How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coa…

Evolution of leaf anatomy in arid environments – A case study in southern African Tetraena and Roepera (Zygophyllaceae)

The dry biomes of southern Africa (Desert, Nama Karoo and Succulent Karoo) are home to a rich and diverse xerophytic flora. This flora includes two morphologically diverse clades of Zygophyllaceae, Tetraena and Roepera (Zygophylloideae), which inhabit some of the most arid habitats in the region. Using a plastid phylogeny of Zygophylloideae we assess whether the evolution of putatively adaptive traits (leaf shape, vasculature, mode of water storage and photosynthetic type: C3 versus C4) coincides with the successful colonisation of environments with different drought regimes within southern Africa. Our results show general niche conservatism within arid habitats in Tetraena, but niche shift…

Phylogeny of Polycnemoideae (Amaranthaceae): Implications for biogeography, character evolution and taxonomy

On the hybrid origin of the C2Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

AbstractC2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary precursor of C4 and/or as the result of hybridization between a C3 and C4 lineage.We compared the expression of photosynthetic traits among populations of the Salsola divaricata agg. (C2) from humid subtropical to arid habitats on the coasts of the Canary Islands and Morocco and subjected them to salt and drought treatments. We screened for enhanced C4-like expression of traits related to habitat or treatment. We estimated species trees with a transcriptome datase…

Phylogeny of Salicornioideae (Chenopodiaceae): Diversification, biogeography, and evolutionary trends in leaf and flower morphology

Chenopodiaceae-Salicomioideae (14-16 gen./c. 90 spp.) are distributed worldwide in coastal and inland saline habitats. Most of them are easy to recognize by their succulent-articulated stem with strongly reduced leaves and by flowers aggregated in dense, thick spike-shaped thyrses. ITS and the atpB-rbcL spacer were sequenced for 67 species representing 14 genera of Salicomioideae and analysed with maximum parsimony and maximum likelihood, a fossil-calibrated molecular clock using the penalized likelihood method, and lineage through time plots. The evolution of stem, leaf, and flower morphology was traced using MacClade. Both molecular markers indicate that the monophyletic Salicomioideae or…

Phylogeny, biogeography, systematics and taxonomy of Salicornioideae (Amaranthaceae/Chenopodiaceae) – A cosmopolitan, highly specialized hygrohalophyte lineage dating back to the Oligocene

De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)

C4 photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C4 from ancestral C3 photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C3 and C4 species have significantly increased our understanding of C4 functioning and evolution. In Chenopodiaceae, a family that is rich in C4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C4, C2, and C3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative …

Towards a complete phylogeny of African Melastomateae : systematics of Dissotis and allies (Melastomataceae)

When do different C4 leaf anatomies indicate independent C4 origins? Parallel evolution of C4 leaf types in Camphorosmeae (Chenopodiaceae).

Broad-scale phylogenetic studies give first insights in numbers, relationships, and ages of C 4 lineages. They are, however, generally limited to a model that treats the evolution of the complex C4 syndrome in different lineages as a directly comparable process. Here, we use a resolved and well-sampled phylogenetic tree of Camphorosmeae, based on three chloroplast and one nuclear marker and on leaf anatomical traits to infer a more detailed picture of C4 leaftype evolution in this lineage. Our ancestral character state reconstructions allowed two scenarios: (i) Sedobassia is a derived C3/C4 intermediate, implying two independent gains of C4 in Bassia and Camphorosma; or (ii) Sedobassia is a…

Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): Implications for systematics, biogeography, flower and fruit evolution, and the origin of C4photosynthesis

 Premise of the study : Atripliceae (Chenopodiaceae), including Atriplex (300 spp.) as the largest genus of the family, are an ecologically important group of steppes and semideserts worldwide. Relationships in Atripliceae are poorly understood due to obscure and potentially convergent morphological characters.  Methods : Using sequence variation of two chloroplast markers ( rbcL gene, atpB-rbcL spacer) and one nrDNA marker (ITS) analyzed with BEAST, we investigated the systematics and biogeography of Atripliceae. We surveyed fl ower morphology and fruit anatomy to study the evolution of fland fruits in the tribe.  Key results : Female fl owers with persistent foliar cover (the diagnosti…

