Dots on Earth with huge genetic diversity: relict flatworm Crenobia alpinain the alpine lakes of Tatra Mountains

Mountain lakes, typical signs of an alpine landscape all around the world, were formed in the western part of the Carpathian Arch about 10,000-15,000 years ago, as remnants of the last continental glaciation. In the Tatra Mountains (Slovak-Polish border), more than 110 permanent lakes of glacial origin and many other small ponds exist. These (sub)alpine lakes, with their specific conditions, are very vulnerable and any change in their environment can largely impact their biodiversity, which is, despite long-term faunistic and ecological research, still not fully recognized. This shortcoming could be strongly improved by molecular approaches, which, even within population-genetic studies, often reveal unsuspected cryptic lineages or potential new species. Our long-term research is aimed at revealing the genetic diversity of aquatic macroinvertebrate species in the alpine environment of the Western Carpathians. One of the currently studied species is the glacial relict flatworm taxon Crenobia alpina (Dana, 1766) (Tricladida: Planariidae), representing an element of the permanent aquatic fauna. Totally, 88 COI haplotypes of C. alpina forming at least five well-separated genetic lineages were identified within 348 individuals collected from 45 lakes and ponds in theTatra Mts. Based on tests of selective neutrality and population stability, C. alpina populations in the Tatra lakes did not overcome recent population expansions or contractions. It seems that great genetic differences between localities and their population stability could be a consequence of the presence of natural topographic barriers (ridges, mountain peaks) dividing the mountains into small and relatively isolated valleys. Moreover, other important factors that could play a significant role are the limited dispersal ability of the species as well as its ability to reproduce asexually. Our findings were also compared with all publicly available sequences (Barcoding of Life Datasystems - BOLD and GenBank) in order to shift our data from a local to a holistic view on C. alpina. Our resultssupport the assumption of Brändle et al. 2017 that C. alpina represents a complex of cryptic lineages or species in Europe. As part of the AquaBOL.sk initiative, the data obtained contribute to the knowledge of genetic variability and barcoding of aquatic organisms in Slovakia.

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Flow modification associated with reduced genetic health of a river-breeding frog, Rana boylii

10.1101/316604 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ryan A. Peek ◽

Sean M. O’Rourke ◽

Michael R. Miller

Keyword(s):

Genetic Diversity ◽

Geographic Distance ◽

Aquatic Organisms ◽

Population Connectivity ◽

Flow Alteration ◽

Population Genetic Differentiation ◽

Flow Modification ◽

Diversity Loss ◽

Rana Boylii

AbstractRiver regulation or flow modification—the hydrological alteration of flow by dams and diversions—has been implicated as a cause of fundamental change to downstream aquatic ecosystems. Flow modification changes the patterns and functionality of the natural flow regime, and has the potential to restrict population connectivity and gene flow in river-dependent organisms. Since population connectivity and the maintenance of genetic diversity are fundamental drivers of long-term persistence, understanding the extent flow modification impacts these critical attributes of genetic health is an important goal for long-term conservation. Foothill yellow-legged frogs (Rana boylii) were historically abundant throughout many western rivers but have declined since the onset of regulation. However, the extent to which R. boylii populations in rivers with altered flow regimes are maintaining connectivity and genetic diversity is unknown. Here we use genetic methods to investigate the impacts of flow alteration on R. boylii to explore their potential for long-term persistence under continued flow modification. We found R. boylii in rivers with flow modification showed striking patterns of isolation and trajectories of genetic diversity loss relative to unregulated rivers. For example, flow modification explained the greatest amount of variance in population genetic differentiation compared with other covariates including geographic distance. Importantly, patterns of connectivity and genetic diversity loss were observed regardless of flow alteration level but were most prominent in locations with the greatest flow modification intensity. Although our results do not bode well for long-term persistence of R. boylii populations under current flow regulation regimes, they do highlight the power of genetic monitoring for assessing population health in aquatic organisms.

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Toxic or Not Toxic, That Is the Carbon Quantum Dot’s Question: A Comprehensive Evaluation with Zebrafish Embryo, Eleutheroembryo, and Adult Models

Polymers ◽

10.3390/polym13101598 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1598

Author(s):

Chih-Yu Chung ◽

Yu-Ju Chen ◽

Chia-Hui Kang ◽

Hung-Yun Lin ◽

Chih-Ching Huang ◽

...

