Search Results (15)

Pampus argenteus, a commercially significant marine species, faces genetic diversity challenges in selective breeding programs. This study implemented a comprehensive molecular strategy to evaluate genetic parameters in wild populations along China’s coast and three successive selected generations. The analysis utilized 19 highly polymorphic microsatellite loci, mtCOI, and mtD-loop sequences to assess genetic structure. Compared with the wild populations, the average number of alleles (N_a: 11.158–12.947), effective alleles (N_e: 5.592–6.502), observed heterozygosity (H_o: 0.626–0.665), expected heterozygosity (H_e: 0.777–0.796), and allele richness (A_r: 10.900–12.510) of the selected populations did not significantly decrease. In the mass selection of the three consecutive generations, the high genetic diversity of the selected population was successfully maintained. The effective population sizes of the first to third generations were estimated to be 83.7, 66.6, and 59.6, respectively. Population differentiation analysis showed minimal genetic divergence (FST = 0.0159–0.0326) with substantial gene flow, supported by clustering patterns indicating panmixia among wild populations from different geographical locations and among the selected populations. Notably, marginal decreases in diversity indices across generations suggest incipient genetic diversity decline, underscoring the imperative for systematic genetic monitoring. These findings validate the current breeding program’s efficacy in maintaining genetic variability while providing a framework for optimizing long-term selection strategies to prevent inbreeding depression. Full article

The shark Squalus albicaudus, categorized by the International Union for Conservation of Nature red list as Data Deficient due to lack of minimal information for classification, is distributed throughout the Brazilian coast. High pressures such as overfishing and anthropic activities, as well as certain biological characteristics, including k strategists, comprise influential shark stocks reduction agents. However, genetic diversity, population structure, connectivity, and effective population size data are still limited for S. albicaudus, indicating the need for further studies. In this context, the genetic variability and population structure of S. albicaudus were investigated herein to test for panmixia. Samples were obtained from coasts of the Brazilian states of Pernambuco, Rio de Janeiro, and São Paulo along the species distribution range, and single nucleotide polymorphisms (SNPs) were assessed by the ddRADseq method. The findings revealed a panmitic S. albicaudus population, explained by certain life strategies, such as polyandry and migratory behavior. Based on the genomic findings reported herein, a single S. albicaudus population should be considered in the study area, indicating the need for specific management and conservation plans at the regional scale. Full article

The Japanese eel (Anguilla japonica) is a commercially important species in East Asia, the abundance of which has rapidly decreased in recent decades. The fishery resource in the Pearl River basin has mainly deteriorated due to overexploitation and habitat degradation. Knowledge on its genetic status is indispensable for resource management. In this study, we explored the temporal genetic structure of A. japonica on the basis of the concatenated sequences of two mitochondrial fragments (mtDNA) and eight microsatellite markers. A total of nine temporal samples (N = 127) were collected during 2019 and 2021 from Jiangmen City, China, which is located in the Pearl River estuary. mtDNA sequence analysis showed a high level of haplotype diversity, and yielded 124 haplotypes with ranging from 9 to 19 in temporal samples. All microsatellite loci were polymorphic among each of the nine temporal samples, with 150 alleles identified across all samples. Pairwise F_ST values were low and nonsignificant according to both mtDNA and microsatellite markers. STRUCTURE analysis showed that all temporal samples were not clearly differentiated from each other. The yielded outcomes supported a panmictic pattern in different temporal A. japonica samples. Therefore, our results call for the management of A. japonica as a single unit and joint conservation strategy of the species, since overexploitation in any region will decrease its global resource. Full article

