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Phylogeny of Barleria overview. (A) A ML IQtree phylogeny of 190 accessions, 185 taxa, based on an alignment of 63,897 RADseq loci assembled in ipyrad, n = 1000 MLBS replicates, colored rectangles denoting subgenera.
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Barleria is a genus of approximately 300 species of herbs, shrubs or, rarely, trees, that is broadly distributed across the Paleotropics. The genus is especially diverse in Tanzania, Angola, and Madagascar. A recent molecular study sampled 53 Barleria species and gathered data for five molecular markers (i.e., four chloroplast loci and the nuclear...
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... best fit model of nucleotide evolution as measured by the Akaike Information Criterion (AIC), Corrected Akaike Information Criterion (AICc), and Bayesian Information Criterion (BIC) was GTR + F + I + G4. Barleria is monophyletic with maximum likelihood bootstrap support (MLBS) of 100% in the IQtree phylogeny (Fig. 5). There is strong support for subg. Barleria (99% MLBS) and, at the 100% MLBS level, for subg. Prionitis, sect. Prionitis, sect. Stellatohirta, and the expanded sect. Somalia (sensu Darbyshire et al. 2019a, which includes former sect. Cavirostrata). All 13 members of sect. Fissimura are part of a clade within subg. Barleria (100% MLBS; ...
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... (Fig. 5). There is strong support for subg. Barleria (99% MLBS) and, at the 100% MLBS level, for subg. Prionitis, sect. Prionitis, sect. Stellatohirta, and the expanded sect. Somalia (sensu Darbyshire et al. 2019a, which includes former sect. Cavirostrata). All 13 members of sect. Fissimura are part of a clade within subg. Barleria (100% MLBS; Fig. ...
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... subg. Prionitis, sect. Prionitis is sister to sect. Stellatohirta, and together these are sister to an expanded sect. Somalia (Fig. 5). Relationships within sect. Prionitis and sect. Stellatohirta are fully resolved and strongly-supported (Figs. 5-7). Within sect. Prionitis, the Quadrispina clade, comprising the northeastern African B. quadrispina Lindau, B. ferox Ensermu & I.Darbysh., B. negelleeensis Ensermu & I. Darbysh., and B. sp. aff. quadrispina, is sister to ...
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... Barleria has seven major lineages, two of single species (i. e., B. oenoetheroides, B. monticola) and five with multiple species: the Crassa, Cristata, Fissimura, Ovata, and Strigosa clades. Relationships among these are strongly supported (Fig. 5). The three sampled accessions of B. cristata, the type species of the genus, are nested within the Cristata clade (Fig. 9). Barleria oenotheroides and B. monticola Oberm. are serially sister to the rest of subg. Barleria. The next clade to diverge is the Strigosa clade, which contains the East African B. holstii Lindau and B. whytei ...
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... of the RADseq data yielded substantially different topologies from ML (Fig. 5) versus coalescent (Fig. S1) approaches. Relationships recovered in the coalescent-based tetrad analysis were poorly supported along the backbone and Barleria was not monophyletic, although the genus appears as monophyletic in all other molecular phylogenetic studies using chloroplast and nrITS markers ( Darbyshire et al., 2019a;McDade ...
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... Barleria RADseq ML phylogeny (Fig. 5) shows a similar overall topology to the cp + nrITS phylogeny of Darbyshire et al. (2019a), but with stronger branch support and some shifts in relationships among taxa within sections and clades. A study by Clugston et al. (2019) found that RADseq sampled almost entirely the nuclear genome of cycads. We did not explicitly test the ...
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... largely independent from the cp + nrITS dataset used by Darby- shire et al. (2019a). Clades that were recovered in both analyses are thus corroborated by independent data sources constituting strong evidence that the species phylogeny has been recovered (Page and Holmes, 1998). Barleria is reconstructed as monophyletic (MLBS 100%) in our study (Fig. 5) and in the topology of Darbyshire et al. (2019a). Likewise, subg. Prionitis and subg. Barleria are also strongly supported as monophyletic in both Darbyshire et al. (2019a) and the present study (Fig. 5). Importantly, the placement of the type species, B. cristata, within the Cristata clade of subg. Barleria was strongly supported ...
