Significant Genetic Structure Research Articles

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

Genetic composition of green sea turtles (Chelonia mydas) at coastal feeding areas of Uruguay

The highly migratory and marine nature of species such as green sea turtles (Chelonia mydas) may hinder understanding of basic life history and impact ensuing management and conservation applications across their full range. To elucidate the linkages between juvenile green turtles foraging in coastal waters of Uruguay in the Southwestern Atlantic Ocean to their future nesting or feeding grounds, this study investigated their genetic composition . A total of 201 tissue samples were collected from turtles that had stranded or were intentionally captured for scientific research along the Uruguayan coast (ca. 33°–35°S) during two sampling periods (2003–2005 and 2009–2014). Samples were pooled for analysis. Twelve mitochondrial control region haplotypes and ten subhaplotypes were identified, all of which had been previously detected at Atlantic or Caribbean nesting beaches. Mixed Stock Analysis revealed that most turtles traced to the Ascension Island rookery, representing a substantial connection to the remote mid-Atlantic island thousands of kilometers distant. Other nesting areas, such as Guinea Bissau in Africa and Trindade Island in Brazil, represented less significant sources. There was no significant temporal or spatial genetic structure within Uruguayan waters, suggesting dispersion along this coast. Despite the geographic distance from the nesting beach, the significant connection to the Ascension Island rookery underscores the importance of considering rookery population size and ocean current influences in understanding source contributions. These findings emphasize the need for conservation efforts, including the maintenance of existing protected areas and the creation of new ones, to ensure the long-term conservation of green turtles connected to various nesting colonies and feeding grounds.

Genetic diversity and population structure of Kawakawa Euthynnus affinis (Cantor, 1849) in Malaysia and its surrounding waters inferred by mitochondrial DNA cytochrome oxidase I and cytochrome b genes

Kawakawa (Euthynnus affinis) is a widely distributed epipelagic tuna, considered among the most economically significant species in the subtropical and tropical waters of the Indo-Pacific region. However, the lack of comprehensive information on the stock structure, management, and conservation of E. affinis populations in Malaysia raises concerns of potential overfishing and depletion of this marine fish. To ensure effective and successful species management, it is imperative to conduct a molecular- based assessment of the stock structure. In the present study, the genetic diversity and population structure of E. affinis in Malaysia and its surrounding waters were investigated using mitochondrial DNA cytochrome oxidase I (COI) and cytochrome b (Cyt b) genes. A total of 390 (COI) and 414 (Cyt b) individuals of E. affinis were sampled from 20 distinct locations situated within five geographic regions: the Straits of Malacca, South China Sea, Sulu Sea, Celebes Sea, and the Arabian Sea. The results revealed that the genetic divergence among 20 populations of E. affinis varied from low to high. The average haplotype diversity (Hd) and nucleotide diversity (π) for COI were calculated to be 0.5131 and 0.0043, respectively. On the other hand, the average haplotype diversity (Hd) and nucleotide diversity (π) for Cyt b were found to be 0.7450 and 0.0162, respectively. The analysis of haplotype distribution revealed that a total of 20 distinct haplotypes were identified for both the COI and Cyt b genes across 20 populations of E. affinis. The analysis of the Neighbor-Joining (NJ) tree and the Minimum Spanning Network (MSN) revealed the formation of three distinct clades among thesamples. AMOVA analysisshowed a significant genetic structure among the 20 populations of E. affinis, as indicated by the COI: FST = 0.5364 (P < 0.05) and Cyt b: FST = 0.9521 (P < 0.05). The neutrality test and mismatch distribution analysis indicated that the E. affinis specimens underwent a period of population expansion. This study marks a significant milestone as the first comprehensive documentation of genetic diversity and population structure of E. affinis across various locations in Malaysia, with an additional pioneering investigation conducted in the waters of Yemen.

Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences

Nemipterus randalli, commonly known as Randall’s threadfin bream, is a commercially important marine finfish. Understanding its genetic structure is critical to effective management and conservation efforts. Previous investigations on population structure in this species were limited by geographic coverage. In this study, we utilized the mitochondrial Cytochrome b gene and nuclear Ribosomal protein gene intron Rp S7 sequences to investigate the population genetic structure, demography and genetic diversity of N. randalli along Indian waters. Our results revealed high haplotype diversity but low nucleotide diversity. AMOVA revealed that the variation among the population was highly significant. Hierarchical AMOVA provided further evidence of significant genetic differentiation between the west and east coasts, which was corroborated by the Bayesian tree and the median-joining network diagram. The mtDNA sequences revealed significant genetic structure between populations based on fixation index analysis following the isolation-by-distance model. Furthermore, the neutrality test and mismatch analysis suggest that N. randalli populations may have experienced a population expansion. However, nuclear marker RpS7, showed a high level of polymorphism, which obscured the population structuring observed with the mitochondrial marker. Consequently, concordant results were not obtained when comparing the mitochondrial and nuclear DNA sequences. The strong genetic differentiation between the east and west coast observed using mitochondrial marker could be attributed to a combination of geographic and environmental factors. These findings lay the groundwork for developing effective conservation and management strategies for N. randalli, considering its genetic structure.

Electronic tags reveal high migratory diversity within largest Atlantic halibut (Hippoglossus hippoglossus) stock

Growing evidence suggests that complex spatial structure occurs within the Scotian Shelf and southern Grand Banks (SSGB) Atlantic halibut stock, yet large knowledge gaps remain about migratory and spawning behaviors. Here, 71 pop-up satellite archival tags were deployed on large Atlantic halibut (FL: 87 - 166 cm) between 2012 and 2020. Migration tracks were successfully reconstructed for 43 fish using a hidden Markov geolocation model, and temperature and depth time series were available for nine fish (total n = 52). Five migratory behaviors were identified: shelf residency, slope residency, shelf-channel migration, shelf-slope migration, and dispersal. The high-resolution data for four of 20 physically recovered tags provided evidence for putative female spawning behavior in deep channels on the continental shelf and along the continental slope between January and February. Additionally, four halibut displayed previously undocumented periods of sustained, oscillatory vertical movement along the continental slope between November and February. The high migratory diversity observed in the SSGB stock supports the existence of multiple resident and migratory contingents in the stock in the apparent absence of significant genetic structure.

Genetic resources of common ash (Fraxinus excelsior L.) in Poland

BackgroundKnowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland.ResultsChloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean AR = 12.35; mean Ho = 0.769; mean He = 0.542) but low differentiation based on nuclear microsatellites (FST = 0.045). Significant spatial genetic structure, consistent with models of isolation by distance, was detected in 14 out of 23 populations. Estimated effective population size was moderate-to-high, with a harmonic mean of 57.5 individuals per population.ConclusionsGenetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands.

Conservation genetics of Notelaea lloydii (Oleaceae) in south‐eastern Queensland, Australia

AbstractHabitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among N. lloydii populations. Therefore, we undertook a genome‐wide single nucleotide polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south‐eastern Queensland. Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that N. lloydii produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un‐bagged flowering and fruiting rates, and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of N. lloydii are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.

Genomics reveals repeated landlocking of diadromous fish on an isolated island.

Landlocking of diadromous fish in freshwater systems can have significant genomic consequences. For instance, the loss of the migratory life stage can dramatically reduce gene flow across populations, leading to increased genetic structuring and stronger effects of local adaptation. These genomic consequences have been well-studied in some mainland systems, but the evolutionary impacts of landlocking in island ecosystems are largely unknown. In this study, we used a genotyping-by-sequencing (GBS) approach to examine the evolutionary history of landlocking in common smelt (Retropinna retropinna) on Chatham Island, a small isolated oceanic island 800 kilometres east of mainland New Zealand. We examined the relationship between Chatham Island and mainland smelt and used coalescent analyses to test the number and timing of landlocking events on Chatham Island. Our genomic analysis, based on 21,135 SNPs across 169 individuals, revealed that the Chatham Island smelt was genomically distinct from the mainland New Zealand fish, consistent with a single ancestral colonisation event of Chatham Island in the Pleistocene. Significant genetic structure was also evident within the Chatham Island smelt, with a diadromous Chatham Island smelt group, along with three geographically structured landlocked groups. Coalescent demographic analysis supported three independent landlocking events, with this loss of diadromy significantly pre-dating human colonisation. Our results illustrate how landlocking of diadromous fish can occur repeatedly across a narrow spatial scale, and highlight a unique system to study the genomic basis of repeated adaptation.

Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants.

Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. To evaluate whether relatedness decreases with local density, we analyzed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation by distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1-3%. The EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

Factors determining fine-scale spatial genetic structure within coexisting populations of common beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.), and sessile oak (Q. petraea (Matt.) Liebl.)

