From 68f6f4d256644399f8d4b7d620f7133625d00eda Mon Sep 17 00:00:00 2001 From: ggserver Date: Tue, 17 Dec 2024 14:42:39 +0000 Subject: [PATCH] Add updates up until 2024-12-17 14:37:35 --- .../52/03CD521DFFED8178FF1B4B45FEAF83B3.xml | 256 ++++++++++++ .../52/03CD521DFFEF8176FF1B4A50FBF08438.xml | 380 ++++++++++++++++++ 2 files changed, 636 insertions(+) create mode 100644 data/03/CD/52/03CD521DFFED8178FF1B4B45FEAF83B3.xml create mode 100644 data/03/CD/52/03CD521DFFEF8176FF1B4A50FBF08438.xml diff --git a/data/03/CD/52/03CD521DFFED8178FF1B4B45FEAF83B3.xml b/data/03/CD/52/03CD521DFFED8178FF1B4B45FEAF83B3.xml new file mode 100644 index 00000000000..deeb8c2038d --- /dev/null +++ b/data/03/CD/52/03CD521DFFED8178FF1B4B45FEAF83B3.xml @@ -0,0 +1,256 @@ + + + +Genetic diversity of populations of Simulium reptans s. l. (Diptera: Simuliidae) in the territory of Russia and Northern Kazakhstan + + + +Author + +Vaulin, Oleg V. +0000-0003-0906-3625 +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. & Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +oleg.v.vaulin@mail.ru + + + +Author + +Petrozhitskaya, Liudmila V. +0000-0001-6201-0368 +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +lusiapetr@yandex.ru + + + +Author + +Novgorodova, Tatiana A. +0000-0002-2795-108X +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +tanovg@yandex.ru + +text + + +Zootaxa + + +2024 + +2024-12-04 + + +5543 + + +3 + + +329 +342 + + + + +https://doi.org/10.11646/zootaxa.5543.3.2 + +journal article +10.11646/zootaxa.5543.3.2 +1175-5326 +14386271 +5672CC43-ADA1-44F8-8E6A-08F1BD1E2F10 + + + + + + +Testing of the allele-specific PCR (AS-PCR) method for identification of + +Simulium reptans + +and + +S. reptantoides + + + + + + + +From examined +122 specimens +, the vast majority (121) had a PCR product predicted for + +S. reptans + +. +One specimen +had an additional band expected for + +S. reptantoides + +. Subsequent sequencing of the COI region revealed a nucleotide substitution near the 3’ end of the corresponding primer annealing site ( +Figure 5 +). Despite the absence of + +S. reptantoides + +among the studied specimens, the spectrum of PCR products of the individual with an additional substitution characteristic of + +S. reptantoides + +indicates the possibility of differentiating these species using the proposed approach. + + + +Sequencing of nuclear rRNA genes + + + +Sequencing of a fragment of the COI gene and two regions of rRNA genes–ITS2 and the D +2 28S +variable region –was performed for several individuals of each sample. Minimal polymorphism was detected for both rDNA sequences. In a number of specimens, polymorphism in ITS2 is expressed in the presence of several variants that differ in insertion/deletion, which makes it difficult to obtain complete reads. + + +In addition to insertions/deletions, polymorphism was noted for the A/T substitution near the 3’ end of the sequence, as well as the overlap of these nucleotides ( +Figure 6 +). All three sequence variants occur in Asian populations; the variant with A/T overlap was noted in all 4 studied ITS2 sequences from the samples collected in the +Murmansk Region +. + + + +FIGURE 5. +Primer annealing sites and multiplex AS-PCR results for samples of + +Simulium reptans + +s.l. +from the Si16 sample (Novosibirsk). +A +–Annealing site of a primer specific for + +S. reptantoides + +; consensus sequences of molecular forms are given, as well as the sequence of a unique individual that we studied. +B +–Annealing site of a primer specific for + +S. reptans + +. +C +–results of electrophoresis of AS-PCR products from the Si16 sample, lane No. 4 corresponds to the unique sample Si16-4, which gives two PCR products, for the remaining specimens only the PCR product with the size predicted for + +S. reptans + +is visible (579 bp). Lane on the right (No. 11)–molecular weight marker 100bp+1.5+3. For +A +and +B +, vertical lines indicate complementary pairs, and the arrow indicates the order of nucleotides in the primer. + + + + +FIGURE 6. +Typical results of ITS2 sequencing of + +Simulium reptans + +s.l. +A +–with nucleotide A in the position in question, +B +–with A/T (W) superposition, +C +–with nucleotide T. + + + +Most of the studied specimens were identical for the D +2 28S +region; two sequences originating from Ust`-Kut ( +Irkutsk Region +) and the +Novosibirsk Region +had a superposition of two nucleotides at the same position. +The D +2 28S +region sequences also differ in three positions from the sequence EF417075, presented in the DNA database and referred to + +S. reptans + +. This result may be associated either with the peculiarities of species identification or with the presence of cryptic