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opencc-zeroApr 2023View details →

Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

Background Abies koreana E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Results Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1,186 bp) of the A. koreana plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. Conclusions These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus.

Fig. 4 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. 4. Divergence time estimation of Vitis inferred from the MCMC tree program in PAML. Blue bars indicate the 95% highest posterior density credibility interval for node ages. Star indicates calibration point. HPD = Highest Posterior Density; Ma = million years ago.

Fig. 3 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. 3. Maximum likelihood (ML) phylogeny and geographic distribution of East Asian grapes. Outgroups are not shown. Approximate ranges of the geographic distribution of the individual species are shown in the maps, using different colors. Tree branches are colored according to the geographic distribution of each species. Orange = Subclade I; yellow = Subclade II; green = Subclade III; Purple and blue tones = Subclade IV. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 1 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. 1. Phylogenetic relationship and ancestral areas of subgenus Vitis. (a) Maximum likelihood (ML) phylogeny of Vitis based on 2068 single-copy orthologous genes. All nodes are supported by 100% bootstrap support except from one, whose support is indicated in the figure. Numbers above branches indicate bootstrap support estimated in RAxML while numbers below branches indicate bootstrap support estimated in PhyML. (b) Ancestral area reconstructions of subgenus Vitis using BBM, implemented in RASP. Possible ancestral ranges and their respective probabilities are shown at each node. Most Likely States (MLS) are shown at the center of each node. The four areas of endemism considered are: (A) North America; (B) Europe and West Asia; (C) Northeastern Asia, North China, and the northern edge of the Himalayas; and (D) Central and South China, northern South Asia, and northern Southeast Asia. Dashed arrows indicate inferred migration routes for subgenus Vitis. Three possible migration routes of subgenus Vitis from North America to Euroasia are shown, i.e., the North Atlantic land bridges (NALB), the Bering land bridge (BLB), and intercontinental long distance dispersal (LDD).

Fig. 6 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. 6. Ecological environments occupied by various Vitis. (a) V. romanetii is one of the highest climbing species of Vitis, which usually occurs in forest habitats. (b) V. sinocinerea is one of the lowest climbing species of Vitis, which usually occurs in shrubby or open habitats.

Fig. 2 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. 2. Maximum likelihood (ML) phylogeny and geographic distribution of North American grapes. Approximate ranges of geographic distribution of species are labeled in the map using different colors. Tree branch colors match the geographic distribution of each species. Blue = Subclade I; Green and purple = Subclade II. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. A.2 in Phylogenomics, biogeography, and adaptive radiation of grapes

Fig. A.2 Gene family analysis. (a) The content of the orthologous genes in different species; (b) Clustering graph of gene family of orthologous genes. (FV: Fragaria vesca; MD: Malus x domestica; VV: Vitis vinifera; PP: Prunus persica; AT: Arabidopsis thaliana).

opennotspecifiedSep 2020View details →

Fig. 1 in Out of the Pan- Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics

Fig. 1. Results of phylogenetic analyses based on 25 regions of 20 nuclear loci from 51 individuals of wild peony species. The maximum likelihood tree inferred using PAUP from the concatenating sequences. Numbers on branches represent support values from maximum likelihood/Bayesian inference (BI) analyses. –, Value below 50%.

opennotspecifiedSep 2020View details →

Fig. 3 in Out of the Pan- Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics

Fig. 3. Strict maximum parsimony consensus trees based on 14 chloroplast genomes (left) and 25 regions of nuclear loci (on the right), showing the origins of Asian Paeonia mairei and European P. arietina, P. officinalis, and P. parnassica (in bold). Paeonia daurica, P. obovata, P. tenuifolia, and P. veitchii (including P. sterniana) served as parents. Colored lines indicate haplotypes from paternal parents. The maternal haplotypes in the tetraploids are phylogenetically closer to those in Asian P. tenuifolia or P. obovata than to those in European species. Italic D, O, T, and V refer to the homologous genomes of P. daurica, P. obovata, P. tenuifolia, and P. veitchii (including P. sterniana), respectively. Numbers on branches represent maximum parsimony bootstrap support percentages equal to or larger than 50.

opennotspecifiedSep 2020View details →

Fig. 2 in Out of the Pan- Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics

Fig. 2. Divergence times from BEAST analysis and biogeographical events in the evolutionary by RASP based on 25 regions of 20 nuclear loci from 52 individuals of all wild peony BEAST. Nodes where dispersals or vicariances occurred are number‐labelled and details

opencc-zeroMay 2023View details →

Data from: Redefining possible: Combining phylogenomic and supersparse data in frogs

