Intra-individual Polymorphism Research Articles

Intra-individual polymorphisms in the mitochondrial COI gene of tick-killing Ixodiphagus wasps parasitizing Haemaphysalis flava ticks.

Ixodid ticks are significant vectors of pathogens affecting both humans and animals. Biological control with natural enemies represents a sustainable tool for managing ticks. However, there is a substantial lack of knowledge about the natural enemies of ticks. Wasps of the genus Ixodiphagus (Encyrtidae) are currently the only known tick-specific parasitoids. While these wasps have been sporadically recorded worldwide, their presence in Eastern Asia is poorly documented. In this study, we investigated the occurrence of Ixodiphagus wasps in field-collected ticks reared on rabbits under laboratory conditions. Ticks were collected from the Hokkaido, Hokuriku, Chugoku, Shikoku, and Kyushu regions in Japan. Out of 1,933 Haemaphysalis ticks attached to rabbits, adult wasps emerged from 15 engorged ticks. All the ticks from which wasps emerged were morphologically and molecularly identified as Haemaphysalis flava. Additionally, wasp DNA was detected in unfed H. flava nymphs using a newly designed Ixodiphagus-specific PCR assay. Among nine experimental sites in the Chugoku region, Ixodiphagus wasps were detected at three sites, with parasitism rates ranging from 1.8% to 8.1%. Finally, the mitochondrial COI genes of four wasp and two tick samples were characterized using shotgun sequencing, direct sequencing and in-fusion cloning approaches. Multiple intra-individual polymorphisms were observed in all the tested samples. Further studies are needed to investigate the relationship between Ixodiphagus wasps and Ixodid ticks. An increased understanding of these parasitoid wasps could contribute to future biological control measures against ticks.

Nuclear DNA segments homologous to mitochondrial DNA are obstacles for detecting heteroplasmy in sugar beet (Beta vulgaris L.).

Heteroplasmy, the coexistence of multiple mitochondrial DNA (mtDNA) sequences in a cell, is well documented in plants. Next-generation sequencing technology (NGS) has made it feasible to sequence entire genomes. Thus, NGS has the potential to detect heteroplasmy; however, the methods and pitfalls in heteroplasmy detection have not been fully investigated and identified. One obstacle for heteroplasmy detection is the sequence homology between mitochondrial-, plastid-, and nuclear DNA, of which the influence of nuclear DNA segments homologous to mtDNA (numt) need to be minimized. To detect heteroplasmy, we first excluded nuclear DNA sequences of sugar beet (Beta vulgaris) line EL10 from the sugar beet mtDNA sequence. NGS reads were obtained from single plants of sugar beet lines NK-195BRmm-O and NK-291BRmm-O and mapped to the unexcluded mtDNA regions. More than 1000 sites exhibited intra-individual polymorphism as detected by genome browsing analysis. We focused on a 309-bp region where 12 intra-individual polymorphic sites were closely linked to each other. Although the existence of DNA molecules having variant alleles at the 12 sites was confirmed by PCR amplification from NK-195BRmm-O and NK-291BRmm-O, these variants were not always called by six variant-calling programs, suggesting that these programs are inappropriate for intra-individual polymorphism detection. When we changed the nuclear DNA reference, a numt absent from EL10 was found to include the 309-bp region. Genetic segregation of an F2 population from NK-195BRmm-O x NK-291BRmm-O supported the numt origin of the variant alleles. Using four references, we found that numt detection exhibited reference dependency, and extreme polymorphism of numts exists among sugar beet lines. One of the identified numts absent from EL10 is also associated with another intra-individual polymorphic site in NK-195mm-O. Our data suggest that polymorphism among numts is unexpectedly high within sugar beets, leading to confusion about the true degree of heteroplasmy.

Variations in the conserved 18S and 5.8S reveal the putative pseudogenes in 18S-ITS1-5.8S rDNA of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae)

Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.

