Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples

Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Multiplexed targeted amplicon sequencing techniques, such as genotyping-in-thousands by sequencing (GT-seq), can provide cost-effective approaches for collecting genetic data from low-quality and quantity DNA samples, making them potentially useful for long-term wildlife monitoring using non-invasive and archival samples. Here, we developed a GT-seq panel as a potential monitoring tool for the American pika (Ochotona princeps) and evaluated its performance when applied to traditional, non-invasive, and archival samples, respectively. Specifically, we optimized a GT-seq panel (307 single nucleotide polymorphisms (SNPs)) that included neutral, sex-associated, and putatively adaptive SNPs using contemporary tissue samples (n = 77) from the Northern Rocky Mountains lineage of American pikas. The panel demonstrated high genotyping success (94.7%), low genotyping error (0.001%), and excellent performance identifying individuals, sex, relatedness, and population structure. We subsequently applied the GT-seq panel to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) collected within the Canadian Rocky Mountains to evaluate its effectiveness. Although the panel demonstrated high efficacy with archival tissue samples (90.5% genotyping success, 0.0% genotyping error), this was not the case for the fecal pellet samples (79.7% genotyping success, 28.4% genotyping error) likely due to the exceptionally low quality/quantity of recovered DNA using the approaches implemented. Overall, our study reinforced GT-seq as an effective tool using contemporary and archival tissue samples, providing future opportunities for temporal applications using historical specimens. Our results further highlight the need for additional optimization of sample and genetic data collection techniques prior to broader-scale implementation of a non-invasive genetic monitoring tool for American pikas.

Population genetics and geometric morphometrics of the freshwater snail Segmentina nitida reveal cryptic sympatric species of conservation value in Europe

Segmentina nitida Müller 1774 is a rare European freshwater snail of drainage ditches and marshland, which has seen a marked decrease in range (~ 80%) over the last 100 years in the UK. This has been attributed to over-dredging of drainage ditches for land management, conversion of grazing marshes to arable farmland, as well as eutrophication. Segmentina nitida is identified as a priority species in the UK Biodiversity Action Plan (UKBAP) that recommends further research to inform reintroduction and translocation for its conservation. We used nuclear markers (microsatellites and ITS2) and a mitochondrial (COI) marker to investigate population structure in S. nitida individuals sampled from Poland, Germany, Sweden, and the UK to identify differences within and between populations. Data based on 2D landmark-based geometric morphometrics of S. nitida shells was used to determine if phenotypic variation followed genetic differentiation. Two distinct genetic lineages of S. nitida were identified in ITS and COI phylogenies as well as cluster analysis of microsatellite markers, one of these lineages was present in eastern Europe (Poland, Sweden- Lineage 2), and one in western Europe (UK, Germany- Lineage 1), with lineages co-occurring in German populations. No genetic admixture was observed in German populations containing both lineages. These two lineages were also distinct in shape, with lineage 2 individuals having significantly wider shells and taller and wider apertures than those in Lineage 1. ~ 85% of shells assigned to the predicted lineage in a discriminant analysis of Procrustes shape coordinates. We infer that S. nitida includes at least one sympatric cryptic species. We discuss the implications of these findings on the conservation status of S. nitida in the UK and Europe.

Diagnostic implications of mycetoma derived from Madurella pseudomycetomatis isolates from Mexico

Background

At the dermatology service of the General Hospital of Mexico City, Mexico, two patients, father and son, with black‐grain mycetoma were seen. The grains were isolated, and the cultured fungi were identified as Madurella mycetomatis based on morphology. Using the M. mycetomatis specific PCR, amplicons of a different size than that of the M. mycetomatis type strain were obtained.

Objective

To determine the causative agent of the two black‐grain mycetoma cases and develop non‐culture‐based diagnostic tools to identify them to the species level.

Methods

The M. mycetomatis specific, the internal transcribed spacer (ITS) region, β‐tubulin (BT) and ribosomal binding protein 2 (RBP2) PCRs were used to confirm the identity of the isolates. Genetic variation was established by amplification fragment length polymorphisms. To determine the antifungal susceptibility profile, the Sensititre™ YeastOne™ assay was used. To develop a species‐specific PCR primers were designed on the sequenced PCR amplicon from the M. mycetomatis specific PCR.

Results

By analyzing the ITS, BT and RBP2 regions the isolates were identified as Madurella pseudomycetomatis. The isolates from father and son were similar but not identical to M. pseudomycetomatis from Venezuela and one from an unknown origin. Madurella pseudomycetomatis isolates were inhibited by itraconazole, posaconazole and voriconazole but showed increased MIC values for amphotericin B and fluconazole. They were not inhibited by the echinocandins and five flucytosine. The two patients were treated with itraconazole resulting in cure for the father while the son was lost to follow‐up. The species‐specific PCR developed for M. pseudomyceotmatis was discriminative and specific.

