Identifying resilient individuals of Pocillopora verrucosa (Ellis & Solander, 1786): insights from diversity assessments for coral restoration

Development of new barcoding loci in gall-forming aphids (Eriosomatinae: Eriosomatini): Comparing three mitochondrial genes, ATP6, ATP8, and COI

To explore the effects of the mutations of ATP6 and ATP8 genes on energy metabolism and genetic structure, we sequenced the ATP6 and ATP8 genes of Ailuropoda melanoleuca. Our results showed that ATP8 is a conserved gene and ATP6 gene is positively selected during the evolution of the giant panda population with a low genetic diversity. Population expansion was observed in the giant panda group. The T179C mutation on Haplotype7 made the production of a potential phosphorylation site. This non-synonymous mutation may occur at the post-translational modification site that have a potential effect on the function of ATP synthase, related to the maintenance of body temperature of pandas at low metabolic rates.

Abstract. Nuryanto A, Komalawati N, Sugiharto. 2019. Genetic diversity assessment of Hemibagrus nemurus from rivers in Java Island, Indonesia using COI gene. Biodiversitas 20: 2707-2717. Green catfish (Hemibagrus nemurus) is a popular freshwater fish that highly exploited in almost all the rivers in Java Island. The exploited population tends to have low genetic diversity. Meanwhile, separated populations might lead to a genetic difference among the river populations. This study aims to investigate the genetic diversity and population variation of H. nemurus collected at eleven rivers across Java Island. The analysis based on 465 bp fragment of the cytochrome c oxidase 1 gene from 140 individuals. Analysis of overall populations proved that H. nemurus had a high gene diversity (h= 0.935±0.016) and nucleotide diversity (π = 0.073±0.036). Within population analysis also showed that H. nemurus populations showed high levels of gene diversity (h= 0.338±0.128 to 1.000±0.022) and nucleotide diversity (π =0.001±0.001 to 0.071±0.038). Those diversity values indicated that H. nemurus had high level of genetic diversity, except for the Citanduy population. Population comparison showed that significant genetic differences observed among populations (p= 0.000 for both variance component and Fst-value). However, pairwise comparison analysis indicated complex pattern of population differentiation. The high genetic diversity and complex pattern of population differentiation have important implication for H. nemurus conservation in Java Island.

The genetic diversity of cultured and wild silver pomfret (Pampus argenteus) populations was analyzed based on mtD-loop and COI gene. The results showed that the average A,T,C and G contents in D-loop were 40.00%,30.55%,16.75% and 12.70%,respectively,and the contents of A + T were 70.55%,higher than those of G + C. In the COI gene,the average A,T,C and G contents in D-loop gene were 25.85%,33.90%,21.30% and 18.85%,respectively,and the contents of A + T were 59.75%,also higher than those of G + C. The total variable sites,number of haplotypes (h),haplotype diversity (Hd),nucleotide diversity (π) and mean pairwise nucleotide differences (k) of two populations based on D-loop were 19,15,0.895,0.007 and 2.505,respectively. The same parameters based on COI gene were 33,17,0.713,0.004 and 2.239,respectively. Based on mtD-loop and COI gene,the genetic diversity of cultured population was lower than that of wild population. The Hd of cultured population based on mtD-loop and COI gene were 0.562 and 0.571,respectively. And the Hd of wild population were 0.891 and 0.801,respectively. The AMOVA analysis based on D-loop showed that the significant genetic divergence existed in cultured and wild populations,while there was no significant genetic divergence when it was analyzed based on COI gene. In conclusion,both D-loop and COI gene were effective molecular markers for analyzing the genetic diversity of silver pomfret population,while the sensitivity of D-loop in detecting the genetic diversity among populations was higher than that of COI gene.