species. + + + +Phylogenetic analysis by COI gene region + + + +Despite the contradiction of data on restriction analysis and the results of species diagnostic PCR, all the studied sequences belonged to + +S. reptans + +( +Figure 7 +). Several groups of COI sequences uniting samples by geographical origin can be distinguished. Specimens of + +S. reptans + +A include a basal group of British specimens, as well as a group including specimens from +Sweden +and from the +Murmansk Region +of +Russia +. Form B of + +S. reptans + +includes the East European branch ( +Slovakia +, +Slovenia +, +Latvia +, +Lithuania +); the Eurasian branch, with a very wide distribution from Northern Europe to Eastern Siberia ( +Great Britain +, +Sweden +, +Norway +, part of the Siberian samples) and the Asian branch (Novosibirsk Region, Krasnoyarsk Krai, Irkutsk Region, Northern +Kazakhstan +). + + +The Eurasian branch corresponds to the +BstF5 +I restriction spectrum of 100+250+350 bp. and +Alu +I restriction spectrum–with one detectable fragment of 230 bp in size. + + +The Asian branch corresponds to the +BstF5 +I restriction spectrum of 600+100 bp. and +Alu +I restriction spectrum with fragments of 180+230 bp in size. + + +Thus, the Asian branch predominates in the Ob-Irtysh basin (Novosibirsk Region, Krasnoyarsk Krai and Northern +Kazakhstan +), while in the Irkutsk Region the proportions of the Asian and Eurasian branches were comparable (Table S3, +Figure 3 +). + + + + \ No newline at end of file diff --git a/data/03/CD/52/03CD521DFFEF8176FF1B4A50FBF08438.xml b/data/03/CD/52/03CD521DFFEF8176FF1B4A50FBF08438.xml new file mode 100644 index 00000000000..ead6b61f86d --- /dev/null +++ b/data/03/CD/52/03CD521DFFEF8176FF1B4A50FBF08438.xml @@ -0,0 +1,380 @@ + + + +Genetic diversity of populations of Simulium reptans s. l. (Diptera: Simuliidae) in the territory of Russia and Northern Kazakhstan + + + +Author + +Vaulin, Oleg V. +0000-0003-0906-3625 +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. & Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +oleg.v.vaulin@mail.ru + + + +Author + +Petrozhitskaya, Liudmila V. +0000-0001-6201-0368 +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +lusiapetr@yandex.ru + + + +Author + +Novgorodova, Tatiana A. +0000-0002-2795-108X +Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. +tanovg@yandex.ru + +text + + +Zootaxa + + +2024 + +2024-12-04 + + +5543 + + +3 + + +329 +342 + + + + +https://doi.org/10.11646/zootaxa.5543.3.2 + +journal article +10.11646/zootaxa.5543.3.2 +1175-5326 +14386271 +5672CC43-ADA1-44F8-8E6A-08F1BD1E2F10 + + + + + + +The features of the genetic structure of population of black flies of the + +Simulium reptans + +s.l. + + + + + + +Our +results, information from other researchers ( + +Kúdela +et al. +2014 + +; +Đuknić 2023 +) and the DNA database indicate significant spatial heterogeneity in the distribution of + +S. reptans + +. +The + +S. reptans + +A form is distributed relatively locally in +northern Europe. The + +S. reptans + +B form is widespread throughout +Eurasia +: from the +British Isles +to +Eastern Siberia +and +Northern +Kazakhstan +. +Based +on the sequence of the standard fragment of the COI gene for + +S. reptans + +B, three branches can be distinguished— +Eastern European +( +Slovakia, Slovenia, Latvia +, +Lithuania +), +Eurasian +(general for +Northern European +and +Asian +habitats) and +Asian +( +Western +and +Eastern Siberia +, +Northern +Kazakhstan +). +The +expected restriction spectra of the COI gene fragment by the +BstF5 +I enzyme differ between the +Eurasian +(100+250+350 bp) and +Asian +(600+100 bp) branches of + +S. reptans +B. Accordingly + +, based on the frequencies of these variants ( +Figure 4 +), it is possible to estimate the predominant mtDNA variants in populations. + +In +Eastern Siberia + +(Ust`- +Kut +), both variants occur with similar frequencies (55 and 45%, respectively), while in the +Ob-Irtysh +basin ( +Novosibirsk region +, +Krasnoyarsk region +and +Pavlodar region +of +Kazakhstan +), the +Asian +branch of mtDNA predominates (88%). +Consequently +, + +S. reptans + +B populations show heterogeneity. +Branches +within + +S. reptans + +B differ in this DNA region by few nucleotide substitutions. +The Asian +branch differs from the +Eurasian +branch by two substitutions, and each of them differs from the +East European +branch by three. +These +distances are comparable to the degree of divergence between the A and B forms of + +S. reptans + +. +The +distance between the nearest tree nodes belonging to + +S. reptans + +A and B is only three substitutions. +Of +particular interest is the actual relationship between forms A and B of + +S. reptans + +. +Are +these forms