Key messageNaturally regenerating populations of common beech, pedunculate, and sessile oaks develop strong spatial genetic structures at adult and seedling stages. Significant genetic relationship occurs between individuals growing up to 60 m apart. This indicates the minimum distance separating trees from which seeds used for reforestation should be harvested to avoid the adverse effects of excessive relatedness among offspring.ContextSpatial genetic structure is an inherent characteristic of naturally regenerating plant populations and has practical implications in forests for the management of genetic resources.AimsWe investigated the extent of spatial genetic structure in three broad-leaved forest tree species (common beech—Fagus sylvatica L.; pedunculate oak—Quercus robur L.; and sessile oak—Q. petraea (Matt.) Liebl.) coexisting in the same nature reserve, explored its variation among species and different life stages (adults/offspring), and tested its possible determinants.MethodsWe explored patterns of spatial distribution of individuals, and using microsatellites, we estimated parameters of spatial genetic structure based on kinship relationships, considering possible sources of variation.ResultsIn adults, the strongest spatial genetic structure was found for Q. petraea (Sp = 0.0187), followed by F. sylvatica (Sp = 0.0133), and the weakest in Q. robur (Sp = 0.0080). It was uniform across different age classes in pedunculate oak but decreased with age in sessile oak. No apparent relationship between age and spatial genetic structure was found in beech. Offspring exhibited significant spatial genetic structure (ranging from 0.0122 in beech to 0.0188 in sessile oak). The cohorts of seedlings having both parents present within the study site had stronger spatial genetic structures than cohorts of seedlings with only one local parent.ConclusionSpatial genetic structure is strong in naturally regenerating populations of heavy-seeded forest trees. Pollen immigration from outside of a local forest stand can significantly decrease the extent of spatial genetic structure in offspring generations.

Population Genetic Structure of a Viviparous Sand Lizard, the Phrynocephalus forsythii in the Tarim Basin, Xinjiang of China

The desert ecosystem occupies an important position in the composition of global biodiversity. The Tarim Basin is located in south Xinjiang of China and has the world’s second largest mobile desert, the Taklamakan Desert. As an endemic species in this region, Phrynocephalus forsythii has been demonstrated to have a potentially high extinction risk due to climate change. In order to understand the overall genetic status and provide accordant conservation strategies for the species, we investigated the genetic diversity and population structure of P. forsythii from 15 sites in the Tarim Basin using 21 highly polymorphic microsatellite markers. We found significant genetic structure across the study region. We also revealed generally low levels of gene flow between the 25 sites, suggesting individual dispersal and migration may be restricted within populations. In addition, geographical distance and ambient temperature might be important factors in explaining the observed genetic structure. Our results will provide a scientific basis for the future protection of P. forsythii in this area, as well as an important reference for the conservation and management of biodiversity in desert ecosystems.

Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River

Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.

Population genetic structure of Kawakawa (Euthynnus affinis Cantor, 1849) in Malaysian waters based on COI gene

Abstract. Binashikhbubkr K, Setyawan AD, Naim DM. 2023. Population genetic structure of Kawakawa (Euthynnus affinis (Cantor, 1849)) in Malaysian waters based on COI gene. Nusantara Bioscience 15: 258-268. Kawakawa (Euthynnus affinis Cantor, 1849) is widely distributed in the subtropical and tropical waters of the Indo-Pacific region. Still, insufficient data about its stock, management, and protection in Malaysia and nearby waters raises concerns about overfishing and depletion. Therefore, to ensure effective and successful management of a species, it is imperative to conduct a molecular-based assessment of the stock structure. The present study investigated the population genetic structure of E. affinis in Malaysian waters using the mtDNA COI gene. Furthermore, the 632 bp segment of the COI region was sequenced in 372 individuals from 19 distinct populations in Malaysian waters. The results revealed that the genetic divergence varied from low to high. The average Haplotype diversity (Hd) and nucleotide diversity (?) were calculated to be 0.5401 and 0.0045, respectively. Examining haplotype distribution unveiled the presence of 22 unique haplotypes within the COI gene of E. affinis. The analysis of the Neighbor Joining (NJ) tree and the Minimum Spanning Network (MSN) revealed the formation of three distinct clades among E. affinis samples. Analysis of Molecular Variance (AMOVA) showed a significant genetic structure among the 19 populations of E. affinis [(FST = 0.5354 (P &lt; 0.05)]. The neutrality test and mismatch distribution analysis indicated that the specimens underwent a period of population expansion. This study is a significant milestone, providing the first comprehensive documentation of the genetic structure of E. affinis in Malaysia.

