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Molecular phylogeny and taxonomy of the genus Disocactus ( Cactaceae ), based on the DNA sequences of six chloroplast markers
Abstract
The genus Disocactus is native to Mexico and Central America and includes 11 species in four subgenera: D. subg. Ackermannia, D. subg. Aporocactus, D. subg. Disocactus and D. subg. Nopalxochia. Phylogenetic reconstruction was carried out with data from DNA sequences using the maximum parsimony and Bayesian inference criteria to explore the monophyly of the genus, its subgenera and its position within Hylocereeae. Six chloroplast markers (matK, psbA-trnH, rpl16, trnL-F, trnQ-rps16 and ycf1) were sequenced in ten species of Disocactus, 17 representatives from the remaining genera of Hylocereeae and five members of outgroups (Acanthocereus, Lemaireocereus and Pereskia). Our phylogenetic analysis supports neither the monophyly of Disocactus as it is currently defined nor that of the subgenera. The clade Disocactus s.str. was recovered for 13 species, including Epiphyllum anguliger, E. crenatum and E. lepidocarpum. Three subclades were observed within this clade, and three well-supported sister-species relationships were recovered: D. eichlamii and D. quezaltecus; D. biformis and D. nelsonii; and D. ackermannii and D. phyllanthoides. Disocactus speciosus subsp. aurantiacus was not recovered in the clade of D. speciosus. Epiphyllum and Pseudorhipsalis are identified as sister clades of Disocactus. Based on the obtained results, a new circumscription for Disocactus is proposed. Citation: Cruz M. Á, Arias S. & Terrazas T. 2016: Molecular phylogeny and taxonomy of the genus Disocactus (Cactaceae), based on the DNA sequences of six chloroplast markers. — Willdenowia 46: 145–164. doi: http://dx.doi.org/10.3372/wi.46.46112 Version of record first published online on 1 April 2016 ahead of inclusion in April 2016 issue.
... Barthlott (in Taylor & Hunt 1991), Anderson (2001), Bauer (2003), and Hunt et al. (2006) maintain this criterion under the argument that Disocactus includes all diurnal and colourful flowers, as is also observed in Aporocactus. The studies of Cruz et al. (2016) and Korotkova et al. (2017) have demonstrated that Aporocactus is a monophyletic group that does not belong to Disocactus and that these genera are not directly related. In those phylogenies, the position of Aporocactus inside the tribe Hylocereeae has not been determined. ...
... The sequences from Aporocactus samples were quality-checked, assembled and edited using Sequencher ® v. 4.8 (Gene Codes, Ann Arbor Michigan USA). The sequences for the species of the genera Acanthocereus, Disocactus, Epiphyllum, Pseudorhipsalis, Strophocactus, Bergerocactus, Cephalocereus, Deamia, and Marshallocereus were obtained from the database of the Laboratory of Systematics of Cactaceae from the Botanical Garden/Institute of Biology, UNAM (Arias et al. 2005, Cruz et al. 2016, Sánchez et al. 2014, Hernández-Hernández et al. 2011) (Appendix 1). Additionally, we included the rps3-rpl16 and trnK-matK sequences from Korotkova et al. (2017) to complete the matrix (Appendix 1). ...
... Phylogenetic relationships of Aporocactus. The results supported the monophyly of the genus Aporocactus (Cruz et al. 2016, Korotkova et al. 2017 and rejected the hypothesis of some authors that Aporocactus is a member of Disocactus because of the similarity in the shape, colour, and diurnal anthesis of these plants, which are presumably pollinated by hummingbirds (Barthlott in Taylor & Hunt 1991, Bauer 2003, Hunt et al. 2006. These results indicated that Aporocactus and Disocactus are independent lineages in different clades and suggest that diurnal anthesis in bright-coloured flowers appeared independently at least two times in Hylocereeae. ...
Background:
Aporocactus is an epiphytic or saxicolous genus that is endemic to Mexico and has a distribution restricted to cloud forests and pine-oak forests. As with many cacti, Aporocactus presents taxonomic conflicts, especially regarding species delimitation, since five species in this genus have been described and accepted by some authors, while others accept only two species.
Questions:
How many species comprise Aporocactus? What are their relationships? Do these species show differences in their climatic preferences?
Studied species:
The five putative species in Aporocactus were investigated.
Study site and dates:
This study was conducted in 2015 and 2016. The collection sites were in Hidalgo, Puebla, Querétaro, Veracruz, and Oaxaca states, Mexico.
Methods:
In this study, phylogenetic analyses were performed using chloroplast DNA markers from different Aporocactus populations and related genera, and ecological niche modeling techniques were also employed.