Understanding Mediterranean‐Californian disjunctions: molecular evidence from Chenopodiaceae‐Betoideae

Chenopodiaceae subfam. Betoideae is distributed in both western Eurasia (four genera) and western North America (one genus). To understand the origin of this disjunction, the phylogeny of the subfamily was reconstructed and dated using ndhF, matK/trnK, tmL-trnF spacer, and ITS sequence variation, penalized likelihood and Langley-Fitch, and calibration with three different fossils. Maximum Parsimony and Maximum Likelihood analyses of the molecular data show that Betoideae are monophyletic, but that relationships of the Himalayan Acroglochin, traditionally included in Betoideae because of the shared possession of a circumscissile capsule, are uncertain. Among the betoidean genera, Beta (excl.…

Salicornia L. (Amaranthaceae) in South Africa and Namibia: rapid spread and ecological diversification of cryptic species

In Salicornia, morphology does not provide reliable diagnostic characters supporting the true extent of evolutionary divergence in the genus, and species concepts have been challenged by molecular analyses. Here, we report the results of an analysis of 91 accessions of the S. meyeriana complex from South Africa and Namibia using the measurements of 38 morphological traits and external transcribed spacer (ETS) sequence data. Morphological data were analysed using discriminant analysis, principal coordinate analysis and nonmetric multidimensional scaling. Phylogenetic divergence was compared with the geographical and ecological diversity of the sampled populations. Tree topology corresponds t…

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l.

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data…

Phylogeny and ecological diversification of South African Sarcocornia (Chenopodiaceae)

Revision of Sarcocornia (Chenopodiaceae) in South Africa, Namibia and Mozambique

Abstract Sarcocornia comprises ca. 20–24 perennial, halophytic herb and shrub species. The genus is distinct from other genera in the Salicornioideae in having flowers that are more or less equal in size, arranged in a row, and with seeds that have a membranous hairy testa and lack perisperm. Sarcocornia is distributed worldwide, mainly in regions characterized by warm-temperate and, to a lesser extent, subtropical climates. The representatives of this genus are found in habitats such as estuarine salt marshes, tidal mud flats, coastal cliffs, inland salt pans, and salt-laden alluvia of intermittent semi-desert and desert streams. Some South African taxa also occur in inland (semi-desert) q…

De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)

C4 photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C4 from ancestral C3 photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C3 and C4 species have significantly increased our understanding of C4 functioning and evolution. In Chenopodiaceae, a family that is rich in C4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C4, C2, and C3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative …

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.

AbstractGene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-base…

Molecular markers indicate the phylogenetic identity of southern Brazilian sea asparagus: first record of Salicornia neei in Brazil

Abstract Molecular phylogenetic analyses based on ETS, ITS and atpB - rbcL spacer sequences assessed the phylogenetic status of the southern Brazil sea asparagus species of the genus Salicornia (Salicornioideae, Amaranthaceae). Accessions of Patos Lagoon estuary (32° S) were obtained from wild plants and two pure line lineages, selected from contrasting prostrate (BTH1) and decumbent (BTH2) ecomorphotypes found locally. Patos Lagoon wild plants, BTH1 and BTH2 f4 progenies showed 100% identical sequences for the atpB - rbcL and ITS spacers, only two mutations for ETS. Comparison of the sequences of these three markers with GenBank records confirmed the identity of Brazilian accessions as Sal…

Gisekia(Gisekiaceae): Phylogenetic relationships, biogeography, and ecophysiology of a poorly known C4lineage in the Caryophyllales

• Premise of the study: Gisekiaceae are a monogeneric family of the core Caryophyllales distributed in arid regions of Africa and Asia. The only widespread species of the genus, Gisekia pharnaceoides, performs C4 photosynthesis based on CO2 compensation point measurements. This study investigates the C4 syndrome and its evolution in Gisekia. The infrageneric relationships, distribution and bioclimatic preferences of Gisekia are also investigated.• Methods: Leaf gas exchange characteristics, activity of Rubisco and major C4 cycle enzymes, and ultrastructural characteristics of mesophyll and bundle sheath cells are studied for Gisekia pharnaceoides. δ13C values and leaf anatomy are analyzed f…