The data available for reconstructing molecular phylogenies have become wildly disparate. Phylogenomic studies can generate data for thousands of genetic markers for dozens of species, but for hundreds of other taxa, data may be available from only a few genes. Can these two types of data be integrated to combine the advantages of both, addressing the relationships of hundreds of species with thousands of genes? Here we show that this is possible, using data from frogs. We generated a phylogenomic dataset for 138 ingroup species and 3,784 nuclear markers (ultraconserved elements, UCEs), including new UCE data from 70 species. We also assembled a supermatrix dataset, including data from 97% of frog genera (441 total), with 1–307 genes per taxon. We then produced a combined phylogenomic-supermatrix dataset (a "gigamatrix") containing 441 ingroup taxa and 4,091 markers, but with 86% missing data overall. Likelihood analysis of the gigamatrix yielded a generally well-supported tree among families, largely consistent with trees from the phylogenomic data alone. All terminal taxa were placed in the expected families, even though 42.5% of these taxa each had >99.5% missing data, and 70.2% had >90% missing data. Our results show that missing data need not be an impediment to successfully combining very large phylogenomic and supermatrix datasets, and they open the door to new studies that simultaneously maximize sampling of genes and taxa.

opencc-zeroMay 2023View details →

Species delimitation beyond phylogenomics: integrative approaches reveal gentoo penguin speciation

Isolation and adaptation to new environments are important steps for reproductive isolation and consequently speciation. Seabirds have low phenotypic variation along their ranges in the absence of clear geographic or environmental barriers to dispersal. Despite the lacking visible phenotypic differences, the number of taxa for the gentoo penguin (Pygoscelis papua, Forster 1781) in the Southern Ocean has been under debate for the last decade, ranging from one to six different taxa. Here, we provide several lines of evidence from genomics, ecology, morphological data, and a complete systematic review that supports four distinctive gentoo penguin species, including the description of a new species. We also provide future niche projections for each of these species. Gentoo penguin genomes (n = 64) recover four main lineages: the northern gentoo (from South America), the southern gentoo (Antarctic Peninsula and maritime Antarctica, south of the Antarctic Polar Front, APF), the southeastern gentoo (from Kerguelen Islands), and the eastern gentoo (colonies located at lower latitudes north of the APF). Our analysis of selection across the genome recovered between 42 and 101 genes under selection for each of the four species, demonstrating that the four species are experiencing differing selective pressures that have caused them to diverge adaptively. The function of these genes affects traits that include reproduction, thermoregulation, osmoregulation, feed efficiency, and morphological variation. Morphological data were taken from museum individuals of all lineages, including from South Georgia gentoos, which have previously been considered a distinct taxon. Multivariate morphological comparisons of all pairs of lineages showed that the northern, southern, southeastern, and South Georgia gentoo penguins are morphologically distinct from each other (p < 0.05 for all pairwise comparisons), while the eastern lineage is intermediate in size and overlaps in morphospace with other lineages. This result also suggests that body size across latitudes is in direct contrast to Bergmann's rule. Here, we describe the southeastern gentoo penguin from Kerguelen Island and confirm the taxonomic rank of gentoos from Macquarie Island and South Georgia Island as subspecies. Species distribution modelling suggests that climate change will expand the favourable space for the southern range expansion of the southern gentoo penguin but would result in a net loss of suitable habitats for compensatory niche shift relocation for the northern and southeastern gentoos. Despite this, amongst the three subantarctic species, the northern and southeastern gentoos possess high neutral and adaptive genetic diversity, including genes related to cold and heat response. This may represent a higher potential to evolve under environmental changes compared with the eastern gentoo penguin; therefore, the future resilience of each species remains uncertain. This study reinforces the urgent need for explicit recognition and protection of the four regional gentoo species based on their genetic, morphological, and ecological distinctiveness.

opencc-zeroAug 2023View details →

Data from: A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes

Alvinellid worms are a family of endemic and closely related species from deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, sister group to the Ampharetidae, occupy a wide range of ecological niches, some of which include the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not yet been studied extensively. It is, however, a complex case with conflicting molecular phylogenies, the main question being the monophyletic or polyphyletic character of the genus Paralvinella. We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets. The study is based on the assembly of several hundred transcripts for 11 of the 14 species described or in description. The results obtained by the most popular phylogenetic inference models (gene concatenation and maximum likelihood, or coalescent-based methods from gene trees) are compared, and an attempt is made to use sequence insertion and deletion information to evaluate and strengthen our choice over the different phylogenies using a newly-developed maximum likelihood method. Although our study does not allow to definitively assert the phylogeny of the Alvinellidae (three species are still missing), we propose to support the initial hypothesis of the monophyly of the Paralvinella proposed by Desbruy`eres and Laubier on the basis of the morphology of the species, in which the species Paralvinella pandorae and Paralvinella unidentata are basal in the genus Paralvinella and grouped together within the subgenus nautalvinella. Following a clock calibration, the radiation of the Alvinellidae, dated between 55 and 78 Myr, took place very rapidly, resulting in high rates of incomplete lineage sorting between the first ancestors and probable gene transfers between the Alvinella, Nautalvinella and the rest of the Paralvinella lineages.

opencc-zeroSep 2023View details →

Supplementary material 2 from: Dagallier L-PMJ, Mbago FM, Couderc M, Gaudeul M, Grall A, Loup C, Wieringa JJ, Sonké B, Couvreur TLP (2023) Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis. PhytoKeys 233: 1-200. https://doi.org/10.3897/phytokeys.233.103096

RAxML maximum likelihood tree of the Monodoreae, based on a concatenated supermatrix of 334 nuclear genes. Bootstrap support values (in %) are given at the nodes