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opencc-zeroDec 2015View details →

Data from: Cultural isolation is greater than genetic isolation across an avian hybrid zone

Elucidating the relationship between genetic and cultural evolution is important in understanding speciation, as learned premating barriers might be involved in maintaining species differences. Here we test this relationship by examining a widely recognized premating barrier, bird song, in a hybrid zone between black-throated green (Setophaga virens) and Townsend's warblers (S. townsendi). We use song analysis, genomic techniques and playback experiments to characterize the cultural and genetic backgrounds of individuals in this region, expecting that if song is an important reproductive barrier between these species, there should be a strong relationship between song and genotype. We show that songs in the hybrid zone correspond to the distinctly different songs found in allopatry but that song and genotype are not tightly coupled in sympatry. Allopatric individuals responded only to local songs, indicating that individuals may have learned to respond to songs they commonly hear. We observed discordance between song and genotype clines; a narrower cline suggests that cultural selection on song is stronger than natural selection on genotype. These findings indicate that song is unlikely to play a role in reproductive isolation between these species, and we suggest that spatial variation in song may nonetheless be maintained by frequency-dependent cultural selection. This decoupling of genes and culture may contribute to hybridization in this region.

opencc-zeroDec 2016View details →

Data from: Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata

Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North-America). Post-dormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in post-dormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F1 and F2 progenies suggest that Bateson-Dobzhansky-Muller-incompatibilities likely act through uniparentally inherited factors. Examination of genome-wide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.

opencc-zeroDec 2013View details →

Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB

The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In the present study we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds, and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation, and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.

opencc-zeroDec 2010View details →

Data from: Relationship between genetic distances and postzygotic reproductive isolation in diploid Fragaria (Rosaceae)

Studies of reproductive isolation are important for understanding speciation and species delimitation. We studied seven components of reproductive isolation at different taxonomic and geographical levels and their relationship with genetic distance in diploid Fragaria. Isolation was only evident between different taxa at later stages (post F1 survivorship) not at the earlier ones of fruit and seed set, F1 seed germination and survivorship. Within F. vesca, isolation at the later stages was positively correlated with genetic distance, but this was not found at interspecific levels. The lack of isolation between F. vesca and the other species at the early stages provide the chance for hybrid formation, but high levels of infertility expressed among the offspring can lead to potentially opposing evolutionary outcomes. Within F. vesca, there was evidence of unexpected isolation promoting evolutionary diversification and incipient speciation. Reproductive isolation values between sympatric and allopatric species pairs were similar and indicate a lack of reinforcement in Fragaria. This, combined with the lack of correlation between genetic distance and isolation at interspecific levels shows that genetic distance is not always proportionally correlated with the degree of isolation in plants and suggests that evolutionary processes may be playing differently in plants compared to animals.

opennotspecifiedJan 2014View details →

FIGURE A9b in Abelisauridae (Dinosauria: Theropoda) from the Late Jurassic of Portugal and dentition-based phylogeny as a contribution for the identification of isolated theropod teeth

FIGURE A9b. (Continued)

opencc-zeroJun 2021View details →

Extended data for: Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea

Background: Antimalarial drug resistance is a major challenge hampering malaria control and elimination. Plasmodium falciparum, the leading causative parasite species, has developed resistance to basically all antimalarials. Continued surveillance of drug resistance using genetic markers provides important molecular data for treatment policies. This study sought to verify the genetic mechanism of resistance to sulfadoxine-pyrimethamine and assess the occurrence of point mutations associated with artemisinin resistance in P. falciparum clinical isolates from Eritrea. Methods: Nineteen dried blood spot samples were collected from patients visiting Adi Quala, Keren and Gash Barka Hospitals, Eritrea. The patients were followed up after receiving treatment with first line artesunate-amodiaquine. Nested polymerase chain reaction and Sanger sequencing techniques were employed to genotype point mutations in the P. falciparum bifunctional dihydrofolate reductase-thymidylate synthase (Pfdhfr, PF3D7_0417200), dihydropteorate synthase (Pfdhps, PF3D7_0810800) and kelch 13 (PfK13, PF3D7_1343700) genes. Results: Eight of nineteen (42%) of the dried blood spot samples were successful for PCR-amplification. Data analyses of the PCR-positive isolates revealed the following point mutations: Pfdhfr N51I in four isolates, C59R in one isolate, S108N in four isolates, a rare non-synonymous substitution V45A in four isolates and Pfdhps K540E in four isolates. No PfK13 point mutations were reported. Conclusions: Pfdhfr C59R and Pfdhps K540E point mutations are reliable markers for the sulfadoxine-pyrimethamine quintuple mutant haplotype combination. These findings highlight first reports in Eritrea, which verify the underlying genetic mechanism of antifolate resistance. Continuous monitoring of the PfK13 marker is recommended.

opencc-zeroDec 2017View details →

Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size

In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).