C 3 –C 4 intermediates may be of hybrid origin – a reminder

Summary The currently favoured model of the evolution of C4 photosynthesis relies heavily on the interpretation of the broad phenotypic range of naturally growing C3–C4 intermediates as proxies for evolutionary intermediate steps. On the other hand, C3–C4 intermediates had earlier been interpreted as hybrids or hybrid derivates. By first comparing experimentally generated with naturally growing C3–C4 intermediates, and second summarising either direct or circumstantial evidence for hybridisation in lineages comprising C3, C4 and C3–C4 intermediates, we conclude that a possible hybrid origin of C3–C4 intermediates deserves careful examination. While we acknowledge that the current model of C…

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Premise of the study The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in s…

Molecular phylogenetics of the Dissochaeta alliance (Melastomataceae): Redefining tribe Dissochaeteae

Phylogeny of Sesuvioideae (Aizoaceae) – Biogeography, leaf anatomy and the evolution of C4 photosynthesis

Abstract Sesuvioideae (Aizoaceae) form a small subfamily of drought-tolerant plants exhibiting leaf succulence, halophytic ecology, and the C4 photosynthetic pathway. Sesuvioideae are sister to the species-rich subfamilies Ruschioideae, Mesembryanthemoideae and Aizooideae that contain many CAM lineages. This close relationship of CAM and C4 taxa identifies the Sesuvioideae as an important clade to address hypotheses of photosynthetic pathway evolution. This study presents a molecular phylogeny of Sesuvioideae based on five markers (atpB-rbcL spacer, rps16 intron, trnL-trnF spacer, petB-petD spacer, ITS) and 51 accessions representing all genera and 37 species. We determined carbon isotope d…

C4-like photosynthesis and the effects of leaf senescence on C4-like physiology in Sesuvium sesuvioides (Aizoaceae).

Sesuvium sesuvioides represents a young C4 lineage with C4-like metabolism: CO2 compensation points range between C4 and C3–C4 intermediate values, and Rubisco was detected in bundle sheath and mesophyll.

A Revision of Sesuvium (Aizoaceae, Sesuvioideae)

Sesuvium and Cypselea are closely related succulent genera within the Sesuvioideae (Aizoaceae). Since Cypselea is nested in Sesuvium in molecular studies and both genera share traits separating them from other members of the subfamily, we propose to include Cypselea in Sesuvium. Sesuvium (incl. Cypselea) comprises 14 species and is distributed worldwide with centres of diversity in southern Africa and North and Central America. Sesuvium comprises erect to procumbent herbs with opposite leaves that often bear conspicuous sheath-like lateral appendages on the petioles (pseudostipules). These and the many-seeded capsules are diagnostic traits, separating Sesuvium from the closely related gener…

<i>Microcnemum coralloides</i> (Chenopodiaceae- Salicornioideae): an example of intraspecific East-West disjunctions in the Mediterranean region

Kadereit, G. & A.E. Yaprak. 2008. Microcnemum coralloides (Chenopodiaceae-Salicornioideae): an example of intraspecific East-West disjunctions in the Mediterranean region. Anales Jard. Bot. Madrid 65(2): 415-426. Microcnemum is a monotypic genus of Salicornioideae comprising rare, annual, hygrohalophytic herbs growing in hypersaline inland lagoons and salt pans. Microcnemum coralloides shows an East-West disjunction in the Mediterranean region: M. coralloides subsp. coralloides occurs in central and eastern Spain while M. coralloides subsp. anatolicum grows in Turkey, Syria, Armenia and Iran. We studied the phylogeny, biogeography and morphological differentiation of M. coralloides. Molecul…

Nothodissotis (Melastomataceae), a new genus from Atlantic Central Africa, including the new species N. alenensis from Equatorial Guinea