The genetic connectivity of the silky shark (Carcharhinus falciformis) across Indonesia

Silky shark (Carcharhinus falciformis) has been listed as CITES Appendix II and Vulnerable by IUCN red list. Reports from Indian, Pacific and Atlantic Ocean showed a sharply declining C. falciformis population every year, including in Indonesia. Despite this issue, information on local and regional genetic population structure of this species is still lacking. In this research, we aim to assess the population condition of C. falciformis across Indonesia Fisheries Management Area (FMAs), using mitochondrial genetic data. A total of 225 fins or tissue samples collected from various traditional fish market and shark-fin exporters across Indonesia, then sequenced using mtDNA control region, yielding 510 bp of sequence. The overall Haplotype diversity is high (h: 0.534 ± 0.035). Meanwhile, the nucleotide diversity (θπ) is low (range of 0.00067 – 0.00201) compared to the Atlantic and Red Sea. In addition, the genetic diversity of C. falciformis in Indonesia is lower than other pelagic shark species. Furthermore, AMOVA and Fst results showed a significant structure between Aceh and other locations in Indonesia. Samples from across Indonesia also showed a certain degree of haplotype sharing but with significant genetic structure with others, additionally, the combined dataset revealed a pattern that is similar to previous studies, which showed that the Atlantic population is different from the rest. The distinct genetic population of C. falciformis observed in Aceh may indicate that this population should be managed separately. Meanwhile, the shared genetic information within the Timor Sea indicates the necessity of establishing a co-management plan between Indonesia and neighbouring countries such as Timor-Leste and Australia to ensure the sustainable use of this marine resource.

Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches

Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame (Sesamum indicum L.) plays a crucial role in Ethiopian agriculture, serving both subsistence and commercial purposes. However, our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited. To address this knowledge gap, we genotyped 368 Ethiopian sesame germplasms, categorizing into four distinct breeding groups: Accessions, landraces, improved varieties, and wild types, using a comprehensive set of 28 polymorphic markers, including 23 simple sequence repeat (SSR) and five Insertion-Deletion (InDel) markers. These markers ensured robust genomic representation, with at least two markers per linkage group. Our results unveiled substantial genetic diversity, identifying a total of 535 alleles across all accessions. On average, each locus displayed 8.83 alleles, with observed and expected heterozygosity values of 0.30 and 0.36, respectively. Gene Diversity and Polymorphic Information Content (PIC) were recorded at 0.37 and 0.35. The percentage of polymorphic loci varied significantly among breeding groups, ranging from 8.00% to 82.40%, indicating high diversity in accessions (82.4%), moderate diversity in improved varieties (31.20%) and landraces (29.60%), and limited diversity in wild types (8.00). Analysis of Molecular Variance (AMOVA) results emphasized significant genetic differentiation among populations, with substantial diversity (P ​< ​0.001) within each population. Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations, while the larger proportion of genetic diversity (92%) resided within each individual sesame population, showcasing heightened diversity within each group. Our study's findings received support from both Bayesian clustering and Neighbor-joining (NJ) analysis, reaffirming the credibility of our genetic structure insights. Notably, Population structure analysis at its highest Δk value (k ​= ​2) revealed the existence of two primary genetic clusters, further subdivided into four sub-populations at k ​= ​4. Similarly, NJ analysis identified two prominent clusters, each displaying additional sub-clustering. In conclusion, our research provides a comprehensive understanding of genetic groups, subpopulations, and overall diversity within Ethiopian sesame populations. These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections. This genetic richness holds promise for breeding and conservation efforts, highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genetic inference of orchid colonization of a Costa Rican lava flow