opencc-zeroJul 2021View details →

Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds

The role of historical factors in establishing patterns of diversity in tropical mountains has been of interest for some time. In these regions, the historical processes of range fragmentation and contraction followed by dispersal are thought to be mediated by the interplay between rugged relief and climate fluctuations and likely explain most of the dynamics of diversification in plants and animals. Although empirical studies addressing the interaction between climate and topography have provided invaluable insights into population divergence and speciation patterns in tropical montane organisms, a more detailed and robust test of such processes in an explicit spatio-temporal framework is still lacking. Consequently, our ability to gain insights into historical range shifts over time and the genomic footprint left by them is limited. Here we used niche modeling and subgenomic population-level datasets to explore the evolution of two species of warbling finches disjunctly distributed across the Montane Atlantic Forest, a Neotropical region with complex geological and environmental histories. Population structure inferences suggest a scenario of three genetically differentiated populations, which are congruent with both geography and phenotypic variation. Demographic simulations support asynchronous isolation of these populations as recently as ~40 kya, relatively stable population sizes over recent time, and past gene flow subsequent to divergence. Throughout the last 800 ky, niche models predicted extensive expansion into lowland areas with increasing overlap of species distributions during glacial periods, with prominent retractions and isolation into higher altitudes during interglacials, which are in line with signs of introgression of currently isolated populations. These results support a dual role of cyclical climatic changes: population divergence and persistence in mountain tops during warm periods followed by periods of expansion and admixture in lower elevations during cold periods. Shallow genetic divergence could be associated with undiscovered cryptic diversity in this global biodiversity hotspot.

opencc-zeroAug 2021View details →

Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of Rhododendron tsusiophyllum, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of R. tsusiophyllum and three populations of R. tschonoskii as an outgroup. Phylogenetic relationships and their habitats suggest that R. tsusiophyllum had evolved and migrated from cold north to warm south regions. We detected clear genetic divergence among populations in three regions of Honshu and the Izu Islands, suggesting restricted migration between them due to isolated habitats on mountains even in the mainland. The three regions have different changes in effective population size, especially, genetic diversity and population size of the Izu Islands are small compared to the others. Further, habitats of populations in the Izu Islands are warmer than those in Honshu, suggesting that they have undergone adaptive evolution. Our study provides evidences of montane rather than insular isolation on genetic divergence, survival of populations and significance of adaptive evolution for island populations with small population size and low genetic diversity, despite close proximity to mainland populations.

opennotspecifiedNov 2008View details →

FIGURE 3 in The largest blindsnake in Mesoamerica: a new species of Typhlops (Squamata: Typhlopidae) from an isolated karstic mountain in Honduras

FIGURE 3. Dorsal and ventral aspects of the preserved holotype of Typhlops tycherus.

opennotspecifiedAug 2021View details →

FIGURE 1 in Diplodia parva sp. nov., a novel species of the family Botryosphaeriaceae isolated from soil in Korea

FIGURE 1. Map showing the location of sampling site.

opencc-zeroSep 2021View details →

Supplementary material 2 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure S2. ML tree generated from LSU sequence data

Figure 3 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure 3 Morphological characters of Coniochaeta sinensis sp. nov. (HMAS 350269) a, b cultures on PDA from the surface and reverse c, d conidiogenous cells e conidiogenous cell that is producing conidia f chlamydospores g, h conidia. Scale bars: 10 μm.

Figure 2 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure 2 Morphological characters of Coniochaeta fibrosae sp. nov. (HMAS 350271) a, b cultures on PDA from the surface and reverse c swollen conidia d, e swollen conidia germinate hyphae f, g conidiogenous cells h conidia. Scale bars: 10 μm.

opencc-zeroSep 2021View details →

Supplementary material 1 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure S1. ML tree generated from ITS sequence data

Figure 1 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure 1 Maximum Likelihood tree constructed using ITS+LSU dataset. Bootstrap support values ≥ 75% and posterior probabilities ≥ 0.95 are indicated above the nodes as ML / PP. The isolates obtained in this study are shown in bold. T = ex-type isolates.

Figure 4 from: Si H-L, Su Y-M, Zheng X-X, Ding M-Y, Bose T, Chang R-L (2021) Phylogenetic and morphological analyses of Coniochaeta isolates recovered from Inner Mongolia and Yunnan revealed three new endolichenic fungal species. MycoKeys 83: 105-121. https://doi.org/10.3897/mycokeys.83.71140

Figure 4 Morphological characters of Coniochaeta mongoliae sp. nov. (HMAS 350270) a, b cultures on PDA from the surface and reverse, c, d conidiogenous cells e, f chlamydospores g, h conidia. Scale bars: 10 μm.

opencc-zeroSep 2021View details →

Targeted sequencing of the five major carbapenemases identified in clinical isolates

This study aimed to evaluate the diagnostic performance of Carba 5 and its impact on the turn-around-time in a clinical microbiology laboratory. Carba 5 was retrospectively evaluated using 78 carbapenemase producers and 23 non-carbapenemase producers confirmed by PCR and sequencing. The performance and time required for carbapenemase identification were prospectively evaluated using 47 carbapenem resistant Enterobacteriaceae isolates, and the results were compared to those obtained using Xpert Carba-R (Cepheid, Sunnyvale, CA, USA).

Sex, Digital Devices, Social Medias and Social Isolation: A study of sexual behavioral during COVID -19 Pandemic

Study data