Results:
The phylogenetic analyses indicated that Aporocactus is composed of only two species: A. flagelliformis and A. martianus. Additionally, the phylogenetic analyses corroborated that Aporocactus is an early diverging group related to Weberocereus and Selenicereus. Finally, niche modeling and niche identity testing indicated that the niches of the two species of Aporocactus are significantly differentiated and niches are more different than would be expected by chance.
Conclusions:
Despite being a genus with only two species, Aporocactus represents a useful model for investigating such topics as the ecology of pollination, genetic populations, and flower development to characterize the evolution of these specialized cacti.
... We chose two chloroplast markers, the rpl16 intron and the intergenic spacer psbA-trnH. In Cactaceae, both markers have been used to resolve phylogenetic relationships (Korotkova et al. 2010;Cruz et al. 2016;Barrios et al. 2020), including Mammillaria (Butterworth and Wallace 2004;Vázquez-Sánchez et al. 2013;Hernández-Hernández et al. 2014); therefore, there are many sequences available in GenBank that can be used to expand the sampling of terminals, including sister groups and outgroups essential for testing the monophyly (Korotkova et al. 2017) of M. ser. Supertextae. ...
... Intron rpl16 was demonstrated to be the most variable and informative marker compared to the intergenic spacer psbA-trnH, which is consistent with previous studies in Cactaceae (Korotkova et al. 2010;Vázquez-Sánchez et al. 2013;Cruz et al. 2016). The molecular characteristics that define the monophyly of M. ser. ...
... In other taxa (e.g., Petalidium Nees, Acanthaceae; Tripp et al. 2017), these problems have been addressed using multiple-locus methods to infer genetic trees, although they require nuclear markers that are not linked with levels of sequence variation according to phy-logenetic questions (Eaton and Ree 2013). To date, no effective nuclear markers have been developed for Cactaceae, and existing markers provide fewer informative sites than chloroplast markers (Cruz et al. 2016). Recently, proposals for nuclear markers have been generated through mining strategies to test hybridization in Opuntia species (Granados-Aguilar et al. 2020). ...
Mammillaria (Cactaceae) taxonomy has been historically problematic due to the morphological variability and sympatry of the species. This has led to several proposals for infrageneric classification, including subgeneric, section and series categories. Mammillaria ser. Supertextae is one of 15 series and is made up of a variable set of species that are mainly distributed in southern Mexico and Central America. However, the phylogenetic relationships within M. ser. Supertextae and its relationship to other Mammillaria taxa are far from fully understood. Here we attempt to elucidate these relationships using complete terminal sampling and newly obtained chloroplast marker sequences and comparing them to Mammillaria species sequences from GenBank. Our phylogenetic analyses showed that M. ser. Supertextae comprises a well-supported monophyletic group that diverged approximately 2.1 Mya and has M. ser. Polyacanthae as its sister group; however, relationships within M. ser. Supertextae remain unresolved. The topology obtained within M. ser. Supertextae must also be interpreted under the distribution shared by these taxa, but it is difficult to differentiate ancestral polymorphisms from possible introgression, given the short time elapsed and the markers used. Our results show that the infrageneric units of M. haageana and M. albilanata can be considered independent evolutionary units. We also suggest that the relationship between M. haageana and M. albilanata is convoluted because their distribution overlaps (mainly towards southern Mexico), with genetic differences that possibly indicate they represent more than two taxonomic entities. One possible explanation is that there could still be gene flow between these taxa, and we might be witnessing an ongoing speciation process. A peer-reviewed open-access journal Cristian R. Cervantes et al. / PhytoKeys 177: 25-42 (2021) 26
... The current Hylocereeae classification and recognized genera date back to the treatment by Barthlott & Hunt (1993) Bauer (2003a) and Aporocactus Lemaire was reinstated by Cruz et al. (2016). ...
... A study using plastid (rpl32-trnL, trnQ-rps16, psbB-trnT) and nuclear sequences (ITS,phyC,Vatp1) showed Hylocereus to be nested within a paraphyletic Selenicereus (Plume et al. 2013). Cruz et al. (2016) carried out a comprehensive sampling of Disocactus, redefined the genus, and provided a species-level synopsis that can serve as taxonomic backbone for it. ...
... Its position within the Hylocereeae remains unresolved. Nevertheless, our results are congruent with those of Cruz et al. (2016) who likewise found Aporocactus distant from Disocactus. Aporocactus was originally established as a genus by Lemaire (1860) but it was not generally accepted afterwards and was included in Cereus [a more detailed classification history of Aporocactus was given by Hunt (1989)]. ...