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... that the species phylogeny has been recovered (Page and Holmes, 1998). Barleria is reconstructed as monophyletic (MLBS 100%) in our study (Fig. 5) and in the topology of Darbyshire et al. (2019a). Likewise, subg. Prionitis and subg. Barleria are also strongly supported as monophyletic in both Darbyshire et al. (2019a) and the present study (Fig. 5). Importantly, the placement of the type species, B. cristata, within the Cristata clade of subg. Barleria was strongly supported (Fig. 9). Furthermore, both analyses recovered sect. Prionitis, sect. Stellatohirta, and an expanded sect. Somalia, encompassing members of the former sect. Cavirostrata, all of which are strongly supported ...
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... (Fig. 5). Importantly, the placement of the type species, B. cristata, within the Cristata clade of subg. Barleria was strongly supported (Fig. 9). Furthermore, both analyses recovered sect. Prionitis, sect. Stellatohirta, and an expanded sect. Somalia, encompassing members of the former sect. Cavirostrata, all of which are strongly supported (Fig. 5). In agreement with Darbyshire et al. (2019a), subg. Barleria includes a strongly supported clade containing members of the former sect. Fissimura, which is nested within the paraphyletic section Barleria sensu Balkwill and Balkwill (1997). In further agreement with Darbyshire et al. (2019a), sect. Chrysothrix sensu Balkwill and ...
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... same sections and subgenera were recovered here (Fig. 5, Figs. S2-S7) and in the cp + nrITS study of Darbyshire et al. (2019a), intra-sectional relationships are different in some cases and are better resolved here. We discuss some of these relationships ...
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... was previously classified first in sect. Stellatohirta based on the presence of stellate trichomes (Balkwill and Balkwill, 1997), and subsequently in sect. Cavirostrata due to the capsule with a beak and four seeds (Darbyshire, 2008b). Barleria descampsii was resolved as sister to B. grandipetala De Wild., another species with stellate trichomes (Figs. 8; S5). In this clade, B. descampsii, B. grandipetala, and B. richardsiae I. Darbysh. are unusual in that the uppermost two corolla lobes are widely divergent such that all five corolla lobes form a single "lip" (Darbyshire et al., 2015). The west African B. maclaudii Benoist, a rare and endangered species (Rokni, 2017) confined to Guinea ...
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... this species was recovered as sister to B. grandis in our study, outside the B. descampsii group (Figs. 8; ...
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... Somalia: Socotra lineage. The Socotra lineage is monotypic, consisting of only B. popovii, a large shrub or treelet from the island of Socotra, where it is currently endangered (Miller, 2004). Barleria popovii is sister to Aucheriana clade + Meyeriana clade (Figs. 8; S5), with strong support. The capsules of Barleria popovii are 4-seeded and prominently beaked as in some members of the Cavirostrata clade, but these Socotran plants have a number of unique characters for sect. Somalia, including a tree-like habit, lepidote scales, a much-reduced, rounded lower corolla lobe, and a capitate stigma ( ...
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... barely-developed branch. Taxa of the Aucheriana clade are found primarily in northeast Africa, the Arabian Peninsula, and India, but extend into East Africa; an undescribed species is known to occur in South Africa (I. Darbyshire, unpubl. data). The sectional type, B. aucheriana, is placed in this clade, sister to B. argentea + B. parviflora ( Figs. 8; ...
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... Barleria-Plants of this subgenus have beak-less capsules that are 4-seeded except in the Fissimura clade, where they are 2-seeded. Seven major clades were recovered with strong support within subg. Barleria (Fig. 5), improving our understanding of relationships within this taxonomically complicated subgenus. Based on studies of Barleria in southern Africa, Obermeyer (1933) recognized seven subsections within her sect. Eubarleria. Balkwill and Balkwill (1997) ...
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... the genus, but especially in subg. Barleria, the RADseq analysis yielded strongly supported clades that may merit sectional or subsectional status. One issue is the potential reinstatement of former sect. Fissimura, which both Darbyshire et al. (2019a) and this analysis resolve within former sect. Barleria (Fig. 5). Because sect. Fissimura is monophyletic and has distinctive characters (most notably, 2-seeded capsules in which the capsule walls tear at the base during explosive dehiscence, a character not found elsewhere in Barleria and closely related genera), it is desirable to resurrect the section. In order to do that, we would have to divide ...