Evidence of hybridization between Galatella villosa and G. linosyris, and a taxonomic reappraisal of the hybrid G. ×subvillosa

At the westernmost distribution of the steppe herbaceous plant, Galatella villosa, in Hungary, Serbia and Ukraine, we recently observed intermediate specimens between this species and its close relative, G. linosyris. We were able to demonstrate the hybrid origin of these individuals by sequencing the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS) region and checking additive polymorphism in the hybrids. In addition, examination of the maternally inherited plastid regions (trnH-psbA and trnL-trnF intergenic spacers) revealed that G. villosa is likely to be the maternal parent in the Hungarian and Ukrainian populations and G. linosyris in the Serbian population. The intermediate forms produced only sterile seeds. The alleged hybrid between the above two species has already been described as G. ×subvillosa based on a very brief diagnosis. Still, the analysis of the morphological characters using linear discriminant analyses clearly separated the holotype of G. ×subvillosa from individuals of G. linosyris × G. villosa. The latter appeared to be morphologically intermediate between populations of G. villosa and G. linosyris. Contrary to the originally stated hybrid origin of the type plants of G. ×subvillosa, morphological evidence indicates the involvement of G. divaricata not G. linosyris. The hybrid G. linosyris × G. villosa is thus described here, as a new nothospecies G. ×feketegaborii. This study highlights the power of easily available molecular phylogenetic tools for demonstrating the hybrid origin of plants and illustrates how additive polymorphism can be distinguished from other types of intraindividual polymorphism in nuclear DNA sequences.

Species composition, geographical distribution and seasonal abundance of the Anopheles maculipennis complex along the Upper Rhine, Germany.

Between May and September 2016, mosquitoes were collected on a biweekly basis at 55 locations with CO2-baited encephalitis vector surveillance traps along the Upper Rhine, Germany, to evaluate the species composition, geographical distribution and abundance of the Anopheles maculipennis complex, some members of this complex being considered vectors of historical malaria in Germany. A total of 2115 Anopheles maculipennis complex specimens were collected during the season, of which a sample of 1252 individuals was determined to species level by amplification of species-specific internal transcribed spacer 2 (ITS2) sequences. A total of 856 individuals of Anopheles daciae (68.37%), 394 Anopheles messeae (31.47%) and 2 Anopheles maculipennis s.s. (0.16%) were recorded. The number and proportion of A. daciae was remarkably higher in the northern meandering zone of the Upper Rhine (843 specimens, 79.90%), than in the more canalised southern furcation zone where A. messeae with 183 collected specimens represented 92.89% of 197 classified individuals. The average number of collected A. maculipennis s.l. individuals per trapping site was 38.45, equalling 0.64% of the total mosquito collection. Despite an increase in imported malaria cases, this comparatively low abundance of A. maculipennis s.l. may indicate a low risk of endemic malaria transmission by members of the A. maculipennis complex today. The proportionally dominance of A. daciae suggests that this species could be suspected the main historical vector of malaria in the Upper Rhine region. Sequence analyses of the ITS2 fragment revealed intraindividual polymorphisms within 3 of 5 diagnostic nucleotides in all specimens of A. daciae, raising the question if additional loci should be considered, to gain further insight into the taxonomical relation to A. messeae.

Unraveling heteroplasmy patterns with NOVOPlasty.

Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been studied across different scientific fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. Before the development of massive parallel sequencing (MPS), most studies of mitochondrial genome variation were limited to short fragments and to heteroplasmic variants associated with a relatively high frequency (>10%). By utilizing ultra-deep sequencing, it has now become possible to uncover previously undiscovered patterns of intra-individual polymorphisms. Despite these technological advances, it is still challenging to determine the origin of the observed intra-individual polymorphisms. We therefore developed a new method that not only detects intra-individual polymorphisms within mitochondrial and chloroplast genomes more accurately, but also looks for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method is capable of detecting heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the sequence for each mitochondrial haplotype (allele). The method is implemented in our open source software NOVOPlasty that can be downloaded at https://github.com/ndierckx/NOVOPlasty.

Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas

AbstractFew botanical studies have explored the potential of nuclear ribosomal DNA (nrDNA) and mitochondrial DNA (mtDNA) data obtained through genome skimming for phylogeny reconstruction. Here, we analyzed the phylogenetic information included in the nrDNA and mtDNA of 44 species of the “Adenocalymma‐Neojobertia” clade (Bignoniaceae). To deal with intraindividual polymorphisms within the nrDNA, different coding schemes were explored through the analyses of four datasets: (i) “nrDNA contig,” with base call following the majority rule; (ii) “nrDNA ambiguous,” with ambiguous base calls; (iii) “nrDNA informative,” with ambiguities converted to multistate characters; and, (iv) “mitochondrial,” with 39 mitochondrial genes. Combined analyses using the nrDNA and mtDNA data and previously published “plastid” datasets were also conducted. Trees were obtained using Maximum Likelihood and Bayesian criteria. The congruence among genomes was assessed. The nrDNA datasets were shown to be highly polymorphic within individuals, while the “mitochondrial” dataset was the least informative, with 0.36% of informative bases within the ingroup. The topologies inferred using the nrDNA and mtDNA datasets were broadly congruent with the tree derived from the analyses of the “plastid” dataset. The topological differences recovered were generally poorly supported. The topology that resulted from the analyses of the “combined” dataset largely resembles the “plastid” tree. These results highlight limitations of nuclear ribosomal DNA and mitochondrial genes for phylogeny reconstruction obtained through genome skimming and the need to include more data from both genomes. The different topologies observed among genomes also highlight the importance of exploring data from various genomes in plant phylogenetics.

Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses.

Genetic associations between mitochondrial DNA (mtDNA) and economic traits have been widely reported for pigs, which indicate the importance of mtDNA. However, studies on mtDNA heteroplasmy in pigs are rare. Next generation sequencing (NGS) methodologies have emerged as a promising genomic approach for detection of mitochondrial heteroplasmy. Due to the short reads, flexible bioinformatic analyses and the contamination of nuclear mitochondrial sequences (NUMTs), NGS was expected to increase false-positive detection of heteroplasmy. In this study, Sanger sequencing was performed as a gold standard to detect heteroplasmy with a detection sensitivity of 5% in pigs and then one whole-genome sequencing method (WGS) and two mtDNA enrichment sequencing methods (Capture and LongPCR) were carried out. The aim of this study was to determine whether mitochondrial heteroplasmy identification from NGS data was affected by NUMTs. We find that WGS generated more false intra-individual polymorphisms and less mapping specificity than the two enrichment sequencing methods, suggesting NUMTs indeed led to false-positive mitochondrial heteroplasmies from NGS data. In addition, to accurately detect mitochondrial diversity, three commonly used tools-SAMtools, VarScan and GATK-with different parameter values were compared. VarScan achieved the best specificity and sensitivity when considering the base alignment quality re-computation and the minimum variant frequency of 0.25. It also suggested bioinformatic workflow interfere in the identification of mtDNA SNPs. In conclusion, intra-individual polymorphism in pig mitochondria from NGS data was confused with NUMTs, and mtDNA-specific enrichment is essential before high-throughput sequencing in the detection of mitochondrial genome sequences.

Intra-individual variation and transcribed pseudogenes in the ribosomal ITS1-5.8S-ITS2 rDNA of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae)

The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). Typically, rDNA is thought to be evolved in a strict concerted evolution pattern, in which show little or even no variations within species, while sequence diversity between species or higher taxa. However, in the present study, we reported a high level of intra-individual polymorphism of ITS1-5.8S-ITS2 rDNA in the genome of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae), suggesting it conformed a non-concerted evolutionary pattern. Three divergent type sequences (Type A, B, and C) differing in length, GC content, secondary structure stability and minimum free energy coexisted in the genome of each studied individual. According to the particular features of ribosomal pseudogenes, Type B and Type C sequences were postulated as pseudogenes. Expression analyses gave clear evidence that both the functional gene and pseudogenes were abundantly transcribed, indicating expression is not an applicable criterion for identifying ribosomal pseudogenes. These findings will enrich useful data for the studies on rDNA evolution in flatfishes, as well as provide fresh insight on the transcribed ribosomal pseudogenes and further consideration of the definition of ribosomal pseudogene.

Genetic polymorphism of Japanese cultivated Rheum species in the internal transcribed spacer region of nuclear ribosomal DNA.

