scholarly journals The value of DNA barcoding in a hotspot area: an example of Rhyacophila tristis (Trichoptera) in the Western Carpathians

2021 ◽  
Vol 4 ◽  
Author(s):  
Jana Bozáňová ◽  
Fedor Čiampor Jr ◽  
Tomasz Mamos ◽  
Michal Grabowski ◽  
Zuzana Čiamporová-Zaťovičová
Keyword(s):  
Genetic Diversity ◽  
Dna Barcoding ◽  
Molecular Diversity ◽  
Population Expansion ◽  
Western Carpathians ◽  
Aquatic Habitats ◽  
Effective Population ◽  
Separate Species ◽  
Mountain System ◽  
W Carpathians

DNA barcoding has proven to be an essential tool in providing molecular tags for animal species. In addition, the value of DNA barcoding undoubtedly consists in giving information about intraspecific genetic diversity, which is of great importance for biodiversity monitoring and conservation assessments. Such data are especially valuable in case of biodiversity hot-spots. Therefore, the aim of our study was to expand the knowledge of the genetic patterns and distribution of the caddisfly Rhyacophila tristis (Trichoptera, Rhyacophilidae) population in one such biodiversity hotspot - The Western Carpathians. The W Carpathians include rich freshwater systems of springs and streams, where molecular diversity and phylogeographic patterns of aquatic fauna are yet to be fully explored. Based on the mitochondrial DNA barcoding fragment (COI-5P) of 161 sequences, two BINs representing distinct lineages within R. tristis were identified. BIN BOLD:AAD5574 occurred in 16 localities to the west and BIN BOLD:ADL4166 in 44 localities more to the east, with contact zone in the middle of the mountain system (Fig. 1). BIN BOLD:AAD5574 occurred at a significantly narrower altitudinal interval compared to BIN BOLD:ADL4166, but we did not record significant differences in molecular diversity between BINs. Likewise, past population growth was found in both lineages. Both BINs started to expand demographically at the beginning of the Last Glacial Maximum, however BIN BOLD: ADL4166 increased its demography more sharply compared to BIN BOLD:AAD5574, moreover the effective population size of BIN BOLD:ADL4166 was much higher. BIN BOLD:ADL4166, showing a significantly wider range of altitude, has probably found higher potential for dispersal to various mountain units in the area of the W Carpathians. Our results showed also that BIN BOLD:ADL4166 is more closely related to the separate R. tristis BIN BOLD: ADL4367 recognized in Bulgaria than to the BIN BOLD:AAD5574 occurring geographically in the same mountain system. Additionally, different patterns of population expansion of BIN BOLD:ADL4166 between springs and streams were found. These differences may have occurred due to specific environmental conditions of the karstic springs, which are considered as relatively isolated aquatic habitats. Our initial study of R. tristis phylogeography in W Carpathians opens several new important questions: Is it possible that BIN BOLD:ADL4166 is expanding from the eastern part of Europe (Bulgaria) to the colder streams in the W Carpathians during the LGM? What role do the W Carpathian springs play in maintaining the genetic diversity and sustainability of R. tristis? Could these relatively isolated aquatic habitats serve as postglacial refugia for R. tristis species? And, maybe also, are they two separate species? This contribution was partially supported by the project VEGA 2/0084/21 and VEGA 1/0127/20.

Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

2012 ◽  
Vol 42 (12) ◽  
pp. 2142-2152 ◽  
Author(s):  
Svetlana A. Semerikova ◽  
Martin Lascoux ◽  
Vladimir L. Semerikov
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Population Decline ◽  
Population Expansion ◽  
Nuclear Marker ◽  
Effective Population ◽  
Species Status ◽  
Siberian Fir ◽  
Low Genetic Diversity

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

scholarly journals Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

2021 ◽  
Author(s):  
Thomas J. Batter ◽  
Joshua P. Bush ◽  
Benjamin N. Sacks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Expansion ◽  
Active Management ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Sex Marker ◽  
Cervus Canadensis ◽  
Population Sizes ◽  
Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

scholarly journals The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10039
Author(s):  
Jana Bozáňová ◽  
Zuzana Čiamporová Zat’ovičová ◽  
Fedor Čiampor Jr ◽  
Tomasz Mamos ◽  
Michał Grabowski
Keyword(s):  
Molecular Diversity ◽  
Molecular Data ◽  
Western Carpathians ◽  
Mountain Area ◽  
Term Survival ◽  
Plot Analysis ◽  
Stable Conditions ◽  
Gene Coi ◽  
Chemical Conditions ◽  
W Carpathians

The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.

scholarly journals DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jana Bozáňová ◽  
Fedor Čiampor ◽  
Tomasz Mamos ◽  
Michal Grabowski ◽  
Zuzana Čiamporová-Zat’ovičová
Keyword(s):  
Genetic Diversity ◽  
Contact Zone ◽  
Distribution Patterns ◽  
Freshwater Ecosystems ◽  
Western Carpathians ◽  
Dna Barcodes ◽  
Mitochondrial Marker ◽  
Demographic Differences ◽  
Freshwater Fauna ◽  
W Carpathians