Based on morphological and phylogenetic evidence, a new genus of Melastomataceae (Melastomateae), Nothodissotis Veranso-Libalah & G.Kadereit, gen. nov., is described from Atlantic Central Africa. Nothodissotis is distinguished from other African Melastomateae genera by its calyx-lobes that are notched at apex and asymmetrical (vs. entire and symmetrical). Nothodissotis includes two species: the type species N.barteri (Hook.f.) Veranso-Libalah & G.Kadereit, comb. nov. (syn. Dissotisbarteri Hook.f.), and the new species N.alenensis Veranso-Libalah & O. Lachenaud, sp. nov., described and illustrated here. Both species are restricted to open vegetation on rock outcrops w…

A taxonomic nightmare comes true: phylogeny and biogeography of glassworts (Salicornia L., Chenopodiaceae)

In this study we analysed ETS sequence data of 164 accessions belonging to 31 taxa of Salicornia, a widespread, hygrohalophytic genus of succulent, annual herbs of Chenopodiaceae subfam. Salicornioideae, to investigate phylogenetic and biogeographical patterns and hypothesise about the processes that shaped them. Furthermore, our aim was to understand the reasons for the notorious taxonomic difficulties in Salicornia. Salicornia probably originated during the Miocene somewhere between the Mediterranean and Central Asia from within the perennial Sarcocornia and started to diversify during Late Pliocene/Early Pleistocene. The climatic deterioration and landscape-evolution caused by orogenetic…

Evolutionary ecology of fast seed germination—A case study in Amaranthaceae/Chenopodiaceae

Abstract Germination is a vulnerable and risky step in a plant’s life cycle. Particularly under harsh environmental conditions, where time windows favourable for seedling establishment and survival are short or unpredictable, germination speed might play a highly adaptive role. We investigated the germination speed of 107 Amaranthaceae s.l. at two different temperatures and related the results to various plant and habitat traits taking into account the molecular phylogenetic relatedness of the species sampled. Germination speed is a fast evolving trait in Amaranthaceae s.l. It evolves towards significantly faster optima in C4 and halophyte lineages, albeit for different reasons. While C4 ph…

Cryptic taxa should have names: Reflections in the glasswort genusSalicornia(Amaranthaceae)

Incongruence between morphology and molecules, i.e., genetic differentiation of lineages that are morphologically identical, or morphological variation among accessions sharing identical genotypes, has been increasingly reported and is most problematic in taxa with reduced morphologies. We here review and discuss these issues for plant taxonomy, taking Salicornia, one of the taxonomically most challenging genera of angiosperms, as a model. We argue in favour of a taxonomic system that remains as much 'workable' as possible for traditional morphology-based taxonomy, but avoids merging genetically widely divergent lineages despite their morphological similarity. Our revised classification of …

Mangleticornia (Amaranthaceae: Salicornioideae) — a new sister for Salicornia from the Pacific coast of South America

Mangleticornia ecuadorensis is a newly recognized monotypic genus from SW Ecuador and adjacent N Peru, where it had previously been identified as Salicornia fruticosa (Arthrocnemum fruticosum) or S. peruviana. It occurs on the coast adjacent to or in Equatorial-Pacific mangroves. Molecular phylogenetic evidence determines that this genus is distinct from and sister to Salicornia sensu lato, and is supported by morphological evidence. The genus is distinguished by a unique combination of characters that are otherwise rare in Salicornioideae: flowers without a visible perianth, anthers and stigmas exserted through pores in the fleshy cortical tissue of the segments, fruit included in the segm…

Variation in leaf anatomical traits relates to the evolution of C4 photosynthesis in Tribuloideae (Zygophyllaceae)

Abstract Tribuloideae (Zygophyllaceae, Zygophyllales) is a warm-climate clade of mostly creeping herbs with an uncertain number of C4 species from at least two genera, raising the possibility of multiple C4 origins within this lineage. To delineate C3 and C4 distributions within Tribuloideae, we conducted a phylogenetic analysis using four genetic markers from 78 accessions of Tribuloideae. δ13C values from 68 Tribuloideae members detected 42 C4 species in the genera Kallstroemia, Tribulopis and Tribulus, and no C4 in Balanites, Neoluederitzia, and Sisyndite. All Kallstroemia are C4, while Tribulopis and Tribulus include C3 species. Two independent C4 origins are supported, one in Tribulus …

Molecular phylogeny and forms of photosynthesis in tribe Salsoleae (Chenopodiaceae).