AbstractThe dispersal and colonization of plant populations allow species to occupy novel habitats, migrate, and undergo range shifts in response to changing environmental factors and, as such, are fundamental ecological processes for ensuring the long‐term persistence of species. Natural landscape disturbance often generates habitats available for colonization. Patterns of colonization and population expansion can be inferred from the levels and partitioning of genetic variation of plant populations with known disturbance histories, such as recent volcanic eruptions. We sampled and mapped 496 individuals from two populations of the colonizing terrestrial orchid, Sobralia chrysostoma, on the 1992 lava flow of Volcán Arenal in central Costa Rica. We used neutral co‐dominant markers to genotype individuals and estimate population genetic statistics. Both populations had high mean levels of genetic diversity (P = 100%; AP = 3.31; He = 0.259) suggesting that the lava flow was colonized by numerous individuals that likely originated from multiple source populations. However, significant spatial genetic structure (SGS) was only present in one population at the smallest distance class (≤2 m) and was low (r = 0.032). That these large and genetically diverse populations had such low SGS and an absence of SGS, respectively is contrary to expectations and differs significantly from the pattern in Epidendrum radicans (Orchidaceae), with which S. chrysostoma is growing sympatrically. Our results suggest that these two populations either consist primarily of immigrant individuals or that seeds produced in situ dispersed over longer distances, thereby producing larger seed shadows and greater overlap of seed shadows.

Insights into the genetic makeup of French Polynesian peripheral populations of the small giant clam Tridacna maxima

Abstract The small giant clam, Tridacna maxima, is distributed from the Red Sea and East African coast to French Polynesia. Across this widespread Indo‐Pacific range, T. maxima shows strong population structure, in agreement with its limited dispersal abilities. Peripheral populations may have smaller effective population sizes, increasing their vulnerability under any environmental changes. Understanding evolutionary processes at play in such regions located at the edges of T. maxima distribution is a prerequisite in the context of transfers and restocking programmes. In this study, giant clams were sampled from 14 atolls and islands within four archipelagos in the peripheral region of French Polynesia, in 2001–2002 and/or in 2012–2013, then genotyped at the COI gene and at nine microsatellite loci. Mitochondrial lineages of T. maxima from French Polynesia diverged from those sampled in Micronesia, Melanesia, the Coral Triangle and the Red Sea by 6.6–7.3%. Within French Polynesia, significant genetic structure was found, indicating restricted gene flow, and it was stable through time. Most of the genetic variation at microsatellite loci was between archipelagos. The most differentiated archipelago was the most geographically isolated (the Austral Islands). The current patterns of genetic structuring of T. maxima in French Polynesia probably result from long‐term genetic isolation with limited dispersal ability. In addition, these results underlined that sufficiently large populations of T. maxima have persisted in the Central Pacific during the last sea‐level regression. Strategies to optimize transfers and restocking programmes should be designed to preserve the genetic diversity and structure observed here, to avoid the risks of altering the genetic structure, allele loss and/or introduction of maladapted alleles in the receiving populations.

Genetic structure shows the presence of small-scale management units in a relict tree species.

Identifying conservation units is crucial for the effective conservation of threatened species. Previous cases are almost exclusively based on large-scale but coarse sampling for genetic structure analyses. Significant genetic structure can occur within a small range, and thus multiple conservation units may exist in narrowly distributed plants. However, small-scale genetic structure is often overlooked in conservation planning especially for wind-pollinated and wind-dispersed trees, largely due to the absence of dense and elaborate sampling. In this study, we focused on a representative endangered relict plant, Metasequoia glyptostroboides. Using both nuclear microsatellites (nSSRs) and chloroplast DNA (cpDNA) fragments, we sampled across the narrow distribution range of this species and determined its conservation units by exploring its genetic structure and historical demography. cpDNA haplotypes were classified into two groups, but mixed in space, suggesting that the existent wild trees of M. glyptostroboides cannot be divided into different evolutionarily significant units. However, using nSSRs, we detected strong spatial genetic structure, with significant genetic differentiation and weak gene flow between the samples in the east of the species' distribution range and other samples. The divergence between the two nSSR groups was dated to the Last Glacial Maximum (c. 19.6 kya), suggesting that such spatial genetic structure has been maintained for a long term. Therefore, these two nSSR groups should be considered as different conservation units, that is, management units, to protect intergroup genetic variations, which is likely to be the outputs of local adaptation. Our findings highlight the necessity to reveal small-scale genetic structure and population demography to improve the conservation strategies of evolutionary potential of endangered plants.

Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors.

Knowledge of genetic structure at the finest level is essential for the conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (Cerastoderma edule) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: (1) the SW British Isles region, highly fragmented due to biogeographic barriers, and (2) Galicia (NW Spain), a putative homogeneous region. A total of 9250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation; however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.