Developing a new molecular marker for aphid species identification: Evaluation of eleven candidate genes with species-level sampling

Silver carp’s (Hypophthalmichthys molitrix) traits and genetic structure are being impacted by artificial proliferation and restocking enhancement. A clear genetic background of cultured silver carp is helpful for exploitation and utilization. Limited research reported the germplasm resources of cultured silver carp. This study was conducted to investigate the genetic diversity of cultured silver carp. Two hundred thirty‐three silver carps were sampled from eight cultured populations in Hubei province, and their population structures were analyzed by mitochondrial COI gene. Average contents of bases T, C, A, and G in the 659 bp COI gene sequence were 30.03%, 26.62%, 26.08% and 17.32%, respectively. And 18 haplotypes were defined from 77 variable nucleotides in COI gene. The haplotypes and nucleotide diversities were 0.604 and 0.00325, respectively. Meanwhile, the highest genetic diversity and lowest genetic diversity were detected in cultured populations from Jianli population (Hd: 0.883 and π: 0.00699) and Yaowan population (Hd: 0.186 and π: 0.00085), respectively. Pairwise fixation index (Fst) analysis revealed that the level of genetic diversity was moderate (Fst: 0.06). The genetic distance between and within populations were 0.00353 and 0.00329, respectively. And the genetic variation occurred mainly within populations (93.42%), but genetic variation between the population was only 6.58%. Therefore, moderate‐level genetic diversity was observed with high haplotype diversity and low nucleotide diversity, suggesting that inbreeding should be avoided among the eight cultured populations in Hubei.

The combination of morphological characteristics and DNA barcodes was used to a systematic study of Hippocampus spinosissimus,laying the foundation for rapid and accurate identification for the medical seahorse species. According to the reported literature and observation on seahorse samples,the typical characteristics of the H. spinosissimus include highly developed spiny,much short nose,single or double cheeks and strongly developed spines bordering pouch. Genomic DNAs of H. spinosissimus and other related seahorse species were extracted using the TIANamp Marine Animals DNA Kit. The COⅠ and ATP6 genes were amplified and sequenced in both directions. After the verification by Blast,the GC content,intraspecific and interspecific genetic distance,and the Neighbor joining( NJ) phylogenetic trees were analyzed by MEGA 7. The lengths of the COⅠ and ATP6 genes were 649 bp and 602-603 bp,respectively,with the average GC content of 39. 96% and 35. 37%. The maximum intraspecific genetic distances in H. spinosissimus based on COⅠ and ATP were both far less than the minimum interspecific genetic distance between H. spinosissimus and other seahorses,suggesting a significant barcoding gap. NJ analysis results of COⅠ and ATP6 exhibited that all H. spinosissimus species clustered together,indicating that the two DNA barcode could identify H. spinosissimus from other seahorses accurately and quickly. In addition,H. spinosissimus shared a close genetic relationship between H. kelloggi according to the NJ tree. Furthermore,there exits three stable subgroup structure of H. spinosissimus,indicating that COⅠ and ATP6 barcodes could be applied the indicator for the geographical ecology research of H. spinosissimus. The results obtained the typical morphological and molecular identification characteristics of H. spinosissimus,which played central roles for the development of species identification. This study provides an important basis data for expanding the medical seahorse resources and ensuring the safety of clinical medicine.

Over the past five decades, approximately one-third of the planet’s live coral cover has been lost, primarily as a consequence of environmental stressors driven by anthropogenic activities, the most severe being the alteration in the periodicity and intensity of El Niño Southern Oscillation (ENSO) events associated with climate change. During the 2023 El Niño event, the coral reef ecosystems in the Mexican Central Pacific experienced a 90% loss of coral cover; however some particular sites acted as refugees with minimal or no loss in the coralline area. Our study describes benthic variability patterns in three of the best-preserved coral reef ecosystems in the Central Mexican Pacific (CMP) region: Chamela Bay, Tenacatita–Barra de Navidad Bays, and Santiago–Manzanillo Bays, each with an average coral cover of ≥ 29%. We analyzed changes in the cover of major benthic groups (corals, algal turf, soft macroalgae, and encrusting calcareous algae) and their relationships with environmental drivers (sea surface temperature, local thermal anomalies, chlorophyll-a levels, and diffuse attenuation coefficient) over thirteen years. Using beta regression models, data were analyzed to determine the local response of each benthic group in response patterns to environmental variability. All three systems showed high resilience to environmental disturbances, with coral cover recovery of up to 74% and regulatory mechanisms that help control the algal blooms. Pronounced seasonal upwelling processes are key to regional environmental variability and may act as stress mitigators during positive ENSO phases. Similarly, the historical ecological processes experienced by each locality have driven the selection, acclimatization, and resilience strategies specific to each benthic community.

