Intraspecific Genetic Variation of Pokea, Batissa violacea (Lamarck, 1818), from Southeast Sulawesi Based on COI Mitochondrial Gene

Community genomics: a community-wide perspective on within-species genetic diversity.

ABSTRACTIntraspecific genetic diversity in wild populations is declining as global change intensifies. Genetic variation within populations of foundation plant species may influence ecological responses to environmental stressors, but remains poorly understood. Here, we examined how intraspecific genetic diversity in salt marsh cordgrass (Spartina alterniflora, hereafter Spartina) affects responses to nutrient addition. Salt marshes are often dominated by Spartina, a partially clonal foundation species that is critical to the structure and ecosystem function of salt marsh habitats. We conducted a two‐way factorial greenhouse experiment to examine plant responses to two levels of intraspecific genetic diversity and two levels of nutrient addition. We genotyped plants and estimated genetic distance and clonal identities. We measured aboveground biomass, belowground biomass, tiller production, and percent nitrogen content of leaf tissue. Nutrient addition had a strong main effect on combined plant responses, but we did not find an impact of intraspecific genetic diversity or the interaction between intraspecific genetic diversity and nutrient addition on the combined plant responses. When we examined plant responses individually, we found that nutrient addition decreased belowground biomass and increased leaf tissue nitrogen content. Nutrient addition interacted with intraspecific genetic diversity to affect tiller production, whereby nutrient addition increased tillers in low genetic diversity pots, but decreased tillers in high genetic diversity pots. Unexpectedly, neither nutrient addition nor intraspecific genetic variation affected aboveground biomass, which may be driven by divergent responses among different plant clones. For example, of the four most common clones (Multilocus Lineages), nutrient addition increased aboveground biomass in the low diversity treatment for two clones, and in the high diversity treatment for another clone. Unlike the well‐established relationship between plant interspecific diversity and ecosystem function, intraspecific genetic diversity of a foundation species did not affect plant responses at a local scale to nutrient addition.

AimAssuming genetic variants are selectively neutral, estimates of intraspecific genetic diversity and population structure should increase simultaneously in parallel to coalescent time, population size and gene flow. However, other processes, such as genetic drift associated with demographic fluctuations, might cause a loss of genetic diversity while not affecting population structure. In this study, we assess large‐scale patterns of estimates of intraspecific genetic variation across species to determine the roles of dispersal, biogeography, divergence time and demographic fluctuations in decoupling genetic diversity and population structure.LocationPristine first‐order streams distributed in seven regions from Neotropical to boreal climate, covering a gradient of habitat persistence through major biogeographical changes (e.g., Pleistocene glaciations).Time period2008–2010.Major taxa studiedFreshwater insect lineages that differ in dispersal propensity.MethodsIntraspecific nucleotide diversity (π) and population structure (ΦST) were estimated for 33 species using 2,128 sequences of the cox1 gene. The correlation between π and ΦST was tested using linear regression models. The geographical distribution of haplotypes was represented in networks. Phylogenetic trees were time calibrated to determine divergence time.ResultsAt a global scale, a positive relationship between π and ΦST was found. Neotropical species showed the highest values of π and ΦST, probably owing to historical environmental stability. Across Europe, the low estimates of π and the wide array of ΦST values and haplotype networks found across species, lineages and latitude were contrary to the biogeographical and dispersal paradigms.Main conclusionsBeyond the macroecological trend found, genetic trajectories of co‐distributed temperate species were disassociated from their functional traits and probably caused by persistent demographic fluctuations associated with local‐scale habitat instability. Overall, the idiosyncratic relationship between π and ΦST across species prevents the establishment of conclusive global patterns and questions the phylogeographical patterns established when studying a reduced number of co‐distributed species.

Onion thrips (Thrips tabaci Lindeman), the cosmopolitan pest, has distributed around Europe, Asia, pacific islands, America, east of Africa and Australia. Because of the tiny body size, short life cycle, and polymorphology with body color from light to dark, it is not only hard to be identified but also impossible to be distinguished their genetic variation among populations. In this study, both genes of nuclear internal transcribed spacer 2 (ITS2) region and mitochondrial cytochrome oxidase subunit I (COI) of onion thrips collected from Pacific Rim were used to detect and analyse their intraspecific genetic diversity. There are 86 sequences successfully to be detected in those onion thrips populations from 13 countries of Pacific Rim with 49 sub-populations. The sequences variation of ITS2 rDNA and COI mtDNA region were 0.4~3.0% and 0~3.1%, respectively. The comparison of sequences in 4 single sample areas, i.e. China, Hawaii, Peru, and Netherlands, showed that the largest variation of ITS2 rDNA region (0.7~0.9%) was found in China populations. The absolute haplotype diversity of ITS2 rDNA region were found in T. tabaci samples of Peru and China (1.00000) and following with America (0.87273), New Zealand (0.83333) and Australia (0.80300). The highest haplotype diversity of COI mtDNA region were found in samples of Netherlands (1.00000) and following with New Zealand (0.83333). The higher fixation index (FST) of ITS2 rDNA region were found between the thrips populations of Taiwan and Mexico (0.60630), and the higher FST of COI mtDNA region were Hawaii and Australia (0.64935), Taiwan and America (0.64739), Taiwan and Australia (0.60240). These indicated that higher frequencies in gene flow, and thus lower genetic diversity, occurring between those two populations. Cloning method was used to study the ITS2 rDNA region composition as the direct sequending of PCR products shown the overlapping at nucleotides positions of 170. The highest haplotype diversity of ITS2 rDNA region was found in populations of Japan (0.9684) with 17 haplotypes totally, in comparing the heterogeneous composition of all specimens. The genetic analyses of both genes indicated that different genetic variations occurring in different populations of T. tabaci from Pacific Rim. Thus, the unexpected introduction of foreign populations of this pest should be avoid to reduce the hybridization adaptation.