Evolution of C3–C4 intermediate and C4 lineages are resolved in Salsoleae (Chenopodiaceae), and a model for structural and biochemical changes for the evolution of the Salsoloid form of C4 is considered.

Tetraploid European Salicornia species are best interpreted as ecotypes of multiple origin

Abstract Salicornia procumbens and S. stricta are two tetraploid European salt marsh species of locally adjacent but ecologically differentiated distribution. Whereas S. procumbens grows in the lowest part of the salt marsh, it is replaced by S. stricta in the middle part (and diploid Salicornias in the upper part). Using AFLPs and a reciprocal transplantation experiment, we investigated whether the two species represent distinct evolutionary lineages. The analysis of AFLP variation clearly showed that both species are not monophyletic. Also, accessions do not cluster according to geographical origin. The transplantation experiment revealed that S. procumbens shows significantly reduced fit…

Typification of the NameKochia saxicola(Chenopodiaceae)

The typification of the name Kochia saxicola Guss. [= Eokochia saxicola (Guss.) Freitag & G. Kadereit] (Chenopodiaceae) is here discussed, and a specimen from the Gussone collection (NAP) is designated as the lectotype. The distribution of the species is given and remarks on its IUCN conservation status are provided.

Tradeoffs in the evolution of plant farming by ants

Diverse forms of cultivation have evolved across the tree of life. Efficient farming requires that the farmer deciphers and actively promotes conditions that increase crop yield. For plant cultivation, this can include evaluating tradeoffs among light, nutrients, and protection against herbivores. It is not understood if, or how, nonhuman farmers evaluate local conditions to increase payoffs. Here, we address this question using an obligate farming mutualism between the ant Philidris nagasau and epiphytic plants in the genus Squamellaria that are cultivated for their nesting sites and floral rewards. We focused on the ants' active fertilization of their crops and their protection against he…

Origin and age of Australian Chenopodiaceae

Abstract We studied the age, origins, and possible routes of colonization of the Australian Chenopodiaceae. Using a previously published rbc L phylogeny of the Amaranthaceae–Chenopodiaceae alliance (Kadereit et al. 2003) and new ITS phylogenies of the Camphorosmeae and Salicornieae, we conclude that Australia has been reached in at least nine independent colonization events: four in the Chenopodioideae, two in the Salicornieae, and one each in the Camphorosmeae, Suaedeae, and Salsoleae. Where feasible, we used molecular clock estimates to date the ages of the respective lineages. The two oldest lineages both belong to the Chenopodioideae ( Scleroblitum and Chenopodium sect. Orthosporum / Dy…

Molecular phylogeny of Camphorosmeae (Camphorosmoideae, Chenopodiaceae): Implications for biogeography, evolution of C4-photosynthesis and taxonomy

Camphorosmeae constitute a species-rich tribe of Chenopodiaceae-Camphorosmoideae that consists mostly of subshrubs and annuals, distributed in steppes and semi-deserts of Australia, Eurasia, North Africa, southern Africa and North America. We study (1) the relationships of Camphorosmeae to major lineages of the closely related Salsoloideae and (2) the diversification of the tribe with focus on the non-Australian members using sequence variation of five different markers (rbcL gene, ndhF gene, atpB-rbcL spacer, psbB-psbH spacer, ITS) and morphological characters. The cpDNA analyses revealed six early-branching lineages in Camphorosmoideae/Salsoloideae (Camphorosmeae, Salsoleae s.str., Caroxy…

Which changes are needed to render all genera of the German lora monophyletic?

53 p., gráf.

Multiple shifts to open habitats in Melastomateae (Melastomataceae) congruent with the increase of African Neogene climatic aridity

International audience; AimAfrican Melastomateae (Melastomataceae) comprise c. 185 species occurring in closed or open habitats throughout sub-Saharan Africa. We sought to reconstruct biogeographical and habitat history, and shifts in diversification rates of African Melastomateae using a well-sampled, dated molecular phylogeny.LocationAmericas, sub-Saharan Africa, Madagascar, SE Asia.TaxonAngiosperms, Melastomataceae, African Melastomateae.MethodsPhylogenetic relationships were estimated based on an extensive sampling of New and Old World Melastomateae, using two nuclear and three plastid markers. Divergence times were estimated in BEAST based on three calibration priors under Bayesian unc…

Linnaeus's folly – phylogeny, evolution and classification ofSedum(Crassulaceae) and Crassulaceae subfamily Sempervivoideae

C3cotyledons are followed by C4leaves: intra-individual transcriptome analysis ofSalsola soda(Chenopodiaceae)

The genome of Salsola soda allows a transition from C3 to C4 photosynthesis. A developmental transcriptome series revealed novel genes showing expression patterns similar to those encoding C4 proteins.

Phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure of the endangered local Lower Elbe river (Germany) endemic Oenanthe conioides (Nolte ex Rchb.f.) Lange (Apiaceae): ITS and AFLP evidence

Abstract Oenanthe conioides is an endangered local endemic of the Lower Elbe river region in Germany where it is found in areas with freshwater tides. Internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) markers were used to investigate its phylogenetic relationships, evolutionary origin, taxonomic status, and genetic structure. Oe. conioides is most closely related to Oe. aquatica and Oe. fluviatilis, and cannot be distinguished from Oe. aquatica by ITS sequence variation. Oe. aquatica is found mainly in standing or slow-flowing freshwater habitats. The AFLP analysis indicated that Oe. conioides may constitute a monophyletic lineage nested within Oe. aquatica…

Argyrella richardsiae, a new species of Melastomataceae from the wet miombo woodlands of south-central Africa

A new species from the wet miombo woodlands of Tanzania and Angola, Argyrella richardsiae Veranso-Libalah & G.Kadereit, sp. nov. (Melastomataceae, Melastomateae), is described and illustrated. Although the widespread Argyrella canescens also occurs in Tanzania and northeastern Angola, A. richardsiae is morphologically most similar to Argyrella bambutorum known only from the Northwest of Cameroon, but differs by its indumentum of glandular trichomes on the entire plant (versus a mixture of stellate and glandular trichomes in other species of Argyrella), leaf-blades with serrulate margins (versus entire margins in A. bambutorum) and lateral nerves that become faint mid-way and never reach…

A broader model for C 4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

C 4 photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C 4 evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO 2 levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C 4 lineages in eudicots. The oldest chenopod C 4 lineage da…

Opposite trends in the genus Monsonia (Geraniaceae): Specialization in the African deserts and range expansions throughout eastern Africa

The African Austroerate Flora stands out by its important species richness. A distinctive element of this flora is Monsonia (Geraniaceae), mostly found in the Namib-Karoo but also in the Natal-Drakensberg, the Somalian Zambezian and the Saharo-Arabian regions. Here, we reconstruct the evolution and biogeographic history of Monsonia based on nuclear and plastid markers, and examine the role of morphological and niche evolution in its diversification using species distribution modeling and macroevolutionary models. Our results indicate that Monsonia first diversified in the Early Miocene c.21 Ma, coinciding with the start of desertification in southwestern Africa. An important diversification…

Phylogeny, biogeography and systematics of Dysphanieae (Amaranthaceae)

After a rather turbulent taxonomic history, Dysphanieae (Chenopodioideae, Amaranthaceae) were established to contain five genera, four of which are monospecific (Cycloloma, Neomonolepis, Suckleya, Teloxys) and geographically restricted, and the fifth genus, Dysphania, having a nearly worldwide distribution and comprising ca. 50 species. This study investigates the phylogeny, biogeography and taxonomy of Dysphanieae. We studied specimens from 32 herbaria to infer morphological differences and distribution areas of the species and sampled 121 accessions representing 39 accepted species of the tribe for molecular phylogenetic analyses. The molecular phylogeny tested generic relationships of th…

Phylogeny and systematics of African Melastomateae (Melastomataceae)