reproductively isolated, having their own gene pools and ecological niches, i.e., are they cryptic species? +Or +is mtDNA divergence just a peculiar variant of neutral intraspecific genetic diversity? +An +indication of genomic divergence between forms A and B could be divergence of nuclear DNA markers. +Sequences +of fragments of nuclear rRNA genes with minimal polymorphism do not demonstrate subdivision between A and B forms. +Thus +, according to ITS2, the samples of + +S. reptans + +A had the same nucleotide sequence as some of the individuals of + +S. reptans +B. According + +to D +2 28S +, only two Asian individuals had variability in the form of superposition in a single position of sequence. The absence of differences in rRNA gene fragments between the studied branches A and B of + +S. reptans + +does not confirm the hypothesis about the divergence of the genomes of A and B forms. It is most likely that these forms are only neutral genetic variants of mtDNA that do not mark separate, reproductively isolated groups of varying degrees. However, in order to clarify the relationships between these forms, it is necessary to conduct additional detailed studies, including an extensive multilocus analysis covering many regions of the genome and carried out for localities where the A and B forms of + +S. reptans + +exist sympatrically. + + + +FIGURE 7. +Maximum likelihood tree constructed from the DNA fragment of the COI gene of + +S. reptans +. + +A branch of + +S. reptantoides + +was used for rooting. The geographical origin of the individuals is indicated. Sequences taken from the NCBI database are designated by corresponding numbers. Bayesian posterior probabilities (above the branches) and bootstrap values (below the branches) are given. + + + +The +habitats of forms A and B of + +S. reptans + +are well defined. +The +features of their distribution can be explained by the difficulties of expansion/mixing of conspecific individuals with different mtDNA variants. +At +the same time, another possible explanation could be the actual genetic isolation of forms A and B and their adaptation to different environmental conditions. +Thus +, + +S. reptans + +A is found in small and medium-sized rivers in +northern Europe +–from Great Britain to the northeast of the +European +part of +Russia +, which is within the boundaries of 54– +69°N +and 2– +30°E +, in conditions from subarctic to temperate continental climate of wet +type +, with an average annual precipitation of +500–600 mm +, mainly on hilly plains and low mountains ( + +50–250 m +above sea level + +) with forest vegetation. + +Simulium reptans + +B is distributed much more widely, mainly on flat, less often low-mountain, forest and steppe landscapes, with a temperate to sharply continental climate, with an annual precipitation of +300–500 mm +. The development of + +S. reptans + +B occurs in both large, medium and small rivers. + + +Unfortunately, we were not able to study material from mid-mountain forest landscapes of Siberia, which somewhat limits the possibilities of comparative analysis with European data on + +Simulium reptans + +s.l. +Due to the lack of information from the mountainous regions of Southwestern Europe, Siberia and Northern +China +, it is currently impossible to evaluate borders of distribution of forms of + +S. reptans + +A and B, taking into account elevational zonation. Provided that the mitochondrial DNA variants corresponding to the A and B forms of + +S. reptans + +mark reproductively isolated and ecologically isolated groups, one would expect that limited populations of + +Simulium reptans + +A could be found on the upper border of the middle mountains, by analogy with the zonal foresttundra. + + +At this stage of the study, the black fly + +Simulium reptantoides + +was not found in the territory of +Russia +and Northern +Kazakhstan +. However, it is too early to make conclusions about the pattern of distribution of this species. According to + +Kúdela +et al. +(2014) + +, the range of + +S. reptantoides + +is not limited to Europe. To obtain a more complete understanding of the distribution of this species and answer the question of whether + +S. reptantoides + +is present in the Asian part of Eurasia, additional studies, including areas with mountain taiga landscapes, are required. + + +According to +Adler (2022) +, the southern part of the range of + +S. reptans + +covers +Greece +, +Italy +, +Portugal +, +Spain +, +Tunisia +, +Turkey +, +Uzbekistan +, North West and north East of +China +. More detailed study in the territory of these countries may expand our understanding of the phylogeography of + +S. reptans + +s.l. + + + + \ No newline at end of file