Theory and empirical evidence show that intraspecific competition can drive selection favouring the use of novel resources (i.e. niche expansion). The evolutionary response to such selection depends on genetic variation for resource use. However, while genetic variation might facilitate niche expansion, genetically diverse groups may also experience weaker competition, reducing density-dependent selection on resource use. Therefore, genetic variation for fitness on different resources could directly facilitate, or indirectly retard, niche expansion. To test these alternatives, we factorially manipulated both the degree of genetic variation and population density in flour beetles (Tribolium castaneum) exposed to both novel and familiar food resources. Using stable carbon isotope analysis, we measured temporal change and individual variation in beetle diet across eight generations. Intraspecific competition and genetic variation acted on different components of niche evolution: competition facilitated niche expansion, while genetic variation increased individual variation in niche use. In addition, genetic variation and competition together facilitated niche expansion, but all these impacts were temporally variable. Thus, we show that the interaction between genetic variation and competition can also determine niche evolution at different time scales.

Population genetics and dispersal of a threatened marsupial mammal, Petrogale penicillata, in southeast Queensland

Seagrasses, marine angiosperms, provide numerous ecosystem services for coastal and estuarine environments. They are often called ‘ecosystem engineer’ as they can modify surrounding marine environments, creating their own habitats. Zostera marine (common name ‘eelgrass’) is one of the seagrass bed-forming species distributed widely in the northern hemisphere including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide including Korea, primarily due to anthropogenic pressure such as climate change and habitat destruction. Although an understanding of the extent of intraspecific genetic diversity and genetic structure of ‘natural’ populations is a key factor in the ultimate success of conservation efforts, little attention has been paid to the population genetic structure of eelgrass populations in South Korea. In the present study, to our knowledge, we are the first to assess the current population genetics status of this species on the entire coasts of South Korea (Jeju Island, South Sea, East Sea and West Sea) in addition to the East China Sea by estimating the levels of genetic diversity and genetic structure using eight microsatellite markers. Eight-hundred-forty specimens were collected from 24 geographic localities in the South Sea (6 populations), East Sea (6), West Sea (4) and Jeju Island (5), which is located approximately 155 km off the southernmost region of the mainland and also in the East China Sea (3). Populations from Jeju Island displayed a much higher rate of asexual reproduction, as indicated by a lower level of clonal diversity and thus significantly lower genetic diversity (allelic richness) compared to other coastal regions. However, Jeju Island populations showed significantly higher levels of inter-population differentiation ( F ST ) than any other regions (p < 0.05), although they are geographically more closely located one another (0.6-26.4 km). Overall, South Korean eelgrass populations were all strongly genetically divergent from one another, suggesting that limited contemporary gene flow has been occurring among populations. Results of FCA (factorial correspondence analysis) suggest that Z.marina populations analyzed here are most likely to form four distinct genetic clusters including Jeju Island, South/West Sea, East Sea and East China Sea. However, a Baysian population assignment test with STURCURE revealed that the most likely number of genetic clusters after Delta K Evanno's correction corresponds to K=7. Microsatellite-based phylogenetic analysis with a Neighbor Joining (NJ) method, indicates that Jeju Island populations are most distantly related, and the South and West Sea populations are most closely related. Small effective population sizes (Ne) and limited population connectivity, particularly for populations in Jeju Island indicate that these island populations may be vulnerable to local extinction under changing environment, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform on conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of Korea for this ecologically important species. To this end, we here suggest that populations from the South Sea can be used as source material through transplantation for the restoration of island populations, given the elevated levels of genetic diversity and also their close evolutionary relationships.

Fish, genes and genomes: contributions to ecology, evolution and management.

