Mitochondrial Control Region Sequences Research Articles

Population genomic analysis of the greater amberjack (Seriola dumerili) in the Mediterranean and the Northeast Atlantic, based on SNPs, microsatellites, and mitochondrial DNA sequences

The greater amberjack (Seriola dumerili) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a/TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.

Population genetic structure of the provincially endangered mainland Eastern Moose (<i>Alces americanus americanus</i>) in Nova Scotia, Canada

Eastern Moose (Alces americanus americanus (Clinton, 1822)) on mainland Nova Scotia (MNS) are declining and experience limited immigration across the Isthmus of Chignecto from the larger population in neighbouring New Brunswick. Provincially Endangered, the recovery strategy for MNS Moose involves mitigating various threats that may lead to local extirpation. We examine genetic diversity of MNS Moose using microsatellite markers and mitochondrial (mtDNA) control region sequences. Genetic similarities with the Alces a. americana population in New Brunswick and the introduced Northwestern Moose (Alces americanus andersoni (= Alces alces andersoni) Peterson, 1952) population on Cape Breton Island are also analysed. Observed heterozygosity for microsatellites for MNS Moose was low and there was also evidence of limited gene flow between Nova Scotia and New Brunswick across the narrow Isthmus of Chignecto that connects these provinces. Consistent with relatively recent colonization of North America by Moose dispersing across the Bering Land Bridge <15 000 years ago, mtDNA haplotypes of MNS Moose were identical or extremely similar to haplotypes found across North America. However, mtDNA diversity was lower in Nova Scotia and New Brunswick than in more central regions of the species’ range. Active measures to maintain habitat that promote connectivity across the Isthmus of Chignecto would likely be valuable for Moose in terms of maintaining genetic variation in the region and reducing inbreeding.

Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan.

Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.

Population genetic diversity in Nezara viridula by analysis of mitochondrial control region sequences

Abstract Here, we examine genetic diversity and dispersal patterns in populations of the agricultural pest Nezara viridula from Argentina using mitochondrial control region sequences. The DNA sequence comparisons of 1837 base pairs of the control region revealed 60 haplotypes determined by a total of 108 variable sites. The observed total haplotype diversity (Hd) value was 0.99, and the nucleotide diversity was 0.00423 and 0.00571 according to π and θW, respectively. The high haplotype diversity and low nucleotide diversity, as well as both neutrality tests and unimodal mismatch distributions, suggested a recent expansion in the populations of N. viridula from Argentina. The expansion of the populations of this insect is probably due to the recent agricultural expansion and intensification of soybean cultivation in this country. No significant levels of genetic differentiation were detected, suggesting that gene flow predominates over genetic drift. In addition, the Bayesian individual assignment analysis revealed that all populations share ancestry. It is probable that the growth in the area cultivated with soybean has generated stable and continuous habitats that allow gene flow among populations of N. viridula. The results of demographic history analysis suggest that the direction of migration of N. viridula would be associated with the growth pattern of soybean crops in Argentina.

Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales.

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.

Genetic data reveal wintering ground affiliation of humpback whales from the Mexican Central Pacific

ABSTRACTTwo groups of humpback whales inhabit the waters off the Pacific coast of Mexico the coastal wintering aggregation in the north (MX), and the southern Mexico/Central America wintering aggregation (S‐MX/CEA) in the south. However, along the coast of the Mexican Central Pacific (MCP), the population affiliation of humpback whales is uncertain. Some studies have concluded that the MCP whales are part of S‐MX/CEA, while others have suggested that the MCP may represent an overlap zone between the two wintering aggregations. In this study, data from 354 biopsy samples were collected over a 12‐year period, to provide insight from genetic information into the affiliation of MCP whales to and the boundaries between the wintering aggregations. Using mitochondrial control region sequences, we found that the majority (73%) of MCP whales are part of MX, but that the boundary between the two wintering aggregations may shift latitudinally depending on environmental conditions. The high haplotypic (h ± SD = 0.859 ± 0.0138) and nucleotide diversity (π ± SD = 0.0145 ± 0.0075) of the MCP whales are also consistent with our sample, including animals from both wintering aggregations. More research is needed to better describe the ranges of the MX and S‐MX/CEA wintering aggregations to ensure their successful conservation and management.

