Estimates Of Gene Flow Research Articles

Damming shapes genetic patterns and may affect the persistence of freshwater fish populations

Abstract River damming threatens freshwater biodiversity worldwide by isolating populations, reducing both gene flow and genetic variation, and affecting the ability of a given population to adapt to environmental changes. Herein, we employed a microsatellite DNA marker panel and a multitemporal approach to assess the effects of damming on the genetic diversity of a long‐lived species from both contemporary and historical perspectives. To accomplish this, we used the migratory catfish Pseudoplatystoma corruscans as a model and sampled it in two South American basins. We tested whether: (1) populations from dammed and undammed environments would display different levels of genetic diversity; (2) ecosystem size would influence the level of genetic diversity; and (3) projected whether fish populations would maintain their current genetic diversity in the long term. Our findings reveal that P. corruscans populations from dammed landscapes with smaller ecosystems showed smaller estimated effective population size, lower genetic diversity, and higher relatedness coefficient than in intermediate ecosystem size in both dammed and undammed environments. We also noticed changes in estimated gene flow and effective population size from both contemporary and historical perspectives, probably because of dams. Predictive genetic diversity analysis revealed a critical scenario for the long‐term persistence of P. corruscans in dammed environments with smaller ecosystem sizes. Our study suggests that anthropogenic barriers have substantially impacted genetic diversity and genetic structuring of the migratory fish P. corruscans. Thus, the formation of conservation policies is urgently needed to avoid local extinctions of this species in fragmented riverscapes. We highlighted the effectiveness of large ecosystems and connectivity between populations in conserving genetic diversity of migratory fishes.

There Is No 'Rule of Thumb': Genomic Filter Settings for a Small Plant Population to Obtain Unbiased Gene Flow Estimates.

The application of high-density polymorphic single-nucleotide polymorphisms (SNP) markers derived from high-throughput sequencing methods has heralded plenty of biological questions about the linkages of processes operating at micro- and macroevolutionary scales. However, the effects of SNP filtering practices on population genetic inference have received much less attention. By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure – SGS) gene flow estimates. We focus specifically on these manifestations in small plant populations, and particularly, in the rare tropical plant species Dinizia jueirana-facao, where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05–0.35) and MD (0–20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σrt = 41.8 m) was ∼ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao, which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no ‘rule of thumb’ for bioinformatic filtering and that relying on default program settings is not advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates.

Population genetic structure of Gymnospermium scipetarum subsp. eddae (Berberidaceae), an endangered Forest endemic from the Southern Apennines (Italy)

Assessing genetic diversity of narrow endemic plants is essential for their conservation. Gymnospermium scipetarum subsp. eddae (Berberidaceae) is an Italian endemic limited to a narrow forest area in the southern Apennines. Here we used random amplified polymorphic DNA (RAPD) markers to investigate population genetic differentiation and diversity in relation to distribution and microhabitat conditions. In all five extant populations and 134 individuals analysed we found a relatively low level of population genetic diversity (average Shannon-Weaver diversity index = 0.280; mean percentage of polymorphic bands = 57.45%; mean Nei’s gene diversity He = 0.187). Percentage of polymorphic bands (PPB) at species level was higher than at the population level (83.33%), while total species diversity (He = 0.210) was comparable to that found in the two southernmost subpopulations. AMOVA revealed a weak differentiation among populations, which shared three genetic pools in their genetic structure. The estimated gene flow among populations was relatively high (mean Nm = 5.320), while the Mantel test revealed no significant correlation between geographical and genetic distances at the population level. We argue that information on genetic diversity of G. eddae have important implications for conservation programmes, particularly for the establishment of ex-situ collections and restocking conservation actions.