In order to develop new domestic production of Rhei Rhizoma (RR) from Rheum specimens cultivated in the Sugadaira Medicinal Plant Cultivation Test Field (SMPCF), the ITS sequences of 12 SMPCF specimens and Chinese Rheum specimens of four species, as well as RR samples produced in North Korea, China and Japan, were determined by subcloning and their sequences were compared. As the ITS sequences of 10 SMPCF specimens showed significant intra-individual polymorphism, identification of pseudogenes was conducted by detecting the three motifs of the 5.8S sequence and the stability of the 5.8S secondary structure. Approximately 46% of sequences obtained from the SMPCF specimens were putative pseudogenes. The maximum likelihood tree based on ITS sequences showed three main groups-the outer group and inner clusters I and II; clones from 10 SMPCF specimens including putative pseudogenes belonged to the outer group. Cluster I was composed of two clades, one including clones from R. officinale specimens and R. palmatum-derived samples with matK genotype Rp9, and another including clones from R. coreanum-derived samples. Cluster II consisted of three clades, one including clones from R. palmatum specimens with genotype Rp5, another including clones mainly from R. tanguticum specimens with genotype Rt4, and the third including clones from R. palmatum or R. tanguticum specimens with various matK genotypes. Clones from SMPCF specimen RC5 showed a close relationship with those from R. tanguticum specimens with matK genotype Rt4, whereas those from specimen RC9 related to R. coreanum-derived samples. As a result, specimens RC5 and RC9 were considered as candidates for the development of domestic RR.

Intra‐individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.

Polymorphism and evolution of ribosomal DNA in tea (Camellia sinensis, Theaceae)

Ribosomal DNA (rDNA) repeats often exhibit a high level of within-species homogeneity, but intra-individual polymorphism of rDNA has been found in Camellia species. In order to reveal the evolutionary pattern of rDNA repeats in tea [Camellia sinensis (L.) O. Kuntze], we identified the 45S rDNA loci, estimated their copy number, and cloned partial regions of them from different PCR products and from digested genomic DNA. The results show that there are 3 loci (6 sites) containing 45S rDNA in the tea genome; they are located at the ends of the short arms of 6 chromosomes and consist of a maximum of ∼6500 repeat units. On one hand, 164 sequences of the 26S rDNA cloned from PCR products contained 147 haplotypes, consisting of 62% pseudogenes, 24% putative functional genes, and 14% PCR-mediated recombinants, suggesting that the 45S rDNA of tea maintains an extremely high level of polymorphism and divergence; on the other hand, rDNA fragments cloned directly from genomic DNA exhibited a very high level of homogeneity: only one of 33 rDNA fragments was from a pseudogene. These results demonstrate that although over 60% of the 26S rDNA sequences identified in PCR products belong to pseudogenes, most 45S rDNA repeats are functional genes and have undergone concerted evolution. In this study, strong PCR bias and PCR-mediated recombination greatly increased the apparent proportion of pseudogenes in PCR products. Phylogenetic analysis and genetic divergence values for 26S rDNA sequences obtained in this study show that many pseudogenes have originated independently from functional genes at different times, and despite thus escaping from concerted evolution, they have failed to be eliminated from the tea genome over a long period, some of them having even produced addition copies by rapid expansion. Importantly, our study suggests that in order to determine the true pattern of evolution of rDNA it is necessary to combine data from more than one method rather than relying only on sequences from PCR products.

강도다리(Platichthys stellatus)에 대한 세포유전학적 연구

【Cytogenetic analysis was conducted to obtain basic information for chromosome manipulation of starry flounder Platichthys stellatus. Nuclear surface area and volume of erythrocyte were $7.60{\pm}0.93{\mu}m^2$ and $12.80{\pm}1.75{\mu}m^3$ , respectively. The haploid DNA content of the species was 0.66 pg/haploid cell which correspond to 93% of olive flounder Paralichthys olivaceus. A karyotype analysis was also carried out with the species using conventional staining and Ag-NOR banding techniques. It was consisted of 48 acrocentric chromosomes and inter-sex or intra-individual polymorphism was not detected in all specimens analyzed. The NOR regions, appearing a terminal position of the short arm of the smallest acrocentric pairs.】

Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing.

Metabarcoding is a powerful tool for exploring microbial diversity in the environment, but its accurate interpretation is impeded by diverse technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-individual polymorphism) that remain poorly understood. To help interpret environmental metabarcoding datasets, we investigated the intracellular diversity of the V4 and V9 regions of the 18S rRNA gene from Acantharia and Nassellaria (radiolarians) using 454 pyrosequencing. Individual cells of radiolarians were isolated, and PCRs were performed with generalist primers to amplify the V4 and V9 regions. Different denoising procedures were employed to filter the pyrosequenced raw amplicons (Acacia, AmpliconNoise, Linkage method). For each of the six isolated cells, an average of 541 V4 and 562 V9 amplicons assigned to radiolarians were obtained, from which one numerically dominant sequence and several minor variants were found. At the 97% identity, a diversity metrics commonly used in environmental surveys, up to 5 distinct OTUs were detected in a single cell. However, most amplicons grouped within a single OTU whereas other OTUs contained very few amplicons. Different analytical methods provided evidence that most minor variants forming different OTUs correspond to PCR and sequencing artifacts. Duplicate PCR and sequencing from the same DNA extract of a single cell had only 9 to 16% of unique amplicons in common, and alignment visualization of V4 and V9 amplicons showed that most minor variants contained substitutions in highly-conserved regions. We conclude that intracellular variability of the 18S rRNA in radiolarians is very limited despite its multi-copy nature and the existence of multiple nuclei in these protists. Our study recommends some technical guidelines to conservatively discard artificial amplicons from metabarcoding datasets, and thus properly assess the diversity and richness of protists in the environment.

