Low Levels Of Genetic Diversity Research Articles

Assessing population genetic structure and diversity and their driving factors in Phoebe zhennan populations

BackgroundPhoebe zhennan, commonly known as “golden-thread nanmu,” is one of the most valuable and protected tree species in China. An accurate understanding of the population genetic structure and its environmental factors is of significance for the protection and selection of new P. zhennan varieties.ResultsSixteen nSSR and six cpSSR markers were used to determine the genetic diversity and population structure of P. zhennan and the effect of environmental factors on the genetic structure. The nSSR markers identified a total of 451 number of alleles (Na), while cpSSR markers detected 20 Na. A relative high level of genetic diversity was observed in the P. zhennan population evidenced by high Shannon’s information index (I) of 0.671 and 2.294 based on cpSSR and nSSR datasets. The low value of fixation index (F) observed from the nSSR dataset indicated low breeding within the population. The genetic differentiation was mainly detected within populations (only 28% and 13% of the variance being between populations according to the nSSR and cpSSR datasets). Among them, the HNSZX (H = 0.469) and SCSZZ (I = 1.943) populations exhibited the highest level of genetic diversity, while the HNXXT (H = 0.041) and SCLJS (I = 0.943) populations exhibited the lowest level of genetic diversity. The average genetic differentiation coefficient (Fst) and gene flow (Nm) were 0.022–0.128 and 1.698–11.373, respectively, which indicated a moderate level of genetic differentiation and a high level of gene flow. STRUCTURE, neighbor-joining clustering, and principal coordinate analysis divided 543 individuals into two or three categories based on the nSSR or cpSSR datasets. Four temperature, three precipitation, five chemical, five physical, and one soil texture variable showed significant effects on the genetic structure and distribution of P. zhennan populations. Compared to nSSR, the genetic differentiation among populations based on cpSSR datasets conformed to the geographic isolation model, suggesting that geographic and genetic distances should be considered for further genetic conservation and breeding utilization. The importance of in situ conservation units, such as populations with a high level of genetic diversity, more private alleles, and haplotypes (e.g., population SCGTS, SCYFS, and YNYJX), should be emphasized. Additionally, breeding, along with artificially assisted population regeneration and restoration, should also be carefully planned, taking into account climate and soil properties at the same time.ConclusionsIn conclusion, this study provided genetic background information for the genetic conservation, management, and utilization of P. zhennan.

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei.

The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa in 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of the CBB, with 93% of the genome assembled into 14 scaffolds. Whole genome sequencing of pooled samples from different populations across Jamaica showed that the CBB harbors low levels of genetic diversity alongside an excess of low-frequency alleles, indicative of a recent genetic bottleneck. The analyses also showed a recent surge in the activity of transposable elements (TEs), particularly LINE/R1 and LTR/Gypsy elements, within CBB populations. Our findings offer first insights into the evolutionary genomics of CBB populations in Jamaica, highlighting the potential role of TEs in shaping the genome of this important pest species.

Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS)

BackgroundAnemone shikokiana (Makino) Makino is a perennial herb of the genus Anemone in the family Ranunculaceae. Endemic to the Shandong Peninsula in China and Shikoku Island in Japan, it is a rare and endangered plant with a narrow, disjunct distribution. It is threatened with extinction and is in urgent need of conservation. Evaluating the genetic diversity of species, revealing the population genetic structure and gene flow, and inferring the population history are of great importance for species conservation, especially for rare and endangered plants.ResultsIn our study, 73 samples from eight wild populations in China were sequenced by Super-GBS, yielding a total of 40.59 G clean reads and 52,231 SNPs. Based on the obtained SNP data set, we evaluated the population genetic diversity, genetic structure, and gene flow of A. shikokiana. A low level of genetic diversity was found (He = 0.1925, Ho = 0.1422). The neighbor-joining (NJ) tree, principal component analysis and ADMIXTURE analysis suggested that these 73 A. shikokiana could be considered as two groups. Pairwise genetic differentiation coefficients (Fst) indicated that genetic differentiation was lower between adjacent populations and higher between geographically separated populations. The gene flow between Kunyu Mountain and Lao Mountain was very low. However, neither of the two regions showed evidence of Isolation by Distance.ConclusionsHere, we revealed the population genetic structure and gene flow of A. shikokiana from the Shandong Peninsula, China. This research provides valuable genetic resources for A. shikokiana and contributes to the scientific and effective conservation of the species.