A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia

Abstract To elucidate the historical biogeography of a species, the patterns of population divergence must be understood, and the evolutionary history of the species must be accurately known. For brown trout (Salmo trutta complex), estimating divergence times remains a challenge due to the lack of well-defined time calibration points and insufficient phylogeographic coverage in previous studies. The present work aims to improve molecular dating of mitochondrial control region sequences by using a multicalibration framework based on the latest paleogeological evidence for dating the origin of Lake Ohrid and two available Salmo fossils, including the overlooked Salmo immigratus. Our results clearly show that, contrary to common belief, the major divisions within the brown trout occurred in the Late Pliocene, not the Pleistocene. The Pliocene origin suggests that the brown trout lineages did not form because of geo(hydro)morphological changes during glaciation cycles but may be the result of orogeny and drainage evolution. In addition, increased sampling, particularly in Serbia, led to the identification of a new haplogroup (da-int) occupying an intermediate position with respect to da-es and da-bs haplogroups. While the control region can delineate brown trout lineages, its phylogenetic resolution is limited, so even extensive sampling could not further resolve the lineage level polytomies.

Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

Genetic structure and phylogeography of the endemic species broadbanded velvetchin Hapalogenys analis in the Northwest Pacific

In recent years, due to high-intensity fishing pressure and environmental pollution, some economically important fish species in the waters of the Northwest Pacific have shown a miniaturization trend as well as a sharp decline in fishery resources. Broadbanded velvetchin Hapalogenys analis is an economically important fish species that is widely distributed in the Northwest Pacific Ocean. To improve the understanding regarding its genetic structure and systematic geographic patterns, 87 mitochondrial control region sequences in four geographically distinct populations in the marginal sea of the Northwest Pacific Ocean were identified and analyzed. Thus, 67 haplotypes were detected in 812-base pair homologous sequences, and the haplotypes were identified as predominantly singletons. Further, genetic diversity and genetic structure analysis revealed that the Chinese and Japanese populations of H. analis had different genetic patterns as well as high levels of genetic differentiation. Furthermore, the population of H. analis expanded in the late Pleistocene and middle Pleistocene. We also identified biogeographical barriers, Pleistocene geological events, ocean circulation, habitat, and life history characteristics as the factors that influenced the population genetic structure and systematic geographical pattern of the broadbanded velvetchin species. This study provides information that can be applied in the conservation, sustainable utilization, and genetic diversity maintenance of H. analis.

A note on genetic isolation of Mediterranean sperm whales (Physeter macrocephalus) suggested by mitochondrial DNA

Thirteen sperm whales were sampled, using sloughed skin, in the Mediterranean Sea during six distinct encounters. Individuals were discriminated using the results of molecular sexing, mitochondrial control region sequencing and microsatellite genotyping (3 loci). Samples from 57 specimens were available from sperm whale strandings on northern European coasts. The first ~ 200bp of the mitochondrial DNA (mtDNA) control region of each sample were sequenced and three different haplotypes were identified. The frequency of each haplotype was significantly different between the Mediterranean Sea and the eastern North Atlantic, suggesting that sperm whales in the two areas comprise different maternal entities.

Phylogeography of the Altai weasel (Carnivora: Mustelidae:Mustela altaica) based on an analysis of mitochondrial control-region haplotypes

AbstractThe phylogeography of the Altai weasel (Mustela altaica) based on mitochondrial control-region sequences was investigated using samples from individuals obtained widely across the species range, including Central Asia, Tibet and southern Siberia. Thirty-four haplotypes were identified among 53 individuals from 32 localities. A maximum-likelihood phylogenetic tree for haplotypes showed two major clades, clades I and II. Clade I contained haplotypes from northern Eurasia, including the continental Far East, Altai Mountains and eastern Kazakhstan. Clade II comprised two subclades: group IIa, with haplotypes from around the Pamir Mountains, and the poorly supported group IIb, with haplotypes from the Tibetan Plateau. High haplotype diversity and low nucleotide diversity for clade I suggest that the range of M. altaica expanded over a relatively short period in northern Eurasia. High haplotype and nucleotide diversity for clade II indicate a longer-term, more stable population resulting from geographical isolation of individuals on the Tibetan Plateau by surrounding mountain ranges. Our study suggests that the ancestral population of M. altaica migrated into Tibet from the outside and has diversified in Tibet, seemingly not supporting the ‘out-of-Tibet’ hypothesis; however, we could not completely refute this hypothesis because an individual having a group IIb haplotype was detected in Mongolia.

Origins and population genetics of sambar deer (Cervus unicolor) introduced to Australia and New Zealand