Keyword(s):

Zebrafish Embryo ◽

Comprehensive Evaluation ◽

Aquatic Organisms ◽

Carbon Quantum Dots ◽

Adult Zebrafish ◽

Fish Embryo ◽

Wide Range ◽

Different Types ◽

Low Toxicity

Carbon quantum dots (CQDs) are emerging novel nanomaterials with a wide range of applications and high biocompatibility. However, there is a lack of in-depth research on whether CQDs can cause acute or long-term adverse reactions in aquatic organisms. In this study, two different types of CQDs prepared by ammonia citrate and spermidine, namely CQDAC and CQDSpd, were used to evaluate their biocompatibilities. In the fish embryo acute toxicity test (FET), the LD50 of CQDAC and CQDSpd was about 500 and 100 ppm. During the stage of eleutheroembryo, the LD50 decreased to 340 and 55 ppm, respectively. However, both CQDs were quickly eliminated from embryo and eleutheroembryo, indicating a lack of bioaccumulation. Long-term accumulation of CQDs was also performed in this study, and adult zebrafish showed no adverse effects in 12 weeks. In addition, there was no difference in the hatchability and deformity rates of offspring produced by adult zebrafish, regardless of whether they were fed CQDs or not. The results showed that both CQDAC and CQDSpd have low toxicity and bioaccumulation to zebrafish. Moreover, the toxicity assay developed in this study provides a comprehensive platform to assess the impacts of CQDs on aquatic organisms in the future.

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Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽

10.3390/d13030126 ◽

2021 ◽

Vol 13 (3) ◽

pp. 126

Author(s):

Emily K. Latch ◽

Kenneth L. Gee ◽

Stephen L. Webb ◽

Rodney L. Honeycutt ◽

Randy W. DeYoung ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Wildlife Management ◽

Field Observations ◽

Adaptive Potential ◽

Population Isolation ◽

Potential Benefits ◽

Wildlife Populations ◽

Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

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Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

Plant Ecology and Evolution ◽

10.5091/plecevo.2018.1366 ◽

2018 ◽

Vol 151 (1) ◽

pp. 48-60

Author(s):

Mi Yoon Chung ◽

Hoa Thi Quynh Le ◽

Sungwon Son ◽

Huai Zhen Tian ◽

Myong Gi Chung

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Geographic Location ◽

Population History ◽

Population Variation ◽

Conservation Strategies ◽

Ancestral Population ◽

Allozyme Diversity ◽

Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

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Soil microbial dynamics and genetic diversity in soil under monoculture wheat grown in different long-term management systems

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2006.12.016 ◽

2007 ◽

Vol 39 (6) ◽

pp. 1391-1400 ◽

Cited By ~ 35

Author(s):

Carmine Crecchio ◽

Maddalena Curci ◽

Antonella Pellegrino ◽

Patrizia Ricciuti ◽

Nunzia Tursi ◽

...

Keyword(s):

Genetic Diversity ◽

Management Systems ◽

Microbial Dynamics ◽

Soil Microbial ◽

Term Management

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An unexpected new record of the Mediterranean orchid, Ophrys bertolonii (Orchidaceae) in Central Europe

Biologia ◽

10.2478/s11756-011-0086-2 ◽

2011 ◽

Vol 66 (5) ◽

Cited By ~ 5

Author(s):

Attila Molnár V ◽

András Máté ◽

Gábor Sramkó

Keyword(s):

Central Europe ◽

New Record ◽

Dispersal Ability ◽

Long Distance Dispersal ◽

Long Distance ◽

Permanent Establishment ◽

Adriatic Coast ◽

Northward Expansion ◽

Mediterranean Plant

AbstractOne flowering specimen of Ophrys bertolonii (s. str.) — a plant with a Circum-Adriatic distribution and hitherto unknown in other regions — was found on 7th May 2010 in the vicinity of Kunadacs (Central Hungary; N 47°00′ E 19°17′). The nearest known populations of this Mediterranean plant inhabit the Adriatic coast (ca. 450 km away) in Croatia, therefore this new occurrence represents a significant long distance dispersal event. The circumstances of the occurrence argue against introduction, but we can not decide now whether this new appearance is temporary or permanent. The permanent establishment of this strictly entomophilous plant requires the presence of its specific pollinator in the close neighbourhood of the habitat. However, no pollination was observed on the three flowers of the plant until 9th May, and one day later the stem had disappeared most likely due to grazing. Whatever the long-term fate of the plant is, this discovery represents a significant long distance (jump) dispersal event, and testifies to the dispersal ability of Ophrys species. Additionally, the appearance of a mature Adriatic plant in Central Europe fits well into the currently observed, climate change driven northward expansion of European orchids, therefore this finding most likely reflects a growing Mediterranean-like climatic influence in the region.

