1. Phylogenomic, biogeographic, and evolutionary research trends in arachnologyscientific monograph Abstract: This book focuses on systematics, biogeography, and evolution of arachnids, a group of ancient chelicerate lineages that have taken on terrestrial lifestyles. The book opens with the questions of what arachnology represents, and where the field should go in the future. Twelve original contributions then dissect the current state-of-the-art in arachnological research. These papers provide innovative phylogenomic, evolutionary and biogeographic analyses and interpretations of new data and/or synthesize our knowledge to offer new directions for the future of arachnology.
Keywords: biogeography, phylogeny, systematics, evolution, arachnology
Published in DiRROS: 09.08.2024; Views: 93; Downloads: 69
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2. Phylogenomic, biogeographic, and evolutionary research trends in arachnologyMatjaž Kuntner, 2022, other scientific articles Abstract: Textbook knowledge tells us that arachnids are a hyper diverse clade of chelicerates that have taken on terrestrial lifestyles. Original papers published in prestigious venues routinely reconstruct details of this purported single terrestrialization event that would have been followed by arachnid diversification on land. However, we are beginning to understand that arachnids are very likely paraphyletic; as such, Arachnida can only circumscribe an assemblage of chelicerates that live terrestrially. If so, arachnid terrestrialization may have taken several independent routes at different historic times. While the diversity and phylogeny of spiders, scorpions and harvestmen may be relatively well documented and understood, additional groups that we deem to be arachnids remain enigmatic and will likely continue to be more or less neglected after this Special Issue. We have here assembled examples of contemporary studies that include both original research as well as reviews focusing on “arachnids” and cover loosely defined biological subdisciplines of phylogenomics, biogeography, and evolution. The latter includes systematics, taxonomy, DNA barcoding, and trait evolution. In this editorial, I introduce the authors of these papers and their featured research, and through this narrative, I pose two questions. The first one is what is arachnology given that arachnids may not be monophyletic? The second question is where should our field be headed toward in the near future?
Keywords: biogeography, phylogeny, systematics, evolution, arachnology
Published in DiRROS: 06.08.2024; Views: 95; Downloads: 40
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3. Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus YDenis Kutnjak, Santiago F. Elena, Maja Ravnikar, 2017, original scientific article Abstract: RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).
IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
Keywords: Potato virus Y, experimental evolution, genetic drift, natural selection, sRNA deep sequencing
Published in DiRROS: 24.07.2024; Views: 148; Downloads: 67
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4. Golden orbweavers ignore biological rules : phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphismMatjaž Kuntner, Christopher A. Hamilton, Ren-Chung Cheng, Matjaž Gregorič, Nik Lupše, Tjaša Lokovšek, Emily Moriarty Lemmon, Alan R. Lemmon, Ingi Agnarsson, Jonathan A. Coddington, Jason E. Bond, 2019, original scientific article Abstract: Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope’s rule (phyletic size increase), Rensch’s rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length
2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch’s rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope’s rule. Allometric analyses reject the converse, Rensch’s rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2–4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97–146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.
Keywords: spiders, evolution of sexual size dimorphism, golden orbweavers, analyses
Published in DiRROS: 24.07.2024; Views: 239; Downloads: 129
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5. The seven grand challenges in arachnid scienceMatjaž Kuntner, 2022, original scientific article Abstract: This perspective identifies the grand challenges in arachnid science: 1. Grasp the arachnid species diversity. There is a need to accelerate taxonomic research to obtain a sense of arachnid species diversity, however, at the same time, taxonomy needs to increase its quality, rigor, and repeatability. 2. Standardize arachnid systematics research. A solid phylogenetic definition and morphological diagnosis of Arachnida and its composing subgroups, usually treated at the rank of order, are needed. Studies should aim to stabilize and standardize phylogenetic efforts at all levels of hierarchy, and systematists should adopt criteria for higher level ranks in arachnid classification. 3. Interpret arachnid trait evolution through omics approaches. Among the field’s grand challenges is to define the genetic diversity encoding for the diverse arachnid traits, including developmental, morphological and ecological characteristics, biomaterials such as silks, venoms, digestive fluids, or allergens and bioproducts that cause diseases. Comparative genomics, transcriptomics, and proteomics will provide the empirical basis for biotechnology to modify arachnid genomes to fit numerous applications. 4. Facilitate biotechnological applications of arachnid molecules and biomaterials. Among the grand field challenges is to define potential applications of arachnid bioproducts from therapeutics to industry. New natural and biodegradable products, e.g. from spider silks, should ease our burden on ecosystems. 5. Utilize arachnids as models in ecological and biogeographic research. Biodiversity inventory sampling and analytical techniques should be extended from spiders to other arachnid groups. Spiders and their webs could be used as environmental DNA samplers, measuring or monitoring ecosystems’ overall biodiversity. Arachnids are excellent models to address biogeographical questions at the global to local scales. 6. Disentangle evolutionary drivers of arachnid diversity. Among the field grand challenges is a more precise evaluation to what extent the emergence of arachnid phenotypes is shaped by classical selection processes, and under what conditions, if any, sexual conflict needs to be invoked. 7. Define effective conservation measures for arachnids in the light of global changes. Effective conservation measures in arachnology should integrate the data from phylogenetic diversity, physiology, ecology, biogeography, and global change biology.