Genetic diversity of mangrove tree species Avicennia marina in eco-geographic regions of Kerala coast, Southern India

The genetic assembly of Avicennia marina (Forsk.) Vierh, Avicenniaceae within and between the three natural mangrove forests of Kerala coast belonging to the districts of Kochi, Kozhikode and Kannur was investigated using Inter Simple Sequence Repeat (ISSR) markers to provide coherent scientific conservation practices. The ten selective ISSR primer combinations of 60 genotypes of Avicennia marina ensured a total of 171 bands of which 84.5% were polymorphic. Gene diversity index H varied from 0.142 Kochi to 0.195 Kozhikode. The mean gene diversity H S was 0.169 and the total gene diversity H T was 0.262 which showed a moderate level of genetic diversity in the studied population. The mangrove Avicennia marina populations showed large genetic difference G ST = 0.3849, indicating that 38% of the total genetic diversity was among the populations and the rest 62% resides within the population. The gene flow estimates Nm = 0.79 shown that natural mangroves of Kerala are in the course of differentiation due to genetic drift. We investigated the genetic distinctiveness of taxonomically confusing species, Avicennia marina and Avicennia officinalis , and resulted in clear demarcation between the two. There is a significant correlation between dendrogram and PCoA designated that extensive distant spreading of seeds between populations of Avicennia marina is comparatively low. The genetic study contributed relatively high diversity and strong differentiation across the three eco-geographic locations. The best remedy to preserve coastal mangrove species like Avicennia marina is to plant the identical species in its respective habitat. Launch, on-site protection zones to safeguard the species and to decrease the impact of human activities would allow its habitats to increase in size through natural regeneration.

Sympatric and independently evolving lineages in the Thoropa miliaris – T. taophora species complex (Anura: Cycloramphidae)

Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.

Development of genic-SSR markers and their application in revealing genetic diversity and population structure in an Eastern and North-Eastern Indian collection of Jack (Artocarpus heterophyllus Lam.)

Jack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.

Assessment of genetic relationships among native and introduced Himalayan balsam (Impatiens glandulifera) plants based on genome profiling.

We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from native and non‐native regions of their distribution. When genetic relationships were explored by PCoA using SNP and SilicoDArT marker data, the first, second, and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada, and Pakistan were grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK–Canada–Pakistan group based on SilicoDArT markers. Constructed trees differentiated individuals into clusters resembling the PCoA patterns. The Bayesian BAPS analysis performed for the SNP data revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan, and the combination of the UK and Canada. Similar clustering was visible in the UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The BAPS analyses conducted for the SilicoDArT data differ slightly: The individuals were distributed in nine clusters, and the Indian cluster exhibited ancestral gene flow with the mixed cluster including Canadian, Pakistani, and UK samples, and one Finnish sample. The AMOVA showed that 45% and 26% of variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. The Bayesian BAPS analyses and the gene flow networks were the most informative tools for resolving relationships among native and introduced plants. It is notable that the small sample sizes for non‐Finnish plant materials may affect the accuracy of the gene flow and other estimates.

Coalescent methods reconstruct contributions of natural colonization and stocking to origins of Michigan inland Cisco (Coregonus artedi)

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish (Coregonus clupeaformis), cisco (C. artedi) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest.

Genetic diversity and population structure assessment using molecular markers and SPAR approach in Illicium griffithii, a medicinally important endangered species of Northeast India

BackgroundIllicium griffithii is an aromatic medicinal tree species that has been listed in the IUCN Red List as an endangered species. Dried seed pods of I. griffithii have a good market potential in the spices and pharmaceutical industries. Fruits are the potential source of shikimic acid and used for the production of oseltamivir (a drug against bird flu). However, in recent years, unscientific harvesting and rampant exploitation of the species has caused a negative and adverse effect on its natural population. Proper knowledge of genetic diversity and population structure is crucial to understand the population dynamics, adaptation, and evolutionary pattern of a particular species for conservation. It was from this view point that the present study was undertaken so as to compare the various types of DNA-based molecular markers namely RAPD, ISSR, DAMD, and SCoT by their efficiency and SPAR approach to evaluate the genetic diversity of I. griffithii as well as to analyze population genetic structure for conservation purpose. ResultA total of 250 discernible bands were generated with 246 bands (98.40 %) being polymorphic in nature. All the primers in combination gave a mean polymorphic information content (PIC) of 0.81 and Rp value (resolving power) of 4.32. Nei’s, Gst, and AMOVA analysis showed similar values of genetic differentiation among populations (Gst = 0.396, FST = 0.30, respectively), revealing a low level of genetic differentiation among the eight sampled populations. I. griffithii with an estimated gene flow value of Nm = 0.761 was significantly low among populations. Clustering pattern obtained with Bayesian structure and PCoA diagram revealed that intermixing of genetic material across populations is only possible when the populations lie close to each other. This is further validated with UPGMA clustering method where a positive correlation of genetic variability with geographical distance among closely related populations could be clearly seen. ConclusionThe result aids in the identification, collection, and preservation of diverse germplasm of I. griffithii from Arunachal Pradesh and Meghalaya of Northeast India. This would further help in understanding the population structure and genetic diversity among other Illicium species in order to formulate effective conservation strategies for the improvement of this endangered taxa.

