Quantifying intraspecific and interspecific trait variability is critical to our understanding of biogeography, ecology and conservation. But quantifying such variability and understanding the importance of intraspecific and interspecific variability remain challenging. This is especially true of large geographic scales as this is where the differences between intraspecific and interspecific variability are likely to be greatest. Our goal is to address this research gap using broad-scale citizen science data to quantify intraspecific variability and compare it with interspecific variability, using the example of bird responses to urbanization across the continental United States. Using more than 100 million observations, we quantified urban tolerance for 338 species within randomly sampled spatial regions and then calculated the standard deviation of each species' urban tolerance. We found that species' spatial variability in urban tolerance (i.e. standard deviation) was largely explained by the variability of urban cover throughout a species' range (R2 = 0.70). Variability in urban tolerance was greater in species that were more tolerant of urban cover (i.e. the average urban tolerance throughout their range), suggesting that generalist life histories are better suited to adapt to novel anthropogenic environments. Overall, species differences explained most of the variability in urban tolerance across spatial regions. Together, our results indicate that (1) intraspecific variability is largely predicted by local environmental variability in urban cover at a large spatial scale and (2) interspecific variability is greater than intraspecific variability, supporting the common use of mean values (i.e. collapsing observations across a species' range) when assessing species-environment relationships. Further studies, across different taxa, traits and species-environment relationships are needed to test the role of intraspecific variability, but nevertheless, we recommend that when possible, ecologists should avoid using discrete categories to classify species in how they respond to the environment.
Two species of Spinitectus Fourment, 1884 have been recorded from southern Africa, namely Spinitectus polli Campana-Rouget, 1961 and Spinitectus petterae Boomker, 1993, both from the Limpopo River system. Spinitectus petterae was described from North African catfish, Clarias gariepinus (Burchell), whereas S. polli infects squeakers, Synodontis spp. During parasitological surveys in the Vaal River system (Orange River catchment), Spinitectus specimens were collected from C. gariepinus. These systems are adjacent but not connected. Therefore, this study aimed to identify the specimens collected using morphological and molecular techniques. The morphological study included light and scanning electron microscopy of whole specimens and excised spicules. Specimens were genetically characterised using 18S rDNA, 28S rDNA and cox1 mtDNA. Additionally, immature specimens of S. petterae were collected near the type locality. Morphological characteristics were most similar to S. petterae from C. gariepinus, whereas genetic data were dissimilar to all available data for the genus. Additional morphological characteristics noted for S. petterae in the present study were the details of the left and right spicule structure and the porous structures on the pseudolabia. Specimens from the Vaal River system differed from those originally described as S. petterae by additional spines posterior to the third ring, lacking caudal alae and variable total body and male oesophagus length. Based on 18S rDNA, haplotypes from the type locality varied only slightly from the study material, supporting the morphological identification. However, 28S rDNA and, more conspicuously, cox1 mtDNA displayed substantial variation between specimens from these localities, which needs further investigation. Haplotypes generated in the present study were highly dissimilar to those characterised for S. petterae from Tanzania and Egypt. Nevertheless, the nematodes collected from C. gariepinus in the Vaal River system are considered S. petterae. This study expands the geographical distribution and adds additional morphological and genetic information for S. petterae, contributing to the limited knowledge of African species of Spinitectus.
- MeSH
- Microscopy, Electron, Scanning MeSH
- Rivers MeSH
- Rhabditida * MeSH
- DNA, Ribosomal MeSH
- Spiruroidea * MeSH
- Catfishes * MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology102: 95-132. doi: 10.3114/sim.2022.102.03.
- Publication type
- Journal Article MeSH
Phytophthora cinnamomi Rands is a cosmopolite pathogen of woody plants which during the last couple of centuries has spread all over the world from its center of origin in Southeast Asia. In contrast to Chinese cork oak (Quercus variabilis Blume) forests native to Asia, which are generally healthy despite the presence of the pathogen, the populations of Cork oaks (Quercus suber L.) in Europe have been severely decimated by P. cinnamomi. The present study aims at identifying the differences in the early proteomic and metabolomic response of these two tree species that lead to their differences in susceptibility to P. cinnamomi. By using micropropagated clonal plants, we tried to minimize the plant-to-plant differences in the defense response that is maximized by the high intraspecific genetic variability inherent to the Quercus genus. The evolution on the content of Phytophthora proteins in the roots during the first 36 h after inoculation suggests a slower infection process in Q. variabilis plants. These plants displayed a significant decrease in sugars in the roots, together with a downregulation of proteins related to carbon metabolism. In the leaves, the biggest changes in proteomic profiling were observed 16 h after inoculation, and included increased abundance of peroxidases, superoxide dismutases and glutathione S-transferases in Q. variabilis plants, which probably contributed to decrease its susceptibility to P. cinnamomi.