Conclusion

Madurella pseudomycetomatis is genetically diverse with same susceptibility profile as M. mycetomatis and causes eumycetoma in Latin America. The M. pseudomycetomatis specific PCR can be used to identify this causative agent to the species level; however, this needs to be validated in an endemic setting.

Testing the Effect of Mountain Ranges as a Physical Barrier to Current Gene Flow and Environmentally Dependent Adaptive Divergence in Cunninghamia konishii (Cupressaceae)

Populations can be genetically isolated by differences in their ecology or environment that hampered efficient migration, or they may be isolated solely by geographic distance. Moreover, mountain ranges across a species’ distribution area might have acted as barriers to gene flow. Genetic variation was quantified using amplified fragment length polymorphism (AFLP) and 13 selective amplification primer combinations used generated a total of 482 fragments. Here, we tested the barrier effects of mountains on gene flow and environmentally dependent local adaptation of Cunninghamia konishii occur in Taiwan. A pattern of genetic isolation by distance was not found and variation partitioning revealed that environment explained a relatively larger proportion of genetic variation than geography. The effect of mountains as barriers to genetic exchange, despite low population differentiation indicating a high rate of gene flow, was found within the distribution range of C. konishii. Twelve AFLP loci were identified as potential selective outliers using genome-scan methods (BAYESCAN and DFDIST) and strongly associated with environmental variables using regression approaches (LFMM, Samβada, and rstanarm) demonstrating adaptive divergence underlying local adaptation. Annual mean temperature, annual precipitation, and slope could be the most important environmental factors causally associated with adaptive genetic variation in C. konishii. The study revealed the existence of physical barriers to current gene flow and environmentally dependent adaptive divergence, and a significant proportion of the rate of gene flow may represent a reflection of demographic history.

Analysis of genetic polymorphisms and tropism in East African Leishmania donovani by Amplified Fragment Length Polymorphism and kDNA minicircle sequencing

Visceral leishmaniasis (VL), the most severe form of leishmaniasis, is caused by Leishmania donovani. In addition to fatal VL, these parasites also cause skin diseases in immune-competent and -suppressed people, post-kala azar dermal leishmaniasis (PKDL) and HIV/VL co-infections, respectively. Genetic polymorphism in 36 Ethiopian and Sudanese L. donovani strains from VL, PKDL and HIV/VL patients was examined using Amplified Fragment Length Polymorphism (AFLP), kDNA minicircle sequencing and Southern blotting. Strains were isolated from different patient tissues: in VL from lymph node, spleen or bone marrow; and in HIV/VL from skin, spleen or bone marrow. When VL and PKDL strains from the same region in Sudan were examined by Southern blotting using a DNA probe to the L. donovani 28S rRNA gene only minor differences were observed. kDNA sequence analysis distributed the strains in no particular order among four clusters (A - D), while AFLP analysis grouped the strains according to geographical origin into two major clades, Southern Ethiopia (SE) and Sudan/Northern Ethiopia (SD/NE). Strains in the latter clade were further divided into subpopulations by zymodeme, geography and year of isolation, but not by clinical symptoms. However, skin isolates showed significantly (p < 0.0001) fewer polymorphic AFLP fragments (average 10 strains = 348.6 ± 8.1) than VL strains (average 26 strains = 383.5 ± 3.8).

Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages

DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.

Population genetic structure of the Culex pipiens (Diptera: Culicidae) complex, vectors of West Nile virus, in five habitats

BACKGROUND

The Culex pipiens complex consists of several morphologically similar, closely related species. In the United States, Cx. pipiens L. is distributed North of 39° latitude, while Cx. quinquefasciatus Say occurs South of 36° latitude; a hybrid zone occurs between these two latitudes including in the Central Valley of California. Members of the Cx. pipiens complex and their hybrids are vectors for West Nile virus (WNv). Hybrid offspring of Cx. pipiens and Cx. quinquefasciatus have been found to have enhanced transmission rates of WNv over those of pure populations of each species. We investigated whether hybrids of Cx. pipiens and Cx. quinquefasciatus occurred more frequently in any of five habitats which were dairies, rural, suburban, and urban areas, and wetlands. In addition, the proportion of alleles unique to Cx. quinquefasciatus and Cx. pipiens found in each habitat-associated population were determined.