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... RADseq tree (Fig. 5) suggests at least four independent transitions of Barleria to Madagascar: the common ancestor of clades in (1) sect. Somalia, (2) sect. Prionitis, and (3) subg. Barleria, and (4) an independent dispersal of the ancestor of B. humbertii (subg. Barleria). A possible fifth transition may include B. glandulostamina and B. humilis and ...
Citations
... compacta and B. tetracantha in Table 2. In the published RADseq phylogeny of Barleria (Comito et al. 2022), B. tetracantha is resolved as sister to a clade comprising B. compacta s.s. and B. brevispina (Fiori) Hedrén, the latter two species forming a morphological "species pair" which are almost inseparable in the vegetative and fruiting states but have very different corolla morphology, B. brevispina being highly zygomorphic with a much reduced and offset abaxial lobe (Malombe and Darbyshire 2010). ...
Two new taxa in Barleria L. sect. Prionitis Nees (Acanthaceae) are described from Somalia, namely Barleria biramosa Defty & I.Darbysh. from central Somalia and B. compacta Malombe & I.Darbysh. subsp. minima I.Darbysh. & Defty from the northeast coastal region. These taxa are further endemics of the Horn of Africa biodiversity hotspot and have highly restricted ranges. Barleria biramosa was previously included within B. punctata Milne-Redh., another range-restricted endemic of the Horn of Africa region form northeast Ethiopia and northern Somalia; an updated description of B. punctata is therefore provided. Notes on the habitat requirements and conservation status (extinction risk) of the species are provided. Barleria biramosa is considered to be globally Endangered whilst B. compacta subsp. minima is currently assessed as Least Concern; the published assessment of Vulnerable for B. punctata is confirmed. With these additions, 11 taxa in 10 species of Barleria sect. Prionitis are currently recognised in Somalia.
... Our molecular dataset of thousands of SNPs was sufficient to resolve the deepest nodes in the phylogeny of Petalidium, but not relationships within the diverse arid clade, which shows low bootstrap support values (Figure 2, Supplementary Figure S1). Such low support was not expected given that RADseq has shown sufficient power to resolve fine-scale phylogenetic relationships in Barleria, a closely related genus of Acanthaceae (Comito et al., 2022). This poor resolution in the shallow part of our phylogeny could be explained by hybridisation or incomplete lineage sorting, both of which may cause conflict among genes for relationships. ...
At present, tropical arid biomes house less woody plant species diversity than tropical moist biomes, which could be due to lower rates of evolutionary diversification in the recent or distant past. Here, we study the evolutionary diversification of Petalidium (Acanthaceae), a genus of 36 species of woody shrubs found in the Namib Desert of southwest Africa, and surrounding areas. We generated a new, nearly fully sampled and temporally calibrated phylogeny for Petalidium using RADseq SNP data and secondary calibrations. We then investigated variation in net diversification rate across the phylogeny, the ancestral climatic niche of lineages and the link between the two. We find that arid climatic conditions are linked with increased rates of net species diversification in the genus. Despite its great age, the Namib Desert clearly hosts young plant radiations. This apparent contradiction can be explained by a scenario of high evolutionary turnover, in this case potentially caused by alternating hyper-arid and relatively mesic phases. Hyper-arid phases could result in high plant mortality and extinction of species, leading to ecological opportunity and diversification during mesic phases. Taken together, our results contribute to a growing body of literature that shows evidence for elevated rates of plant diversification in the Quaternary in arid biomes across the globe.
... A molecular phylogenetic study of Isoglossinae and allies based on three loci (nrITS, trnT-L and trnS-G) by Kiel et al. (2006) Tripp et al. 2017;Darbyshire et al. 2020;Comito et al. 2022). With such a project still to be initiated for Isoglossinae, a pragmatic interim solution is needed to allow the description of the known novelties from Madagascar to proceed. ...
