Low Genetic Diversity Research Articles

Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae).

Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.

Introduced Herbivores Threaten the Conservation Genetics of Two Critically Endangered Single-Island Endemics, Crambe sventenii and Pleudia herbanica.

Crambe sventenii Pett. ex Bramwell & Sunding and Pleudia herbanica (A.Santos & M.Fernández) M.Will, N.Schmalz & Class.-Bockh. are two single-island endemic species from Fuerteventura (Canary Islands), inhabiting the same areas and similar habitats. They are under the "Critically Endangered" category due to historical herbivore pressure, mainly goats, leading to habitat fragmentation and poor population recruitment. The main aim of our study was to provide insights into the conservation genetics and habitat suitability of these two species. For this purpose, we sampled all known populations on the island and developed two new sets of microsatellite markers. Moreover, to assist restoration plans, we performed species distribution models to determine the most suitable areas for reintroduction. While Crambe sventenii is highly fragmented, with low genetic diversity indices in some populations, Pleudia herbanica's genetic structure is quite homogeneous, grouped in three main regions, with signs of inbreeding and an overall low genetic diversity. Both species could present moderate to high levels of autogamy. Our findings can provide guidance to local governments regarding conservation actions to be implemented in the field, like the identification of propagule sources and new suitable areas for restoration.

Exploring changes in social spider DNA methylation profiles in all cytosine contexts following infection.

Living at high density and with low genetic diversity are factors that should both increase the susceptibility of organisms to disease. Therefore, group living organisms, especially those that are inbred, should be especially vulnerable to infection and therefore have particular strategies to cope with infection. Phenotypic plasticity, underpinned by epigenetic changes, could allow group living organisms to rapidly respond to infection challenges. To explore the potential role of epigenetic modifications in the immune response to a group-living species with low genetic diversity, we compared the genome-wide DNA methylation profiles of five colonies of social spiders (Stegodyphus dumicola) in their natural habitat in Namibia at the point just before they succumbed to infection to a point at least six months previously where they were presumably healthier. We found increases in genome- and chromosome-wide methylation levels in the CpG, CHG, and CHH contexts, although the genome-wide changes were not clearly different from zero. These changes were most prominent in the CHG context, especially at a narrow region of chromosome 13, hinting at an as-of-yet unsuspected role of this DNA methylation context in phenotypic plasticity. However, there were few clear patterns of differential methylation at the base level, and genes with a known immune function in spiders had mean methylation changes close to zero. Our results suggest that DNA methylation may change with infection at large genomic scales, but that this type of epigenetic change is not necessarily integral to the immune response of social spiders.

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa: implications for future breeding and research studies

Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, alongside and understanding of the genetic diversity and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity, and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified thirteen distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported, and may not be universal across all organ-types. From a global analysis, SG3 was only significant higher expressed in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Genetic diversity, population structure and ecological niche modeling of Thyrinteina arnobia (Lepidoptera: Geometridae), a native Eucalyptus pest in Brazil

Thyrinteina arnobia (Lepidoptera: Geometridae) is a native American species. Despite its historical importance as an insect pest in Eucalyptus plantations, more information is needed regarding the population diversity, demography, and climatic variables associated with its distribution in different regions of Brazil. We used a phylogeographic approach to infer the genetic diversity, genetic structure, and demographic parameters of T. arnobia. We also conducted an ecological niche modeling (ENM) to predict suitable areas for T. arnobia occurrence in Brazil and other countries worldwide. Although T. arnobia populations have low genetic diversity in Brazil, we identified mitochondrial haplogroups predominating in different Brazilian regions and high ФST and ФCT values in AMOVA, suggesting a low frequency of insect movement among these regions. These results indicate that outbreaks of T. arnobia in Eucalyptus areas in different regions of Brazil are associated with local or regional populations, with no significant contribution from long-distance dispersal from different regions or biomes, suggesting that pest management strategies would be implemented on a regional scale. In Brazil, the demographic and spatial expansion signals of T. arnobia seem to be associated with the history of geographical expansion of Eucalyptus plantations, a new sustainable host for this species. ENM indicated that isothermality and annual rainfall are critical climatic factors for the occurrence of T. arnobia in tropical and subtropical areas in the Americas. ENM also suggested that T. arnobia is a potential pest in Eucalyptus areas in all Brazilian territory and in regions from Africa, Asia, and Oceania.

Exploration of Genetic Variation and Population Structure in Bergenia ciliata for its Conservation Implications.

Bergenia ciliata (Haw.)Sternb. is a perennial medicinal herb distributed in Indian Himalayan Region(IHR). A total of eight populations of B.ciliata were collected from diverse locales of IHR, and 17 EST-SSR markers were used in this study. The present study revealed moderate genetic diversity at the locus level with the mean number of alleles (Na = 7.823), mean number effective of alleles (Ne = 3.375), mean expected heterozygosity (He = 0.570), and meanShannon's diversity index (I = 1.264). The MSR (He = 0.543, I = 1.067) and DRJ populations (He = 0.309, I = 0.519) revealed the highest and lowest genetic diversity at the population level, respectively. AMOVA analysis showed that 81.76% of genetic variation was within populations, 10.55% was among populations, and 7.69% was among the regions. In addition, a moderate to high level of differentiation was found among the populations (FST = 0.182), which could be indicative of low to moderate gene flow (Nm = 0.669) in the B. ciliata populations. UPGMA and PCoA analysis revealed that eight populations could be differentiated into two groups, while the structure analysis of the 96 individuals differentiated into three groups. The Mantel test showed a positive relationship between genetic and geographical distance. The findings of this study will provide the development of conservation and germplasm management strategies for this valuable medicinal species.

Population genetic structure and range limits of Prostanthera cineolifera (Lamiaceae), a vulnerable shrub with a patchy distribution

AbstractIntegrating molecular data is essential for clarifying the distributions and genetic structures of species that have histories of misidentification and misapplication of names. There has been confusion about the species limits of the Vulnerable Prostanthera cineolifera with respect to morphologically similar specimens in the Hunter Valley, New South Wales, Australia and morphologically dissimilar specimens in the Lower Hawkesbury Valley, New South Wales, and from north-eastern New South Wales. To test the species limits of P. cineolifera, and related taxa, specimens were collected from across the range and augmented with herbarium specimens. We used morphometric analysis of 18 morphological characters across 51 samples. Using the DArTseq reduced representation sequencing platform, 4010 single-nucleotide polymorphisms (SNPs) across 110 individuals were recovered for molecular analysis. Both morphological and molecular analyses produced three concordant clusters (A) P. cineolifera, (B) a group sharing similarities with P. sp. Hawkesbury (B.J.Conn 2591), and (C) a group allied with P. lanceolata and P. ovalifolia. These results indicate that the specimens form north-eastern New South Wales are more likely to be P. lanceolata, not P. cineolifera, and that specimens from the Lower Hawkesbury are of an undescribed species with the phrase name P. sp. Hawkesbury (B.J.Conn 2591). Within P. cineolifera there was pronounced genetic differentiation among populations. Little evidence of inbreeding was observed, but the newly recognised, more isolated populations had the lowest genetic diversity. This study provides new information about the range of the species and its genetic structure that informs the conservation priorities for this species.

Analysis of the genetic diversity of Tahe red deer and population structure of Cervus elaphu/hanglu/canadensis

The Tahe red deer is currently the largest breeding population of antlered Cervus elaphus in China. It has unique characteristics such as drought and roughage tolerance, high antler yield and early sexual maturity. It is a high-quality provenance for cultivating high-yield Cervus elaphus breeds and is also the subject of study on the origin, evolution, and classification of Cervus elaphus. The breeding quantity of Tahe red deer has decreased significantly in recent years due to the influence of feeding conditions and consumer market. This has resulted in a serious threat to its genetic resources. To provide a scientific theoretical basis for the protection of the Tahe red deer population, we performed PCR amplification and direct sequencing of the AMELY2, DBY and SRY genes of the Y chromosome, and the ND1, COX1, ATP6, ND5, Cyt b and D-loop regions of the mtDNA, and analysed their genetic diversity and population genetic structure. The results showed high haplotype diversity and low nucleotide diversity in both the Y chromosome and mtDNA genes. The phylogenetic tree and haplotype network diagram, constructed using white-lipped deer as the outgroup, indicate that Tahe red deer has two distinct ancestral types. The phylogenetic tree, based on the Cyt b gene and D-loop region, reveals that the Cervus elaphus/hanglu/canadensis is divided into three clades: western, central, and eastern. Tahe red deer, C.h.bactrianus, and C.h.hanglu are clustered in the central clade. The study results indicate that Tahe red deer has low genetic diversity and two distinct ancestor types. It is speculated that the central clade is either the earliest differentiation from the ancestor species or the closest to it.

Range-wide population genomic structure of the Karner blue butterfly, Plebejus (Lycaeides) samuelis.

The Karner blue butterfly, Plebejus (Lycaeides) samuelis, is an endangered North American climate change-vulnerable species that has undergone substantial historical habitat loss and population decline. To better understand the species' genetic status and support Karner blue conservation, we sampled 116 individuals from 22 localities across the species' geographical range in Wisconsin (WI), Michigan (MI), Indiana (IN), and New York (NY). Using genomic analysis, we found that these samples were divided into three major geographic groups, NY, WI, and MI-IN, with populations in WI and MI-IN each further divided into three subgroups. A high level of inbreeding was revealed by inbreeding coefficients above 10% in almost all populations in our study. However, strong correlation between F ST and geographical distance suggested that genetic divergence between populations increases with distance, such that introducing individuals from more distant populations may be a useful strategy for increasing population-level diversity and preserving the species. We also found that Karner blue populations had lower genetic diversity than closely related species and had more alleles that were present only at low frequencies (<5%) in other species. Some of these alleles may negatively impact individual fitness and may have become prevalent in Karner blue populations due to inbreeding. Finally, analysis of these possibly deleterious alleles in the context of predicted three-dimensional structures of proteins revealed potential molecular mechanisms behind population declines, providing insights for conservation. This rich new range-wide understanding of the species' population genomic structure can contextualize past extirpations and help conserve and even enhance Karner blue genetic diversity.

Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity

Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity

Low Genetic Variation Contrasts With Variable Morphotypes in Neoscytalidium dimidiatum From the Philippines and Their Aggressiveness to Dragon Fruit Species

ABSTRACTNeoscytalidium dimidiatum is an asexual, opportunistic and necrotrophic pathogen that causes the devastating stem canker disease of dragon fruit species (Selenicereus spp.). Despite this, information about its intraspecific diversity remains lacking. Examination of the morphological variations of 40 N. dimidiatum isolates hosted by S. megalanthus, S. monacanthus and S. undatus from eight allopatric regions in the Philippines detected three distinct morphotypes. Sequencing of three partial gene markers (ITS, ACT and TUB2) of representative isolates revealed low intraspecific genetic diversity of the pathogen from the three hosts. Phylogenetic analysis of internal transcribed spacer (ITS) sequences of the isolates in this study and worldwide collections of the phytopathogen in the GenBank database infers similar founding populations and the possible specificity of the dragon fruit‐infecting N. dimidiatum. Pathogenicity and aggressiveness assay of the isolates on detached stems of dragon fruit did not detect host specificity to S. monacanthus and S. undatus. However, some isolates (i.g., MBDF0802A, MBDF0808B, MBDF0339A and MBDF0007A) significantly had shorter latent period to the stems of S. undatus than S. monacanthus. A higher aggressiveness component of lesion size development on S. undatus stems by isolates from S. monacanthus was recorded suggesting a possible directional selection of highly aggressive N. dimidiatum in this host. This is the first population study on the phenotypic traits and the genetic structure of N. dimidiatum. Valuable inputs for further study of the pathogen are provided, which may help inform the design of management options for stem canker disease of dragon fruit.

The Low Genetic Diversity of Dientamoeba fragilis Isolates in Southwest Turkey and Analysis of Clinical Findings.

Dientamoeba fragilis (D. fragilis) is a common intestinal protozoan with a global distribution. In the present study, we aimed to determine genetic diversity of D. fragilis isolates with multilocus sequence typing (MLST) in the southwest of Turkey and analyse the clinical findings. The study included faecal samples from 200 individuals in Aydin, Turkey. The positivity of D. fragilis was determined with 18S rRNA gene-based PCR assay. Six nested-PCR reactions were set to amplify partial D. fragilis housekeeping genes in the positive samples. The sequences were aligned with the references from GenBank to detect nucleotide polymorphisms and haplotypes. Additionally, the clinical findings and demographic characteristics of patients were statistically analysed between D. fragilis-infected and non-infected cases. The positivity of D. fragilis was 16% (32 out of 200 cases) with 18S rRNA based-PCR, and all were classified as "genotype 1". The analysis of six MLST loci revealed different haplotypes only at one locus; the remaining five loci exhibited no polymorphisms. The haplotypes in the present study were identical to at least one previously reported reference, except the locus "large subunit of RNA polymerase II" locus. There were no significant differences in any of the clinical findings or demographic characteristics between the infected and non-infected groups. Our study revealed a low genetic diversity of D. fragilis isolates from Turkey, like other countries including Italy, Denmark, the UK, Australia, and Brazil. The high degree of sequence similarity in housekeeping genes indicated the clonal distribution of D. fragilis.

Genetic structure and climate niche differentiation among populations of Leopardus geoffroyi.

Geoffroy's cat (Leopardus geoffroyi) is a small-sized felid native to South America. Given the species' distribution covering a wide variety of habitats, and the presence of high levels of anthropization in part of its range, it is possible that genetically differentiated groups exist and that they occupy different climatic niches. We assessed patterns of contemporary genetic diversity and structure in the species across most of its range, characterizing each inferred genetic group based on ecological niche models. We genotyped 11 microsatellites for 142 samples covering most of Geoffroy's cat distribution, and investigated patterns of genetic structure and diversity, applying spatial and nonspatial Bayesian clustering methods and a spatial principal component analysis. We created ecological niche models for each genetic cluster, evaluating whether these clusters occupy different climatic spaces and display differences in the suitability of different values of the climatic variables analyzed. We identified two genetic clusters, one in the north-northeast and the other in the south-southwest of the species' distribution. These clusters showed moderate FST values between them and differences in dispersal/genetic diversity. We found isolation-by-distance patterns globally and within each cluster. We observed lower expected heterozygosity compared with other studies and a north-south gradient in allelic richness. The southern cluster showed lower genetic variability and a more restricted climatic niche suggesting that this group is more vulnerable to the effects of the current context of climate change. Individuals from the southern genetic cluster are under different pressures, likely a product of the particularly dry habitat they occupy. Climatic variables associated with habitat suitability suggest the southern cluster has affinity for the arid and semiarid conditions present in its distribution. Conservation measures should consider the genetic structure observed and differences in climatic spaces to maintain the evolutionary potential of the species.

Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.

Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of thirteen individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e., Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.

Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France

Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways.

Two outbreaks and sporadic occurrences of Candida auris from one hospital in China: an epidemiological, genomic retrospective study.

To investigate the clinical relevance, origin, transmission, and resistance of Candida auris (C. auris) isolates from two outbreaks and sporadic occurrences from one hospital in China. A total of 135 C. auris isolates were collected. Clinical characteristics were obtained and antifungal susceptibility testing (AFST) was performed using the method of broth microdilution. Phylogenetic tree, WGS analysis, and single nucleotide polymorphisms (SNPs) were used to determine the origin, transmission, and resistance mechanisms. A total of 31 patients (91.2%, 31/34) received invasive medical procedures and 13 patients (38.2%, 13/34) had antifungal agents before C. auris infection/colonization, except one patient whose clinical information was missing. Only 4 cases of C. auris candidemia were observed. 18 patients died, 13 patients recovered, and the outcomes of 3 patients were not available. A total of 35 C. auris isolates, which were successfully cultivated and the first isolated or harbored specific drug-resistant phenotype from each patient, were selected to be sequenced and further analyzed. C. auris isolates presented low genetic variability and belonged to clade I, possibly originating from BJ004-H7 in Beijing. All 35 isolates were resistant to Fluconazole (FCZ) and amphotericin B (AMB), and 3 isolates were resistant to caspofungin (CAS). Mutations in ERG11 and FKS1 were linked to reduced azole and echinocandin susceptibility, respectively. Two outbreaks of highly clonal, multidrug-resistant C. auris isolates within the medical facility were reported. The intensive performance of disinfection measures helped block in-hospital transmission. Understanding the epidemiology, drug resistance and management of C. auris will be helpful for implementing effective infection control and treatment strategies.

Individual and social heterosis act independently in honey bee (Apis mellifera) colonies.

Heterosis occurs in individuals when genetic diversity, i.e., heterozygosity, increases fitness. Many advanced eusocial insects evolved mating behaviors, including polyandry and polygyny, which increase inter-individual genetic diversity within colonies. The possibility of this structure of diversity to improve group fitness has been termed social heterosis. Neither the independence of individual and social heterosis nor their relative effect sizes have been explicitly measured. Through controlled breeding between pairs of Western honey bee queens (Apis mellifera L.; n=3 pairs) from two distinct populations, we created inbred colonies with low genetic diversity, hybrid colonies with high heterozygosity, and mixed colonies (combining inbred workers from each population) with low heterozygosity and high social diversity. We then quantified two independent traits in colonies: survival against bacterial challenge and maintenance of brood nest temperature. For both traits, we found hybrid and mixed colonies outperformed inbred colonies but did not perform differently from each other. During immune challenge assays, hybrid and mixed colonies experienced hazard ratios of 0.49 (95% CI [0.37, 0.65]) and 0.69 (95% CI [0.50, 0.96]) compared to inbred colonies. For nest temperatures, hybrid and mixed colonies experienced 1.94±0.97°C and 2.82±2.46°C less thermal error and 0.14±0.11°C2 and 0.16±0.06°C2 less thermal variance per hour than inbred lines. This suggests social and individual heterosis operate independently and may have similar effect sizes. These results highlight the importance of both inter- and intra-individual diversity to fitness, which may help explain the emergence of polyandry/polygyny in eusocial insects and inform breeding efforts in these systems.

Variable Craniofacial Shape and Development among Multiple Cave-Adapted Populations of Astyanax mexicanus.

Astyanax mexicanus is a freshwater fish species with blind cave morphs and sighted surface morphs. Like other troglodytic species, independently evolved cave-dwelling A. mexicanus populations share several stereotypic phenotypes, including the expansion of certain sensory systems, as well as the loss of eyes and pigmentation. Here, we assess the extent to which there is also parallelism in craniofacial development across cave populations. Since multiple forces may be acting upon variation in the A. mexicanus system, including phylogenetic history, selection, and developmental constraint, several outcomes are possible. For example, eye regression may have triggered a conserved series of compensatory developmental events, in which case we would expect to observe highly similar craniofacial phenotypes across cave populations. Selection for cave-specific foraging may also lead to the evolution of a conserved craniofacial phenotype, especially in regions of the head directly associated with feeding. Alternatively, in the absence of a common axis of selection or strong developmental constraints, craniofacial shape may evolve under neutral processes such as gene flow, drift, and bottlenecking, in which case patterns of variation should reflect the evolutionary history of A. mexicanus. Our results found that cave-adapted populations do share certain anatomical features; however, they generally did not support the hypothesis of a conserved craniofacial phenotype across caves, as nearly every pairwise comparison was statistically significant, with greater effect sizes noted between more distantly related cave populations with little gene flow. A similar pattern was observed for developmental trajectories. We also found that morphological disparity was lower among all three cave populations versus surface fish, suggesting eye loss is not associated with increased variation, which would be consistent with a release of developmental constraint. Instead, this pattern reflects the relatively low genetic diversity within cave populations. Finally, magnitudes of craniofacial integration were found to be similar among all groups, meaning that coordinated development among anatomical units is robust to eye loss in A. mexicanus. We conclude that, in contrast to many conserved phenotypes across cave populations, global craniofacial shape is more variable, and patterns of shape variation are more in line with population structure than developmental architecture or selection.

Comparison of two cultivation methods for domesticating wild red algal eucheumatoids for use in the seaweed industry

AbstractEucheumatoid cultivation is an important alternative livelihood for small-scale farmers in coastal areas in east Malaysia. Over the last 50 years, the same clones of the red eucheumatoid Kappaphycus alvarezii and Kappaphycus striatus have been vegetatively propagated for cultivation resulting in low genetic diversity. This has made the cultivars more vulnerable to pests and diseases, which has been further exacerbated by climate change. There is an urgent need, therefore, to develop new cultivars that are resilient to pests and diseases, as well as environmental change. In this study, wild eucheumatoids were collected from four regions in Semporna, East Malaysia: Kerindingan, Sibuhun, Sebangkat and Omadal. These eucheumatoids were then grown at a commercial seaweed farm in Silungun, Semporna using two methods: i) tie-tie and ii) basket net for 60 days and their performance was evaluated based on growth and survival rates. A higher mean specific growth rate (SGR) was recorded by wild-collected Kappaphycus spp. (2.15 ± 1.90% day−1) and Eucheuma denticulatum (2.83 ± 3.27% day−1) when tie-tie was used. However, survival of the wild-collected eucheumatoids was better with the basket net, which led to a reduction in grazing and prevented detachment from culture lines. Of 212 original individuals, 72 survived throughout the study, despite the prevalence of pests and ice-ice disease. Of these, 46.15% Kappaphycus spp. and 50.75% E. denticulatum survived when cultivated using the basket net and 17.20% Kappaphycus spp. and 30.77% E. denticulatum survived when cultivated using tie-tie. The mean SGR and survival rate were significantly correlated with temperature, salinity, pH, current velocity and rainfall (p &lt; 0.05). The surviving wild-collected Kappaphycus spp. and E. denticulatum have the potential to be developed into new cultivars for possible commercial use.

Genetic diversity evaluation of Luculia yunnanensis, a vulnerable species endemic to Yunnan, Southwestern China based on morphological traits and EST-SSR markers.

Luculia yunnanensis is a vulnerable species endemic to Yunnan Province, Southwestern China, which has high ornamental value. Its wild population has not been fully protected and utilized for a long time, which is not conducive to the long-term stable development of this species. Genetic diversity assessment is the basis and prerequisite for the conservation of rare species. In this study, 21 phenotypic traits and 17 highly polymorphic EST-SSR markers were used to analyze the genetic diversity and genetic structure of 164 individuals from six L. yunnanensis populations. The coefficient of variation of 21 phenotypic traits ranged from 11.76% to 52.58% (mean=21.72%), and the coefficient of variation of 18 traits was less than 30%. The average values of Ne, I, Ho and He were 1.710, 0.619, 0.384, and 0.352, respectively. The genetic diversity of LLO (Ho = 0.476 and He = 0.426) and LCM (Ho = 0.424 and He = 0.381) populations in Lushui County was highest. The GDX populations (Ho = 0.335 and He = 0.269) isolated by Gaoligong Mountain had the lowest genetic diversity. The AMOVA results showed that 13.04% of the genetic variation was among populations and 86.96% was within populations. The average phenotypic differentiation coefficient of phenotypic traits among populations was 18.69%. The results of phenotypic and genetic variation analysis were consistent, indicating that the most of variation exists within population. Genetic structure, UPGMA clustering and PCA analysis results showed that the populations of L. yunnanensis had obvious geographical divisions, and the populations distributed in the southern region and distributed in the northern region of the Nujiang River clustered into one group respectively. Combining the results of phenotypic and molecular markers, we recommend that give priority to the protection of LLO, LCM and GDX population, in order to ensure the sustainable utilization of L. yunnanensis germplasm resources.