The tribe Hylocereeae are represented by mainly Central American-Mexican epiphytic, hemi-epiphytic and climbing cacti. They are popular due to their spectacular nocturnal flowers and have some importance as crops grown for their edible fruits. We present the first comprehensive phylogenetic study of the Hylocereeae sampling 60 out of the 63 currently accepted species and 17 out of 19 infraspecific taxa. Based on four plastid regions (trnK/matK, the rpl16 intron, rps3-rpl16, and trnL-F) we find a highly supported core Hylocereeae clade that also includes Acanthocereus and Peniocereus p.p., while Strophocactus is depicted as polyphyletic and is resolved outside of the Hylocereeae tribe. The clades found within Hylocereeae agree, in general terms, with the currently accepted genera but none of the genera are entirely monophyletic in their current circumscription. A new concept for the Hylocereeae is presented to include the genera Acanthocereus (incl. Peniocereus p.p.), Aporocactus, Disocactus, Epiphyllum, Selenicereus (incl. Hylocereus and Weberocereus p.p.), Pseudorhipsalis, Kimnachia gen. nov., and Weberocereus. New nomenclatural combinations are provided to make these genera monophyletic. The genus Deamia is reinstated for Strophocactus testudo and S. chontalensis, while Strophocactus is newly circumscribed to include S. wittii, Pseudoacanthocereus brasiliensis, and P. sicariguensis. Both genera are excluded from Hylocereeae. A taxonomic synopsis of Hylocereeae is provided.
... Britton and Rose (1963) divided Selenicereus and Hylocereus into different genera from morphology. However, based on many plastids and nuclear DNA sequences, morphology and anatomical data, it was proved that the two genera were not separated, and Hylocereus was nested in Selenicereus (Arias et al. 2005;Gómez-Hinostrosa et al. 2014;Plume et al. 2013;Miguel Á ngel et al. 2016). Different perspectives on classification standards and limited genomic information further complicated the taxonomic definition of this genus. ...
... However, it is worth noting that S. monacanthus, once classified as Hylocereus (synonym: H. lemairei), is more closely related to S. anthonyanus, the traditional Selenicereus species. Our results support the previous studies, namely the two genera were not separated, and they have a very close phylogenetic relationship (Arias et al. 2005;Gómez-Hinostrosa et al. 2014;Plume et al. 2013;Miguel Á ngel et al. 2016). However, considering the existence of interspecific or even intergeneric hybridization for Selenicereus plants (Tel-Zur et al. 2004), it is one-side to perform phylogenetic inferences about species with hybridization origin based on organelle genomes, as organelles are matrilineal inheritance . ...
Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.
Supplementary information:
The online version contains supplementary material available at 10.1007/s12298-021-01121-z.
... ), Deamia (Cerén et al. 2018, Cephalocereus , Disocactus Lindl. (Cruz et al. 2016), and Hylocereeae (Korotkova et al. 2017). ...
... Taxon sampling The seven species of Peniocereus recognized in recent taxonomic syntheses (Guzmán et al. 2003;Hunt 2016) and all the genera of the subtribe Pachycereinae (Arias and Terrazas 2006;Tapia et al. 2017;Cerén et al. 2018) were included in the present study. Additionally, one or two species per genus from the subtribe Echinocereinae were selected to represent the sister clade of Pachycereinae (Arias et al. , 2005Hernández-Hernández et al. 2011;Sánchez et al. 2014 Arias et al. (2005), Sánchez et al. (2014), Cruz et al. (2016), Tapia et al. (2017), andCerén et al. (2018). Voucher information and GenBank accession numbers for the samples used in this study are listed in "Appendix 1". ...
The genus Peniocereus contains distinctive cacti with slender stems and thickened roots. The phylogenetic relationship of Peniocereus to other members of the subtribe Pachycereinae is unresolved, and a sister group for the genus has not been suggested in previous molecular phylogenies. Therefore, this study aims to corroborate the monophyly of Peniocereus, to determine the relationships within the genus, to clarify their relationship with Nyctocereus, and to reconstruct the ancestral states for eight morphological characters and the areas of distribution. Five chloroplast markers (rpl16, petL-psbE, psbA-trnH, trnL-trnF, and rpl32-trnL) and a broad outgroup represented by all genera of the subtribes Pachycereinae and Echinocereinae were used in phylogenetic analyses. The results strongly supported the monophyly of Peniocereus, which comprises P. greggii, P. johnstonii, P. lazaro-cardenasii, P. marianus, P. striatus, P. viperinus, and P. zopilotensis. The genus was sister to the Pachycereus group, which comprises Carnegiea, Lophocereus, Marshallocereus, Nyctocereus, and Pachycereus (including Backebergia and Pterocereus). The scandent branches, slender stems, and papillose epidermis are ancestral characters to Peniocereus. A complex region including the Pacific Lowlands, the Balsas Basin, and the Sonoran Desert was inferred as the ancestral area for the genus. This work provides the most comprehensive phylogeny of the subtribe Pachycereinae.