Different rates of pollen and seed gene flow cause branch‐length and geographic cytonuclear discordance within Asian butternuts

Summary Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance.We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance.Our findings indicate that the chloroplast genome had substantially deeper divergence (branch‐length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation‐by‐distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome.Altogether, this study highlights a critical role of sex‐biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.

Restoration of Abundance and Dynamics of Coastal Fish and Lobster Within Northern Marine Protected Areas Across Two Decades

This article reviews a suite of studies conducted in a network of coastal Marine Protected Areas (MPAs) in Skagerrak, Southeast Norway. In 2006, Norway’s first lobster reserves were implemented, with the aim of protecting European lobster (Homarus gammarus) through a ban on fixed gear. A before–after control-impact paired series (BACIPS) monitoring program was initiated to evaluate effects of protection on depleted lobster populations. Experimental trapping and capture-recapture techniques were combined to track demography of populations, also including movement of individuals within and beyond MPAs and adjacent control areas. Further, population genetics and parentage studies were applied, allowing for estimation of gene flow, and novel work on sexual selection in lobsters. Additional studies have evaluated MPA effects on coastal cod (Gadus morhua), and on commercially harvested labrids (Ctenolabrus rupestrisandSymphodus melops) and anadromous brown trout (Salmo trutta). Together, these studies reported effects of protection pertaining to increased population density, survival, body size and phenotypic diversity, changes in emigration and interaction with surrounding fisheries, and alteration of selection pressure on morphological- and behavioral traits. Designation of MPAs in close collaboration with fishers and managers, long-term monitoring, inclusion of citizen science and evolving research protocols—also including fisheries data—have revealed novel effects of protection and harvesting on marine populations, thus providing substantial contributions to conservation science. Moreover, knowledge of MPA effects on coastal species has impacted harvest regulations showing the utility of MPAs as empirically documented management tools in Norway.

A response to Justen etal. 2020: Estimating hybridization rates in the wild: Easier said than done?

We consider four key challenges related to estimating per-individual rates of hybridization in wild birds: (1) what is the meaning of the term "hybrid"?, (2) the importance of distinguishing between shared DNA sequences and on-going hybridization between populations, (3) the perils of focusing exclusively on known hybrid zones, and (4) the implications of very low rates of per individual hybridization. Because our focus is on using phenotype to recognize hybrids, we define a hybrid as an individual with a phenotype that is intermediate between two parental species. We emphasize the value of quantifying the rate of between-species mating that is ongoing in current populations and distinguish this endeavor from estimates of gene flow between populations based on genomic analysis, which can reflect both current and ancient hybridization. We restate the importance of quantifying per individual rates of hybridization among all birds without prejudging which birds are presumed to engage in hybridization. And finally, we emphasize that evidence for strong prezygotic sorting is not necessarily evidence that mate choice is a driver of speciation.

Mining and characterization of genic-microsatellites associated with sucrose synthesis and their utility in population structure analysis in sugarcane

