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FIG. 5 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)

FIG. 5. — Photomicrographs of thin slides: A, Planktonic foraminifera () and ferroan euhedral dolomite crystals () (S# 09); B, dolomitized zone () with planktonic foraminifera (), radiolarians () and ostracods () (S# 25); C, contact of the foraminiferal wackestone and packstone patch (S# 22); D, radiolarian rich facies showing radiolarians () and calcispheres () (S# 18); E, Heterohelix sp. () along with radiolarians () and ostracods () (S# 17); F, dolomitized zone between the lime mudstone (MS) and wackestone (WS) (S# 11); G, tectonic induced fracturing (S# 07); H, radiolarians () and zoned ferroan dolomite crystals in the mudstone facies (S# 11); I, well rounded feldspar grains (S# 38); J, chert lithic (S# 36); K, ferruginous matrix (S# 37); L, quartz () and feldspar () grains in Hangu Formation (S# 38). Scale bars: A-C, F, G, 200 µm; D, E, H-L, 100 µm.

FIG. 1 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)

FIG. 1. — Regional geological map after Burg (2011). The red square corresponds to studied location at Dhudial.

FIG. 9 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)

FIG. 9. — Sketch showing the platform evolution through different stages. The platform geometry in the early Campanian time (Stage I) during deposition of Kawagarh Formation was characterized by a steeper ramp. An incised valley and sequence boundary developed in Stage II during Selandian and the platform configuration became much gentler during the Thanetian (Stage III) as the accommodation space filled up.

FIG. 7 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)

FIG. 7. — Chart showing the sequence stratigraphic framework, sea level changes and paleoecology of the Dhudial Section.

FIG. 8 in Foraminiferal biostratigraphy, facies and sequence stratigraphy analysis across the K-Pg Boundary in Hazara, Lesser Himalayas (Dhudial Section)

FIG. 8. — Chart showing the planktonic foraminiferal distribution and biozones of the Dhudial Section.

opencc-by-4.0Jan 2022View details →

Supplementary Data for "Sequencing the Pandemic: Rapid and High-Throughput Processing and Analysis of COVID-19 Clinical Samples for 21st Century Public Health"

Supplementary material for F1000 methods manuscript. Includes raw sequencing metrics for two COVID sequencing methodologies, as well as a complete cost breakdown for each methodology.

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Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes

Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole alignments may be done, and release new bioinformatics tools that implement statistically sound methods of dealing with multiple comparisons (i.e., by controlling the family-wise error rate or the false discovery rate). Using the new software to analyse an alignment of amino acids encoded by 116 flavivirus genomes, we reveal, for the first time, that these genomes are unlikely to have evolved under stationary, reversible, and homogeneous Markovian conditions.

opencc-zeroJun 2022View details →

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Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

opencc-zeroJun 2022View details →

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Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)

Background: Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species. Results: The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap. Conclusions: The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

opencc-zeroJun 2022View details →

opencc-by-4.0Aug 2022View details →

Data and analysis script to support "Multi-site analysis of sequence in leaf-out and flowering reveals evidence of local adaptation"

Data files and R script used to download and analyze plant leaf-out and flowering observations maintained by the USA National Phenology Network to evaluate the consistency of leaf-out and flowering among species pairs over multiple years.

Fig. 3 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)

Fig. 3. Predicted secondary structure of the rrnl in the Acanthacorydalis orientalis mt genome. Roman numerals denote the conserved Watson-Crick base pairing and dot (•) indicates G-U base pairing.

Fig. 4 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)

Fig. 4. Predicted secondary structure of the rrns in the A. orientalis mt genome. Roman numerals denote the conserved domain structure. Dash (-) indicates Watson-Crick base pairing and dot (•) indicates G-U base pairing.

Fig. 1 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)

Fig. 1. Mitochondrial genome map of Acanthacorydalis orientalis. The tRNAs are denoted by the color blocks and are labeled according to the IUPACIUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription

Fig. 2 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)

Fig. 2. Inferred secondary structure of 22 tRNAs of the Acanthacorydalis orientalis mt genome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dash (-) indicates Watson-Crick bonds and dot (·) indicates GU bonds.

Fig. 5 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)

Fig. 5. Phylogenetic relationships among the sequenced Megaloptera insects. Numbers at the nodes are Bayesian posterior probabilities (left) and ML bootstrap values (right).

Fig. 6 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis

Fig. 6. The phylogenetic relationship of Bonasa among Galliformes based on the complete mitogenome. Branch lengths and topologies were obtained from Maximum Likelihood analyses. The numbers were the bootstrap values of MP/ML/BI trees in turn. * indicates that MP or BI tree was inconsistent with ML tree.

Fig. 4 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis

Fig. 4. The structure of CR in Bonasa sewerzowi mitochondrial genome and comparasion with B. bonasia.

Fig. 5 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis

Fig. 5. Nucleotide composition of different partitions from two Bonasa mitogenomes. AT-skew, (A-T)/(A+T); GC-skew, (G-C)/(G+C); PCG-1st, the first codon positions of PCGs; PCG-2nd, the second codon positions of PCGs; PCG-3rd, the third codon positions of PCGs.

Fig. 3 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis

Fig. 3. The srRNA secondary structure of Bonasa sewerzowi mitogenome and comparasion with B. bonasia. The different nucleotides in B. bonasia was pointed out.

Fig. 1 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis

Fig. 1. Gene map of the B. sewerzowi mitochondrial genome. Transfer RNA genes are designated by single-letter amino acid codes. L1, L2, S1, and S2 denote trnL (uur), trnL (cun), trnS (ucn) and trnS (agy), respectively.