The study of natural selection and local adaptation is a thriving field of research. Local adaptation is driven by environment components and results in locally adapted phenotypes with higher fitness relative to other phenotypes from other locations in the species range. Tests of local adaptations have traditionally been done using transplant experiments, but the advent of next-generation sequencing methods have allowed the study of local adaptation to move from a phenotypic to a genomic approach. By using genome scans and state-of-the-art statistical tests, researchers can identify genes putatively under selection and study the genomic architecture of local adaptation, which often includes the observation of clustering of adaptive genes concentrated in fewer genomic regions known as “genomic islands of divergence”. The two species of North Atlantic eels, the European and the American eel, are excellent species for studying selection since they are panmictic and present large population sizes, show a wide distribution range across extremely heterogenous environments, and are subject to high mortalities. We reviewed studies of natural selection and local adaptation in American eel, European eel, between life cycle stages, between European and American eel. Finally, we discussed genome architecture in relation to local adaptation in eels and the role of both genetic (i.e., local adaptation) and non-genetic (i.e., phenotypic plasticity) in the survival of eels across their distribution range. Full article

The giant mottled eel, Anguilla marmorata, is at high risk of extinction due to overfishing of glass eels and elvers to provide stock for eel farming. In Vietnam, information on the genetic diversity and population structure of this species, which is necessary for resource management, is limited. In order to address this paucity of information, sequencing of the entire mitochondrial control region (mtDNA) was carried out for 176 individuals collected from central Vietnam. The sequences were investigated using various genetic, phylogenetic and population analyses. A total of 165 distinct haplotypes were identified. The percentage of variation within and among populations was 99.26% and 0.74%, respectively. The fixation index was low (0.007) and not significant (p = 0.096). Therefore, panmixia and a lack of significant population genetic structuring seem likely for A. marmorata in central Vietnam. Most sampled eels were genetically similar to eels found in North Pacific populations (Japan, Taiwan and the Philippines), except for one sample from Quang Tri and two samples from Binh Dinh, which had high values of genetic identity (97% to 99%) with South Pacific populations (Tahiti, Fiji, New Caledonia and Papua New Guinea). Taken together, we suggest that A. marmorata from the North and South Pacific populations co-exist in central Vietnam. Full article

The thin-lipped grey mullet Chelon ramada (Risso, 1827) is a catadromous species that is distributed along the Northeast Atlantic, from the Norwegian coastline down to Mauritania, on the African coast (20–60° N, 18° E–42° W), and displays diverse patterns of habitat use and migratory behaviors. This widely distributed species is observed in large shoals throughout coastal areas and in brackish and freshwater environments, yet no previous studies have addressed the population’s genetic structure. To study the patterns of genetic variation, gene flow and connectivity in the C. ramada distribution range), 457 fin clips sampled from 14 locations (Portuguese coast, Bay of Biscay, North seas, Celtic sea, Western Mediterranean and Eastern Mediterranean) were genotyped using 11 microsatellite DNA markers. No significant genetic differentiation among locations or geographic clustering of samples was observed, which points towards the existence of a unique genetic group. The results suggest strong gene flow from the Western Mediterranean to the Portuguese coast (Nm = 1) and vice versa (Nm = 0.87). The Portuguese coast has displayed the highest values of gene flow with all the sampling sites ([0.4–0.6]) whereas Northeast Atlantic coast and Eastern Mediterranean maintained symmetrical lower values of gene flow that ranged between [0.20–0.30]. The present study provides evidence that high levels of gene flow are maintained within the distribution range, contributing to the existence of a panmictic population. Full article

Norway spruce, economically and ecologically one of the most important European forest tree species, rapidly declines due to massive bark beetle outbreaks across many countries. As a prerequisite of ecosystem stability facing climate changes of uncertain predictions, the reforestation management promoting locally adapted resources of broad genetic diversity should be prioritized, especially in nature conservation areas. In our case study carried out in the national park, Krkonoše Mountains (the Giant Mountains, the Czech Republic), we demonstrated a tree breeding strategy aiming at maximizing genetic diversity. More than four hundred unique Norway spruce accessions were genotyped on 15 microsatellite loci (N_e = 5.764, I = 1.713 and H_e = 0.685). Two core collection selection approaches were proposed to establish a new deployment population providing local gene sources of high genetic diversity. Namely, the Core Hunter selection algorithm, with average entry-to-nearest-entry distance (EN) optimization, was applied to identify the most diverse core collection set with the highest genetic diversity parameters obtained for 57 selected individuals (N_e = 6.507, I = 1.807, and H_e = 0.731). The latter core collection method proposed is innovative, based on choosing appropriate genotypes from a clustered heatmap. For simplicity, we demonstrated the principle of selection strategy on a reduced dataset. It is vital to promote panmixia of a newly established production population from a core collection to complete the conservation breeding effort. Thus, we demonstrated the utilization of the Optimum Neighborhood Algorithm (ONA) deployment that outperformed other deployment algorithms, especially in the case of balanced clone representation and uneven shapes of planting plots. We believe that the case study presented can be generalized and considered as a guideline for analogical tree breeding intentions. Full article

