Unknown Lineage Research Articles

Phylogeography and species distribution modeling unveil unnoticed Pliocene diversity: the case of a montane Iberian bush-cricket, Antaxius spinibrachius (Orthoptera: Tettigoniidae)

Abstract The geographic distribution and systematics of many groups of insects are still understudied across large geographic areas of the Iberian Peninsula. This lack of knowledge and the fact that many species have a complex evolutionary history due to the existence of “refugia within refugia” have hindered the taxonomic description of the true biodiversity in the Iberian Peninsula. Here, we discuss the evolutionary history of a flightless Iberian bush-cricket Antaxius spinibrachius (Fischer, 1853) using 1 nuclear and 2 mitochondrial markers. We applied species distribution modeling to design sampling strategies in climatically favorable areas and to detect missing isolated populations or unknown lineages. Following the species distribution modeled using all of the presence records available, we discovered 4 new isolated populations in Sierra Madrona, Serra de São Mamede, Sierra de Montánchez, and Sierra de la Demanda. Phylogenetic analyses recovered 2 major Pliocene lineages with a north–south geographic speciation pattern in the Iberian Peninsula. This north–south vicariant event split the common ancestor of these species on either side of the Tagus Valley, probably associated with the Pliocene climate change and the reorganization of paleobasins of the western Iberian Peninsula during the Miocene–Pliocene. We described the southern Iberian Plateau lineage of Antaxius as a new species of bush-cricket based on phylogenetic and morphological evidence, Antaxius oretanus sp. nov. We assessed the conservation status of the new species as “VU B2ab(iii,v)” under the IUCN criteria.

Understanding Rhododendron intraspecific compatibility in botanic garden collections for species conservation

Context Controlled pollination is an important technique for maintaining intraspecific diversity in integrated plant conservation practices, particularly in genera such as Rhododendron, where open pollination usually produces hybrids with unknown paternal lineages. Aims This study investigated the capacity for viable seed set from self- and intraspecific cross-pollination for Rhododendron taxa in different categories of the International Union for Conservation of Nature (IUCN) Red List, to guide conservation management of threatened species in botanic garden collections. Methods The following five taxa of subsection Maddenia were studied: R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), R. nuttallii (Near Threatened), and R. excellens (Vulnerable). Controlled pollination was performed on selected garden accessions, and seed germination was tested at an alternating temperature regime of 15/25°C, 8 h photoperiod, and ~6 μmol m−2 s−1 photosynthetic photon flux density (PPFD). Key results Intraspecific compatibilities varied among different taxa and between self- and outcross treatments. X-ray images for Rhododendron seeds showed low capacity to predict seed germination. Neither X-ray scan nor fungicide (Ridomil) treatment showed any adverse impact on seed germination, which has positive implications for seed-banking and subsequent raising of Rhododendron seedlings. Conclusions Controlled intraspecific pollination can be used to maintain diversity of ex situ accessions for selected Rhododendron species. However, the zero or low compatibility demonstrated in some species, such as R. excellens, suggests that these species may require a different approach. Implications Intraspecific pollination should be evaluated for each Rhododendron species before a propagation program is initiated in ex situ conservation.

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers.

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.

Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification

Abstract Sengis (Macroscelidea) are members of the Afroinsectivora, a group of mammals belonging to the supercohort Afrotheria. Sengis’ low population densities and their distribution, which includes politically unstable regions with ongoing armed conflicts, hinder contemporary sampling of comprehensive datasets. We overcome this obstacle for the species Petrodromus tetradactylus, one of the most widely distributed sengi species, by utilizing 44 historical museum samples from multiple natural history museums. These historical samples were combined with newly generated or published data of 11 modern samples, thus creating a dataset of 55 P. tetradactylus individuals covering most of the species’ distribution. Phylogenetic reconstruction with 11 nuclear loci in conjunction with mostly complete mitochondrial genomes reveals multiple deeply divergent and formerly unknown lineages within this monotypic genus, highlighting the need for a taxonomic revision. Furthermore, we can show that the assumed allopatric distribution of P. tetradactylus in Central Africa most likely represents a sampling artifact. Biogeographic character mapping indicates that the African forest system and its dynamics through climate fluctuations shaped the evolutionary and biogeographic history of this taxon. We show that lineages within Petrodromus that were able to adapt to dryer woodland ecosystems are much more widely distributed than lineages restricted to moist forest systems. The evolution and radiation of the four-toed sengi (P. tetradactylus) mirrors the patterns of its distant relative, the giant sengis (Rhynchocyon) in both ecotype variation and overall distribution, implying a significant influence of climate and landscape features in shaping diversification.