Current generic delimitation in subtribe Isoglossinae of Acanthaceae is discussed using available morphological and molecular data. Particular consideration is given to the small genera endemic to Madagascar — Celerina Benoist, Melittacanthus S.Moore, Sphacanthus Benoist and the illegitimate Conocalyx Benoist — and how these relate to the current circumscription of Isoglossa Oerst. The relative merits and challenges of recognising a broadly circumscribed Isoglossa are considered. Isoglossa s.l. is readily recognisable by combining a bilabiate corolla, with an androecium comprising two bithecous stamens and lacking staminodes, and with the presence of gürtelpollen (i.e. bipororate pollen, circular in apertural view and with a pronounced interapertural “girdle” of tectate exine), whilst the segregate genera as currently defined are not separable morphologically. However, the limited molecular phylogenetic data available to date indicate that Isoglossa s.l. is paraphyletic. Pending further molecular studies of this group to clarify generic delimitation, it is proposed that all new taxa in bithecous Isoglossinae should be described in Isoglossa as an interim solution . Four new species of Isoglossa are described: I. eburnea Onjalal. & I.Darbysh., I. pterocalyx I.Darbysh. & Phillipson, I. pseudoanisotes I.Darbysh. and I. conocalyx I.Darbysh. & Callm., the lattermost of which is based on Conocalyx laxus Benoist nom. illegit. In addition, Justicia onilahensis Benoist (including Ritonia poissonii Benoist) and Anisotes perplexus T.F.Daniel, Letsara & Martín-Bravo are transferred to Isoglossa , and three names within Justicia L. are synonymised within existing taxa in Isoglossinae. Lectotypes are selected for Sphacanthus brillantaisia Benoist, S. humbertii Benoist and Justicia subpaniculata Benoist (= Celerina seyrigii Benoist var. egena Benoist).
... Other methods to sub-sample the genome include restriction site-associated sequencing (RAD-seq; Gnirke et al. 2009) and Hyb-seq (Lemmon et al. 2012;Weitemier et al. 2014). These are relatively low-cost skimming methods that have been successfully used for plant phylogenomic studies (Eaton and Ree 2013;McKain et al. 2018;Dodsworth et al. 2019;Hale et al. 2020), including studies of Acanthaceae Daniel and Tripp 2018;Comito et al. 2022;Darbyshire et al. 2020;Tripp and Darbyshire 2020). While RADseq and Hyb-seq are effective at generating sequence data from across the genome for multiple samples, data can only be combined if the same restriction enzymes or baits are used to prepare the samples. ...
... Sampling-Sixteen species of Acanthaceae were sampled in the present study to trial a method of combining genome skims and transcriptomes for phylogenetic analysis. Taxa were chosen to represent the major lineages of Acanthaceae based on McDade et al. (2008) and summarized in Tripp et al. (2022) with an emphasis on sampling representatives from the BAWN clade (10 species) to test for monophyly of Barleria and guide our research in this group (Comito et al. 2022). Six sampled taxa represent other major lineages of Acanthaceae whose phylogenies have been recently studied in greater detail, with the exception of Acanthus (Tripp 2007;Tripp et al. 2013;Fisher et al. 2015;Kiel et al. 2017Kiel et al. , 2018. ...
... Notably, the branches leading to the BAWN clade, the BAW clade and the Whitfieldeae are here more strongly supported. As in the cp 1 nr-ITS tree, the 10 single-copy loci RAxML tree returned moderate to no support for these branches, and the branching order of Barleria (Fig. 4) is inconsistent with topologies from the 587 loci data set (Fig. 3), as well as with other studies of Barleria (Darbyshire et al. 2019;Comito et al. 2022). Ten single-copy loci do not adequately resolve this part of the tree. ...
Acanthaceae is a family of tropical flowering plants with approximately 4900 species. Despite remarkable variation in morphological traits, research on patterns of character evolution has been limited by uncertain relationships among some of the major lineages. We sampled 16 taxa from these major lineages to estimate a phylogenomic framework using a combination of five newly sequenced shotgun genome skims plus seven new and four publicly available transcriptomes. We used OrthoFinder2 to infer a species tree with strong branch support. Except for the placement of Crabbea , our results corroborate the most recent chloroplast and nrITS sequence-based topology. Of 587 single copy loci, 10 were recovered for all 16 species; a RAxML tree estimated from these 10 loci resulted in the same topology as other datasets assembled in this study, with the exception of relationships among three sampled species of Barleria ; however, branch support was lower compared to the tree reconstructed using more data. ABBA-BABA tests were conducted to investigate patterns of introgression involving Crabbea ; few nucleotides supported alternative topologies. SplitsTree networks of the 587 loci and 6136 orthogroup trees revealed conflict among the branches leading to Andrographideae, Whitfieldieae, and Neuracanthus . A principal components analysis in treespace found no distinct clusters of trees. Our results based on combined genome skim and transcriptome sequences strongly corroborate the previously published chloroplast and nr-ITS-based phylogeny of Acanthaceae with increased resolution among Barlerieae, Andrographideae, Whitfieldieae, and Neuracanthus . This advance in our knowledge of Acanthaceae relationships will allow us to investigate character evolution and other phenomena within this diverse group of plants in studies with increased taxon sampling.