Geographical variation and genetic diversity of Parashorea chinensis germplasm resources.

Parashorea chinensis is a rare monodominant species in southwest China known for its production of high-quality timber, is facing decline due to its narrow distribution, human interference and habitat destruction. However, there are no reports on genetic diversity and geographical variation of phenotypic traits of P. chinensis. In this study, phenotypic characters and genetic diversity of 15 germplasms resources from five provenances in southwest China were investigated, and their relationships with geographical and environmental factors was discussed. Our results revealed a rich phenotypic diversity among the germplasms, with variation coefficients ranging from 3.63% to 45.49%. Among the studied germplasms, NP03 from Napo and ML02 from Mengla region exhibited superior phenotypic traits. Notably, NP03 also demonstrated the highest genetic diversity. Genetic differentiation analyses including genetic differentiation coefficient (0.6264) and gene flow (0.3736) illustrated that genetic variation was most prevalent among populations. Furthermore, redundancy analysis showed that temperature related factors (maximum air temperature, annual mean temperature and minimum air temperature) significantly affected phenotypic variation. Similarly, altitude, longitude, latitude, annual mean precipitation and the minimum air temperature significantly impacted the level of genetic diversity. The molecular variation of the natural population of P. chinensis followed a certain geographical pattern. Our finding indicated abundant phenotypic variation among P. chinensis germplasms. However, populations exhibited low levels of genetic diversity alongside high genetic differentiation, potentially contributing to the species' rarity. Based on our results, NP03 and ML02 germplasm could be used as the parents for breeding superior germplasm of P. chinensis. Overall, this study provides valuable insights into germplasm diversity and conservation, genetic improvement, and utilization of P. chinensis.

Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam’s famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Genetic Attributes and Conservation of an Endangered Giant Water Bug Species, Diplonychus esakii Miyamoto and Lee, 1966 (Hemiptera: Belostomatidae).

Diplonychus esakii, a water bug from the family Belostomatidae, plays an important role in freshwater ecosystems as one of the top predators. In this study, we investigated the genetic diversity and population structure of D. esakii by analyzing 318 specimens across 27 sites in South Korea. We found that the populations of D. esakii possess 11 haplotypes with a haplotype diversity of 0.623. This represents a relatively low level of genetic diversity compared to other known belostomatids and endangered species. AMOVA and FST analyses revealed significant genetic differentiation among populations, with most populations harboring only 1-2 haplotypes, suggesting restricted gene flow between populations and a low level of genetic diversity. This low genetic diversity and limited gene flow suggest a potential vulnerability to environmental changes and an increased risk of extinction, indicating that D. esakii should be designated as a protected species in South Korea as part of future conservation efforts. Based on the results of this study, Upo Wetland, which maintains relatively high levels of genetic diversity and Jeju Island, which, despite its lower genetic diversity compared to the mainland, does not share haplotypes with other regions, should be considered key conservation units for this species. This study highlights the importance of incorporating genetic information into conservation status assessments under the Red List Categories and Criteria and also emphasizes the need to evaluate this species on the Korean Red List. The data provided here will serve as essential baseline information and valuable resources for the development of effective conservation strategies.

Diversidad y estructura genética de <i>Lobelia villaregalis</i> (Campanulaceae), especie en peligro endémica de Jalisco, México