Melastomateae are the most species-rich (185 spp./13 gen.) and morphologically diverse tribe within the African Melastomataceae. In this study we present the first in-depth phylogenetic analysis of African Melastomateae using sequences generated from one nuclear (nrITS) and two plastid spacers (accD-psaI, psbK-psbL) sampling 183 accessions representing 75 African, 10 Madagascan and 7 Asian species and a broad outgroup sampling. We infer phylogenetic relationships using maximum likelihood, maximum parsimony and Bayesian approaches and propose a revised generic classification of African Melastomateae based on our molecular trees in combination with a careful reassessment of morphological vari…

Phylogenetic placement of Cailliella praerupticola (Melastomataceae), a rare, monospecific lineage from Guinea, West Africa

The genus Cailliella includes a single species, C. praerupticola, restricted to a sandstone plateau region in Coyah, Dubreka, Forecariah and Kindia Prefectures, Guinea, West Africa. Until its rediscovery in 2016, this species was known only by the type gathering made in 1937. We provide an emended description, photographs of living material, locality and habitat data, and a discussion of its conservation status. We further designate a lectotype for C. praerupticola. On the basis of morphology, Cailliella had been considered an isolated member of the tribe Melastomateae, possibly sister to Melastomastrum. We tested the classification of Cailliella by means of a phylogenetic analysis of C. pr…

A new species ofHalocnemumM.Bieb. (Amaranthaceae) from southern Turkey

Halocnemum yurdakulolii Yaprak is described as the second species of the previously monotypic genus Halocnemum. The species is endemic to the Goksu Delta in southern Turkey. The main morphological characteristics that separate H. yurdakulolii from H. strobilaceum (Pall.) M.Bieb. are growth form and spike morphology. Apart from these morphological differences, the species show a clear genetic differentiation. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 716–721.

Carbon isotope composition of plant photosynthetic tissues reflects a Crassulacean Acid Metabolism (CAM) continuum in the majority of CAM lineages

Abstract The stable carbon isotope composition of plant tissues, commonly expressed as δ13C, holds a wealth of information about photosynthetic pathway, water relations and stress physiology. Crassulacean acid metabolism (CAM) is a derived form of photosynthesis that allows plants to fix carbon at a higher water-use efficiency compared to the ancestral C3 photosynthesis. While the central carbon-fixing enzyme of C3 plants, Rubisco, strongly discriminates against the heavy 13C isotope, CAM is characterized by a dual use of Rubisco and the much less discriminating PEP carboxylase as carbon-fixing enzymes, causing the δ13C values of CAM plant tissues to be generally less negative than those fo…

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in su…

Molecular markers indicate the phylogenetic identity of southern Brazilian sea asparagus: first record of Salicornia neei in Brazil

Abstract Molecular phylogenetic analyses based on ETS, ITS and atpB - rbcL spacer sequences assessed the phylogenetic status of the southern Brazil sea asparagus species of the genus Salicornia (Salicornioideae, Amaranthaceae). Accessions of Patos Lagoon estuary (32° S) were obtained from wild plants and two pure line lineages, selected from contrasting prostrate (BTH1) and decumbent (BTH2) ecomorphotypes found locally. Patos Lagoon wild plants, BTH1 and BTH2 f4 progenies showed 100% identical sequences for the atpB - rbcL and ITS spacers, only two mutations for ETS. Comparison of the sequences of these three markers with GenBank records confirmed the identity of Brazilian accessions as Sal…

Data from: A revision of Sesuvium (Aizoaceae, Sesuvioideae)

Sesuvium and Cypselea are closely related succulent genera within the Sesuvioideae (Aizoaceae). Since Cypselea is nested in Sesuvium in molecular studies and both genera share traits separating them from other members of the subfamily, we propose to include Cypselea in Sesuvium. Sesuvium (incl. Cypselea) comprises 14 species and is distributed worldwide with centres of diversity in southern Africa and North and Central America. Sesuvium comprises erect to procumbent herbs with opposite leaves that often bear conspicuous sheath-like lateral appendages on the petioles (pseudostipules). These and the many-seeded capsules are diagnostic traits, separating Sesuvium from the closely related gener…