Intra-individual ITS polymorphism and hybridization in Pulmonaria obscura Dumort. and Pulmonaria angustifolia L. (Boraginaceae)

Internal transcribed spacer (ITS) is used as a molecular marker in most phylogenetical analyses in Boraginaceae, an unplaced group in the current angiosperm phylogeny. However, there is no knowledge on intra-individual polymorphism of ITS in Boraginaceae. Difficulties in PCR and sequencing of ITS in Pulmonaria species mentioned in the literature may be seen as indirect evidence of intra-individual polymorphism. This study aims to detect intra-individual polymorphism of ITS1–5.8S–ITS2 in rare species Pulmonariaangustifolia L. and common species Pulmonariaobscura Dumort. Cloning of ITS sequences of P. angustifolia, P. obscura and putative hybrid specimens from mixed population showed intra-individual polymorphism of ITS1–5.8S–ITS2 in all specimens, whereas most of them also contained pseudogenic sequences. Intra-individual sequence divergence of ITS1 and ITS2 spacers was similar in the P. angustifolia and mixed population and significantly higher than in P. obscura. P. angustifolia specimens had nucleotide polymorphisms characteristic to both P. angustifolia and P. obscura and part of P. angustifolia sequences clustered into mostly P. obscura clade on the neighbour-joining trees based on ITS1 sequence and ITS2 sequence and structure data. These results suggest a hybrid origin of all P. angustifolia populations studied. Thus, outbreeding depression is a likely explanation for the decline in populations near the northern border of distribution area of rare species P. angustifolia. Hybrid origin of the whole P. angustifolia is also probable; the central population from Poland showed a similar pattern of polymorphism as distribution edge populations.

ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex.

The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogenetic network analyses indicate additivity of parental ITS variants in both synthetic and natural hybrids. The triploid synthetic hybrids are genetically much closer to their maternal progenitors, probably due to ploidy dosage effects, although exhibiting a paternal-like leaf morphology. The natural hybrids are genetically and morphologically closer to the putative paternal progenitor species. Secondary structures of ITS1-5.8S-ITS2 were rather conserved in all taxa. The observed similarities in ITS polymorphisms suggest that the natural apomict R. variabilis is an ancient hybrid of the diploid sexual species R. notabilis and the sexual species R. cassubicifolius. The additivity pattern shared by R. variabilis and the synthetic hybrids supports an evolutionary and biogeographical scenario that R. variabilis originated from ancient hybridization. Concerted evolution of ITS copies in R. variabilis is incomplete, probably due to a shift to asexual reproduction. Under the condition of comprehensive inter- and intraspecific sampling, ITS polymorphisms are powerful for elucidating reticulate evolutionary histories.

Testing a Hypothesis of Intergeneric Allopolyploidy in Vine Cacti (Cactaceae: Hylocereeae)

Abstract Allopolyploidy is common in angiosperms, but only rarely involves different genera. One hypothesized case of intergeneric allopolyploidy is Hylocereus megalanthus, a member of Cactaceae tribe Hylocereeae, a group of vine cactus species, some of which are known for their edible fruits (“pitahaya” or “dragon fruit”). This polyploid species has been interpreted as morphologically intermediate between Hylocereus and Selenicereus. Plastid and nuclear ribosomal DNA ITS sequences from all H. megalanthus individuals sampled are either identical (plastid), or form a monophyletic clade despite considerable intraindividual polymorphism (ITS). Plastid and ITS phylogenies both show H. megalanthus nested within a well-supported Hylocereus, which in turn is nested within a paraphyletic Selenicereus. The absence of more than one lineage of ITS in H. megalanthus is consistent with autopolyploidy, but could be due to inter-homoeologue concerted evolution. Numerous low-copy nuclear genes were tested for utility in ...