The Red-backed Shrike (Lanius collurio) is a medium-sized, carnivorous passerine, occurring throughout the western Palearctic. As with numerous other bird species, its numbers are declining, mainly due to anthropogenic factors. Therefore, revealing the population structure and genetic diversity is paramount in ensuring the survival of the species. However, until present, only mitochondrial DNA has been targeted to reveal the genetic structure of the species. These studies suggested a panmictic population structure. In this study, we employed next-generation sequencing of 88 Red-backed Shrikes from 11 countries and used single nucleotide polymorphisms (SNPs)) to investigate the population structure. Even with such high-resolution DNA data, we found considerable genetic variability, but our results indicate no genetic structure in the Red-backed Shrike, suggesting a panmictic population. Migrant birds from Israel and Kuwait could not be attributed to breeding populations. Panmixia is the genetic legacy of the widespread and continuous distribution of the species, high locomotion capacities, and, most importantly, the numerous ice ages from the past few million years, which forced various populations to retract to refugia and expand their ranges several times, and to interbreed both in the glacial refugia and during warm periods in Eurasia. Full article

Determining migratory connectivity within and among diverse taxa is crucial to their conservation. Insect migrations involve millions of individuals and are often spectacular. However, in general, virtually nothing is known about their structure. With anthropogenically induced global change, we risk losing most of these migrations before they are even described. We used stable hydrogen isotope (δ²H) measurements of wings of seven species of butterflies (Libytheana carinenta, Danaus gilippus, Phoebis sennae, Asterocampa leilia, Euptoieta claudia, Euptoieta hegesia, and Zerene cesonia) salvaged as roadkill when migrating in fall through a narrow bottleneck in northeast Mexico. These data were used to depict the probabilistic origins in North America of six species, excluding the largely local E. hegesia. We determined evidence for long-distance migration in four species (L. carinenta, E. claudia, D. glippus, Z. cesonia) and present evidence for panmixia (Z. cesonia), chain (Libytheana carinenta), and leapfrog (Danaus gilippus) migrations in three species. Our investigation underlines the utility of the stable isotope approach to quickly establish migratory origins and connectivity in butterflies and other insect taxa, especially if they can be sampled at migratory bottlenecks. We make the case for a concerted effort to atlas butterfly migrations using the stable isotope approach. Full article

Sea anemones are sedentary marine animals that tend to disperse via planktonic larvae and are predicted to have high population connectivity in undisturbed habitats. We test whether two sea anemone species living in two different tidal zones of a highly disturbed marine environment can maintain high genetic connectivity. More than 1000 loci with single-nucleotide polymorphisms (SNPs) were obtained with double-digest RADseq for 81 Stichodactyla haddoni and 99 Entacmaea quadricolor individuals to test for population genetic structure. We find evidence that both species predominantly propagate via sexual reproduction, and asexual reproduction is limited. We observe panmixia that indicates the absence of effective dispersal barriers for these species living in a highly anthropogenically disturbed environment. This is positive news for both species that are also found in the aquarium trade. More fundamentally, our results suggest that inhabiting different parts of a shallow reef may not affect a species’ population connectivity nor favour asexual reproduction. Full article

Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low F_ST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used. Full article