Background: Lobelia villaregalis is an endemic and endangered species in Jalisco, Mexico. Knowing the structure and genetic diversity of populations of species at risk can contribute to improving strategies for their conservation. This information has not been generated for L. villaregalis. Questions: 1) Does L. villaregalis present low levels of genetic diversity?, 2) Are there genetic differences between its populations?. Studied species: Lobelia villaregalis T.J. Ayers (Campanulaceae: Lobelioideae), herbaceous perennial. Study site and dates: During 2018-2020, field work was carried out in El Bosque La Primavera Natural Protected Area, in Zapopan, Jalisco, in order to locate new populations of the species and collect leaf material. Methods: The diversity and genetic structure of 87 individuals in five populations were evaluated using ISSR molecular markers. Results: The average genetic diversity of L. villaregalis is low (He = 0.057, P = 48.17 %, I = 0.110) as well as the total diversity (HT = 0.069). Molecular analysis of variance showed that most of the genetic variation (92 %) occurred within populations. The Mantel test indicates that there is no correlation between the genetic distances and the geographical distances for the five populations of the species (R = 0.64, P = 0.18). With the genetic assignment analysis, 4 groups were identified, however there is no genetic structure (GST = 0.060). Conclusions: Lobelia villaregalis requires urgent actions of conservation to maintain the genetic diversity present in all its populations, giving the highest priority to three of them.

Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics

The muskox (Ovibos moschatus), an integral component and iconic symbol of arctic biocultural diversity, is under threat by rapid environmental disruptions from climate change. We report a chromosomal-level haploid genome assembly of a muskox from Banks Island in the Canadian Arctic Archipelago. The assembly has a contig N50 of 44.7 Mbp, a scaffold N50 of 112.3 Mbp, a complete representation (100%) of the BUSCO v5.2.2 set of 9225 mammalian marker genes and is anchored to the 24 chromosomes of the muskox. Tabulation of heterozygous single nucleotide variants in our specimen revealed a very low level of genetic diversity, which is consistent with recent reports of the muskox having the lowest genome-wide heterozygosity among the ungulates. While muskox populations are currently showing no overt signs of inbreeding depression, environmental disruptions are expected to strain the genomic resilience of the species. One notable impact of rapid climate change in the Arctic is the spread of emerging infectious and parasitic diseases in the muskox, as exemplified by the range expansion of muskox lungworms, and the recent fatal outbreaks of Erysipelothrix rhusiopathiae, a pathogen normally associated with domestic swine and poultry. As a genomics resource for conservation management of the muskox against existing and emerging disease modalities, we annotated the genes of the major histocompatibility complex on chromosome 2 and performed an initial assessment of the genetic diversity of this complex. This resource is further supported by the annotation of the principal genes of the innate immunity system, genes that are rapidly evolving and under positive selection in the muskox, genes associated with environmental adaptations, and the genes associated with socioeconomic benefits for Arctic communities such as wool (qiviut) attributes. These annotations will benefit muskox management and conservation.

Update of the Genetic Variability of Monkeypox Virus Clade IIb Lineage B.1.

From 1 January 2022 to 31 May 2024, the World Health Organization (WHO) reported 97,745 laboratory-confirmed Mpox cases, including 203 deaths, across 116 countries. Despite a 2.3% decrease in new cases in May 2024 compared to April 2024, significant regional variations persist. The African Region reported the highest proportion of new cases, while other regions experienced mixed trends. Phylogenomic analyses of the Mpox virus Clade IIb lineage B.1 reveal stable genetic variability with minimal diversification. The Bayesian Skyline Plot indicates a generally stable viral population size with a modest peak in late 2023, followed by a decline. In general, the data indicate that the MPXV outbreak is primarily localized within a few consistent geographic clusters. The virus's evolution is relatively slow, as indicated by its stable genetic variability, and Clade IIb lineage B.1 does not currently show signs of rapid genetic changes or population growth. The current low level of genetic diversity should not lead to complacency. Ongoing genomic surveillance is essential for effective outbreak management and understanding. This monitoring is crucial for identifying any shifts in the virus's behavior or transmission, allowing for prompt public health responses and adjustments. In addition, continued vigilance is necessary to detect any new variants that might influence the outbreak's trajectory.

A Sister Species for the Blue Crab, Callinectes sapidus? A Tale Revealed by Mitochondrial DNA.

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species.

Examining intra-host genetic variation of RSV by short read high-throughput sequencing.