Sucrose content is a highly valued trait in sugarcane breeding that is regulated by several genes. Tracking of multiple genes involved in the expression of a complex trait in a highly heterozygous crop like sugarcane during the breeding programme is a huge challenge. Trait tagging through expressed sequence tags (ESTs) derived molecular markers has been considered as powerful tool because they are encoded by functionally relevant elements of the genome and directly linked with the target traits. Functional markers related to sucrose content are very limited in sugarcane, which hindered the genetic improvement of this trait. Seventy-three sucrose rich and fifteen low sucrose clones chosen from twelve full-sib families were used for the study on the development and characterization of genic microsatellites associated with sucrose synthesis. A total of 186 alleles were obtained, with an average of 6.20 alleles per microsatellite marker. Polymorphism Information Content (PIC) values were ranged from 0.31 to 0.83, with a mean value of 0.61. The average values of gene diversity (GD) and resolving power (RP) were 0.60 and 5.14, respectively. The present study identified genic SSR markers for four major enzymes viz., CA076844187 (FK), CA155160295 (SREBF), CA163325191,213 (SREBF), TA38405-4547232 (PPFK), and CA135596178, 225 (DFPP) which could be useful to identify sucrose rich clones in the initial testing stages of the selection programme in sugarcane. Analysis of molecular variance (AMOVA) showed 74 per cent of the total variation within population and 26 per cent among population. The EST-SSR primers showed a high allelic polymorphism, as demonstrated by high genetic diversity estimates (I =1.17, Ho = 0.78). The low mean values of fixation index (FST = 0.078) and the high estimates of gene flow (Nm = 4.166) indicates the low level of population differentiation and maximum genetic exchange between two populations. Based on SSR marker data, eighty-eight clonal accessions were classified broadly into high and low sugar population which corresponded to the molecular diversity of the sucrose specific alleles through structure analysis and principal coordinate analysis. Key wordsSugarcane, sucrose content, genic-microsatellites, AMOVA, population structure

Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.

On the potential of Angiosperms353 for population genomic studies.

PREMISEThe successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full‐gene sequences in population‐level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested.METHODSUsing herbarium specimens from a 50‐year‐old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias.RESULTSWe identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)—typically between 0.002 and 0.010, with most variation found in flanking non‐coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics.DISCUSSIONAngiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades‐old herbarium specimens.

Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers

Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

Independent origins of populations from Dehong State, Yunnan Province, and the multiple introductions and post-introduction admixture sources of mile-a-minute (Mikania micrantha) in China

Abstract Mile-a-minute (Mikania micrantha Kunth) is a tropical American species and has become a worldwide invasive weed. It was first introduced to mainland China in 1983 in Yingjiang City, Dehong State, Yunnan Province. To assess the origins of populations from Dehong State, Yunnan Province, the genetic structure of 427 individuals from 11 M. micrantha populations from Yunnan, Guangxi, Hainan, and Guangdong provinces were analyzed. A total of 28 alleles were detected in 12 nuclear microsatellite loci. Genetic diversity at the population level was relatively high. An analysis of molecular variance showed that most of the variation occurred within populations (82.73%), and only 18.27% occurred among populations. The genetic differentiation coefficient (FST) was 0.183. The estimated gene flow (Nm) from FST was 1.116. The independent origins of four populations collected from Dehong State, Yunnan Province, was determined by the unweighted pair-group method with arithmetic means clustering and STRUCTURE analysis. Three gene clusters and one admixture gene cluster were found. A Mantel test of pairwise Nei’s genetic distances and pairwise geographic distances revealed no evidence for isolation by distance (r = 0.068, P = 0.343). These results suggest that the post-introduction admixture caused by multiple introductions and high gene flow might contribute to the evolutionary adaptation of M. micrantha. These results could provide a scientific basis for the management of invasive M. micrantha.

Multilocus Sequence Analysis of Selected Housekeeping- and Pathogenicity-Related Genes in Venturia inaequalis.

The relationship between housekeeping and pathogenicity-related genes and virulence or avirulence towards the primary Malus resistance genes (R) has not been previously studied for Venturia inaequalis fungus, the causal agent of apple scab. In this study, the sequences of two housekeeping genes encoding elongation factor alpha (EF-1α) and β-tubulin and two previously unstudied effector genes of V. inaequalis from mannosidase and glucosidase families of 100 strains collected from apple cultivars with Rvi6, Rvi1, and Rvi17 and without known scab resistance genes were submitted to the analyses. Based on the phylogenetic and diversity data, as well as recombination analyses of the sequenced regions, we assessed the phylogenetic relationships and genetic structure of the pathogen within the species and the evolutionary forces that are currently acting upon this microorganism. The topology of the obtained phylograms demonstrates the lack of a relationship between the phylogenetic position of the strain and the host cultivar and the geographical origin or race of the strain. The isolates from different hosts were differentiated but did not form diagnosable, distinct phylogenetic groups. These results suggest that the analyzed genes may be too conserved to reflect the adaptation of pathogens to apple genotypes with different R genes; thus, they do not adequately reflect race discrimination. In contrast, based on variation and gene flow estimation, genetic divergence was observed among strains virulent to apple trees containing Rvi6. The results of this study confirmed a lack of free recombination between strains and demonstrated that the analyzed regions are in linkage disequilibrium and contain non-random polymorphisms associated with the strain.