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Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Animals ◽

10.3390/ani11082193 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2193

Author(s):

Angelika Podbielska ◽

Katarzyna Piórkowska ◽

Tomasz Szmatoła

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

First Generation ◽

Expected Heterozygosity ◽

Hybrid Detection ◽

Average Coefficient ◽

Mixed Origin ◽

Generation Hybrid

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

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Risk Assessment of Malakite with the Active Substances Dithianon and Pyrimenthanil

European Journal of Nutrition & Food Safety ◽

10.9734/ejnfs/2019/v9i430075 ◽

2019 ◽

pp. 312-314

Author(s):

Torsten Källqvist ◽

Merete Grung ◽

Katrine Borgå ◽

Hubert Dirven ◽

Ole Martin Eklo ◽

...

Keyword(s):

Risk Assessment ◽

Surface Waters ◽

Plant Protection ◽

Aquatic Organisms ◽

Toxicity Tests ◽

Concentration Addition ◽

Active Ingredients ◽

Active Substances ◽

Assessment Factor

The plant protection product Malakite (BAS 669 01 F), containing the active substances dithianon and pyrimethanil, is a fungicide against scab in pome fruits. Products containing these active plant protection substances are approved in Norway, but not with both substances in the same product. The Swedish Chemicals Agency (KemI) has as zonal Rapporteur Member State (zRMS) of the Northern Zone evaluated the product Malakite and decided on non-approval due to the observation of unacceptable effects in exposed birds, aquatic organisms, non-target arthropods and earthworms. On request from The Norwegian Food Safety Authority, the VKM Panel on Plant Protection Products has discussed the available data and the report prepared by KemI, and has concluded as follows on the questions raised: On the refinement of DT50 in long term risk assessment for birds: It is the view of the VKM panel that the refinement is not acceptable because the analysis using first order kinetics seems not in line with a realistic and sufficiently conservative approach for the data provided. Furthermore, field studies from more sites are required. On the long term cumulative effects of the active substances on birds: VKM shares the view of KemI, that the combined sub-lethal and reproduction effects should be assessed because the mode of action of the two ingredients has only been shown in fungi, and since the mechanisms in birds could be different. On the reduction of assessment factor for fish: VKM opposes to the reduction of assessment factor for dithianon in fish because the data from acute toxicity tests cannot be extrapolated to chronic toxicity, and because the factor should reflect not only the variation in interspecies sensitivity, but also the uncertainty involved in extrapolation from laboratory tests to the field situation. On the choice of end point in risk assessment for fish: The VKM panel considers the NOEC of dithianon for fish determined from the study at pH 7.9 not to be adequate for the more acidic Norwegian surface waters, and recommends using the data from the test performed at pH 6.5. On the formulation studies for aquatic organisms: It is the opinion of the VKM panel that the formulation studies may be used together with corresponding studies with the active ingredients as long as the studies compared are performed and evaluated according to the same principles. However, VKM notes that the formulation tests as well as the tests of the active ingredients have been performed at high pH values, which are not representative to most Norwegian surface waters. Thus, the toxic effect of dithianon shown in these tests are likely to be lower than expected under typical conditions in Norway. On the assessment factors for concentration addition in fish: It is the opinion of the VKM panel that a reduction in assessment factor for one component in a mixture cannot be used for a formulation containing components for which a similar reduction has not been accepted. On effect studies of active substances and formulations on non-target arthropods: The VKM panel shares the view of KemI that the risk assessment should be based on all available information, including the studies presented for the active substances. On the endpoint in earthworm risk assessment: VKM supports the view of KemI that the observed effects of pyrimethanil on reproduction of earthworms should be considered in the risk assessment of Malakite.