AbstractThe region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.

scholarly journals The first step towards a DNA barcode reference database for mayflies (Ephemeroptera) of Slovakia

2021 ◽  
Vol 4 ◽  
Author(s):  
Patrik Macko ◽  
Tomáš Derka ◽  
Fedor Čiampor Jr ◽  
Zuzana Čiamporová-Zaťovičová
Keyword(s):  
Genetic Diversity ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Primary Source ◽  
Western Carpathians ◽  
Reference Database ◽  
Mtdna Coi ◽  
Phylogenetic Lineages ◽  
Baetis Rhodani

Mayflies (Ephemeroptera) represent a small but diverse order of amphibiotic insects, whose larvae contribute to several essential processes in freshwater habitats, such as bioturbation and bioirrigation, decomposition, nutrient cycling, and also serve as a primary source of nutrients for numerous organisms. Due to their cosmopolitan distribution and high-quality water requirements, they are also important indicators of ecosystem health and an integral part of biomonitoring protocols. Although the Slovak mayfly fauna is well researched, studies on genetic diversity, including DNA barcoding, are still lacking. The absence of the comprehensive DNA barcode reference libraries from various biogeographical regions and the presence of so-called cryptic lineages may prevent further efficient use and application of new approaches to aquatic ecosystem biomonitoring (Biomonitoring 2.0) based on eDNA analyses. Therefore, in the initial stage of our research, we bring the first insight into the genetic diversity of mayflies (based on mtDNA COI-5P barcoding fragment) from 47 localities of Slovakia mostly situated in the biogeographically significant Western Carpathians' territory. A total of 403 sequences of 42 morphologically determined species were added to the BOLD (Barcode of Life Data System) database, representing more than 1/3 of the mayfly fauna of Slovakia and covering 10 of 16 families. Sequences of these species were finally assigned to 62 BINs (Barcode Index Numbers) in BOLD (Fig. 1), whereby sequences of 12 species were divided into more than one BIN, indicating the presence of cryptic lineages. The largest number of BINs was represented by widely distributed species such as Baetis rhodani Pictet, 1843-1845 (6 BINs), Habroleptoides confusa Sartori & Jacob, 1986 (4 BINs) and Ecdyonurus venosus (Fabricius, 1775) (3 BINs). The sequences of the remaining nine species were split into two BINs. Maximum intraspecific variability (calculated by K2P) of some representatives was surprisingly high [e.g., E. venosus – 27.1 %; Baetis muticus (Linneaus, 1758) – 23.6 %; Caenis luctuosa (Burmeister, 1839) – 23.34 %, Baetis rhodani – 18.66 % and B. vernus Curtis, 1834 – 15.25 %] and far exceeded the level of intraspecific variability of the COI fragment based on the BOLD standards. The sequences of 23 individuals determined as Habroleptoides confusa, Baetis rhodani, B. buceratus Eaton, 1870, Caenis beskidensis Sowa, 1973 and Torleya major (Klapálek, 1905) created seven unique BINs, which represent the distant phylogenetic lineages of already existing BINs, that are currently unique to Slovakia. The coexistence of Baetis rhodani individuals of two different BINs was confirmed at five localities. Our study indicates clear importance of more detailed sampling and DNA barcoding due to the presence of unexpected intraspecific genetic diversity of mayflies captured in a relatively small area of the Western Carpathians.

scholarly journals Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11846
Author(s):  
Vikas Vohra ◽  
Narendra Pratap Singh ◽  
Supriya Chhotaray ◽  
Varinder Singh Raina ◽  
Alka Chopra ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Diversity ◽  
Bubalus Bubalis ◽  
Breeding Strategy ◽  
North India ◽  
Genetic Admixture ◽  
Advisory Group ◽  
Effective Population ◽  
Morphometric Variation

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Evolutionary genetics of small populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Evolutionary Genetic ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 112
Author(s):  
Monika Bielecka ◽  
Bartosz Pencakowski ◽  
Marta Stafiniak ◽  
Klemens Jakubowski ◽  
Mehdi Rahimmalek ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Performance ◽  
Carnosic Acid ◽  
Limited Information ◽  
Metabolomic Analysis ◽  
Separate Species ◽  
Flight Mass Spectrometry ◽  
Aerial Parts ◽  
Central Asian ◽  
Aromatic Species

Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH-psbA and ITS2 barcodes to clarify the relationships between these two taxa. Metabolomic analysis demonstrated that aerial parts are more similar than roots and none of the major compounds stand out as distinct. Sugiol in S. yangii leaves and carnosic acid quinone in S. abrotanoides were mostly responsible for their chemical differentiation, whereas in roots the distinction was supported by the presence of five norditerpenoids in S. yangii and two flavonoids and one norditerpenoid in S. abrotanoides. To verify the metabolomics-based differentiation, we performed DNA authentication that revealed S. yangii and S. abrotanoides to be very closely related but separate species. We demonstrated that DNA barcoding coupled with parallel LC-MS profiling constitutes a powerful tool in identification of taxonomically close Salvia species.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

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