Genetic connectivity in allopatric seabirds: lack of inferred gene flow between Northern and Southern Buller’s albatross populations (Thalassarche bulleri ssp.)

ABSTRACT The Buller’s albatross species complex is composed of two asynchronously breeding subspecies, the Northern Buller’s albatross (Thalassarche bulleri platei) and Southern Buller’s albatross (Thalassarche bulleri bulleri). The aim of this study was to test for genetic differentiation between Northern and Southern Buller’s albatross and to reassess genetic connectivity between these populations. Genotyping-by-Sequencing (GBS) was used to estimate gene flow and genome-wide divergence using 13 T. b. platei and 40 T. b. bulleri samples. The STACKS de novo and reference guided pipelines were used to call single nucleotide polymorphisms (SNPs) for three data sets: one each for Northern and Southern Buller’s and a third for both taxa together. The number of SNPs in each de novo data set was relatively consistent from 12,148 to 11,898 for Northern and Southern Buller’s albatross collections, respectively. A random subsample of 1000 SNPs from each of the two groups indicated that mean per-site nucleotide diversity and heterozygosity were slightly higher for Northern Buller’s albatross (π = 0.335; HE = 0.322) than for either of the two Southern Buller’s albatross breeding colonies (π = 0.286 and 0.294; HE = 0.275 and 0.288). Both STRUCTURE and discriminant analysis of principal components (DAPC) consistently showed differentiated clusters corresponding to Northern and Southern Buller’s but did not resolve population structure among Southern Buller’s breeding populations. These results indicate that an asynchronous breeding season likely limits gene flow between Northern and Southern Buller’s albatross and have important implications for the taxonomic status of Buller’s albatrosses.

Genetic Diversity Analysis, Population Structure and Gene-flow Estimates among Citrus Macroptera Mont. Collections from Garo Hills, Meghalaya using SPAR Approach

North East India is extremely rich in natural resources and is a biodiversity hotspot. Many plant species, including Citrus are known to have originated from this region. Citus macroptera Mont. is a wild, endangered species which have been found to exist naturally in various parts of this region, including Meghalaya. To access the genetic variability among genotypes and their phylogeny, 30 genotypes of wild C. macroptera Mont. were collected from Garo Hills of Meghalaya. Single primer based DNA markers viz. RAPD, ISSR, DAMD were utilized to ascertain genetic diversity. The percentage polymorphic bands for RAPD, ISSR, DAMD were found to be 97.71%, 94.67% and 100% respectively. ISSR showed the highest values for both RP (7.67) and MI (5.03) highlighting its efficacy in determining genetic variations. A concatenated approach, Single Primer Amplification Reaction (SPAR) was also followed to assess their genetic diversity. Dendogram generated from SPAR data showed that the South-West Garo Hills population is the most recently evolved amongst all others while West Garo Hills collections retain an ancestral position in the evolutionary time-frame. Population genetics parametres such as Gene flow (Nm) and the diversity among populations (GST) were found to be 1.9894 and 0.2009 respectively. Gene flow estimates (Nm>1) suggests appreciable gene flow in the populations. AMOVA data further supported this with high percentage of variations (92%) within populations whereas variations among populations were about 8% only. Shannon’s information index (I) values and Nei’s gene diversity (h) varied between 0.303-0.423and 0.201-0.285 respectively. The use of SPAR method yields a clear and concise picture of the underlying genetic variabilities, and a detailed and comprehensive data analysis will help conceive efficient and sustainable conservation strategies for this important plant.