Phylogenetics of Asian Small-Clawed Otters (Aonyx cinereus) in West Sumatra.

<b>Background and Objective:</b> The presence of Asian small-clawed otters (<i>Aonyx cinereus</i>) in West Sumatra has been reported from ecological data in the form of footprints and feces, while its genetic information has not been reported yet. This genetic information needs to be reported along with the determination of <i>A. cinereus</i> as a vulnerable species and is experiencing population decline by the International Union for Conservation of Nature (IUCN). This study aimed to determine the phylogenetic relationship of <i>A. cinereus</i> found in West Sumatra with other regions. <b>Materials and Methods:</b> The samples used were <i>A. cinereus</i> stool collected from several wetland locations in West Sumatra. <i>Aonyx cinereus</i> DNA was extracted from stool samples following the QIAamp Fast DNA Stool Mini Kit protocol (Qiagen). Amplification was performed using the CO1 gene. The IQTree was used to provide phylogenetic information on <i>A. cinereus</i> and MEGA 7 was used to determine the uncorrected genetic distance of <i>A. cinereus</i>. <b>Results:</b> <i>Aonyx cinereus</i> clustered to form three sub-clusters namely <i>A. cinereus</i> Sundaland, Laos lineage and unknown lineage. <i>Aonyx cinereus</i> Sundaland consists of <i>A. cinereus</i> West Sumatra and <i>A. cinereus</i> Sarawak, Malaysia which are closely related with a genetic distance of 0.68%. Moreover, compared to <i>A. cinereus</i> from unknown lineage (including Captive Copenhagen Zoo) and Laos lineage, <i>A. cinereus</i> of West Sumatra had a genetic distance of 0.68-1.20 and 4.18%, respectively. <b>Conclusion:</b> Wetland conversion and the role of humans have influenced the obstacle to connectivity among populations that cause genetic variation.

Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.

A new species of the genus Amolops (Amphibia: Ranidae) and the first national record of Amolops vitreus from China

Abstract The torrent frogs of the genus Amolops represent a great anuran diversification in southern China and Southeast Asia. Previous studies have shown that, the diversity of this genus still remains underestimated. During herpetological surveys from 2021 to 2022, several Amolops specimens were collected from the international border regions of southwestern Yunnan Province, China. Herein, we utilized molecular phylogenetic and morphological data to identify these specimens. Our findings indicate the presence of a separate and previously unknown lineage in the A. viridimaculatus group, which we formally describe as a new species. Furthermore, the specimen from Xishuangbanna National Nature Reserve clustered with A. vitreus from the paratype, supporting the morphological diagnosis. Therefore, we describe a new species and a new species record for China. Our study contributes to the species richness of the genus Amolops as well as the diversity of amphibians in China. Notably, our discovery brings the total number of Amolops species to 85 and the total number of torrent frog species known to occur in China to 53. In addition, our study further confirmed that Yunnan and Indochina Peninsula have similar faunal composition, implying that more studies are needed to achieve a complete understanding of the species diversity and distribution pattern.

Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.

The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.