Keywords: diversity, systematics, arachnids, evolution, biomaterials
Published in DiRROS: 18.07.2024; Views: 152; Downloads: 82
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6. A new locality for the blind loach, Eidinemacheilus smithi (Teleostei: Nemacheilidae) in Iranian Zagros : a morpho-molecular approachMohammad Javad Malek-Hosseini, Yaser Fatemi, Hamid Reza Esmaeili, Tjaša Lokovšek, Matjaž Kuntner, 2022, original scientific article Abstract: Four obligate cave fish species have been recorded from Zagros in Iran: Garra typhlops (Bruun and Kaiser, 1944), G. lorestanensis (Mousavi-Sabet and Eagderi, 2016), G. tashanensis (Mousavi-Sabet, Vatandoust, Fatemi and Eagderi, 2016) and Eidinemacheilus smithi (Greenwood, 1976). So far, the only known locality of the latter has been the Loven cave. Here, we extend the known range of the Zagros blind loach (E. smithi) by reporting a new locality, the Tuveh spring, located 31 km south of Loven. We combine morphological evidence with the calculated K2P genetic divergences of 1.39% between Tuveh and Loven to confirm that these populations are conspecific. Our discovery of the second E. smithi population has implications for the conservation of this rare and vulnerable species.
Keywords: fishes, caves, evolution, Irano-Anatolian hotspot
Published in DiRROS: 17.07.2024; Views: 147; Downloads: 121
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7. Evaluation of methods and processes for robust monitoring of SARS-CoV-2 in wastewaterOlivera Maksimović, Živa Lengar, Zala Kogej Zwitter, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2022, original scientific article Abstract: The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
Keywords: waste water, method evolution, virus detection, SARS-CoV-2
Published in DiRROS: 17.07.2024; Views: 128; Downloads: 108
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8. The Middle Pleistocene human metatarsal from Sedia del Diavolo (Rome, Italy)Alessandro Riga, Antonio Profico, Tommaso Mori, Riccardo Frittitta, Alessia Nava, Lucia Mancini, Diego Dreossi, Davorka Radovčić, Hannah Rice, Luca Bondioli, Damiano Marchi, 2024, original scientific article Abstract: The peopling of Europe during the Middle Pleistocene is a debated topic among paleoanthropologists. Some authors suggest the coexistence of multiple human lineages in this period, while others propose a single evolving lineage from Homo heidelbergensis to Homo neanderthalensis. The recent reassessment of the stratigraphy at the Sedia del Diavolo (SdD) site (Latium, Italy), now dated to the beginning of marine isotope stage (MIS) 8, calls for a revision of the human fossils from the site. In this paper, we present the morphometric, biomechanical and palaeopathological study of the second right metatarsal SdD2, to both re-evaluate its taxonomical affinities and possibly determine the levels of physical activity experienced by the individual during lifetime. Results demonstrate the persistence of archaic features in SdD2 suggesting new insights into the technology and hunting strategies adopted by Homo between MIS 9 and MIS 8.
Keywords: anthropology, evolution, palaeontology
Published in DiRROS: 23.05.2024; Views: 248; Downloads: 328
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9. Tuning the long-term corrosion behaviour of biodegradable WE43 magnesium alloy by PEO coatingJulia Nachtsheim, Songyun Ma, Jaka Burja, Barbara Šetina, Bernd Markert, 2023, original scientific article Keywords: long-term degradation, in vitro corrosion mechanisms: biodegradable, magnesium, DMEM fluid, hydrogen evolution, PEO coating
Published in DiRROS: 20.05.2024; Views: 244; Downloads: 130
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