The floodwater mosquito Aedes caspius is a competent vector of several human pathogens and has a global distribution across Asia, Europe, Africa, and the Americas. This study aimed to investigate the genetic diversity and population genetic structure of Ae. caspius from Iran. Aedes caspius mosquitoes were collected from Iran, and genetic diversity was assessed using the mitochondrial DNA-encoded cytochrome c oxidase subunit I (mtDNA-COI) gene. BLAST analysis confirmed the morphological identification of all specimens as Ae. caspius, with 100% similarity to GenBank sequences. Haplotype diversity (Hd) and haplotype diversity variance of the Ae. caspius mosquitoes based on the COI gene were found to be 0.954 and 0.00006, respectively. Nucleotide diversity (Pi) of the Ae. caspius sequences based on the COI gene was calculated to be 0.01495, with 56 segregation sites identified. Phylogenetic analysis demonstrated high genetic diversity in Iranian Ae. caspius populations, suggesting its long-standing establishment in Iran and indicating its native status. The origin of this population in Iran may be linked to populations from the United Arab Emirates (UAE), Pakistan, China, and Europe. Further studies should explore the genetic variability of Ae. caspius in various countries and continents.

The hard clam Meretrix lamarckii is ecologically and economically important in the coastal regions of China. In this study, we evaluated the genetic diversity and population structure of six M. lamarckii populations in the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit 1 (COI) and cytochrome b (Cytb) genes. We obtained 582bp of partly sequences comprising 28 novel haplotypes of COI gene from 138 specimens and 1168bp of partly sequences comprising 22 novel haplotypes of Cytb gene from 125 specimens. The haplotype diversity of COI and Cytb genes ranged from 0.606 to 0.862 and 0.562 to 0.863, respectively. The nucleotide diversity ranged from 0.0015 to 0.0038 in COI gene and ranged from 0.0007 to 0.0032 in Cytb gene. Thus, there is moderate-level genetic diversity in M. lamarckii in the China Sea. The F-statistics showed that the Zhoushan (ZS) and Xiangshan (XS) populations were significantly (P < 0.01) differed from the populations of Wenzhou (WZ), Zhangpu (ZP), Shantou (ST), and Zhanjiang (ZJ) in both COI and Cytb genes. Both haplotypes network and plot of STRUCTURE analysis suggested obviously genetic divergence between East China Sea and South China Sea regions. Knowledge on genetic variation and population structure of M. lamarckii populations along the Southeast China Sea obtained from this study will support the aquaculture management and conservation of M. lamarckii in China.

The complete mitochondrial genome of Chinese green hydra, Hydra sinensis (Hydroida: Hydridae) is a linear molecule of 16,189 bp in length, containing 13 protein-coding genes, small and large subunit ribosomal RNAs, methionine and tryptophan transfer RNAs, a pseudogene consisting of a partial copy of COI and terminal sequences at two ends of the linear mitochondrial DNA. The A + T content of the overall base composition of H-strand is 77.2% (T: 41.7%; C: 10.9%; A: 35.5%; and G: 11.9%). COI and ND1 genes begin with GTG as start codon, while other 11 protein-coding genes start with a typical ATG initiation codon. COII, ATP8, ATP6, COIII, ND5, ND6, ND3, ND1, ND4 and COI genes are terminated with TAA as stop codon, ND4L ends with TAG, ND2 ends with TA and Cyt b ends with T.