... The phylogeny given by Darbyshire et al. [1] represents only one sample of it. Comito et al. [4] generated ddRAD sequencing data for multiple specimens of B. cristata collected from the USA (CSULB Greenhouse (LOB)), China (Gooligong Shan Biodiversity Survey 15,945 (CAS)) and Nepal (Grey-Wilson, C. Phillips 865B (K)). But in order to compare those specimens with Indian specimens, there is a need to generate ddRAD sequencing data from Indian B. cristata morphotypes. ...
Barleria cristata L., commonly known as the Philippine violet, is native to South Asia. It is an ornamental plant and is also used for the treatment of a variety of diseases. In India, it is found throughout the country in many forms, varying in its floral attributes (calyx and corolla) and habitat. In order to understand the species limits in B. cristata, we studied morphological as well as palynological variation and assessed the phylogenetic relationships among five different morphotypes. The studied morphotypes (populations) came from three phytogeographical regions, namely the Western Ghats, the Deccan Peninsula and the Western Himalaya. The naturally occurring populations from the Deccan Peninsula and the Western Himalaya showed conspicuous differences in their morphology. All the morphotypes had oblate spheroidal, tri-brevicolporate and honey-combed pollen grains which differed only in their quantitative parameters. The distinct-looking morphotypes, namely, Nandi Hills, Uttarakhand and cultivated morphotypes, could not be separated based on pollen characters. Phylogenetic analyses based on chloroplast DNA sequences revealed that our samples formed a clade sister to the B. cristata specimen used in the previous study. The genetic variation within morphotypes was not enough for the genomic regions investigated; however, it revealed among morphotype genealogies in detail. Phylogenetic analyses showed that there were three monophyletic groups within the B. cristata complex that exhibited some morphological differences. Nevertheless, based on the present sampling, it is not possible to delimit these morphotypes at specific or infraspecific level. To reach such conclusions, further investigations like sampling this species across its distribution range in India and assessment of intraspecific relationships, and their cytogenetical characterization should be done.
... The genus was last treated in full in southern Africa by Obermeyer (1933), and whilst this was an excellent account, our knowledge of the genus has increased significantly in the proceeding 89 years through large numbers of additional collections and field observations and through a range of taxonomic, floristic and phylogenetic studies (e.g. Balkwill & Balkwill 1997;Darbyshire 2015;Darbyshire et al. 2019aDarbyshire et al. , 2019bDarbyshire et al. , 2021Comito 2019;Comito et al. 2022). New, highly range-restricted species continue to be discovered in southern Africa. ...
... Samples of some of these species were included in a recent RADseq molecular phylogenetic study of Barleria (Comito 2019;Comito et al. 2022). In that study, Barleria soutpansbergensis was resolved in a clade of subg. ...
Two new species of Barleria subg. Barleria (Acanthaceae) are described from the Soutpansberg Centre of Plant Endemism in Limpopo Province of South Africa: Barleria soutpansbergensis and B. spinosissima . The habitat requirements, conservation status and taxonomic affinities of each species are discussed. Barleria soutpansbergensis is considered to be closely allied to the widespread and frequently cultivated southern African species B. obtusa , whilst B. spinosissima is morphologically most similar to B. bremekampii which has a restricted distribution in northern South Africa and Zimbabwe. Remarkably, the two new species are postulated to occasionally hybridise within the Soutpansberg. Both species are currently assessed as of Least Concern despite their restricted ranges. Barleria spinosissima is noted to be amongst the most densely spiny species of Barleria and, indeed, is a contender as one of the spiniest species of plant in South Africa.