Context Some populations of introduced species cause significant undesirable impacts but can also act as reservoirs for genetic diversity. Sambar deer (Cervus unicolor) are ‘Vulnerable’ in their native range and invasive in Australia and New Zealand. Genetic data can be used to determine whether these introduced populations might serve as genetic reservoirs for declining native populations and to identify spatial units for management. Aims We aimed to identify the provenance of sambar deer in Australia and New Zealand, and to characterise their genetic diversity and population structure. Methods We used mitochondrial control region sequences and 18 nuclear microsatellite loci of 24 New Zealand and 63 Australian sambar deer collected across continuous habitat in each location. We estimated genetic diversity and population differentiation by using pairwise FST, AMOVA, and Structure analyses. We compared our data with 27 previously published native and invasive range sequences to identify phylogenetic relationships. Key results Sambar deer in Australia and New Zealand are genetically more similar to those in the west of the native range (South and Central Highlands of India, and Sri Lanka), than to those in the east (eastern India, and throughout Southeast Asia). Nuclear genetic diversity was lower than in the native range; only one mitochondrial haplotype was found in each introduced population. Australian and New Zealand sambar deer were genetically distinct but there was no population structure within either population. Conclusions The genetic differences we identified between these two introduced populations at putatively neutral loci indicate that there also may be underlying diversity at functional loci. The lack of population genetic structure that we found within introduced populations suggests that individuals within these populations do not experience barriers to dispersal across the areas sampled. Implications Although genetic diversity is reduced in the introduced range compared with the native range, sambar deer in Australia and New Zealand harbour unique genetic variants that could be used to strengthen genetic diversity in populations under threat in the native range. The apparent high levels of gene flow across the areas we sampled suggest that localised control is unlikely to be effective in Australia and New Zealand.

Population structure and genetic connectivity reveals distinctiveness of Irish harbour seals (Phoca vitulina) and implications for conservation management

Abstract The identification of discrete intraspecific units, such as genetically informed management units (MUs), is important to effectively develop and implement conservation strategies for protected species. Harbour seals (Phoca vitulina) occurring in Irish waters are currently viewed as a single nationwide panmictic population (and hence MU), although this assumption is not based on any knowledge of population structure because of the lack of available genetic data. Thus, the present study used mitochondrial control region sequences and between nine and 11 microsatellite loci from harbour seals from Ireland and Northern Ireland (up to n = 123) and adjacent UK/European waters (up to n = 289) to provide insights into the genetic population structure and diversity of harbour seals in the areas studied. Within the island of Ireland, genetic analyses revealed the presence of three genetically distinct local populations, characterized by high genetic diversity, hereby defined as: East Ireland (EI), North‐west & Northern Ireland (NWNI), and South‐west Ireland (SWI). Using previously published and newly generated data, a subsequent wider scale analysis revealed that the EI and SWI local populations were genetically distinct from neighbouring UK/European areas, whereas seals from the NWNI area could not be distinguished from a previously identified Northern UK metapopulation. Migration rate estimates showed that NWNI receives migrants from North‐west Scotland, with NWNI acting as a genetic source for both SWI and EI. The present study provides the most comprehensive genetic assessment of harbour seals in European waters to date, with findings indicating that conservation strategies for harbour seals in Irish waters should be amended to accommodate at least three genetically distinct local populations/MUs. The use of approaches considering both ecological and genetic parameters is recommended for future assessments and delineation of units of ecological relevance for conservation management purposes.

Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific.

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n= 1818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size-based investigation of population structure and phylogeography of this species in the ETP to date.

Population genetic structure of Bryde’s whales (Balaenoptera brydei) on the central and western North Pacific feeding grounds

The genetic structure of Bryde’s whale ( Balaenoptera brydei) on the central and western North Pacific feeding grounds was investigated using a total of 1195 mitochondrial control region sequences and 1182 microsatellite genotypes at 17 loci in specimens collected from three longitudinal areas, 1W (135°E–165°E), 1E (165°E–180°), and 2 (180°–155°W). Genetic diversities were similar among areas and a haplotype network did not show any geographic structure, while an analysis of molecular variance found evidence of genetic structure in this species. Pairwise FST and [Formula: see text] estimates and heterogeneity tests attributed this structure to weak but significant differentiation between areas 1W/1E and 2. A Mantel test and a high-resolution analysis of genetic diversity statistics showed a weak spatial cline of genetic differentiation. These findings could be reconciled by two possible stock structure scenarios: (1) a single population with kin-association affecting feeding ground preference and (2) two populations with feeding ground preference for either area 1W or area 2. An estimated dispersal rate between areas 1W and 2 indicates that both scenarios should be considered as a precautionary principle in stock assessments.

Genetic evidence for a single stock of giant tiger prawns Penaeus monodon in demarcated prawn fishing zones of Tanzania

AbstractTanzania demarcated three prawn fishing zones along its coast to spread fishing pressure and help the prawn fishery to recover. However, it is unknown whether the demarcated zones correspond to the genetic stock structure of the world's most commercially important prawn, the giant tiger prawn (Penaeus monodon). Thus, this study used partial mitochondrial control region sequences (534 base pairs) to test the hypotheses that (1) giant tiger prawns in Tanzania's demarcated prawn fishing zones are a single stock and (2) the giant tiger prawns on the Tanzanian coast experienced a recent demographic expansion. The sequences showed high haplotype diversity (h = 0.998–1.0) and low nucleotide diversity (θπ = 1.89%–2.24%). The neutrality test and mismatch analysis showed that the hypothesis of recent demographic expansion could not be rejected. The analysis of molecular variance revealed low and insignificant fixation indices between the zones (FST = 0.00025, p > 0.05; ΦST = −0.00027, p > 0.05), suggesting that the three demarcated fishing zones constitute a single stock and that fishers may be targeting the same stock. Furthermore, it was discovered that Zone 2 has the potential to replenish depleted areas; thus, it should be prioritised in future conservation planning.

