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Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics

ABSTRACT: Australia harbours a rich and highly endemic orchid flora with over 90% of native species found nowhere else. However, little is known about the assembly and evolution of Australia’s orchid flora. Here, we used a phylogenomic approach to infer evolutionary relationships, divergence times and range evolution in Pterostylidinae (Orchidoideae), the second largest subtribe in the Australian orchid flora, comprising the genera Pterostylis and Achlydosa. Phylogenetic analysis of 75 plastid genes provided well-resolved and supported phylogenies. Intrageneric relationships in Pterostylis were clarified and monophyly of eight of 10 sections supported. Achlydosa was found to not form part of Pterostylidinae and instead merits recognition at subtribal level, as Achlydosinae. Pterostylidinae were inferred to have originated in eastern Australia in the early Oligocene, coinciding with the complete separation of Australia from Antarctica and the onset of the Antarctic Circumpolar Current, which led to profound changes in the world’s climate. Divergence of all major lineages occurred during the Miocene, accompanied by increased aridification and seasonality of the Australian continent, resulting in strong vegetational changes from rainforest to more open sclerophyllous vegetation. The majority of extant species were inferred to have originated in the Quaternary, from the Pleistocene onwards. The rapid climatic oscillations during the Pleistocene may have acted as important driver of speciation in Pterostylidinae. The subtribe underwent lineage diversification mainly within its ancestral range, in eastern Australia. Long-distance dispersals to southwest Australia commenced from the late Miocene onwards, after the establishment of the Nullarbor Plain, which constitutes a strong edaphic barrier to mesic plants. Range expansions from the mesic into the arid zone of eastern Australia (Eremaean region) commenced from the early Pleistocene onwards. Extant distributions of Pterostylidinae in other Australasian regions, such as New Zealand and New Caledonia, are of more recent origin, resulting from long-distance dispersals from the Pliocene onwards. Temperate eastern Australia was identified as key source area for dispersals to other Australasian regions.

SUBMITTER: Nargar K

PROVIDER: S-EPMC9277221 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background and aimsAsparagaceae subfamily Nolinoideae is an economically important plant group, but the deep relationships and evolutionary history of the lineage remain poorly understood. Based on a large data set including 37 newly sequenced samples and publicly available plastomes, this study aims to better resolve the inter-tribal relationships of Nolinoideae, and to rigorously examine the tribe-level monophyly of Convallarieae, Ophiopogoneae and Polygonateae.MethodsMaximum likelihood (ML) and Bayesian inference (BI) methods were used to infer phylogenetic relationships of Nolinoideae at the genus level and above. The diversification history of Nolinoideae was explored using molecular dating.Key resultsBoth ML and BI analyses identically recovered five clades within Nolinoideae, respectively corresponding to Dracaeneae + Rusceae, Polygonateae + Theropogon, Ophiopogoneae, Nolineae, and Convallarieae excluding Theropogon, and most deep nodes were well supported. As Theropogon was embedded in Polygonateae, the plastome phylogeny failed to resolve Convallarieae and Polygonateae as reciprocally monophyletic. Divergence time estimation showed that the origins of most Nolinoideae genera were dated to the Miocene and Pliocene. The youthfulness of Nolinoideae genera is well represented in the three herbaceous tribes (Convallarieae, Ophiopogoneae and Polygonateae) chiefly distributed in temperate areas of the Northern Hemisphere, as the median stem ages of all 14 genera currently belonging to them were estimated at <12.37 Ma.ConclusionsThis study recovered a robust backbone phylogeny, providing new insights for better understanding the evolution and classification of Nolinoideae. Compared with the deep relationships recovered by a previous study based on transcriptomic data, our data suggest that ancient hybridization or incomplete lineage sorting may have occurred in the early diversification of Nolinoideae. Our findings will provide important reference for further study of the evolutionary complexity of Nolinoideae using nuclear genomic data. The recent origin of these herbaceous genera currently belonging to Convallarieae, Ophiopogoneae and Polygonateae provides new evidence to support the hypothesis that the global expansion of temperate habitats caused by the climate cooling over the past 15 million years may have dramatically driven lineage diversification and speciation in the Northern Hemisphere temperate flora.