... The present study intends to reconstruct evolutionary relationships within Monechma s.l. in the context of the wider classification of the Justicioid lineage and towards understanding the diversification of this ecologically important lineage. A RADseq phylogenetic approach is used in light of the considerable success that this method has provided in resolving phylogenetic relationships within other major lineages of Acanthaceae, including Petalidium [6], Louteridium S. Watson [30], Ruellieae [31], Barleria [32] and New World Justicia [33]. The sampling of species of Monechma s.l. is here expanded to include ca. ...
Monechma Hochst. s.l. (Acanthaceae) is a diverse and ecologically important plant group in sub-Saharan Africa, well represented in the fire-prone savanna biome and with a striking radiation into the non-fire-prone succulent biome in the Namib Desert. We used RADseq to reconstruct evolutionary relationships within Monechma s.l. and found it to be non-monophyletic and composed of two distinct clades: Group I comprises eight species resolved within the Harnieria clade, whilst Group II comprises 35 species related to the Diclipterinae clade. Our analyses suggest the common ancestors of both clades of Monechma occupied savannas, but both of these radiations (13 mya crown ages) pre-date the currently accepted origin of the savanna biome in Africa, 510 mya. Diversification in the succulent biome of the Namib Desert is dated as beginning only 1.9 mya. Inflorescence and seed morphology are found to distinguish Groups I and II and related taxa in the Justicioid lineage. Monechma Group II is morphologically diverse, with variation in some traits related to ecological diversification including plant habit. The present work enables future research on these important lineages and provides evidence towards understanding the biogeographical history of continental Africa.
With ca. 375 species worldwide, Ruellia is a morphologically diverse and geographically widespread lineage of flowering plants. The majority of these species (ca. 275 of 375) occur in the New World (NW), with most of these occurring in the tropics and only about 65 occurring in temperate regions. In the NW, the genus spans some 77° of latitude, ranging from the northern United States (Wisconsin) to northeastern Argentina (Córdoba) and southern Uruguay (Canelones). In this study, we generated ddRAD molecular sequence data for 187 of 275 species of NW Ruellia (ca. 68% of NW species) to reconstruct phylogenetic relationships within this lineage. Coupled with morphological and ecological information, we used this well‐resolved and strongly supported molecular phylogeny to delimit 15 sections of NW Ruellia . Representing the first comprehensive attempt in ca. 125 years, we present a revised classification for NW Ruellia , which places a total of 205 species in the following sections: Ruellia sect. Aphragmia , sect. Blechum , sect. Boreosilva , sect. Brasilia , sect. Cerradicola , sect. Chiropterophilae , sect. Chromatoruellia , sect. Eurychanes , sect. Gymnacanthus , sect. Mexicanae , sect. Physiruellia , sect. Ruellia , sect. Siphonacanthus , sect. Stephanophysum , and sect. Strobiliformes . Nomenclatural innovations in this study include the description of several new sections, new combinations, and new names proposed. Our study complements an earlier reclassification of Old World species to provide a globally unique perspective on the taxonomy and phylogeny of a geographically widespread lineage of flowering plants.
Background and aims – Ochna holstii and its allies represent an ecologically important group in a variety of lowland to montane habitats in tropical eastern and southern Africa. Identifying and delimiting species within this group has proved challenging due to a lack of variation in morphological characters. We combine genomic-scale data of multiple accessions per species with morphological data to generate a taxonomic revision for the Ochna holstii complex using a multi-evidence approach.
Material and methods – A total of 50 samples representing eight species were analysed using target enrichment and a custom bait kit. Phylogenetic analysis was conducted using the multi-species coalescent model and a concatenation maximum likelihood method, and gene tree discordance was investigated. Herbarium specimens of the O. holstii complex were studied in detail for informative morphological characters, supplemented where possible from field collections, and a full taxonomic revision is provided.
Key results – Within Ochna sect. Schizanthera Clade I, our study confirms that all species are monophyletic and supported by morphological data with the exception of O. holstii , which is paraphyletic. A new species, O. mchanga , previously confused with O. polyneura , is described, and the placement of another recently described species, O. maguirei , is confirmed for the first time using molecular data.
Conclusion – The widespread montane tree Ochna holstii is non-monophyletic in its current circumscription and likely gave rise to the more range-restricted O. oxyphylla and O. stolzii. We suggest that an integrated taxonomy approach, using both molecular and morphological data, is essential for deciphering difficult species relationships in Ochna .
As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.
