phylogenetic placement
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Castanea ◽  
2022 ◽  
Vol 86 (2) ◽  
Nicholas Koenig ◽  
Megan Scholer ◽  
Tara Littlefield ◽  
Brad R. Ruhfel

Zootaxa ◽  
2022 ◽  
Vol 5087 (3) ◽  
pp. 441-450

This study targets two specimens of a morphologically highly unusual pill scarab from Cameroon. The original morphology-inspired hypothesis that these beetles represent a new genus is refuted. Instead, a phylogenetic analysis of 90 terminals and 3231 aligned DNA positions linked both specimens with the Afrotropical genus Melanophilharmostes Paulian, 1968. Both Cameroonian specimens are herein described as Melanophilharmostes tuber Grebennikov, new species. Re-evaluation of the morphological characters of this species in light of molecular results corroborated this taxonomic decision by detecting all three morphological autapomorphies of the genus: the presence of setae and horseshoe-shaped microsculpture on the dorsal body surface, as well as the presence of the lateral carina on each elytron. Except for a single representative of the genus Melanophilharmostes placed within the genus Pseudopterorthochaetes Paulian, 1977 (interpreted as an analytical artifact), both genera are sister groups, in agreement with the pre-existing morphology-based hypothesis. Both genera, together with the Malagasy/Comorian genus Synarmostes Germar, 1843 and monotypic Balleriodes Grebennikov, 2021 from Tanzania, constitute the strongly supported Synarmostes group of genera.  

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Jason C. Hyun ◽  
Jonathan M. Monk ◽  
Bernhard O. Palsson

Abstract Background With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for “comparative pangenomics” that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants. Results Applied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species’ phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain’s mutation enrichment is strongly function-dependent. Conclusions These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.

2021 ◽  
Vol 46 (4) ◽  
pp. 1026-1032
Bruno S. Amorim ◽  
Patricia Melchionna Albuquerque ◽  
Duane F. Lima

Abstract— Myrcia longipetiolata, a new species of Myrcia, is here described and illustrated. With a phylogenetic hypothesis, we show that this species belongs to Myrcia clade 10, a morphologically recognized and narrowly distributed group of species, which was recently discovered. Myrcia longipetiolata resembles M. unana due to its long leaves, acute or acuminate leaf apex, cuneate leaf base, long petioles, and they share the same area of occurrence. Myrcia longipetiolata differs from M. unana by its larger leaves, larger number of leaf secondary veins, marginal vein more distant from the leaf margin, lanceolate bracteoles, smaller and truncate, rounded, or apiculate calyx lobes with whitish to yellowish trichomes, and smaller floral disc. Besides the phylogenetic placement of M. longipetiolata within the genus, morphological comparisons with related species and comments on its distribution, habitat, and conservation status are also provided.

Phytotaxa ◽  
2021 ◽  
Vol 527 (2) ◽  
pp. 125-133

Gibellula is an exclusively spider-pathogen genus, with most species immediately recognized by their distinctive conidial state, but also including the teleomorphic states of these fungi that were previously included in the rejected genus Torrubiella. Two sexual specimens and an asexual morph specimen were collected from Anhui Province, China, and were recognized as the same species based on molecular evidence. Its asexual morph differs from Gibellula pulchra, to which it is morphologically similar, in having shorter verrucose conidiophores with slightly smaller metulae, phialides and conidia. Its sexual morph is characterized by producing superficial and elongate ellipsoid small perithecia with short asci on a cream-yellow mycelial mat covering the host. Multi-locus (SSU, LSU, TEF, and RPB1) phylogenetic analyses showed that the specimens belong to a strongly supported subclade, and formed a sister subclade with G. pulchra and Gibellula sp. A combination of morphological characteristics and its phylogenetic placement confirmed that these unique specimens are a new species, which is described as Gibellula flava.

2021 ◽  
Vol 12 (1) ◽  
Xing Guo ◽  
Dongming Fang ◽  
Sunil Kumar Sahu ◽  
Shuai Yang ◽  
Xuanmin Guang ◽  

AbstractChloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

2021 ◽  
Vol 22 (1) ◽  
Rhys A. Farrer

Abstract Background Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. Results HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from under the MIT License. Conclusions HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 597
Laura N. Sutherland ◽  
Kyle E. Schnepp ◽  
Gareth S. Powell ◽  
Seth M. Bybee

The tribe Plesioclytini was recently erected for a single genus of cerambycine longhorn beetle. The group was diagnosed from a proposed sister lineage, the diverse Clytini; however, a formal phylogenetic analysis was not performed due to limitations in data availability. Here, we present a phylogenetic reconstruction from five loci, that Plesioclytini is not sister to Clytini, but is instead only distantly related. Subsequent morphological investigations provide additional support for this placement.

Zootaxa ◽  
2021 ◽  
Vol 5068 (1) ◽  
pp. 81-98

Two new species of Rhinogobius found in streams on central part of Palawan Island, Philippines are described. The two new species, Rhinogobius estrellae and Rhinogobius tandikan share unique transverse rows of sensory papillae on the cheek with Rhinogobius similis Gill, 1859, but differ from the latter in fin ray counts, arrangement of the scales, etc. The two new species are distinguished from each other by the pectoral-fin ray count, the longitudinal- and predorsal-scale counts, and colouration of the body. Rhinogobius estrellae new species and R. tandikan new species have been found allopatrically in a stream within Malatgao River system flowing into the Sulu Sea and in the Cayulo River flowing into the South China Sea, respectively. The Malatgao River system is the southernmost habitat of the genus Rhinogobius. Rhinogobius similis had been considered as the only member of the most basal lineage of this genus, but our mitochondrial genome analysis suggested that the two new species are additional members of this lineage. They are considered to be relicts of their common ancestor with R. similis, which probably had a wider distribution.  

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