Role of generalists, specialists and opportunists in Nitrospira community assembly in soil aggregates from nearby cropland and grassland areas in a campus

Nitrospirota is an essential contributor to nitrification. However, the community assembly mechanism of such organisms in soil aggregates from nearby but different ecosystems is unclear. We quantitatively measured the relative contributions of generalists, opportunists and specialists to the Nitrospira community assembly. Nitrospira were more abundant in agricultural soils than in grasslands and were relatively enriched in microaggregates in both agricultural (AS) and grassland soils (GS). These findings could be explained by the neutral pH of AS and the relatively high organic carbon quantity of the aggregates. The community variation in Nitrospira was driven by both ecosystem and aggregate size fractions, with dispersal and drift dominating the assembly process, partly explained by macro- and microaggregates with higher organic quality that can reduce selection pressures to enrich Nitrospira species (indicated by a higher α diversity), supporting more stochastic processes (drift and dispersal limitations) in community assembly. Generalists belonging to Namibia soil cluster 2, followed by unknown Nitrospira and other lineage II members, contributed to the stochastic assembly, as indicated by a high normalized stochasticity ratio (NST) value of 0.618. A total of 89.7 % and 5.6 % of the ASVs were defined as opportunists and generalists, respectively. Opportunists expand their taxonomic affiliation from Nitrospira lineages I, II, V, and grassland metagenome lineages to unknown lineages, and almost all specialists cannot be assigned to a known lineage or a subcluster. We observed that the NSTs for Opportunists and specialists were approximately 0.472 and 0.247, respectively, suggesting that the assembly of opportunists was less dominated by stochastic processes than was that of generalists, while the assembly of specialists highly relied on deterministic processes. Indeed, limited variation in the abundances of opportunists and specialists was significantly explained by the soil properties, agreeing that variable selection slightly contributed to Nitrospira community assembly. We also highlighted that each specialist with an unknown affiliation could be a new species or variant from Nitrospira in “specific” micro-environments, as indicated by the fact that one species occurred in only a few soil aggregate size fractions. The present study presents a case in which the stochastic process of Nitrospira community assembly in soil aggregates from two nearby ecosystems with mild environmental conditions could be explained by a high proportion of opportunists plus generalists and a few microhabitat specialists.

Sequence introgression from exogenous lineages underlies genomic and biological differences among Cryptosporidium parvum IOWA lines

The IOWA strain of Cryptosporidium parvum is widely used in studies of the biology and detection of the waterborne pathogens Cryptosporidium spp. While several lines of the strain have been sequenced, IOWA-II, the only reference of the original subtype (IIaA15G2R1), exhibits significant assembly errors. Here we generated a fully assembled genome of IOWA-CDC of this subtype using PacBio and Illumina technologies. In comparative analyses of seven IOWA lines maintained in different laboratories (including two sequenced in this study) and 56 field isolates, IOWA lines (IIaA17G2R1) with less virulence had mixed genomes closely related to IOWA-CDC but with multiple sequence introgressions from IOWA-II and unknown lineages. In addition, the IOWA-IIaA17G2R1 lines showed unique nucleotide substitutions and loss of a gene associated with host infectivity, which were not observed in other isolates analyzed. These genomic differences among IOWA lines could be the genetic determinants of phenotypic traits in C. parvum. These data provide a new reference for comparative genomic analyses of Cryptosporidium spp. and rich targets for the development of advanced source tracking tools.

Environmental DNA metabarcoding of foraminifera for biological monitoring of bottom water and sediments on the Takuyo-Daigo Seamount in the northwestern Pacific