The genetic structure of organisms results from the interactions between life history traits and the ecological and demographic characteristics of the landscape that shape the intra- and interpopulation genetic variation in space and time. In this study, we used a species restricted to islands of grassland vegetation in southern Brazil to investigate the effects of its naturally fragmented distribution on diversity and genetic structure patterns. Diversity and intra- and interpopulational genetic structure were analyzed using polymorphisms of eight nuclear microsatellite markers in 205 individuals of T. hatschbachii and Bayesian and multivariate methods. At the intrapopulation level, populations presented low genetic diversity and strong spatial genetic structure, indicating a greater spatial autocorrelation until ∼50-500 m. At the interpopulation level, genetic variation partitioned into two geographically structured genetic clusters. Gene flow through pollen was more efficient than gene flow by seeds. Genetic structure was influenced locally by seed and pollen dispersal dynamics and regionally by fragmentation of the grassland landscape. This study highlights the importance of geological barriers, and potentially a role for genetic drift, in influencing diversification of species in subtropical grasslands of southern Brazil.

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.

BackgroundMosquito control is needed to prevent dengue fever, which is mainly spread by Aedes albopictus in China. Application of insecticides is one of the main mosquito control methods; however, this approach can fail due to the knockdown resistance (kdr) gene mutation that causes decreased sensitivity to insecticides in Ae. albopictus. The kdr mutation patterns among different regions in China differ significantly. However, the underlying mechanism and factors that influence kdr mutation remain unclear. To explore the potential influence of genetic background on the development of insecticide resistance in Ae. albopictus, we analyzed the genetic structure of Ae. albopictus populations in China and its correlation with major kdr mutations.MethodsWe collected Ae. albopictus from 17 sites in 11 provinces (municipalities) across China from 2016 to 2021 and extracted the genomic DNA from individual adult mosquitoes. We selected eight microsatellite loci for genotyping, and based on microsatellite scores, we estimated intraspecific genetic diversity, population structure, and effective population size. The association between the intrapopulation genetic variation and F1534 mutation rate was evaluated by the Pearson correlation coefficient.ResultsBased on variation analysis of the microsatellite loci of 453 mosquitoes representing 17 populations throughout China, more than 90% of the variation occurred within individuals, whereas only about 9% of the variation occurred among populations, indicating that field populations of Ae. albopictus are highly polymorphic. The northern populations tended to belong to gene pool I (BJFT 60.4%, SXXA 58.4%, SDJN 56.1%, SXYC 46.8%), the eastern populations tended to belong to pool III (SH 49.5%, JZHZ 48.1%), and the southern populations tended to belong to three different gene pools. Moreover, we observed that the greater the fixation index (FST), the lower the wild-type frequency of F1534 of VSGC.ConclusionsThe degree of genetic differentiation among Ae. albopictus populations in China was low. These populations were divided into three gene pools, in which the northern and eastern pools are relatively homogeneous, while the southern gene pool is heterogeneous. The possible correlation between its genetic variations and kdr mutations is also noteworthy.Graphical

Intraspecific genetic variation in mitochondrial 16S rRNA and COI genes in domestic and wild populations of Huaguizhikong scallop Chlamys nobilis Reeve

Background: Coilia mystus is an important commercial and ecologically species. In recent years, its resources have declined sharply. It is very important to establish management unit for better protect this species. At present, the population genetic structure of C. mystus from the adjacent waters has not been studied. The current study aimed to study the population genetic structure of C. mystus from the adjacent waters, so as to establish the management unit for better protect and management its resources. Methods: Samples of 144 C. mystus individuals were collected from 4 localities of LS, CM, ZS and WZ for total genomic DNA extraction. PCR amplification was carried out by the common pairs of primers and the target amplification products were separated, purified and sequenced. The COI sequences and genetic diversity were analyzed by a series of sequence analysis software. Result: The results identified low genetic diversity and significant genetic differentiation of C. mystus from Yangtze Estuary and its adjacent waters. The influence factors of genetic diversity including historical factors, anthropogenic activity, habitation and a low rate of gene flow were discussed. The present work will conducive to the establishment of management unit for better protection and utilization of this species.

Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (HT) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (FST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise FST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.

Persian leopards Panthera pardus saxicolor have been extirpated from over 84% of their historic range and are now limited to rugged landscapes of West Asia and the Caucasus. Understanding and maintaining genetic diversity and population connectivity is important for preventing inbreeding and genetic drift, both of which can threaten population viability. All previous analyses of intraspecific genetic variation of West Asian leopards based on the NADH dehydrogenase subunit 5 gene have reported low mitogenomic diversity. In the current study, we sequenced 959 bp of the mtDNA cytochrome b gene to describe the spatial genetic structure of 22 wild Persian leopards across Iran, which hosts most of the subspecies extant range. The findings based on phylogenetic trees and median-joining network indicated that leopards from Iran formed a distinct subclade, i.e., P. p. saxicolor. The AMOVA analysis showed significant differentiation (88.55%) between the subclades of Persian leopards and other Asian leopards. The lowest levels of haplotype (0.247) and nucleotide (0.00078) diversity were estimated in Persian leopards from Iran. Mitochondrial genome sequencing revealed only two closely related haplotypes. There was no evidence for recent sudden demographic expansion scenario in Persian leopards. The low diversity in cytochrome b gene could potentially be brought about by selective pressure on mitochondria to adapt to oxidative stress and higher metabolic rates in cold environments.