Revealing the genetic population structure in abundant avian species is crucial for understanding speciation, conservation, and evolutionary history. The Red-backed Shrike Lanius collurio, an iconic songbird renowned for impaling its prey, is widely distributed as a breeder across much of Europe, Asia Minor and western Asia. However, in recent decades, many populations have declined significantly, as a result of habitat loss, hunting along migration routes, decrease of arthropod food, and climate change e.g., severe droughts in Africa. Within this context, gene flow among different breeding populations becomes critical to ensure the survival of the species, but we still lack an overview on the genetic diversity of the species. In this paper, we analyzed the mitochondrial cytochrome b gene (mtDNA) and the cytochrome c oxidase subunit 1 gene (mtDNA) of 132 breeding Red-backed Shrikes from across the entire breeding range to address this knowledge gap. Our results revealed consistent genetic diversity and 76 haplotypes among the Eurasian populations. Birds are clustered in two major groups, with no clear geographical separation, as a direct consequence of Pleistocene glaciations and apparent lineage mixing in refugia. This has led to genetic panmixia. Full article

Currently, there has been an increasing demand on seed orchard designs with respect to mitigating inbreeding in advanced generations or facing severe mortality at sites. Optimum Neighborhood Algorithm design (ONA) excels in solving these issues, as shown in two case studies. The first demonstrates the application of the ONA for populating empty positions in an existing orchard. Following this concept, the ONA can be used for upgrading existing orchards, where only high-value parents are retained and new parents are introduced, thus avoiding the genetic penalty associated with the establishment of new-generation seed orchards. The second illustrates benefits of combining the ONA with the Minimum Inbreeding (MI) seed orchard design. Utilizing the MI, distances among clonal rows of selected clones were maximized on the orchard grid while the remaining single-tree positions were populated by ONA. Full article

Oscillations of periods with low and high temperatures during the Quaternary in the northern hemisphere have influenced the genetic composition of birds of the Palearctic. During the last glaciation, ending about 12,000 years ago, a wide area of the northern Palearctic was under lasting ice and, consequently, breeding sites for most bird species were not available. At the same time, a high diversity of habitats was accessible in the subtropical and tropical zones providing breeding grounds and refugia for birds. As a result of long-term climatic oscillations, the migration systems of birds developed. When populations of birds concentrated in refugia during ice ages, genetic differentiation and gene flow between populations from distinct areas was favored. In the present study, we explored the current genetic status of populations of the migratory European bee-eater. We included samples from the entire Palearctic-African distribution range and analyzed them via mitochondrial and nuclear DNA markers. DNA data indicated high genetic connectivity and panmixia between populations from Europe, Asia and Africa. Negative outcomes of Fu’s Fs and Tajima’s D tests point to recent expansion events of the European bee-eater. Speciation of Merops apiaster started during the Pliocene around three million years ago (Mya), with the establishment of haplotype lineages dated to the Middle Pleistocene period circa 0.7 Mya. M. apiaster, which breed in Southern Africa are not distinguished from their European counterparts, indicating a recent separation event. The diversification process of the European bee-eater was influenced by climatic variation during the late Tertiary and Quaternary. Bee-eaters must have repeatedly retracted to refugia in the Mediterranean and subtropical Africa and Asia during ice ages and expanded northwards during warm periods. These processes favored genetic differentiation and repeated lineage mixings, leading to a genetic panmixia, which we still observe today. Full article

The Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensive population genetics analysis was based on 1400 Gb of whole-genome sequence (WGS) data from 84 eels. It demonstrated that a Japanese eel group from the Kuma River differed from other populations of the same species. Even after removing the potential adapted/selected single nucleotide polymorphism (SNP) data, and with very small differences (fixation index [Fst] = 0.01), we obtained results consistently indicating that panmixia does not occur in Japanese eels. The life cycle of the Japanese eel is well-established and the Kuma River is in the center of its habitat. Nevertheless, simple reproductive isolation is not the probable cause of non-panmixia in this species. We propose that the combination of spawning area subdivision, philopatry, and habitat preference/avoidance accounts for the non-panmixia in the Japanese eel population. We named this hypothesis the “reproductive isolation like subset mapping” (RISM) model. This finding may be indicative of the initial stages of sympatric speciation in these eels. Full article