Foraminifera are adapted to a wide range of environments, and environmental DNA (eDNA) metabarcoding of foraminifera should facilitate development of new environmental indicators. In this study, we used eDNA metabarcoding to evaluate the discrepancy between planktic and benthic foraminifera molecular communities identified in bottom water and short sediment cores. The molecular community was compared to foraminiferal shells in sediment traps set on the seafloor. Samples were collected in June and August around the Takuyo-Daigo Seamount in the western subtropical Pacific Ocean. Approximately 40% of amplicon sequence variants (ASVs) pertained to unknown foraminiferal lineages in sediment samples, compared with only 22% in bottom water. Bottom water contained benthic foraminifera and taxonomically unassigned lineages, which were attributed to resuspended particles. In bottom water, 100 ASVs were assigned to planktic foraminifera. ASVs assigned to Candeina nitida were most abundant and accounted for 36%–86% of planktic foraminiferal ASVs. In sedimentary DNA, Globigerinita glutinata was the most abundant among 33 ASVs of planktic foraminifera. However, transparent shells in sediment traps contained more spinose species, such as Globigerinoides ruber, whereas C. nitida was not found and few G. glutinata were detected. This discrepancy between the three samples may be due to the species-specific preservation, to polymerase chain reaction biases, and/or to low abundance of planktic foraminifers. In sedimentary DNA, 893 ASVs were assigned to high-level foraminiferal taxa. Among benthic foraminiferal lineages, monothalamids were most abundant, as reported in other deep-sea regions. Molecular communities formed one cluster above the boundary at which ASVs sharply decrease across the three cores. Our results suggest that depth within the sediment core can affect foraminiferal ASVs, but the distance between sites up to 200 m did not strongly affect ASVs of sedimentary DNA at least above the boundary at which ASVs sharply decrease. Sequences of foraminiferal DNA in sediment decreased linearly in core PC02-A1, but exponentially in core PC03-B3. The decline of foraminiferal ASVs may reflect both the decreases in numbers of living foraminifera and degradation of DNA in sediment, related to the particle mixing depth.

Host-associated genetic differentiation and origin of a recent host shift in the generalist parasitic weed Phelipanche ramosa.

Branched broomrape, Phelipanche ramosa (L.) Pomel, is a globally distributed parasitic weed of economic importance. In Europe, where it is native, it can infest several crops, notably tomato, tobacco, and hemp. In western France, it has recently adapted to a new host crop, oilseed rape, causing substantial damage. The aim of this study was to investigate the evolutionary relationships and genetic differentiation among P. ramosa populations infesting different hosts. We collected 1611 P. ramosa samples from 109 fields cultivated with six different crops (oilseed rape, tobacco, hemp, tomato, lentil, and celery) and distributed among six European countries. All samples were genotyped for ten microsatellite loci and a subset of samples was sequenced for two nuclear genes and two chloroplast genes. Genetic differentiation among populations was high (F ST = 0.807) and mainly driven by differentiation among different host crops, with no significant geographic structure. Genetic structure analysis identified up to seven biologically meaningful clusters that matched with host crops of origin. Reconstructed networks of sequence haplotypes and multilocus SSR genotypes showed a large genetic divergence between samples collected on oilseed rape and samples collected on other crops. The phylogeny inferred from DNA sequences placed samples collected from oilseed rape as a basal lineage. Approximate Bayesian Computations were used to compare different evolutionary scenarios of divergence among the three main genetic clusters, associated, respectively, with oilseed rape, tobacco, and hemp as host crops. The best-supported scenario indicated that P. ramosa infesting oilseed rape derived recently from an ancient, unknown lineage. Our results suggest that a more complete description of the genetic diversity of P. ramosa is still needed to uncover the likely source of the recent adaptation to oilseed rape and to anticipate future new host shifts.

Fakhr al-Din al-Razi's Usage of The Poetic and Grammatical Citation to Guide The Qur'anic Recitations (Qira’at) in His Interpretation of (Mafatih al-Ghayb)

There is no doubt that reliance on the poetic grammatical citation in directing the Quranic recitations is of great importance, as the interpreter is indispensable in some places from citing a verse of poetry in directing a specific recitation from the recitations (Qira’at). In addition, the grammatical poetic evidence, including what is consecutive and frequent attributed, while others through an unknown lineage. As well as different Quranic recitations according to the languages and dialects of the Arabs (including mutawatir and so on), which makes those interested in linguistics and recitations, seek to know that how to deal with (Al-Fakhr Al-Razi in his interpretation “Mafatih Al-Ghayb”) this poetic grammatical elements, and how did he use it to explain the aspects of the recitations in it. Herein lies the research problem. The importance of the research is that the poetic grammatical citation came to control the difference of the recitations and direct their meaning in order to give preference to the strongest meaning and the most correct way. This research also took the descriptive approach based on the analysis of the poetic citation's passage, the placement of the reason of his citing, the opinion of Al-Fakhr Al-Razi about it, and the comparison between the poetic citation and the recitation, because of the difference in acceptance and rejection. This research came in Ten topics and a conclusion that includes the findings of the researcher, the most important of which are: that Fakhr al-Din al-Razi used in his interpretation of (Mafatih al-Ghayb) poetic and grammatical citation to guide the Quranic recitations. And that the citation he cited for directing the recitation was from the well-known eras of Argumentation, and Fakhr al-Din al-Razi was subject to the grammatical rules of the Qur’anic recitations and marveled at the approach of grammarians who preferred to prove a language with an unknown verse and did not recommend proving it with a continuous seventh recitations.