Molecular evidence of cryptic speciation, historical range expansion, and recent intraspecific hybridization in the Neotropical seasonal forest tree Cedrela fissilis (Meliaceae)

Molecular phylogeography can lead to a better understanding of the interaction between past climate events, large-scale vegetation shifts, and the evolutionary history of Neotropical seasonal forests. The endangered timber tree species Cedrela fissilis is associated with seasonal forests and occurs throughout South America. We sampled C. fissilis from 56 sites across the species’ range in Brazil and Bolivia and obtained sequence data for nuclear and chloroplast DNA. Most specimens (149 out of 169) exhibited intraindividual polymorphism for the nuclear internal transcribed spacer (ITS). Cloning and an array of complementary sequence analyses indicated that the multiple copies of ITS were functional paralogs – concerted evolution in C. fissilis appeared to be incomplete. Independent Bayesian analyses using either ITS or cpDNA data revealed two separate phylogenetic lineages within C. fissilis that corresponded to populations located in separate geographic regions. The divergence occurred in the Early Pliocene and Late Miocene. We argue that climate-mediated events triggered dispersal events and split ancestral populations into at least two large refugial areas of seasonal forest that were located to the east and west of the present day Cerrado. Upon recent climate amelioration, formerly isolated lineages reconnected and intraspecific hybridization gave rise to intraindividual polymorphism and incomplete concerted evolution in C. fissilis.

DNA barcodes for Mexican Cactaceae, plants under pressure from wild collecting

DNA barcodes could be a useful tool for plant conservation. Of particular importance is the ability to identify unknown plant material, such as from customs seizures of illegally collected specimens. Mexican cacti are an example of a threatened group, under pressure because of wild collection for the xeriscaping trade and private collectors. Mexican cacti also provide a taxonomically and geographically coherent group with which to test DNA barcodes. Here, we sample the matK barcode for 528 species of Cactaceae including approximately 75% of Mexican species and test the utility of the matK region for species-level identification. We find that the matK DNA barcode can be used to identify uniquely 77% of species sampled, and 79-87% of species of particular conservation importance. However, this is far below the desired rate of 95% and there are significant issues for PCR amplification because of the variability of primer sites. Additionally, we test the nuclear ITS regions for the cactus subfamily Opuntioideae and for the genus Ariocarpus (subfamily Cactoideae). We observed higher rates of variation for ITS (86% unique for Opuntioideae sampled) but a much lower PCR success, encountering significant intra-individual polymorphism in Ariocarpus precluding the use of this marker in this taxon. We conclude that the matK region should provide useful information as a DNA barcode for Cactaceae if the problems with primers can be addressed, but matK alone is not sufficiently variable to achieve species-level identification. Additional complementary regions should be investigated as ITS is shown to be unsuitable.

High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes

Molecular studies of six species from the ancient extant seed plant Cycas, covering a wide range of its morphological diversity and all major areas of distribution, revealed a high level of intra-individual polymorphism of the internal transcribed spacer (ITS1, 5.8S, and ITS2) region, indicative of incomplete nrDNA concerted evolution. Through a range of comparisons of sequence characteristics to functional cDNA ITS copies, including sequence length and substitution variation, GC content, secondary structure stability, the presence of a conserved motif in the 5.8S gene, and evolutionary rates, the PCR amplified divergent genomic DNA ITS paralogs were identified as either putative pseudogenes, recombinants or functional paralogs. This incomplete ITS concerted evolution may be linked to the high number of nucleolar organizer regions in the Cycas genome, and the incomplete lineage sorting due to recent species divergence in the genus. Based on the distribution of a 14bp deletion, an early evolutionary origin of the pseudogenes is indicated, possibly predating the diversification of Cycas. Due to their early origin combined with the unconstraint evolution of the ITS region in pseudogenes, they accumulate high levels of homoplastic mutations. This leads to random relationships among the pseudogenes due to long-branch attractions, whereas the phylogenetic relationships inferred from the functional ITS paralogs grouped the sequences in species specific clades (except for C. circinalis and C. rumphii). The findings of our extensive study will have a wide significance, for the evolution of these molecular sequences, and their utilization as a major marker for reconstructing phylogenies.