... Britton & Rose [7] gave early de nitions of the two based on morphology, but Bauer [8] believed that "the transfer of Selenicereus to Hylocereus" made Britton & Rose's classi cation concept no longer applicable. Finally, based on a large number of plastid and nuclear DNA sequences, morphology and anatomical data, it was proved that the two genera were not separated, and Hylocereus was nested in Selenicereus [9][10][11][12]. The increasing quality and widespread cultivation of pitaya, as well as different viewpoints and limited genomic information, have further complicated the taxonomic de nition of this genus. ...
... However, it is worth noting that S. monacanthus, once classi ed as Hylocereus (synonym: H. lemairei), is more closely related to S. anthonyanus, the traditional Selenicereus species. Our results support the previous studies, namely the two genera were not separated, and Hylocereus was nested in Selenicereus [9][10][11][12]. However, considering the existence of interspeci c or even intergeneric hybridization for Selenicereus plants [55], it is one-side to perform phylogenetic inferences about species with hybridization origin based on organelle genomes, as organelles are matrilineal inheritance [56]. ...
Background: Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandiflorus and S. validus, and carried out a comprehensive comparative analysis.
Results: The four Selenicereus plastomes all have a typical quartile structure. The plastome size ranged from 133,146 bp to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the IR regions had undergone a dramatic expansion and formed a previously unreported SC/IR border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Phylogenetic analysis indicated that Hylocereus was nested in Selenicereus.
Conclusion: Our study enriches the plastomic resources in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.
... Molecular studies recovered Hylocereeae as a monophyletic group with maximum support (Cruz et al. 2016;Korotkova et al. 2017;Cruz 2018). Currently, eight genera are recognized based on chloroplast DNA: Acanthocereus, Aporocactus, Disocactus, Epiphyllum, Kimnachia, Pseudorhipsalis, Selenicereus, and Weberocereus (Korotkova et al. 2017). ...
... These three characters differentiate Disocactus from other genera that have stems with two ribs. Moreover, Epiphyllum anguliger and E. crenatus shared these characters with the other species of Disocactus and support Cruz et al. (2016) conclusions to transfer both species to Disocactus. Although Pseudorhipsalis, Kimnachia, and Epiphyllum have two ribs, Pseudorhipsalis is distinguished by the lignified cortical cells, the differential secondary growth, and cubic crystals in the cortical cells. ...
The Hylocereeae is a monophyletic group in which eight genera are recognized based on molecular data. However, relationships between the genera remain partially resolved. In this study, combined analyses of molecular and structural characters
for Hylocereeae were carried out with the aims of fnding structural synapomorphies that support the genera and to resolve
relationships between them. We studied sixty-nine species of the eight genera of Hylocereeae, as well as six Echinocereeae
species as outgroup using light microscopy and scanning electron microscopy. Thirty-six morpho-anatomical characters
were incorporated into a matrix and analyzed in combination with sequences of four chloroplast DNA regions. Phylogenetic
analyses using maximum parsimony, maximum likelihood, and Bayesian inference yielded a robust phylogenetic hypothesis
and showed morphological synapomorphies. Four of the genera (Acanthocereus, Aporocactus, Epiphyllum, and Kimnachia)
have at least one structural synapomorphy. Disocactus and Pseudorhipsalis can be recognized by a combination of characters, while Selenicereus and Weberocereus cannot be recognized by any structural vegetative character. There are structural
synapomorphies that allow recognizing relationships between genera. The cortical and vascular characters are as important
as the epidermal traits, a condition that had not been reported for another group within Cactaceae.
... Estos autores incluyeron a Acanthocereus horridus, una especie catalogada como endémica a Guatemala dentro de la Flora Mesoamericana (Ulloa-Ulloa et al., 2021); Peniocereus chiapensis, cuya distribución se limita a la depresión central de Chiapas en México y algunas áreas adyacentes a Guatemala (Gómez-Hinostrosa y Hernández, 2005); Disocactus biformis, cuya presencia en Honduras constituye una confusión en su distribución geográfica (Cerén et al., 2017); Disocactus cinnabarinus, sinónimo de D. speciosus subsp. cinnabarinus y distribuida solo en México y Guatemala (Cruz et al., 2016); además, apuntan que Nopalea hondurensis es una especie diferente de Opuntia hondurensis, sin embargo, actualmente es aceptada la inclusión de Nopalea en Opuntia (Pineda y Oyuela, 2020). ...