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New kid on the block: Research of alpine-lake macroinvertebrates in the Tatra Mountains enhanced by DNA barcoding and metabarcoding

ARPHA Conference Abstracts ◽

10.3897/aca.4.e64945 ◽

2021 ◽

Vol 4 ◽

Author(s):

Ondrej Vargovčík ◽

Zuzana Čiamporová-Zaťovičová ◽

Fedor Čiampor Jr

Keyword(s):

Large Scale ◽

Environmental Changes ◽

Human Impacts ◽

Sampling Error ◽

Alpine Lakes ◽

Alpine Lake ◽

Tatra Mountains ◽

Aquatic Communities ◽

Wide Range ◽

The Tatra Mountains

State of ecosystems and biodiversity protection are becoming the key interests for modern society due to climate change and negative human impacts (Leese 2018). Environmental changes in freshwaters are indicated also by benthic communities, especially in sensitive ecosystems like alpine lakes (Fjellheim 2009). Moreover, remoteness and isolation of alpine lakes make them a source of biodiversity, which is worth conserving (Hamerlík 2014). A promising tool for efficient large-scale monitoring of aquatic communities is DNA metabarcoding (Leese 2018). In this study, we applied metabarcoding to analyse macrozoobenthos of 12 lakes in the Tatra Mountains, using benthic bulk samples and eDNA filtered from water (Fig. 1). In compliance with recent publications, eDNA amplified with BF3/BR2 primers resulted in high percentage of non-invertebrate reads (Leese 2021). Based on in silico tests with the obtained sequences, we confirm that the recently developed EPTDr2n primer enables minimizing non-target amplification even with eDNA filtered from alpine-lake water (Elbrecht and Leese 2017). This ability is facilitated by 3’ end of the primer and we observed the two important mismatches in non-target sequences from our study (Leese 2021). Thus, our future analyses of eDNA (and bulk-sample fixative) will benefit from the new primer. Concerning bulk samples, a wide range of invertebrate taxa was assigned to the OTUs and they showed good congruence with previous studies using morphological determination (e.g. Krno 2006). Certain differences with (and among) the previous records per lake were observed, which could suggest ecological changes, but at the moment the influence of sampling error cannot be excluded. In eDNA, several taxa were congruent with the previous records, but their amount and read abundance was considerably lower due to non-target amplification. Apart from that, filling gaps in barcoding databases remains one of our priorities, as identification to species or genus level was not yet possible for some invertebrate OTUs. In addition, we subjected the NGS data to denoising and abundance-filtering in order to explore haplotype-level diversity (Andújar 2021). Although more comprehensive conclusions will be possible only after obtaining data from more lakes and years, already the two metabarcoding experiments presented here enabled us to efficiently detect within-species genetic diversity and identify a large variety of taxa, including groups that would otherwise be omitted or very challenging to identify. This underlines the potential of DNA methods to provide valuable ecological and biodiversity data across the tree of life for modern biomonitoring. This study was realized with support from VEGA 2/0030/17 and VEGA 2/0084/21.

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Testing successful Business Model using System Dynamics

International Journal of Production Management and Engineering ◽

10.4995/ijpme.2019.10807 ◽

2019 ◽

Vol 7 ◽

pp. 91

Author(s):

J. Ganzarain ◽

M. Ruiz ◽

J.I. Igartua

Keyword(s):

System Dynamics ◽

Business Model ◽

Business Models ◽

Industrial Sector ◽

Continuous Change ◽

Dynamic Complexity ◽

Holistic View ◽

Short And Long Term ◽

Systemic View

In our increasingly globalised economy, managing continuous change whilst remaining competitive and dynamic has become a central issue for firms in the industrial sector. One of the elements for obtaining this competitiveness is the value creation model of the firm. The most important challenges in firms are characterised by dynamic complexity which makes it difficult to understand factors in their context. Consequently management and decision making is hindered (Antunes et al., 2011). Business models are characterised by complexity and dynamism. Performance of the firm is a complex topic determined by the large amount of variables that can be involved in the system, and the different effects that influence the system in the short and long term. Due to this complexity a systemic view is required, that is, an holistic view of the whole system. Such a systemic view enables managers to make decisions based on evidence rather than intuition and personal experiences, as they understand how the whole system works. Thus, the main aim of this research is to use an empirical tool such as System Dynamics (SD), to support and sustain firms in the identification of new constructs related to their Business Model (BM).

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