Introduction: The 1997-98 El Niño event caused massive coral bleaching and mortality in the Central Mexican Pacific (CMP). Punta de Mita alone used to harbor more than 30 % of the coral coverage in this region, with a mono-specific Pocillopora coverage. The 1997-1998 ENSO event caused massive coral mortality reducing live coral coverage to &lt; 5 %. Despite being considered a coral region unlikely to recover, recent restoration efforts have been implemented to rehabilitate the coral community. Objective: To assess coral recovery by analyzing the coral growth and survival rates of branching Pocillopora species at Punta de Mita. Methods: Healthy coral fragments of opportunity were re-attached to the natural substrata using zip ties and measured considering their growth in terms of maximum length and width (cm) to determine their annual extension rates. Results: After 50 weeks, corals duplicated their size, with a mean growth of ~ 4 cm year-1. After 100 weeks (2 years), corals triplicated their size, increasing on average 8–9 cm in each diameter. Conclusions: Successful coral reef restoration activities in the Central Mexican Pacific are the result of Pocillopora’s physiological processes, such as fast growth rates, and recent life-history traits, like the ability to cope with thermal anomalies, which enable them to thrive in a dynamic region severely affected by natural and anthropogenic perturbations. Indeed, a region considered unlikely to recover has regained its live coral cover from &lt; 5 % in 1998 up to 15 % in 20 years. This demonstrates the importance of assisting natural coral recovery with restoration efforts, especially in coral locations that, despite environmental perturbations, have proven to be resilient and may become coral refugia areas under the current climate change scenario.

Mosquito-borne diseases profoundly affect public health through the induction of illness, economic burden, and the emergence of epidemics. Efficient control techniques, encompassing vector management, vaccinations, public awareness, and enhanced healthcare infrastructure, are essential for mitigating their impacts. Aedes vittatus is increasingly recognised as a possible vector for several viral illnesses, presenting an escalating threat to both humans and animals. Genetic analysis of Aedes. vittatus is crucial for formulating targeted and sustainable mosquito control tactics. Population genetics research elucidates resistance mechanisms and vector competence, thereby supporting public health initiatives in disease prevention. This study will investigate the genetic diversity and provenance of Aedes. vittatus populations gathered from several regions in India to address this gap. The collected data will be essential for enhancing comprehension and management of this species. This research examined the genetic diversity of Aedeses vittatus populations utilising the DNASp software tool. Haplotype diversity (Hd), nucleotide diversity (π), the average number of pairwise nucleotide changes, and the counts of synonymous and non-synonymous mutations were analysed. Neutrality tests, such as Tajima’s D, Fu and Li’s D+ and F+, and R2 statistics, were performed. Fifteen sequences were obtained from GenBank, revealing seven haplotypes (H = 7) and a haplotype diversity of 0.819. The sequencing investigation indicated that of the 933 nucleotides analysed, 59.31 were synonymous and 240.69 were non-synonymous. The mean pairwise nucleotide differences (k) was 11.124, although the nucleotide diversity (π) was very modest at 0.03708. The research found 43 polymorphic sites (S = 43) and documented a total of 43 mutations (Eta = 43). Analysis of pairwise nucleotide differences revealed 43 segregating sites. Harpending's raggedness measure (R² = 0.1126) lacked statistical significance (P &gt; 0.05), suggesting demographic stability among Aedes. vittatus populations in India. Fu and Li’s D+ test value (1.41960) was statistically significant (P &lt; 0.05), however Fu and Li’s F+ test value (0.87642) was not statistically significant (P &gt; 0.10). Furthermore, Fu's F statistic (3.499) was positive, indicating the influence of balanced selection in preserving genetic diversity. Strobeck’s S statistic was 0.093, although Tajima’s D value (-0.68003) lacked statistical significance (P &gt; 0.10). The predicted shape parameter for the discrete Gamma distribution was 1.4123. The Tamura-Nei model (+G) was employed to simulate evolutionary rate variations among sites, incorporating five substitution rate categories with mean evolutionary rates of 0.18, 0.46, 0.78, 1.24, and 2.35 substitutions per site. The nucleotide composition of Ae. vittatus COI sequences was: A = 29.83%, T/U = 39.43%, C = 15.55%, G = 15.18%. Genomic research underscores the impact of evolutionary forces on genetic diversity, with balanced selection maintaining stability in Aedes. vittatus populations. Some genetic areas change slowly due to functional restrictions, whereas others acquire mutations rapidly, indicating dynamic flexibility. Comprehending these genetic patterns is crucial for evaluating the evolutionary potential of Aedes. vittatus, especially regarding its adaptation to environmental changes and its involvement in disease transmission. These insights are essential for public health, underscoring the necessity for ongoing genetic research to guide vector control measures and avert mosquito-borne illness outbreaks.

