Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Molecular Phylogenetics and Evolution, Год журнала: 2025, Номер 204, С. 108293 - 108293

Опубликована: Янв. 23, 2025

Язык: Английский

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Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Ilex rotunda Thunb.

Forests, Год журнала: 2024, Номер 15(7), С. 1117 - 1117

Опубликована: Июнь 27, 2024

Ilex rotunda Thunb. stands as a representative tree species in subtropical evergreen broad-leaved forests, widely distributed across southeast Asia. This holds significant value forestry due to its ecological resilience and adaptability. Although researchers have conducted in-depth research on the plastid genome (plastome) of I. rotunda, mitochondrial (mitogenome) this has remained undocumented. In present study, we successfully sequenced assembled mitogenome. The mitogenome circular structure is 567,552 bp total length, with GC content 45.47%. composition encompasses 40 protein-coding genes, along 3 rRNA genes 19 tRNA genes. Notably, exhibits universal distribution repetitive sequences, but length repeats contributes relatively small proportion (4%) whole mitogenome, suggesting that do not serve primary cause amplification mitogenomes. Collinear analysis indicates very conservative within Aquifoliales species. Additionally, our identified 51 fragments genomic DNA, which migrated from plastome into five remaining intact. Eventually, phylogenetic analyses based plastomes mitogenomes 36 angiosperms determine be basal group campanulids. study establishes bedrock for prospective investigations molecular breeding research.

Язык: Английский

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Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 195, С. 108064 - 108064

Опубликована: Март 19, 2024

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, is distributed worldwide in temperate tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera ca. 160 species, restricted eastern Australia, New Zealand, Guinea. species show an impressive range growth habit, from small herbs ericoid subshrubs medium-sized trees. They live a wide habitats are often dominant subalpine alpine vegetation. Despite well-supported circumscription Celmisiinae, uncertainties have remained about their internal relationships classification at genus levels. This study exploited recent advances high-throughput sequencing build robust multi-gene phylogeny for subtribe Celmisiinae. target enrichment Angiosperms353 bait set hybpiper-nf paragone-nf pipelines were used retrieve, infer, assemble orthologous loci 75 taxa representing all main putative clades within subtribe. Because diploidised ploidy level as well missing data assemblies, uncertainty remains surrounding inference orthology detection. However, based on variety gene-family sets, coalescent concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy gene-families caused some problems, but estimated phylogenies well-resolved. phylogenomic evidence supported three clades: Pleurophyllum clade (Pleurophyllum, Macrolearia Damnamenia), mostly Zealand Subantarctic Islands, Celmisia mainland Shawia (including 'Olearia pro parte' Pachystegia) Australia results presented here add accumulating support efficient method documenting plant diversity.

Язык: Английский

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Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 198, С. 108136 - 108136

Опубликована: Июнь 22, 2024

Язык: Английский

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Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Опубликована: Май 27, 2024

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking step-change in the generation of data phylogenetic inference. While this advancement facilitated resolution many relationships, conflict continues to be reported, often attributed genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common evolution. The proliferation methods designed analyse target presence these can overwhelming researchers, especially students. In review, we guide researchers through bioinformatic workflow, with particular focus on robust inference conflict. Through highlight key considerations reducing artefactual conflict, synthesise strategies managing paralogs, explain causes measurement summarise current investigating biological underlying draw from examples Australian flora, review is broadly relevant any researcher working data. We conclude inherent inevitable but when properly managed, provide unprecedented insight into extraordinary complex histories plants.

Язык: Английский

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Target capture sequencing clarifies key relationships in the Eriostemon group (Rutaceae: Zanthoxyloideae) and supports a reclassification of Philotheca, including the recognition of two new genera

Taxon, Год журнала: 2025, Номер unknown

Опубликована: Фев. 6, 2025

Abstract The Eriostemon group (Rutaceae) is a clade of 16 genera and ~ 209 species endemic to Australia, New Zealand Caledonia. Recent efforts address taxonomic phylogenetic uncertainty in the using plastome nuclear ribosomal DNA sequences have made some progress but also highlighted problematic areas that require further research. In particular, current circumscription Philotheca known be non‐monophyletic, unclear relationships prevented reclassification group. We generated target capture data Angiosperms353 universal bait kit conducted analyses on with aims resolving uncertain backbone clarifying . Our results uncovered extensive cytonuclear discordance group, conflict between our phylogenies previous observed several key tree. Despite this, positions polyphyletic lineages were consistent enough across enable confident genus, which presented herein. Two sections , P. sect. Corynonema Erionema are raised generic rank under names Erioseira respectively. Cyanochlamys transferred into genus Muiriantha type section retained becomes entirety genus. Appropriate nomenclatural changes transfer all currently recognised subspecies their respective this new classification.