Host Cells of Leucocytozoon (Haemosporida, Leucocytozoidae) Gametocytes, with Remarks on the Phylogenetic Importance of This Character.

Leucocytozoon parasites remain poorly investigated in comparison to other haemosporidians. The host cell inhabited by their blood stages (gametocytes) remains insufficiently known. This study aimed to determine the blood cells inhabited by Leucocytozoon gametocytes in different species of Passeriformes and to test if this feature has a phylogenetic importance. We microscopically analyzed blood films stained with Giemsa from six different bird species and individuals and used PCR-based methods for parasite lineage identification. The DNA sequences obtained were applied for phylogenetic analysis. Leucocytozoon parasite from the song thrush Turdus philomelos (cytochrome b lineage STUR1), the blackbird Turdus merula (undetermined lineage), the garden warbler Sylvia borin (unknown lineage) inhabited erythrocytes, a parasite from the blue tit Cyanistes caeruleus (PARUS4) infects lymphocytes, while in the wood warbler Phylloscopus sibilatrix (WW6) and the common chiffchaff Phylloscopus collybita (AFR205) they were found inhabiting thrombocytes. Parasites infecting thrombocytes were closely related, while the parasites infecting erythrocytes were placed in three different clades, and the one found in lymphocytes was placed in a separate clade. This shows that the determination of host cells inhabited by Leucocytozoon parasites can be phylogenetically important and should be considered in future species descriptions. Noteworthy, phylogenetic analysis might be used for the prediction of which host cells parasite lineages might inhabit.

Unveiling the Genomic Basis of Chemosensitivity in Sarcomas of the Extremities: An Integrated Approach for an Unmet Clinical Need.

Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) can be considered as a spectrum of the same disease entity, representing one of the most common adult soft tissue sarcoma (STS) of the extremities. While MFS is rarely metastasizing, it shows an extremely high rate of multiple frequent local recurrences (50-60% of cases). On the other hand, UPS is an aggressive sarcoma prone to distant recurrence, which is correlated to a poor prognosis. Differential diagnosis is challenging due to their heterogeneous morphology, with UPS remaining a diagnosis of exclusion for sarcomas with unknown differentiation lineage. Moreover, both lesions suffer from the unavailability of diagnostic and prognostic biomarkers. In this context, a genomic approach combined with pharmacological profiling could allow the identification of new predictive biomarkers that may be exploited for differential diagnosis, prognosis and targeted therapy, with the aim to improve the management of STS patients. RNA-Seq analysis identified the up-regulation of MMP13 and WNT7B in UPS and the up-regulation of AKR1C2, AKR1C3, BMP7, and SGCG in MFS, which were confirmed by in silico analyses. Moreover, we identified the down-regulation of immunoglobulin genes in patient-derived primary cultures that responded to anthracycline treatment compared to non-responder cultures. Globally, the obtained data corroborated the clinical observation of UPS as an histotype refractory to chemotherapy and the key role of the immune system in determining chemosensitivity of these lesions. Moreover, our results confirmed the validity of genomic approaches for the identification of predictive biomarkers in poorly characterized neoplasms as well as the robustness of our patient-derived primary culture models in recapitulating the chemosensitivity features of STS. Taken as a whole, this body of evidence may pave the way toward an improvement of the prognosis of these rare diseases through a treatment modulation driven by a biomarker-based patient stratification.