Ligula intestinalis (Cestoda: Diphyllobothriidea) is a cosmopolitan tapeworm parasite characterized by a complex life cycle that includes freshwater fish infection. Ligula disrupts host reproduction, and causes ecological imbalances. Despite its broad geographic distribution and ecological significance, molecular data for South American populations have been lacking, leaving a critical gap in understanding its genetic diversity and evolutionary history. To address this, we conducted the first molecular characterization of L. intestinalis plerocercoid larvae isolated from the native fish Orestias agassizii in Lake Titicaca, Peru. Using Illumina next-generation sequencing, we assembled a complete mitochondrial genome of 13,657bp, containing 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. The mitogenome exhibited an A + T-rich composition (66.3%) and contained over 580 repetitive elements, primarily concentrated within its control region. Comparative analyses with European and Asian mitogenomes revealed substantial regional differences in nucleotide diversity and amino acid composition, with closer similarity observed between South American and Asian lineages. Genes atp6, nad5, and nad6 showed the highest variability, whereas cox1 demonstrated significant intercontinental divergence yet remained conserved within South America, reflecting both phylogeographic patterns and strong functional constraints. Phylogenetic inference based on mitochondrial markers (cytb, cox1, and nd1) confirmed the Titicaca specimen as a distinct South American lineage, closely related to the Nearctic lineage. These findings enhance our understanding of L. intestinalis mitogenomic diversity, emphasize the importance of geographic isolation in parasite diversification, and provide an essential genomic resource for future evolutionary and ecological research in high-altitude ecosystems.

Reproductive strategy can play a significant role in invasion success and spread. Asexual and sexual reproduction may confer different advantages and disadvantages to a founding population, resulting in varying impacts on genetic diversity and the ability to invade. We investigate the role of reproductive mode in two species of non-native hydromedusae (Maeotias marginata and Moerisia sp.) in the San Francisco Estuary (SFE). Both species can reproduce asexually and sexually. We employed 7–8 microsatellite markers to determine overall genetic diversity and to investigate contributions of asexual and sexual reproduction to the populations. We found both species had high levels of genetic diversity (Average HE = 0.63 and 0.58, Number individuals sampled = 111 and 277, for M. marginata and Moerisia sp. respectively) but also detected multiple individuals in clonal lineages. We identified the same clones across sampling locations and time, and the index of asexual reproduction (R) was 0.89 for M. marginata and 0.91 for Moerisia sp. Our results suggest both species maintain high population genetic diversity through sexual reproduction, in combination with asexual reproduction, which allows rapid propagation. In addition, we conducted genetic sequence analyses at the ribosomal ITS1 marker, using samples of Moerisia sp. from the SFE and M. lyonsi from Chesapeake Bay. We found 100 % sequence similarity showing that Moerisia sp. in the SFE and Chesapeake Bay are the same species. The two hydromedusae studied here possess the means to propagate rapidly and have high genetic diversity, both of which may allow them to successfully adapt to changing environments and expand their invasions.