METHODS

Amplified fragment length polymorphism (AFLP) markers were used to compare the population structure of the Cx. pipiens complex from each habitat to geographically distant populations considered pure Cx. pipiens and Cx. quinquefasciatus. Structure analyses were used to assign individuals to either Cx. pipiens, Cx. quinquefasciatus, or hybrids of the Cx. pipiens complex. The ancestry of hybrids (F1, F2, or backcrossed) in relation to the two parent populations was estimated for each Central Valley population. Loci unique to the pure Cx. pipiens population and the pure Cx. quinquefasciatus population were determined. The proportion of loci unique to Cx. pipiens and Cx. quinquefasciatus populations were subsequently determined for each population from the five Merced habitats and from the Oroville California population. The unique loci found in Merced populations and not in Cx. pipiens or Cx. quinquefasciatus were also determined. A principal components analysis was run, as was an analysis to determine loci under putative selection.

RESULTS

The Structure Harvester analysis found K = 3, and the Culex pipiens complex mosquitoes formed a genetic cluster distinct from Cx. quinquefasciatus and Cx. pipiens. Individuals collected from each habitat were nearly all hybrids. However, Cx. pipiens complex collected near dairies had more individuals categorized as Cx. pipiens than collections from the other habitats. None of the mosquitoes collected in Merced or Oroville were considered pure Cx. quinquefasciatus. Significant genetic divergence was detected among the Cx. pipiens complex from the five habitats in Merced; Cx. pipiens complex mosquitoes from dairies were divergent from the urban and suburban populations. New Hybrids analysis found that individuals from all five Merced habitat-associated populations and the population from Oroville were primarily categorized as hybrids backcrossed to the Cx. pipiens population. Finally, all five habitat-associated populations shared more alleles with Cx. pipiens than with Cx. quinquefasciatus, even though the pure Cx. quinquefasciatus population was more geographically proximate to Merced. Results from the principal component analysis, and the occurrence of several unique loci in Merced populations, suggest that Cx. pipiens molestus may also occur in the habitats sampled.

CONCLUSIONS

Nearly all mosquitoes in the five habitats in Merced in the Central Valley of California area were hybrids of Cx. pipiens and Cx. quinquefasciatus, consisting of hybrids backcrossed to Cx. pipiens. Habitat-associated mosquitoes collected near dairies had more individuals consisting of pure Cx. pipiens, and no mosquitoes from Merced or Oroville CA classified as pure Cx. quinquefasciatus. The genetic distances among Cx. pipiens and Cx. quinquefasciatus, and hybrid populations agree with previous studies using other molecular markers. Cx. pipiens hybrids in Merced shared more alleles with Cx. pipiens than Cx. quinquefasciatus which was unexpected, since Merced is geographically closer to the northern limit of Cx. quinquefasciatus distribution. Culex pipiens molestus may occur in more habitats in the Central Valley than previously suspected, which warrants further investigation. Future studies could investigate the vector competence of hybrids backcrossed to either Cx. pipiens or Cx. quinquefasciatus parent for their ability to transmit West Nile virus.

Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2–9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, F_ST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (Φ_PT = 0.252–0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.

Occasional hybridization between a native and invasive Senecio species in Australia is unlikely to contribute to invasive success

Background

Hybridization between native and invasive species can facilitate introgression of native genes that increase invasive potential by providing exotic species with pre-adapted genes suitable for new environments. In this study we assessed the outcome of hybridization between native Senecio pinnatifolius var. pinnatifolius A.Rich. (dune ecotype) and invasive Senecio madagascariensis Poir. to investigate the potential for introgression of adaptive genes to have facilitated S. madagascariensis spread in Australia.

Methods

We used amplified fragment length polymorphisms (141 loci) and nuclear microsatellites (2 loci) to genotype a total of 118 adults and 223 seeds from S. pinnatifolius var.pinnatifolius and S. madagascariensis at one allopatric and two shared sites. We used model based clustering and assignment methods to establish whether hybrid seed set and mature hybrids occur in the field.

Results

We detected no adult hybrids in any population. Low incidence of hybrid seed set was found at Lennox Head where the contact zone overlapped for 20 m (6% and 22% of total seeds sampled for S. pinnatifolius var. pinnatifolius and S. madagascariensis respectively). One hybrid seed was detected at Ballina where a gap of approximately 150 m was present between species (2% of total seeds sampled for S. madagascariensis).