Every viral infection entails an evolving population of viral genomes. High-throughput sequencing technologies can be used to characterize such populations, but to date there are few published examples of such work. In addition, mixed sequencing data are sometimes used to infer properties of infecting genomes without discriminating between genome-derived reads and reads from the much more abundant, in the case of a typical active viral infection, transcripts. Here we apply capture probe-based short read high-throughput sequencing to nasal wash samples taken from a previously described group of adult hematopoietic cell transplant (HCT) recipients naturally infected with respiratory syncytial virus (RSV). We separately analyzed reads from genomes and transcripts for the levels and distribution of genetic variation by calculating per position Shannon entropies. Our analysis reveals a low level of genetic variation within the RSV infections analyzed here, but with interesting differences between genomes and transcripts in 1) average per sample Shannon entropies; 2) the genomic distribution of variation 'hotspots'; and 3) the genomic distribution of hotspots encoding alternative amino acids. In all, our results suggest the importance of separately analyzing reads from genomes and transcripts when interpreting high-throughput sequencing data for insight into intra-host viral genome replication, expression, and evolution.

Dissecting the invasion history of Spotted-Wing Drosophila (Drosophila suzukii) in Portugal using genomic data

BackgroundThe invasive pest Spotted-Wing Drosophila, Drosophila suzukii (Matsumura), causes extensive damage and production losses of soft-skinned fruits. Native to Asia, the species has now spread worldwide, with first reports in Portugal in 2012. In this study, we focus on the genomic signatures of the recent Portuguese invasion, in the context of worldwide patterns established in previous works. We analyzed whole genome pool sequencing data from three Portuguese populations (N = 240) sampled in 2019 and 2021.ResultsThe correlation of allele frequencies suggested that Portuguese populations are related to South European ones, indicating a Mediterranean invasion route. While two populations exhibited levels of genetic variation comparable to others in the invasive range, a third showed low levels of genetic diversity, which may result from a recent colonization of the region. Genome-wide analyses of natural selection identified ten genes previously associated with D. suzukii’s invasive capacity, which may have contributed to the species’ success in Portugal. Additionally, we pinpointed six genes evolving under positive selection across Portuguese populations but not in European ones, which is indicative of local adaptation. One of these genes, nAChRalpha7, encodes a nicotinic acetylcholine receptor, which are known targets for insecticides widely used for D. suzukii control, such as neonicotinoids and spinosyns. Although spinosyn resistance has been associated with mutations in the nAChRalpha6 in other Drosophila species, the putative role of nAChRalpha7 in insecticide resistance and local adaptation in Portuguese D. suzukii populations encourages future investigation.ConclusionsOur results highlight the complex nature of rapid species invasions and the role of rapid local adaptation in determining the invasive capacity of these species.

Molecular Identification Validates Morphological Identification of Javanese Cardamom from Banyumas in Central Java, Indonesia

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation.

Genomic analysis of NE Atlantic sardine (Sardina pilchardus) reveals reduced variation in a recently established North Sea population and directs reconsideration of management units.

The European sardine (Sardina pilchardus) is under intense fishing pressure and exhibits distributional/abundance shifts linked to environmental change. The current understanding of population demographics needed for sustainable management is uncertain due to concerns that previous genetic studies lacked resolution and limited sampling of sardine north of the Bay of Biscay. To address these issues, we performed mtDNA sequencing and genome wide SNP analysis of samples collected across the Bay of Biscay, Celtic Sea, English Channel and North Sea. The complete SNP data reported a lack of structure throughout the sampled area compatible with high gene flow. A consensus suite of positive outlier SNPs was identified which reported a significant correlation with geographical distance with the largest differentiation between the southern Bay of Biscay and North Sea samples which also reported a significant mtDNA ΦST. While the roles of dispersal limitation and environmental heterogeneity underpinning this require further study, this adds to growing evidence that selection is influencing sardine population structure against a background of high gene flow. The results indicate that while there may be a level of demographic independence between North Sea and South Biscay sardine, the current delimitation of central (Biscay) and northern (Channel and Celtic Sea) operational stocks may misrepresent connectivity between the Biscay and Channel. The North Sea sample exhibited markedly lower mtDNA and nuclear variation than other samples. As sardine have only recently invaded the North Sea such reduced genetic variation is compatible with predictions for peripheral leading-edge populations but contrasts with patterns for other small pelagic species and emphasises the need to consider species-specific genetic structure in ecosystem-based management. Nascent management of the North Sea sardine fishery must ensure that current low levels of genetic diversity are not eroded further as this may decrease the species adaptive potential and inhibit its expansion.

Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes.

Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.

Analysis of the genetic structure of populations of the terrestrial mollusk <i>Caucasotachea vindobonensis</i> (Helicidae) in conditions at the eastern border of the range using microsatellite markers

BACKGROUND: Assessing the genetic structure of populations of rare and vulnerable species provides useful information for developing conservation strategies. AIM: The aim of the study was to study the genetic structure of Caucasotachea vindobonensis populations in the south of the Central Russian Upland using SSR markers. MATERIALS AND METHODS: Genetic structure of the populations was studied using eight microsatellite markers, first identified by the authors for the species under study. Fragment analysis of PCR products was carried out on an automatic capillary DNA sequencer Nanophore 05 (Russia). A total of 498 individuals from 24 populations were studied. RESULTS: A total of 59 alleles were isolated in the eight studied SSR loci, of which 21 (36%) turned out to be private. At the same time, private alleles were found in eleven studied populations, which is 46% of their total number. According to the data obtained, the effective number of alleles (Ae) averaged 1.6 ± 0.06, the Shannon index (I) was 0.45 ± 0.03, and the level of expected heterozygosity (He) was 0.27 ± 0.021. A high level of spatial subdivision of population gene pools was noted (Fst = 0.47 ± 0.08) with a fairly low level of gene flow (Nm = 1.15 ± 0.91). PCA analysis showed that the populations of the central and eastern parts of the south of the Central Russian Upland form a closely related group, different from other populations of the region. Calculation of the effective abundance using the LD method showed that Ne varies in different groups of snails from 0.6 to infinity. CONCLUSIONS: Populations of C. vindobonensis in the south of the Central Russian Upland live in conditions of significant isolation, as evidenced by the high degree of differentiation of the studied groups. The analysis of principal components based on genetic distances according to Nei and Wright’s F-statistics indicate a pronounced division of populations in the study area into two clusters, which is probably associated with the historical features of landscape formation. Calculation of effective numbers indicates the high viability of the majority of the studied populations. At the same time, some groups of snails are clearly in a depressed state, which is reflected in low levels of genetic diversity and their effective size.

Contrasting patterns of spatial genetic structure in endangered southern damselfly (Coenagrion mercuriale) populations facing habitat fragmentation and urbanisation

AbstractAimHuman‐induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra‐population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining.LocationWe studied two areas: one in semi‐natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species' range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France).MethodsWe genotyped 2743 individuals from 128 populations using 11 microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding and genetic relatedness), the extent of genetic differentiation and population affiliations (sPCAs) within the two areas. We also examined fine‐scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS) method.ResultsNorthern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation.Main ConclusionsThese results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures.

Ecological genetics of isolated loach populations indicate compromised adaptive potential

Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.

Effects of inbreeding on reproductive success in endangered North Atlantic right whales.

Only approximately 356 North Atlantic right whales (Eubalaena glacialis) remain. With extremely low levels of genetic diversity, limited options for mates, and variation in reproductive success across females, there is concern regarding the potential for genetic limitations of population growth from inbreeding depression. In this study, we quantified reproductive success of female North Atlantic right whales with a modified de-lifing approach using reproductive history information collected over decades of field observations. We used double-digest restriction site-associated sequencing to sequence approximately 2% of the genome of 105 female North Atlantic right whales and combined genomic inbreeding estimates with individual fecundity values to assess evidence of inbreeding depression. Inbreeding depression could not explain the variance in reproductive success of females, however we present evidence that inbreeding depression may be affecting the viability of inbred fetuses-potentially lowering the reproductive success of the species as a whole. Combined, these results allay some concerns that genetic factors are impacting species survival as genetic diversity is being retained through selection against inbred fetuses. While still far fewer calves are being born each year than expected, the small role of genetics underlying variance in female fecundity suggests that variance may be explained by external factors that can potentially be mitigated through protection measures designed to reduce serious injury and mortality from human activities.

Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China

Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense.