High Level Of Genetic Diversity Research Articles

Characterization of the Coding Sequence of the MC1R (Melanocortin 1 Receptor) Gene of Ayam Cemani Black Chickens

Plumage color is one of the most important traits characterizing chicken breeds. Black-boned chickens constitute a specific group of breeds with a unique phenotype. One of the representatives is the Indonesian Ayam Cemani. The extraordinary black phenotype results from a specific chromosomal rearrangement. We used complete CDS of crucial color-related gene MC1R, which plays a key role in melanin distribution but has not been previously studied in Ayam Cemani. It turned out that Ayam Cemani individuals possess a newly found non-synonymous mutation G355A resulting in amino acid substitution D119N. Together with the presence of G274A (E92K), the new missense variant enabled us to distinguish a new extended black allele at the E locus. All of the investigated birds were heterozygous in terms of the new mutation. Previous studies and our own results indicate a high level of genetic variation within the MC1R gene within and between chicken breeds. Besides the key mutations that make it possible to distinguish particular major alleles, there are also numerous substitutions that give haplotypes more characteristics for individual breeds.

Comparative genomics and evolutionary analysis of dengue virus strains circulating in Pakistan.

Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogenetic analysis demonstrated the circulation of all four dengue virus serotypes (DENV-1, -2, -3, and -4) with prevalent genotypes III and V within DENV-1, cosmopolitan genotype within DENV-2, genotype III within DENV-3, and genotype I within DENV-4 during 2006-2014. Based on the complete envelope region, genome-wide residue signature and genetic diversity indicate that there is a high level of genetic diversity among DENV-1 strains, while DENV-3 strains exhibit the least genetic diversity. Comparative analysis of all four DENV serotypes revealed that certain codons in DENV-2 and -4 were subject to strong purifying selection, while a few codon sites in the envelope region showed evidence of positive selection. These findings provided valuable insights into the comparative genomics and evolutionary pattern of DENV strains reported from Pakistan. Whether those characteristics conferred a fitness advantage to DENV-1 genotypes within a specific geography and time interval warrants further investigations. The findings of the current study will contribute to tracking disease dynamics, understanding virus transmission and evolution, and formulating effective disease control strategies.

African Local Pig Genetic Resources in the Context of Climate Change Adaptation.

Africa is home to a wide diversity of locally adapted pig breeds whose genetic architecture offers important insights into livestock adaptation to climate change. However, the majority of these inherent traits have not been fully highlighted. This review presents an overview of the current state of African pig genetic resources, providing highlights on their population and production statistics, production system, population diversity indices, and genomic evidence underlying their evolutionary potential. The study results reveal an incomplete characterization of local pig genotypes across the continent. The characterized population, however, demonstrates moderate to high levels of genetic diversity, enough to support breeding and conservation programs. Owing to low genetic differentiation and limited evidence of distinct population structures, it appears that most local pig populations are strains within larger breeds. Genomic evidence has shown a higher number of selection signatures associated with various economically important traits, thus making them potential candidates for climate change adaptation. The reportedly early evidence of hybridization with wild suid groups further suggests untapped insights into disease resistance and resilience traits that need to be illuminated using higher-density markers. Nevertheless, gene introgression from commercial breeds is prevalent across Africa; thus, efforts to realize and utilize these traits must increase before they are permanently depleted.

Population genetic analysis of Plasmodium vivax vir genes in Pakistan.

Plasmodium vivax variant interspersed repeats (vir) refer to the key protein used for escaping the host immune system. Knowledge in the genetic variation of vir genes can be used for the development of vaccines or diagnostic methods. Therefore, we evaluated the genetic diversity of the vir genes of P. vivax populations of several Asian countries, including Pakistan, which is a malaria-endemic country experiencing a significant rise in malaria cases in recent years. We analyzed the genetic diversity and population structure of 4 vir genes (vir 4, vir 12, vir 21, and vir 27) in the Pakistan P. vivax population and compared these features to those of the corresponding vir genes in other Asian countries. In Pakistan, vir 4 (S=198, H=9, Hd=0.889, Tajima's D value=1.12321) was the most genetically heterogenous, while the features of vir 21 (S=8, H=7, Hd=0.664, Tajima's D value =-0.63763) and vir 27 (S =25, H =11, Hd =0.682, Tajima's D value=-2.10836) were relatively conserved. Additionally, vir 4 was the most genetically diverse among Asian P. vivax populations, although within population diversity was low. Meanwhile, vir 21 and vir 27 among all Asian populations were closely related genetically. Our findings on the genetic diversity of vir genes and its relationships between populations in diverse geographical locations contribute toward a better understanding of the genetic characteristics of vir. The high level of genetic diversity of vir 4 suggests that this gene can be a useful genetic marker for understanding the P. vivax population structure. Longitudinal genetic diversity studies of vir genes in P. vivax isolates obtained from more diverse geographical areas are needed to better understand the function of vir genes and their use for the development of malaria control measures, such as vaccines.

Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape.

This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.

Genetic diversity analysis of Saccharosydne procerus in Hunan region, China.

Saccharosydne procerus serves as a significant alternative host for parasitoids of the important rice pest, rice planthoppers. Rearing S. procerus on the water bamboo plants near rice field can provide a parasitic site for parasitic wasps during the idle period of rice fields, thereby stabilizing the number of parasitoids and suppressing the number of rice planthoppers in the field. However, limited understanding of genetic diversity of S. procerus restricts its application. Therefore, this study aims to analyze the genetic diversity of S. procerus in Hunan region. In this study, 16 geographical populations of the S. procerus from the Hunan region were used. After screening, ISSR primers were employed for polymorphism detection. POPGENE32 software was used for genetic diversity analysis, and UPGMA clustering was applied for statistical analysis of different geographical populations to generate an evolutionary tree. Eleven ISSR primers were screened, resulting in the detection of 194 amplification locus, of which 126 were polymorphic. The average percentage of polymorphic locus was 64.95%. The mean Nei's gene diversity (H) was 0.2475, the mean Shannon's Information index (I) was 0.3708, and the Genetic diversity index among populations (Gst) was 0.3800. Cluster analysis identified three groups, with most populations concentrated in the second group, indicating no clear genetic structure. This suggests that the 16 populations of S. procerus exhibit high levels of genetic diversity.

Assessment of the genetic similarity between the novoaltayskaya horse breed and the original breeds by microsatellite DNA loci

The research was carried out for the purpose of a comparative assessment of the allele pool of the Novoaltayskaya horse breed and the breeds that participated in its creation. The experimental sample included 5736 horses, including: Novoaltayskaya breed – 363, Altai – 39, Lithuanian Heavy Draft – 159, Russian Heavy Draft – 617, Soviet d Heavy Draft – 288, Orlov trotter – 4,177, Budenny – 93. Population genetic analysis was performed using generally accepted methods. The following indicators were determined: the total number of alleles at 17 loci, the average number of alleles per locus, the level of polymorphism, observed and expected heterozygosity, coefficients of intrapopulation inbreeding, genetic similarity and genetic distances. It was established that horses of the Novo-Altai breed had the highest level of genetic diversity (154 alleles) and polymorphism (Ae = 4,909). Analysis of genetic differentiation showed the absence of intrapopulation inbreeding in the groups of Altai, Lithuanian Heavy Draft and Budenny breeds. Groups of horses of the Novoaltayskaya, Orlov trotter, Russian Heavy Draft and Soviet Heavy Draft breeds were distinguished by a slight deficiency of heterozygotes. It has been established that horses of the Novoaltayskaya and Heavy Draft breeds are characterized by a high frequency of occurrence of the HTG6 O allele, and the Altai breed is characterized by a high frequency of occurrence of the HTG4 M allele. A number of loci of alleles identical in spectrum to those of the Altai, Russian Heavy Draft and Soviet Heavy Draft breeds were identified in the Novoaltayskaya horse. Cluster analysis demonstrated a high level of genetic similarity of horses of the Novoaltayskaya breed with the Russian Heavy Draft (0,903) and Altai (0,899) breeds. As part of the study, using molecular genetic markers, new data was obtained on horses of seven breeds, with the help of which it is possible to improve breeding programs in horse breeding, allowing to control the biodiversity and genetic similarity of populations, preserving the originality and heterogeneity of the allele pool of horses of different breeds.

Reintroduction of Armeria maritima ssp. elongata by sowing and planting in a 20-year restoration project: Is there an impact on genetic variation?

Reintroduction is a frequently used method to restore populations of endangered species. However, it has hardly been tested whether there is a pronounced genetic impact resulting from different propagule types used for restoration. To address this knowledge gap, we carried out a pilot study based on a 20-years practical experiment, in which new populations of the rare and endangered herb Armeria maritima ssp. elongata were founded using seeds and/or young plants. The experiment took place in a nature reserve protecting a declining nutrient-poor sand-dune habitat. To evaluate if there was an effect of propagule type on genetic variation of restored populations, we compared populations of A. maritima ssp. elongata started by direct seeding, planting of seedlings and both seeding & planting. Using molecular markers (AFLPs), we observed slightly higher levels of genetic diversity within restored compared to the source population. Genetic diversity was comparable in populations restored by different propagules, and genetic differentiation between the source and restored populations was absent. Our study provides a first piece of evidence that both seeds and young plants can be applied successfully in population restoration projects. We suggest to further test the impact of the reintroduction methods on restoration outcomes under different experimental settings, e.g. using species with different life history traits.

The Complex Genetic Legacy of Hybridization and Introgression between the Rare Ocotea loxensis van der Werff and the Widespread O. infrafoveolata van der Werff (Lauraceae).

Hybridization and introgression are complex evolutionary mechanisms that can increase species diversity and lead to speciation, but may also lead to species extinction. In this study, we tested the presence and genetic consequences of hybridization between the rare and Ecuadorian endemic O. loxensis van der Werff and the widespread O. infrafoveolata van der Werff (Lauraceae). Phenotypically, some trees are difficult to identify, and we expect that some might in fact be cryptic hybrids. Thus, we developed nuclear microsatellites to assess the existence of hybrids, as well as the patterns of genetic diversity and population structure in allopatric and sympatric populations. The results revealed high levels of genetic diversity, even in the rare O. loxensis, being usually significantly higher in sympatric than in allopatric populations. The Bayesian assignment of individuals into different genetic classes revealed a complex scenario with different hybrid generations occurring in all sympatric populations, but also in allopatric ones. The absence of some backcrossed hybrids suggests the existence of asymmetric gene flow, and that some hybrids might be more fitted than others might. The existence of current and past interspecific gene flow also explains the blurring of species boundaries in these species and could be linked to the high rates of species found in Ocotea.

Study of the Karachay Population Based on the Analysis of Ten Polymorphic DNA Loci

Genetic structure of Karachai population has been studied based on analysis of 10 autosomal DNA markers (diallelicand multiallelic): CCR5∆32, ACE, D7S23(KM19) STR/THOI, STR/FABP, STR/IVS6a, VNTR/PAH, VNTR/DAT1, VNTR/eNOS VNTR/APOB. The total number of sample makes up 485 individuals who are residents of five Karachai regions: Karachaevsky, Prikubansky, Malokarachayevsky, Ust-Dzhegutinsky and the city of Cherkessk, the capital of the Republic of Karachaevo-Cherkessia. Analysis of allele’s frequency of autosomal DNA markers in Karachay geographic subgroups shows considerable genetic differentiation between them. The highest level of genetic diversity for Karachay people on dialle system is set at the locus ID/ACE, Hobs = 0.513, on multi-allele system isat the locus STR/THOI, Hobs = 0.792. The average value of the observed heterozygosity per locus is 0.466, varying from 0.441 in Ust-Dzhegutinsky to 0.503 in Cherkessk. The level of genetic differences between Karachai groups (FST = 0.007) is inside the variance defined in the previously studied peoples, Mari (FST = 0.0024), Udmurt (FST = 0.0048), Chuvash (FST = 0.006), Tatars (FST = 0.0075) and Bashkir (FST = 0.008).

Performance evaluation of the new Access HIV Ag/Ab combo assay on the DxI 9000 Access Immunoassay Analyzer

Fourth-generation HIV immunoassays have been developed to reduce the window period of detection during seroconversion period, allowing for the detection of early and established infections. The aim of this work was to evaluate a newly developed assay, Access HIV Ag/Ab combo on the novel high throughput DxI 9000 Access Immunoassay Analyzer (Beckman Coulter, Inc.). The assay allows for simultaneous qualitative detection and differentiation of HIV-1 p24 antigen and HIV-1/2 antibodies.Assay performance was compared to two gold standard assays, the Abbott Architect HIV Ag/Ab Combo and Roche Elecsys HIV Duo, and assessed in a multicenter study, using a wide panel of samples (n > 9000, clinical samples and viral lysates) representative of genetic diversity for both antibodies and antigens, early phases of infection, negative, and cross-reacting samples.The clinical sensitivity was 100 % for clinical samples as well as for viral lysates. Data on viral lysates and early detection on seroconversion panels showed a better result with the Access assay. Analytical sensitivity showed a limit of p24 detection determined around 0.2 IU/mL. The overall specificity was 99.91 %, and no interference was found using the potentially cross-reactive samples.In conclusion, the Access HIV Ag/Ab combo assay demonstrated its ability for accurate diagnosis of chronic as well as primary HIV infections on the DxI 9000 Analyzer, despite the high level of genetic diversity of these viruses.

Emergence of genetic diversity and multi-drug resistant Clostridium perfringens from wild birds

BackgroundClostridium perfringens (C. perfringens) is an important zoonotic microorganism that can cause animal and human infections, however information about the prevalence status in wild birds of this pathogenic bacterium is currently limited.ResultIn this study, 57 strains of C. perfringens were isolated from 328 fecal samples of wild birds. All the isolates were identified as type A and 70.18% of the isolates carried the cpb2 gene. Antimicrobial susceptibility testing showed that and 22.80% of the isolates were classified as multidrug-resistant strains. The MLST analysis of the 57 isolates from wild birds was categorized into 55 different sequence types (STs) and clustered into eight clonal complexes (CCs) with an average of 20.1 alleles and the Simpson Diversity index (Ds) of 0.9812, and revealed a high level of genetic diversity within the C. perfringens populations. Interestingly, the isolates from swan goose were clustered in the same CC while isolates from other bird species were more scattered suggesting that a potential difference in genetic diversity among the C. perfringens populations associated with different bird species.ConclusionC. perfringens exhibits a wide range of host adaptations, varying degrees of antimicrobial resistance, and a high degree of genetic diversity in wild birds. Understanding the prevalence, toxin type, antimicrobial resistance, and genetic diversity of C. perfringens in wildlife populations is essential for developing effective strategies for disease control and management.

Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus.

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.

Genetic Analysis and Construction of a Fingerprint for Licensed Triadica sebifera Cultivars Using SSR Markers.

Triadica sebifera is an important landscaping tree species because of its colorful autumn leaves. In recent years, some cultivars have been bred and licensed, but it can be difficult to identify them from their morphological traits due to their similar phenotypes. To explore the genetic relationships and construct a fingerprint of the cultivars, the licensed T. sebifera cultivars were analyzed using SSR markers. A total of 179 alleles were identified among the 21 cultivars at 16 SSR loci, and these alleles exhibited a high level of genetic diversity (He = 0.86). The genetic variations mainly occurred among cultivars based on an analysis of molecular variance (AMOVA). According to phylogenetic analysis, principal coordinate analysis (PCoA), and Bayesian clustering analysis, the genetic relationships were independent of geographic distances, which may be mainly due to transplantations between regions. Some cultivars with different leaf colors showed obvious genetic differentiation and may be preliminary candidates for cross-breeding. Finally, the fingerprint for the licensed cultivars was constructed with two SSR markers. The results of this study can provide technical support for the application and legal protection of licensed Triadica sebifera cultivars.

Whole-genome mutagenesis of whiteleg shrimp (Litopenaeus vannamei) by ARTP and analysis of its mutational characteristics

Artificial induction has been widely employed to generate genetic resources with increased mutation rates for subsequent selection. To assess the potential of physical mutagenesis in shrimp breeding, we utilized Atmospheric and Room Temperature Plasma (ARTP) to induce mutations in fertilized eggs from four different families of Litopenaeus vannamei. Treatment durations ranged from 2 to 12 min. The results revealed a significant decrease in hatching rates among the ARTP-treated groups, ranging from 3.22% to 67.81%, with more substantial reductions observed in longer treatment durations. Following a 90-day mixed rearing test, we found no statistically significant differences (P > 0.05) in the average body weight of 743 shrimps across the 13 mutagenesis groups compared to the control group. However, variations in weight were observed in the 22 largest or smallest sample groups, with 12 groups displaying an average increase of 8.69% and 10 groups showing an average decrease of 9.97% compared to their respective controls. Regarding fitness traits, seven treatment groups from two families exhibited higher median lethal times or mean survival times against WSSV compared to the control group, while two treatment groups demonstrated improved resistance to ammonium nitrogen. Genomic resequencing analysis was conducted on growth sampling groups, identifying a total of 2,718,961 SNPs and 331,172 Indels in the treatment group. The mutation rate in the treatment group was 2.148 × 10−3, significantly higher than the control group's rate of 5.275 × 10−5. Within the treatment group, 17,104 specific non-synonymous SNPs were identified in the exons of 7780 genes, markedly surpassing the control group's count of 121 SNPs and 110 genes. GO annotation analysis revealed an even distribution of mutations induced by ARTP across various biological processes, cellular components, and functions. Furthermore, KEGG enrichment analysis demonstrated a significant enrichment trend in metabolic pathways, both in terms of gene count and FDR value. A total of 42 KEGGs and several potential growth-related genes, including IGF1 and AMY2, previously confirmed to be highly correlated with growth in L. vannamei, were identified. In conclusion, a feasible method for whole-genome mutagenesis in shrimp zygotes was developed in this study. Tests on economic traits revealed that ARTP can generate mutant individuals with either a greater degree of variation or superior traits. Resequencing revealed the presence of numerous mutation SNPs involved in various biological processes and contribute to a higher level of genetic diversity. These results suggest that ARTP can be utilized to enhance the available genetic variation in shrimp breeding, thereby providing valuable materials and methods for genetic breeding in whiteleg shrimp.

Genetic prospective of a local invader: the strange pattern of Pontastacus leptodactylus population structure in Greece and Turkey based on microsatellite DNA.

The combination of the increasing demand of freshwater crayfish exports, the reduced population sizes due to overfishing, the crayfish plague epidemics and the habitat degradation, have led to unrecorded translocations of Pontastacus leptodactylus in Greek lakes. In the present study, the genetics of five narrow clawed crayfish (P. leptodactylus) populations were studied, namely three translocated populations inhabiting in Northern Greece, one native Greek population from Evros river and one potential progeny source population from Turkey. Nine microsatellite loci previously designed for the specific species were investigated, in order to assess the levels of genetic diversity and further to confirm the origin of these translocated populations some decades after the translocation events. Our results confirmed that the source population for the translocated Greek population is the Turkish lake Eğirdir. Further, despite the low values of the number of alleles, heterozygosity, and FST the populations were generally diverse, providing evidence for local adaptation. The low values of FIS for the translocated populations in combination with the high values of gene flow, possibly indicate the existence of re-introducing events. Apart from the translocated populations, high levels of genetic diversity and heterozygosity were observed in Evros population, suggesting it as a possible unit for future conservation purposes both as a donor population for reintroduction purposes as well as a unique gene pool protection source. To the best of our knowledge this is the first study dealing with the genetic composition of Greek P. leptodactylus populations from Nothern Greece, operating as a first step towards the development of proper management practices for restocking events and monitoring of translocated populations.

Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, Colombia.

The adaptative responses and divergent evolution shown in the environments habited by the Cichlidae family allow to understand different biological properties, including fish genetic diversity and structure studies. In a zone that has been historically submitted to different anthropogenic pressures, this study assessed the genetic diversity and population structure of cichlid Caquetaia kraussii, a sedentary species with parental care that has a significant ecological role for its contribution to redistribution and maintenance of sedimentologic processes in its distribution area. This study developed de novo 16 highly polymorphic species-specific microsatellite loci that allowed the estimation of the genetic diversity and differentiation in 319 individuals from natural populations in the area influenced by the Ituango hydroelectric project in the Colombian Cauca River. Caquetaia kraussii exhibits high genetic diversity levels (Ho: 0.562-0.885; He: 0.583-0.884) in relation to the average neotropical cichlids and a three group-spatial structure: two natural groups upstream and downstream the Nechí River mouth, and one group of individuals with high relatedness degree, possibly independently formed by founder effect in the dam zone. The three genetic groups show recent bottlenecks, but only the two natural groups have effective population size that suggest their long-term permanence. The information generated is relevant not only for management programs and species conservation purposes, but also for broadening the available knowledge on the factors influencing neotropical cichlids population genetics.

Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data.

Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai-Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.

Genetic assessment of eight zoo populations of golden snub-nosed monkey (Rhinopithecus roxellana) implication to the conservation management of captive populations.

Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.

The effect of terrain on the fine-scale genetic diversity of sub-Antarctic Collembola: A landscape genetics approach.

Biodiversity patterns are shaped by the interplay between geodiversity and organismal characteristics. Superimposing genetic structure onto landscape heterogeneity (i.e., landscape genetics) can help to disentangle their interactions and better understand population dynamics. Previous studies on the sub-Antarctic Prince Edward Islands (located midway between Antarctica and Africa) have highlighted the importance of landscape and climatic barriers in shaping spatial genetic patterns and have drawn attention to the value of these islands as natural laboratories for studying fundamental concepts in biology. Here, we assessed the fine-scale spatial genetic structure of the springtail, Cryptopygus antarcticus travei, which is endemic to Marion Island, in tandem with high-resolution geological data. Using a species-specific suite of microsatellite markers, a fine-scale sampling design incorporating landscape complexity and generalised linear models (GLMs), we examined genetic patterns overlaid onto high-resolution digital surface models and surface geology data across two 1-km sampling transects. The GLMs revealed that genetic patterns across the landscape closely track landscape resistance data in concert with landscape discontinuities and barriers to gene flow identified at a scale of a few metres. These results show that the island's geodiversity plays an important role in shaping biodiversity patterns and intraspecific genetic diversity. This study illustrates that fine-scale genetic patterns in soil arthropods are markedly more structured than anticipated, given that previous studies have reported high levels of genetic diversity and evidence of genetic structing linked to landscape changes for springtail species and considering the homogeneity of the vegetation complexes characteristic of the island at the scale of tens to hundreds of metres. By incorporating fine-scale and high-resolution landscape features into our study, we were able to explain much of the observed spatial genetic patterns. Our study highlights geodiversity as a driver of spatial complexity. More widely, it holds important implications for the conservation and management of the sub-Antarctic islands.