Groundwater Amphipods of the Hyporheic Interstitial: A Case Study from Luxembourg and The Greater Region

Hyporheic interstitials are ecologically dynamic and often neglected aquatic environments. In this study, groundwater amphipods (Niphargidae, Pseudoniphargidae and Crangonyctidae) were sampled in hyporheic interstitials throughout Luxembourg and The Greater Region and specimens were analyzed by DNA barcoding. Sites characterized by gravel or coarse sand and high flow velocities of incoming water were the most species- and specimen-rich. A total of 11 species were detected, of which the Niphargus aquilex lineage EF of the N. aquilex cryptic species complex and juveniles of N. schellenbergi dominated the data set, but an unknown lineage of the N. aquilex-complex was also found. Some regions appeared to be devoid of groundwater amphipods. We hypothesize that underlying sandstone formations resulting in low sediment porosity may prevent physical colonization, but also that historical water pollution may have a long-lasting effect, either through the persistence of contaminants in the sediment or low recolonization rates of affected populations. In summary, our approach expanded regional species inventories, confirmed known occurrences, and validated previously questionable or historical morphology-based detections. In addition, the collection of absence data provided valuable insights into local extinctions. Finally, DNA-based distribution data are needed to gather information on the ecological affinities of groundwater amphipods to understudied hyporheic interstitial environments.

Revealing anole diversity in the highlands of the Northern Andes: New and resurrected species of the Anolis heterodermus species group

The Anolis heterodermus group comprises eight big-headed and short-legged lizard species from the highlands of the northernmost South American Andes. Recent studies revealed unknown lineages within this group that had previously been categorized as a species complex. By widely sampling and applying an integrative taxonomic framework, we (1) assessed the species diversity of the group using a molecular dataset (two mitochondrial and one nuclear markers) along with an inclusive morphological study (scalation, scale configuration and ornamentation, morphometrics, and dewlap and body colour patterns); and (2) we inferred the evolutionary relationships within this species group. Our analyses confirmed the formerly reported differentiation between populations of those high-altitude lizards, and we identified several unknown evolutionary lineages. Our results provided evidence for the existence of nine distinct, independently evolving evolutionary lineages in the heterodermus group. As a result, we described two morphologically and genetically highly distinct lineages as species new to science (A. quimbayasp. nov. and A. tequendamasp. nov.). We redescribed A. heterodermus and erected as a valid species Anolis richteri, a previously described synonym of A. heterodermus. A taxonomic key for the identification of species of the Phenacosaurus clade was presented. The identification of two additional poorly-known lineages suggested that the diversity of this group of lizards is still unknown; therefore, it is necessary to establish measurements for the group´s conservation, as well as to perform fieldwork and revision of herpetological collections to identify possible hidden diversity within the group.

COI-Barcoding and Species Delimitation Assessment of Toad-Headed Agamas of the Genus Phrynocephalus (Agamidae, Squamata) Reveal Unrecognized Diversity in Central Eurasia

We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards.

Sores of boreal moose reveal a previously unknown genetic lineage of parasitic nematode within the genus Onchocerca.

Long-standing reports of open sores on the hind legs of moose (Alces alces) have been recorded in Alaska (as well as Canada, Europe, and Michigan), eliciting concerns about causes and infection. We used histological and genomic methods to investigate the sores from 20 adult moose on the Kenai Peninsula, Alaska. We paired this with thermal imagery and molt scoring of adult moose to further describe sore formation and understand its timing. Severe, ulcerative and eosinophilic dermatitis was found in all moose with sores present, and microfilariae within intraepidermal pustules were additionally found in four samples. Genetic analysis of sores from moose revealed a previously unknown genetic lineage of Onchocerca. Adult moose molt and lose their barrier of protection against flies in June and July during peak fly activity, leaving them vulnerable and allowing the development of sores. In summary, our results indicate that the cause for the sores on the hindleg of moose is a previously unknown genetic lineage of Onchocerca, probably transmitted by black flies, in timing with the molt cycle of adult moose. These sores leave moose exposed to pathogens, making them vulnerable, and challenging their health and fitness.