Se documentó la distribución de la familia Cactaceae en Honduras. Un archivo con 285 registros bibliográficos y ejemplares de herbario fue generado, el cual permitió reconocer 40 especies de cactáceas (incluyendo taxones infraespecíficos) distribuidas en 17 de los 18 departamentos de Honduras. El género Opuntia es el más diverso con 8 especies y la especie con mayor número de recolectas en el territorio hondureño es Rhipsalis baccifera. El área con mayor presencia de recolectas se ubica en los valles de la zona central del país entre los departamentos de Comayagua, Francisco Morazán y El Paraíso. Este análisis expone la importancia de la información brindada por las colecciones biológicas para realizar estudios sobre distribución de especies. Sin embargo, es necesario sustentar este trabajo con estudios de campo para evaluar la situación actual de las poblaciones y evidenciar otros puntos de distribución, ya que los hábitats de preferencia de las cactáceas en Honduras son muy amenazados por actividades agrícolas y el desarrollo urbanístico.
... For the circumscription of the epiphyte families, we followed the classification of APG IV (The Angiosperm Phylogeny Group, 2016) and at the species level that of The Plant List (2013) and Tropicos (2020). In the case of some families such as Bromeliaceae, Cactaceae, and Orchidaceae, the studies of some taxonomic specialists were considered (Schuiteman and Chase, 2015;Cruz et al., 2016;Espejo-Serna and López-Ferrari, 2018). ...
Background and Aims
Epiphytes are an important component of tropical forests, also they are sensitive to disturbance and deforestation caused by humans, since they depend on their host trees and the micro environmental conditions that these provide. The aim of this study was to analyze the differences in species richness, composition, and vertical distribution of epiphytic angiosperms between areas with natural and disturbed forest at the Northern Coast of Jalisco state, Mexico.
Methods
The presence/absence of epiphytic angiosperms was evaluated in each vertical zone of a selected tree, as well as those present in the understory, both in natural and disturbed sites in three types of vegetation (gallery forest, oak forest, tropical semideciduous forest) with a total of 30 plots of 20 m × 20 m in six sites. Alpha diversity was calculated for each site, as well as species turnover (beta diversity) between habitats. An analysis of variance was performed to determine if there was a significant difference in species richness between sites and, also to compare the height and diameter at breast height (DBH) of the host trees. Multivariate analyzes were used to group the sites according to their floristic composition. Furthermore, a linear regression was performed to detect any relationship between the number of species and the phorophyte structure.
Results
We recorded 45 species, 29 genera and nine families of epiphytic angiosperms. The most diverse families were Bromeliaceae and Orchidaceae and the richest genus was Tillandsia . Although the disturbed sites had more species, a significant difference in richness was not found, except for the disturbed gallery forest. Epiphytic angiosperms presented a high beta diversity, since the sites shared only between 2 and 18% of the recorded species. The inner portion of the canopy (Z3 and Z4) hosted most of the species in all sites and the understory had a high representation of epiphytes except for the disturbed oak forest, where these were absent. A relationship between the DBH and the number of species was found only at the disturbed sites, however, it was highly influenced by the high number of taxa registered in disturbed gallery forest. Therefore, the size of the trees could not be considered a factor in determining the diversity of epiphyte species.
Conclusion
The diversity of epiphytic angiosperm species from the North Coast of Jalisco has not been severely affected by the human disturbance. Most of the species have morphological and physiological adaptations that allow their establishment and survival in adverse climatic conditions. Our results suggest that epiphytic angiosperms cannot be considered as a good indicator for natural or disturbed environments in this region but should be considered in environmental conservation, as they present a high beta diversity.
... (Ritz & al. 2016), Copiapoa Britton & Rose (Larridon & al. 2015;Larridon & al. 2018a), Disocactus Lindl. (Cruz & al. 2016), Cephalocereus Pfeiff. (Tapia & al. 2017), Echinocactus Link & Otto (Vargas-Luna & al. 2018, Epithelantha F. A. C. Weber ex Britton & Rose , Eriosyce Phil. ...
This data paper presents a largely phylogeny-based online taxonomic backbone for the Cactaceae compiled from literature and online sources using the tools of the EDIT Platform for Cybertaxonomy. The data will form a contribution of the Caryophyllales Network for the World Flora Online and serve as the base for further integration of research results from the systematic research community. The final aim is to treat all effectively published scientific names in the family. The checklist includes 150 accepted genera, 1851 accepted species, 91 hybrids, 746 infraspecific taxa (458 heterotypic, 288 with autonyms), 17,932 synonyms of accepted taxa, 16 definitely excluded names, 389 names of uncertain application, 672 unresolved names and 454 names belonging to (probably artificial) named hybrids, totalling 22,275 names. The process of compiling this database is described and further editorial rules for the compilation of the taxonomic backbone for the Caryophyllales Network are proposed. A checklist depicting the current state of the taxonomic backbone is provided as . All results are also available online on the website of the Caryophyllales Network and will be constantly updated and expanded in the future.