Project description:Subfamily Nandinoideae Heintze (Berberidaceae), comprising four genera and ca. 19 species, is disjunctively distributed in eastern North America vs. Eurasia (eastern Asia, Central Asia, Middle East, and southeastern Europe), and represents an ideal taxon to explore plastid phylogenomics and plastome evolution in Berberidaceae. Many species of this subfamily have been listed as national or international rare and endangered plants. In this study, we sequenced and assembled 20 complete plastomes, representing three genera and 13 species of Nandinoideae. Together with six plastomes from GenBank, a total of 26 plastomes, representing all four genera and 16 species of Nandinoideae, were used for comparative genomic and phylogenomic analyses. These plastomes showed significant differences in overall size (156,626-161,406 bp), which is mainly due to the expansion in inverted repeat (IR) regions and/or insertion/deletion (indel) events in intergenic spacer (IGS) regions. A 75-bp deletion in the ndhF gene occurred in Leontice and Gymnospermium when compared with Nandina and Caulophyllum. We found a severe truncation at the 5' end of ycf1 in three G. altaicum plastomes, and a premature termination of ropC1 in G. microrrhynchum. Our phylogenomic results support the topology of {Nandina, [Caulophyllum, (Leontice, Gymnospermium)]}. Within the core genus Gymnospermium, we identified G. microrrhynchum from northeastern Asia (Clade A) as the earliest diverging species, followed by G. kiangnanense from eastern China (Clade B), while the rest species clustered into the two sister clades (C and D). Clade C included three species from West Tianshan (G. albertii, G. darwasicum, G. vitellinum). Clade D consisted of G. altaicum from northern Central Asia, plus one species from the Caucasus Mountains (G. smirnovii) and three from southeastern Europe (G. odessanum, G. peloponnesiacum, G. scipetarum). Overall, we identified 21 highly variable plastome regions, including two coding genes (rpl22, ycf1) and 19 intergenic spacer (IGS) regions, all with nucleotide diversity (Pi) values > 0.02. These molecular markers should serve as powerful tools (including DNA barcodes) for future phylogenetic, phylogeographic and conservation genetic studies.

Project description:Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae. Simultaneously, nine monophyletic lineages were revealed in Cynodonteae: supersubtribe Boutelouodinae, subtribes Tripogoninae, Aeluropodinae, Eleusininae, Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. Within the tribe of Cynodonteae, the basal lineage is supersubtribe Boutelouodinae and Tripogoninae is sister to the remaining lineages. The clade formed of Aeluropodinae and Eleusininae is sister to the clade composed of Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. The clade comprising Dactylocteniinae and supersubtribe Gouiniodinae is sister to the clade comprising Cleistogenes, Orinus, and Triodiinae. Acrachne is a genus within Eleusininae but not within Dactylocteniinae. Molecular evidence determined that Diplachne is not clustered with Leptochloa, which indicated that Diplachne should not be combined into Leptochloa. Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas the recently proposed subtribe Orininae was not supported. Cynodonteae was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving its phylogenetic relationships. Ancestral state reconstructions of morphological characters showed that the most recent common ancestor (MRCA) of Chloridoideae has a panicle, multiple florets in each spikelet, the peaked type of stomatal subsidiary cells, and a saddle-shaped phytoliths, while the ancestral morphological characters of Cynodonteae are the panicle, peaked type of stomatal subsidiary cells, sharp-cap cell typed and equal-base-cell microhair, and square-shaped phytoliths. Overall, plastome phylogenomics provides new insights into the phylogenetic relationships and morphological character evolution of Chloridoideae.

Project description:BackgroundThe "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence.ResultsAlthough the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected.ConclusionsMolecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.

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Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics

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