Anthropogenic influences on genetic diversity and differentiation of the clearhead icefish (Protosalanx hyalocranius), as revealed by mitochondrial and microsatellite DNA markers

The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. For the past few decades, the wild resources of P. hyalocranius have markedly decreased due to human activities such as overfishing, hydro-projects and water pollution. Meanwhile, P. hyalocranius has been widely introduced into lakes and reservoirs of northern China and some have become established, invasive populations, leading to detrimental effects on ecosystems. Using mitochondrial control region sequences and nine microsatellite DNA markers, the aim of this study was to assess to what extent human activities could impact the genetic diversity and population structure of P. hyalocranius, and explore the sources of the invasive Heilong River population based on genetic characterization. Based on mitochondrial DNA, the average haplotype diversity and nucleotide diversity among six populations were 0.737 and 0.0029 respectively. Based on microsatellite markers, the observed (HO) and expected (HE) heterozygosities in each population ranged from 0.481 to 0.565 and 0.478 to 0.565, respectively. Both mitochondrial and microsatellite markers indicated the genetic diversity in Chaohu Lake was the lowest. HO and HE of the two anadromous populations (Liao River Estuary and Yalu River Estuary) were close to Chaohu Lake and relatively low among all populations. The pairwise Dest values showed high and significant genetic differentiation between Taihu Lake and other populations. There was no evidence of genetic differentiation between Chaohu Lake and the two anadromous populations. No significant reduction of genetic diversity was observed in the Heilong River population. Bottleneck analysis showed that the two anadromous populations may have experienced a recent genetic bottleneck. DIYABC analysis suggested that the sources of the invasive Heilong River population were Taihu and Hongze lakes, with a greater genetic contribution from Hongze Lake. Therefore, the anadromous populations of P. hyalocranius may have suffered more impacts from human activities than the strictly freshwater populations. Among freshwater populations, Chaohu Lake should also be paid more attention in fisheries management. In addition, our study demonstrated that multiple introductions can give rise to high genetic diversity in an invasive population.

Population structure, phylogeography and demographic history of Tenualosa ilisha populations in the Indian Ocean region inferred from mitochondrial DNA sequence variation

Understanding evolutionary processes reshaping the genetic structure in the context of environmental changes is an important component of sustainable management for the fisheries resources. In this study, we analyzed mitochondrial control region sequence to reveal population structure, phylogeography and demographic history of six populations of hilsa shad (Tenualosa ilisha) in the Indian Ocean regions (Andaman Sea, Bay of Bengal, Arabian Sea and Persian Gulf). High haplotype diversity was found in all of the populations of T. ilisha. The Analysis of Molecular Variance and FST comparisons revealed high level of genetic variation and divergence between populations of the Bay of Bengal and Arabian Sea. Four cryptic genetic barriers were found for the studied populations of T. ilisha, and the highest degree of population divergence was found between the Western Indian Ocean (Arabian Sea and Persian Gulf) and Eastern Indian Ocean (Andaman Sea and Bay of Bengal) regions based on the Voronoï tessellation of BARRIER analysis. The gene flow analysis detected almost no migration between Eastern and Western part of the Indian Ocean regions. Besides, one-way migration was found from Pakistan of Arabian Sea to Kuwait population of Persian Gulf. Demographic history of population expansion and long stable population varied for different populations of hilsa shad. Distinct cryptic genetic barriers, limited gene flows and complex evolutionary process resulted in a significant population genetic and phylogeographic structure, and intricate demographic histories of T. ilisha populations. Further, the study provided valuable insights for conserving and managing of this fishery resource in its broad geographical coverage.

Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route.

Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.

Strong genetic structure and limited connectivity among populations of Clark’s Anemonefish (Amphiprion clarkii) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due to limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clark’s Anemonefish (Amphiprion clarkii) based on 209 individuals from 16 samples sites in the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and eight nuclear microsatellite loci. Results provided evidence of a significant genetic structure (mtCR: Φst = 0.42, Φct = 0.64; microsatellites: Fst = 0.01, Fct = 0.05). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor) and Eastern (Biak) IMA populations, with almost no gene flow. This matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.