Citation: Korotkova N., Aquino D., Arias S., Eggli U., Franck A., Gómez-Hinostrosa C., Guerrero P. C., Hernández H. M., Kohlbecker A., Köhler M., Luther K., Majure L. C., Müller A., Metzing D., Nyffeler R., Sánchez D., Schlumpberger B. & Berendsohn W. G. 2021: Cactaceae at Caryophyllales.org – a dynamic online species-level taxonomic backbone for the family. – Willdenowia 51: 251–270.
Version of record first published online on 31 August 2021 ahead of inclusion in August 2021 issue.
Data published through: http://caryophyllales.org/cactaceae/Checklist
... A total of 39 morphological characters was compiled (Online Resource 4) from field data, herbarium materials [DES, HAC, HAJB, JBSD, MEXU, NY; acronyms follow Thiers (2018)] and living collections (National Botanical Garden, University of Havana). In addition, a majority of the information of genera outside of Leptocereus was compiled through bibliographic review (Britton and Rose 1920;Bravo-Hollis 1978;Barthlott and Hunt 2000;Anderson 2001;Hunt et al. 2006;Sánchez-Salas et al. 2009;Ostolaza 2011;Cruz et al. 2016;Franco 2017;Rosas 2017;Tapia et al. 2017;Areces-Mallea 2017). The matrix of morphological characters (Online Resource 5) was coded with binary and multistate characters and edited in Mesquite 3.02 (Maddison and Maddison 2015). ...
Leptocereus is an Antillean genus of thin-stemmed cacti with 17 described species. We carried out a phylogenetic reconstruction with plastid DNA sequence data and a combined analysis with a set of 39 morphological characters using Maximum Likelihood and Bayesian inference criteria to explore the monophyly of the genus. We further analyzed the evolution of eight morphological characters to interpret the circumscription of Leptocereus and test for putative synapomorphies for the clade. Five plastid markers (trnL-F, trnQ-rps16, psbA-trnH, petL-psbE, and rpl16) were sequenced for fifteen species of Leptocereus, seven species of the related genera (Armatocereus, Dendrocereus, Strophocactus) and ten species from Hylocereeae, Pachycereinae, Stenocereinae were used as outgroup taxa. Our phylogenetic analyses suggest that Leptocereus is paraphyletic with a clade of the two Dendrocereus species nested within it. All Cuban species constitute a monophyletic group, as do the species of Hispaniola and Puerto Rico, which are sister to the Cuban clade + Dendrocereus clade. No morphological character analyzed here was synapomorphic for the genus, but sunken areoles in the depressions of the ribs were a character present in all subclades of Leptocereus. Based on our molecular data and extensive fieldwork, a new circumscription of Leptocereus is proposed, which includes three new combinations (Leptocereus albellus comb. et stat. nov., L. nudiflorus comb. nov., L. undulosus comb. nov.).
... In molecular phylogenies previously published, Selenicereus species were recovered as monophyletic [47,48], while the same works reported the position of Disocactus in the tribe Hylocereeae as uncertain. In addition, the controverted taxonomy of some members of Disocactus, such as the subspecies of D. speciosus, was attributed to the high morphological variability of the stems, spines and flowers [49,50]. The same controverted systematic context was addressed in a study combining molecular and morphological data for the genus Echinocereus by Sanchez et al. [51]. ...
Pyrolysis coupled to gas chromatography and mass spectrometry (Py-GC/MS) is a fast analytical technique used to characterize different lignocellulosic materials. Additionally, cheminformatics allows processing the vast amount of information obtained from Py-GC/MS for the classification of such materials. Here we characterized the lignocellulosic matrix of the spines in species of Cactaceae by Py-GC/MS; omic tools were used for processing the mass spectra in order to classify the species and identify chemical characters with taxonomic value. Fresh spines samples were collected from mature individuals belonging to 15 species of Cactaceae with known phylogenies. All samples were cleaned by ultrasonication and sequential Soxhlet extraction. Milled samples were analysed by Py-GC/MS and mass spectra were deconvoluted, identified, aligned and annotated using omic tools before the multivariate analysis. A total of 451 compounds were identified and aligned: ketones, esters, alcohols, furans and hydrocarbons were the main classes. Furan, furfural, butane and ethylene oxide were the main derivatives produced from carbohydrates, while the p-hydroxyphenyl (H) and guaiacyl (G) derivatives, as well as catechols, were the only compounds produced from lignin. Abundance patterns shared by different clusters of species were identified, obtaining a good resolution at the genus level. Lignin derivatives were preponderant for the identification of some groups of species, such as those of Cacteae, Selenicereus-Deamia and Opuntia. An incongruent clustering for Disocactus and Echinocereus species was found; environmental effects and characters convergence are evoked as the probable causes. A good taxonomic correspondence was obtained by combining the clustering and factorization analyses.