- Publication type
- Journal Article MeSH
PURPOSE: Even though the taxonomy of bat-infesting chiggers has been studied extensively, information about the distribution and morphological variability of many species is still lacking. In fact, the only available distribution records for several species are their type localities. The purpose of this paper is to broaden the knowledge of the Indonesian group. METHODS: Hosts and chiggers were captured from April 2018 to March 2020 in Bali and Nusa Penida Islands in Indonesia by using standard bat-capturing and parasite-collecting methods. A list of bat-infesting chiggers in Indonesia was compiled by searching the public databases using specific keywords. RESULTS: When compared with already published data on type specimens, the physical measurements and morphology of Whartonia diosi, W. maai and Grandjeana sinensis revealed only minor differences that fell within intraspecific variability of the mentioned species. Two species (W. diosi and G. sinensis) are recorded here for the first time outside of their type localities (Panay Island in the Philippines and China) and, in both cases, represent the first records for Indonesia. The checklist summarizes all 16 species in 9 genera of bat-infesting chiggers collected from 12 bat species belonging to 5 families all collected on 8 Indonesian islands. CONCLUSION: Indonesia comprises more than 17,000 islands, is home to over 200 bat species, and harbors hundreds of still undiscovered caves. With such a huge potential for chigger diversity and endemism, it is likely that our results document only a fraction of the actual diversity.
- MeSH
- Chiroptera * MeSH
- Mite Infestations * MeSH
- Humans MeSH
- Trombiculidae * anatomy & histology MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
- Geographicals
- China MeSH
- Indonesia MeSH
Necrophagous blowflies (Diptera: Calliphoridae) are of great importance particularly during investigations of suspicious deaths. Many studies have analyzed the distribution of blowflies based on pig experiments and baited trapping; however, data from real case scenarios are rarely used. In this article, the distribution of blowflies found during investigations of 160 real cases during 1993-2007 in Switzerland is evaluated based on habitat, altitude, and season. Ten species of blowflies were present in 145 out of the 160 cases. The most common species was Calliphora vicina, which occurs throughout the year and was present in 69 % of all cases. Lucilia sericata, Calliphora vomitoria, and L. caesar were identified among the rest of the flies as species of great forensic importance mainly due to their distributional patterns. After a comparison with a similar dataset from Frankfurt, Germany, some surprising differences were determined and discussed. The biggest discrepancies between our dataset and the German dataset were in the occurrences of L. sericata (30 % vs. 86 %, respectively), Phormia regina (5 % vs. 43 %), and L. ampullacea (1 % vs. 45 %). The life-history strategies and intraspecific behavioral variability of blowflies remain understudied, although they can be essential for an unbiased approach during a death investigation. Further research and comparison of occurrence patterns across the area of distribution of blowflies are therefore needed and recommended.
Lacking fur, living in eusocial colonies and having the longest lifespan of any rodent, makes naked mole-rats (NMRs) rather peculiar mammals. Although they exhibit a high degree of polymorphism, skeletal plasticity and are considered a novel model to assess the effects of delayed puberty on the skeletal system, scarce information on their morphogenesis exists. Here, we examined a large ontogenetic sample (n = 76) of subordinate individuals to assess the pattern of bone growth and bone microstructure of fore- and hindlimb bones by using histomorphological techniques. Over 290 undecalcified thin cross-sections from the midshaft of the humerus, ulna, femur, and tibia from pups, juveniles and adults were analyzed with polarized light microscopy. Similar to other fossorial mammals, NMRs exhibited a systematic cortical thickening of their long bones, which clearly indicates a conserved functional adaptation to withstand the mechanical strains imposed during digging, regardless of their chisel-tooth predominance. We describe a high histodiversity of bone matrices and the formation of secondary osteons in NMRs. The bones of pups are extremely thin-walled and grow by periosteal bone formation coupled with considerable expansion of the medullary cavity, a process probably tightly regulated and adapted to optimize the amount of minerals destined for skeletal development, to thus allow the female breeder to produce a higher number of pups, as well as several litters. Subsequent cortical thickening in juveniles involves high amounts of endosteal bone apposition, which contrasts with the bone modeling of other mammals where a periosteal predominance exists. Adults have bone matrices predominantly consisting of parallel-fibered bone and lamellar bone, which indicate intermediate to slow rates of osteogenesis, as well as the development of poorly vascularized lamellar-zonal tissues separated by lines of arrested growth (LAGs) and annuli. These features reflect the low metabolism, low body temperature and slow growth rates reported for this species, as well as indicate a cyclical pattern of osteogenesis. The presence of LAGs in captive individuals was striking and indicates that postnatal osteogenesis and its consequent cortical stratification most likely represents a plesiomorphic thermometabolic strategy among endotherms which has been suggested to be regulated by endogenous rhythms. However, the generalized presence of LAGs in this and other subterranean taxa in the wild, as well as recent investigations on variability of environmental conditions in burrow systems, supports the hypothesis that underground environments experience seasonal fluctuations that may influence the postnatal osteogenesis of animals by limiting the extension of burrow systems during the unfavorable dry seasons and therefore the finding of food resources. Additionally, the intraspecific variation found in the formation of bone tissue matrices and vascularization suggested a high degree of developmental plasticity in NMRs, which may help explaining the polymorphism reported for this species. The results obtained here represent a valuable contribution to understanding the relationship of several aspects involved in the morphogenesis of the skeletal system of a mammal with extraordinary adaptations.
