Figure 2 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
Methods of concatenation and coalescence. (A) Concatenation method joins all gene sequences of each species into each super-gene sequence. These super-gene sequences are then used in aligning and building phylogeny trees; (B) Coalescence method extracts the same gene sequences from all species and merges them into each single parallel-gene sequence file. Then all parallel-gene sequence files are aligned separately to build trees. Finally, all those trees are computed to get the final tree.
Source publication
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of...
Contexts in source publication
Context 1
... the development of next-generation sequencing and computational phylogenomics, the reconstruction of angiosperm phylogenies from multiple genes has relied upon concatenation methods [18]. The concatenation method concatenates multiple gene sequences of each species and treats them as one alignment to generate a phylogenetic tree ( Figure 2A). As the number of subsampled nuclear genes increases, the result of concatenation analyses becomes dependable [18]. ...
Context 2
... demonstrated that using concatenated data, species tree estimation performed deficiently and was statistically inconsistent even under stable population size without selection or population stratification. In addition to concatenation method, recent studies have also taken advantage of coalescence method for phylogenetic analysis [20,21].This method first computes gene trees by the individual gene sequences and then aggregates all gene trees to obtain the final species tree ( Figure 2B) [15]. Goncalves and colleagues [22] conducted a phylogenetic analysis of 78 plastid genes, and their results showed that the phylogenetic tree inferred by the coalescence method was reliable. ...
Context 3
... extracting 50 unique genes, we constructed the phylogenetic trees using each individual gene. However, most of the 50 chloroplast gene trees ( Figure S2) showed chaotic phylogenetic relationships. For example, matK, ndhF, rbcL and rpoC1 genes (Figure 4), which are commonly used to construct phylogenetic trees, indicated that species of the genus Juglans failed to group together. ...
Context 4
... entire chloroplast coding sequence (CDS) and protein sequences (entire-genes) of each species (Table 2) were concatenated to make super sequences (Figure 2A) using in-house Linux scripts. The super-entire-CDSs and super-entire-protein sequences of all the chloroplast genomes were acquired. ...
Context 5
... gathering common coding gene sequences into common files, a total of 73 specific gene sequence files were acquired (Table S4). These 73 CDS and protein sequences were used to contract the parallel-entire-genes phylogeny trees ( Figure 2B). Similarly, the alignment of each specific sequence file was also created using MAFFT v7.271 and constructed phylogenetic trees using IQtree with the same parameters as described in unique chloroplast genes above. ...
Citations
... The topologies inferred from the chloroplast genomes are shown in Fig. 2 (left). Carya was reconstructed as monophyletic with a strong support value (MP-BS = 100%, ML-BS = 100%, PP-BI = 1.00), which is consistent with previous studies (Zhang et al. 2013, Luo et al. 2021). The phylogenetic relationships indicate that the newly identified species is a sister to Carya tonkinensis with high support values (MP-BS = 100%, ML-BS = 100%, PP-BI = 1.00). ...
Carya luana sp. nov., a new species of Juglandaceae from Guizhou, China, is described and illustrated. The new species is easily distinguished from other Carya species by having lanceolate leaflets and obovate fruits with a 4–6 mm thick husk, but is otherwise morphologically close to C. tonkinensis and C. kweichowensis . Based on phylogenetic reconstruction of whole plastomes, C. luana is the sister of C. tonkinensis , while formed a clade with C. tonkinensis and C. hunanensis on ITS. A morphometric analysis demonstrate that C. luana , C. tonkinensis and C. kweichowensis are morphologically distinct. The conservation status of C. luana is assessed as Endangered (EN) according to the IUCN Red List Categories and Criteria. A new identification key to all Asian Carya species is provided.
... In the original publication [1], there was a mistake in Table 2 as published. Minor errors were found in the number of tRNA and rRNA genes, CDS length and GC content in Table 2. ...
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