... Few years later, analyses with a greater sampling and more molecular markers allowed to delimit genera with high support as in Gymnocalycium Pfeiff. (Demaio et al. 2011); Opuntia Mill (Majure et al. 2012); some genera in tribe Rhipsalideae (Korotkova et al. 2011;Calvente et al. 2011); genera in tribe Cacteae (Vázquez-Sánchez et al. 2013); and several genera in Echinocereeae (Arias et al. 2005;Sánchez et al. 2014) and Hylocereeae (Cruz et al. 2016;Korotkova et al. 2017). The results of those studies have allowed to construct a natural classification as is preferred in phylogenetic systematics (Wheeler 2004). ...
Phylogenies based on molecular characters has dominated publications rather than those based on morphological characters. Some authors have defended the use of morphology in phylogenetic reconstruction. In Cactaceae few studies have been made combining molecular and morphological characters. A good example about the use of morphology in phylogenetic analysis has been addressed in Echinocereus. Echinocereus is a morphologically diverse genus including 67 species that have been grouped into eight taxonomic sections based on morphological traits. Previous molecular phylogenetic analyses did not show entirely the relationships in Echinocereus species, and did not provide useful characters to recognize clades. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses resulted mostly congruent. However, relationships of E. poselgeri did not agree between analyses. A second bayesian analysis using long-branch extraction test resulted in a topology with a morphologically congruent position of E. poselgeri. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The clades did not recover the recent infrageneric classification. As a consequence, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which are supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.
... The trnL-F spacer had the greatest number of phylogenetically informative sites, including three synapomorphies that support the monophyly of Epithelantha and it contributes characters in the delimitation of six of the eleven putative species. This marker has been used mainly in phylogenetic analyses (Vázquez-Sánchez et al. 2013;Cruz et al. 2016;Korotkova et al. 2017, among others), and we confim that it provided resolution at both the species and genus levels. ...
The genus Epithelantha (Cactaceae, Cactoideae, Cacteae) is native to Mexico and the southern USA and includes several uncertain species and ambiguous phylogenetic relationships. We applied multivariate analysis to a set of nine quantitative characters and six qualitative characters and we used Bayesian inference and maximum likelihood to reconstruct the phylogeny of Epithelantha using molecular data from four chloroplast regions (petL-psbE, psbA-trnH, trnL-F, and trnQ-rps16). Eleven taxa were collected in 39 localities where digital images of five individuals were taken. A correlation analysis allowed us to eliminate correlated characters. A discriminant canonical analysis (DCA) for quantitative characters and principal components analyses with mixed data (PCA mix) for quantitative and qualitative characters identified the length of the flower, number of spines, areole length/width ratio, the expansion of the hilar region of the seed, multicellular sculpture, and the relief of the periclinal wall as the most variable characters. The partial least squares-discriminant analysis (PLS-DA) allowed us to recognize nine of eleven taxa. As a complement, the molecular data matrix included 68 substitutions and 12 indels between the four markers. The 39 terminals analyzed were recovered in nine strongly supported clades, confirming the results of multivariate analyses. Epithelantha was recovered as a monophyletic group strongly supported by four substitutions and an indel, with Turbinicarpus being the sister group. Based on our results, we include a taxonomic synthesis of Epithelantha where we recognize ten species, propose two new combinations, designate seven lectotypes, and provide a key for species.
... For instance, it includes species with and without spinules in the exine, variable shape (subprolate to oblate-spheroidal), and polar area index is either small, medium or large. Moreover, the generic limits of Hylocereus and Selenicereus have changed over time Cruz et al. 2016;Korotkova et al. 2017). Pollen size, the absence of spinules and the morphological characters in species such as S. minutiflorus and S. stenopterus suggest they might belong to a genus other than Hylocereus or Selenicereus. ...
Hylocereeae is one of the nine tribes in the subfamily Cactoideae (Cactaceae), for which the limits and recognition of genera have been controversial. Essentially, this group comprises epiphytic and hemiepiphytic genera with stems modified as climbing structures. The aim of this paper is to examine pollen attributes in representative species of genera of Hylocereeae, focusing on Selenicereus whose current circumscription comprises Hylocereus and three Weberocereus species, to find whether significant potentially apomorphic and/or autapomorphic systematic characters can be discovered. Utilizing SEM and light microscopy, 25 pollen characters were observed and measured. Tribe Hylocereeae is stenopalynous, with pollen grains isopolar and radially symmetrical monads, mostly tricolpate, except in Kimnachia , Pseudoripsalis and Weberocereus , whose pollen grains are pantocolpate. Seven attributes (five qualitative and two continuous) exhibited useful variation and were coded. The character of brevicolpate pollen grains was shared by Kimnachia ramulosa and Pseudorhipsalis amazonica . Convex quadrangular outline in the polar view was shared by Weberocereus tunilla and S. glaber . The absence of spinules on the exine was shared by S. minutiflorus and S. stenopterus. The largest pollen grain, found in Selenicereus megalanthus , might be correlated with polyploidy. Selenicereus is the taxon with the highest variation in pollen attributes, including species with an exine with or without spinules and variable polar area index and shape (subprolate or oblate-spheroidal).