- MeSH
- Femur anatomy & histology MeSH
- Humerus anatomy & histology MeSH
- Mole Rats MeSH
- Osteogenesis physiology MeSH
- Tibia anatomy & histology MeSH
- Ulna anatomy & histology MeSH
- Bone Development physiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Leishmania spp. are important pathogens causing a vector-borne disease with a broad range of clinical manifestations from self-healing ulcers to the life-threatening visceral forms. Presence of Leishmania RNA virus (LRV) confers survival advantage to these parasites by suppressing anti-leishmanial immunity in the vertebrate host. The two viral species, LRV1 and LRV2 infect species of the subgenera Viannia and Leishmania, respectively. In this work we investigated co-phylogenetic patterns of leishmaniae and their viruses on a small scale (LRV2 in L. major) and demonstrated their predominant coevolution, occasionally broken by intraspecific host switches. Our analysis of the two viral genes, encoding the capsid and RNA-dependent RNA polymerase (RDRP), revealed them to be under the pressure of purifying selection, which was considerably stronger for the former gene across the whole tree. The selective pressure also differs between the LRV clades and correlates with the frequency of interspecific host switches. In addition, using experimental (capsid) and predicted (RDRP) models we demonstrated that the evolutionary variability across the structure is strikingly different in these two viral proteins.
- MeSH
- Leishmania virology MeSH
- Leishmaniasis virology MeSH
- Humans MeSH
- RNA, Viral analysis MeSH
- RNA-Dependent RNA Polymerase genetics MeSH
- RNA Viruses genetics MeSH
- Capsid Proteins genetics MeSH
- Viral Proteins genetics MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Sex chromatin is a conspicuous body that occurs in polyploid nuclei of most lepidopteran females and consists of numerous copies of the W sex chromosome. It is also a cytogenetic tool used to rapidly assess the W chromosome presence in Lepidoptera. However, certain chromosomal features could disrupt the formation of sex chromatin and lead to the false conclusion that the W chromosome is absent in the respective species. Here we tested the sex chromatin presence in 50 species of Geometridae. In eight selected species with either missing, atypical, or normal sex chromatin patterns, we performed a detailed karyotype analysis by means of comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH). The results showed a high diversity of W chromosomes and clarified the reasons for atypical sex chromatin, including the absence or poor differentiation of W, rearrangements leading to the neo-W emergence, possible association with the nucleolus, and the existence of multiple W chromosomes. In two species, we detected intraspecific variability in the sex chromatin status and sex chromosome constitution. We show that the sex chromatin is not a sufficient marker of the W chromosome presence, but it may be an excellent tool to pinpoint species with atypical sex chromosomes.
- MeSH
- Species Specificity MeSH
- In Situ Hybridization, Fluorescence MeSH
- Karyotype MeSH
- Moths genetics MeSH
- Sex Chromosomes genetics MeSH
- Sex Chromatin metabolism MeSH
- Comparative Genomic Hybridization MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
European brown hare (Lepus europaeus Pallas 1778) is a broadly distributed lagomorph species in Europe, recognized as a host for Ixodes ricinus and reservoir of a wide range of pathogens with zoonotic potential. Even though Lepus europaeus represents an important game animal in Central Europe, the data available on Anaplasma phagocytophilum in this lagomorph are scarce. In this study, three populations of brown hare from distinct localities in the Czech Republic were analysed for the presence of Anaplasma phagocytophilum DNA. We used standard qPCR, targeting the msp2 gene and adapted the same assay also for digital droplet PCR. Out of 91 samples, these two methods identified 9 and 12 as positive, respectively. For taxonomic analysis, we amplified the groEL gene from five of six samples that were found positive by both methods. In phylogenetic analyses, this haplotype belongs to ecotype 1, and to the subclade with isolates from cervids and I. ricinus. Our findings underline the importance of correct result interpretation and positivity cut-off set-up for different detection methods of A. phagocytophilum. This bacterium is characterized by a high intraspecific variability and highly sensitive detection itself, is not enough. Detailed molecular typing is necessary to define the zoonotic potential of different strains and their natural reservoirs.
- MeSH
- Anaplasma phagocytophilum * genetics MeSH
- Phylogeny MeSH
- Ixodes * microbiology MeSH
- Hares * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