Conclusions

We found no evidence of adult hybrid plants at two shared sites. Hybrid seed set from both species was identified at low levels. Based on these findings we conclude that introgression of adaptive genes from S. pinnatifolius var. pinnatifolius is unlikely to have facilitated S. madagascariensis invasions in Australia. Revisitation of one site after two years could find no remaining S. pinnatifolius var. pinnatifolius, suggesting that contact zones between these species are dynamic and that S. pinnatifolius var. pinnatifolius may be at risk of displacement by S. madagascariensis in coastal areas.

Population structure within the one-dimensional range of a coastal plain katydid

Biogeography plays a significant role in species’ dispersal, and in turn population structure, across the landscape. The North American katydid Neoconocephalus melanorhinus belongs to a genus with high mobility. Unlike other members of the genus, N. melanorhinus is a salt marsh specialist restricted to a narrow corridor along the Atlantic and Gulf coasts. In addition, their range crosses at least one known biogeographic barrier and possesses biogeographic characteristics of the stepping-stone as well as the hierarchical island model of dispersal. Using AFLP markers we searched for areas that conform to the predictions of isolation by distance and for areas of non-uniform increases in genetic variance, indicative of isolation by barrier. We found significant genetic differentiation between all twelve sampled sites. Isolation by distance was the predominant pattern of variation across their range. In addition, we saw possible evidence of two biogeographic barriers to gene flow, one at the Atlantic-Gulf divide and the other along the Gulf coast. We also observed a change in body size across the range. Body size, as measured by male hind femur length, correlated closely with latitude, a possible indication of differential selection across the species range.

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.

Environmental (in)dependence of a hybrid zone: Insights from molecular markers and ecological niche modeling in a hybrid zone of Origanum (Lamiaceae) on the island of Crete

The role of environment and the relative significance of endogenous versus exogenous selection in shaping hybrid zones have been crucial issues in the studies of hybridization. Recent advances in ecological niche modeling (ENM) offer new methodological tools, especially in combination with the genotyping of individuals in the hybrid zone. Here, we study the hybrid zone between the widely known spices Origanum onites and Origanum vulgare ssp. hirtum in Crete. We analyze the genetic structure of both parental taxa and their hybrid Origanum × intercendens using AFLP markers on 15 sympatric and 12 allopatric populations and employ ecological niche modeling and niche similarity tests to study their niche patterns. We complement these analyses with seed viability measurements. Our study revealed that the hybridizing taxa O. onites and O. vulgare ssp. hirtum and the resulting genotypic classes showed geographical and environmental niche similarities based on the predictions of ENMs and the subsequent similarity tests. The occurrence of the hybrid zone is not directly dependent on environmental factors which favor the fitness of the hybrid compared to the parental taxa, but rather on aspects such as historical factors and management practices, which may contribute to the localization and maintenance of the contact zone between parental species. Our results suggest that if a minimum required niche differentiation between genotypic classes is not achieved, environmental dependence might not have a prominent role on the outcome of the hybridization.

Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex

PREMISE OF THE STUDY

Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions.

METHODS

We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs).

KEY RESULTS

Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation.

CONCLUSIONS

Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.

Simple regression models as a threshold for selecting AFLP loci with reduced error rates

Background

Amplified fragment length polymorphism is a popular DNA marker technique that has applications in multiple fields of study. Technological improvements and decreasing costs have dramatically increased the number of markers that can be generated in an amplified fragment length polymorphism experiment. As datasets increase in size, the number of genotyping errors also increases. Error within a DNA marker dataset can result in reduced statistical power, incorrect conclusions, and decreased reproducibility. It is essential that error within a dataset be recognized and reduced where possible, while still balancing the need for genomic diversity.

Results

Using simple regression with a second-degree polynomial term, a model was fit to describe the relationship between locus-specific error rate and the frequency of present alleles. This model was then used to set a moving error rate threshold that varied based on the frequency of present alleles at a given locus. Loci with error rates greater than the threshold were removed from further analyses. This method of selecting loci is advantageous, as it accounts for differences in error rate between loci of varying frequencies of present alleles. An example using this method to select loci is demonstrated in an amplified fragment length polymorphism dataset generated from the North American prairie species big bluestem. Within this dataset the error rate was reduced from 12.5% to 8.8% by removal of loci with error rates greater than the defined threshold. By repeating the method on selected loci, the error rate was further reduced to 5.9%. This reduction in error resulted in a substantial increase in the amount of genetic variation attributable to regional and population variation.

Conclusions

This paper demonstrates a logical and computationally simple method for selecting loci with a reduced error rate. In the context of a genetic diversity study, this method resulted in an increased ability to detect differences between populations. Further application of this locus selection method, in addition to error-reducing methodological precautions, will result in amplified fragment length polymorphism datasets with reduced error rates. This reduction in error rate should result in greater power to detect differences and increased reproducibility.