilic Coreoleuciscus species can be explained by the colonizer hypothesis that the endemic freshwater fish originated from the common ancestor in continental region.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13258-022-01243-y.

Wing geometry and genetic analyses reveal contrasting spatial structures between male and female Aedes aegypti (L.) (Diptera: Culicidae) populations in metropolitan Manila, Philippines

The population genetic structure of Aedes aegypti (Linnaeus, 1762) has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine its population structure but these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between its male and female populations using phenotypic and genetic data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila. Five mosquito populations comprised of female (n = 137) and male (n = 49) adult mosquitoes were used in this study. All mosquito individuals underwent geometric morphometric (26 landmarks), and genetic (11 microsatellite loci) analyses. Results revealed that F_ST estimates (genetic) were 0.055 and 0.009 while Q_ST estimates (phenotypic) were 0.318 and 0.309 in in male and female populations, respectively. Wing shape variation plots showed that male populations were distinctly separated from each other while female populations overlapped. Similarly, discriminant analysis of principal components using genetic data revealed that male populations were also distinctly separated from each other while female populations showed near-overlapping populations. Genetic and phenetic dendrograms showed the formation of two groups in male populations but no groups in female populations. Further analysis indicated a significant correlation (r = 0.68, p = 0.02) between the genetic and phenetic distances of male populations. Bayesian analysis using genetic data also detected multiple clusters in male (K = 3) and female (K = 2) populations, while no clusters were detected using the phenotypic data from both sexes. Our results revealed contrasting phenotypic and genetic patterns between male and female Ae. aegypti, indicating that male populations were more spatially structured than female populations.