Язык: Английский

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Selecting a Window Size for the Analysis of Whole Genome Alignments using AIC

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 7, 2025

A bstract The variation of evolutionary histories along the genome presents a challenge for phylogenomic methods to identify non-recombining regions and reconstruct phylogenetic tree each region. To address this problem, many studies used non-overlapping window approach, often with an arbitrary selection fixed sizes that potentially include intra-window recombination events. In study, we proposed information theoretic approach select size best reflects underlying alignment. First, simulated chromosome alignments reflected key characteristics empirical dataset found AIC is good predictor accuracy in correctly recovering topologies Due issue missing data datasets, then designed stepwise applied method genomes erato - sara Heliconius butterflies great apes. We butterflies’ chromosomes ranged from < 125bp 250bp, which are much shorter than those previous study even though difference did not significantly change most common across genome. On other hand, apes’ 500bp 1kb proportion major topology (grouping human chimpanzee) falling between 60% 87%, consistent findings. Additionally, observed notable impact stochastic error concatenation when using small large windows, respectively. For instance, apes was 50% 250bp but reached almost 100% 64kb windows. conclusion, our highlights challenges associated selecting analyses proposes as more objective way optimal whole alignments.

Язык: Английский

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Australian biogeography, climate-dependent diversification and phylogenomics of the spectacular Chamelaucieae tribe (Myrtaceae)

Australian Systematic Botany, Год журнала: 2025, Номер 38(1)

Опубликована: Фев. 21, 2025

Chamelaucieae is a diverse tribe in Myrtaceae with ~800 species 37 genera distributed across Australia. We applied target capture sequencing using the Angiosperms353 probe set for 131 taxa as part of Genomics Australian Plants initiative. Sampling all (36) from 10 11 named subtribes, we present phylogenomic analysis tribe. This approach has allowed us to better resolve subtribal relationships tribe, resulting an updated classification and additional subtribe (total 12 subtribes including Triplarininae). Despite these advances, phylogenetic placements Stenostegiinae, Astarteinae, Micromyrtinae remain equivocal resolution should be focus future research. constructed dated phylogeny this genomic dataset investigate tribe’s biogeographic history diversification dynamics. estimate that crown radiation occurred Eocene (c. 42 Ma), ancestral area origin Australia unresolved. Subsequent divergence mostly south-west Western frequent dispersals there into semi-arid arid interior since Miocene (20 Ma). Dispersals out northern eastern were limited confined dispersal events interior. Using paleoenvironmental models show after initial radiation, declined rapidly until Eocene–Oligocene boundary extinction pulse event subsequently more slowly present, modest increase during Middle Climatic Optimum. No significant rate shifts detected within clades except Chamelauciinae. There was no geographic-dependent Our results add growing literature revealing high plant diversity due time accumulation attributed long-term climatic stability rather than elevated rates.

Язык: Английский

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A framework phylogeny of the diverse guinea-flowers (Hibbertia, Dilleniaceae) using high-throughput sequence data

Australian Systematic Botany, Год журнала: 2025, Номер 38(2)

Опубликована: Март 20, 2025

Hibbertia is the largest genus in Dilleniaceae and one of Australian plant genera, with ~350 current more than 100 known undescribed species Australia. We present first published phylogeny based on rigorous sampling Hibbertia. As part Genomics for Plants Stage II, 95 were newly sequenced using Angiosperm353, OzBaits nuclear plastid bait sets, resulting 402 79 loci that subsampled to retain most phylogenetically useful 300 60 respectively. Nuclear phylogenies reconstructed concatenation coalescent approaches, further analysed Quartet Sampling. found four subgenera within are robustly supported as monophyletic recovered 14 major clades, both datasets, two (subg. Hemistemma subg. Hibbertia). However, many relationships between these clades unresolved discordant. Some incongruence was also detected trees. Discordance particularly high eastern clade Hemistemma. Possible causes this discordance, discussed.

Язык: Английский

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Multiple instances of river-lake introgression in the adaptive radiation of sailfin silversides in Wallace’s Dreampond

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 18, 2025

Abstract While adaptive radiations significantly contribute to the world’s biodiversity, much is unknown about genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate speciation process by generating diversity on which diversifying selection act. Sailfin silverside fishes (Telmatherinidae) in Malili Lakes system Sulawesi have diversified within last 2 million years. We assembled annotated a chromosome-scale reference genome riverine sailfin Telmatherina bonti generated whole sequences all species Lake Matano, South Sulawesi, Indonesia, one oldest deepest lakes. reconstructed phylogenetic relationships radiation silversides inferred past ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins roundfins. However, we found mismatches between morphology-based taxonomic assignments genome-wide relationships. signs both old river-dwelling T. lacustrine sharpfin group, as shown elevated D-statistic, f4-ratio f-branch statistic. Levels excess allele sharing three most common declined with increasing distance from river-inlet, indicating at lake-river interface. This combination radiating flock makes Matano particularly valuable study fundamental mechanisms driving under genomic exchange. The phylogenomic framework elaborated this provides foundation for studies processes shaping charismatic radiation.

Язык: Английский

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