... The early diverging members of Core Cactoideae I clade are south American, generally columnar cacti, such as Corryocactus or Neoraimondia , followed by a clade composed of mostly shrubby, epiphytic or prostrate cacti (Epiphylum, Selenicereus, Leptocereus, Acanthocereus, Disocactus, etc.) with flowers already differentiated toward novel pollination by bats or hummingbirds. This last clade, corresponding to the tribe Hylocereeae, has been studied in more detail using chloroplast sequences showing that traditionally recognized genera, such as Hylocereus and Selenicereus, were nonmonophyletic (Cruz et al. 2016;Korotkova et al. 2017). These lineages are found through tropical regions of the Caribbean, México, Central America, and Florida (Anderson 2001). ...
Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.
... There is evidence of at least five climbing or epiphyte lineages, possibly shrubs, that diversified independently (Korotkova et al., 2010, Tapia et al., 2017. In Mesoamerica, most of the Hylocereeae genera and one Echinocereeae genus (Deamia) have diversified into climbing, hemi-epiphytic or epiphytic growth forms (Cruz et al., 2016, Korotkova et al., 2017, Tapia et al., 2017; therefore, it is of great interest to know the processes and structures involved in their adaptation. ...
Deamia montalvoae sp. nov. (Cactaceae) from the Mesoamerican region (El Salvador, Guatemala, and Mexico) is described and illustrated based on morphological and molecular evidences. The new species is morphologically characterized by stems up to 2 cm in diameter, 7−8-ribbed, flowers (23−)27−30 cm long, with pericarpel covered by bristles and trichomes, but without spines; fruit 5−6 cm long and pale-red, covered by bristles and trichomes, with white flesh; seeds 3.1−3.5 mm long, dark brown, with a smooth microrelief. The phylogenetic analysis using two introns, rpl16 and trnL-trnF, and a spacer, psbA-trnH, shows that D. testudo is the sister species of D. montalvoae and D. chontalensis.
... The exact placement within Hylocereeae of this species long remained controversial and it has been moved back and forth. For instance, Hunt et al. (2006) accepted it as a species of Disocactus Lindl., whereas Lodé (2015) studies confirm that it is best accommodated in Disocactus (Cruz et al., 2016). (4): 346-347. ...
Recent field work in Gran Canaria (Canary Islands, Spain), mostly in March and April 2017, yielded first records of 10 species of Cactaceae, all originally introduced as ornamentals. Cylindropuntia bigelovii, C. imbricata, C. prolifera, Disocactus speciosus, Opuntia lindheimeri and O. microdasys are locally naturalized or likely to become so, whereas Ferocactus herrerae, Harrisia tetracantha, Lophocereus schottii and Trichocereus
spachianus are considered casuals. All these species are illustrated, georeferenced localities provided and
other useful information, especially with regard to their identification and invasion status (in Gran Canaria as
well as elsewhere in the world) are also presented. The presence of two further species, Opuntia monacantha
and O. robusta, both often considered doubtful in the Canary Islands, is confirmed from Gran Canaria. New
data are also provided for Opuntia leucotricha and O. pilifera, two species that were recently recorded for the
first time for Gran Canaria, that seem to have increased.
... Collections at the DBG and the Botanical Garden of Instituto de Biologia (JBIB) in México City, for example, have been used for a variety of evolutionary and ecological studies. These include phylogenetic and cytogenetic studies of the prickly pear cacti or nopales and relatives (Majure et al. 2012a, 2012b, Majure and Puente 2014 and, more broadly, the entire family Cactaceae Cruz et al. 2016). Likewise, collections at DBG and JBIB are being used extensively in phylogenomic and ecophysiological studies (Williams et al. 2014, Hultine et al. 2016 to fill in evolutionary gaps in our knowledge of the family Cactaceae. ...
The family Cactaceae contains some of the most iconic species of succulent plants, many of which are valued for their cultural, economic, and ecological value. However, over 75% of all species of cacti are in decline, largely because of the effects global environmental changes (GEC), including climate change. Mitigating the impacts of GEC on cacti will require a coordinated effort that combines conservation, research, and education. Botanical gardens are uniquely positioned to lead such an effort because their living collections and programs focus on conservation and research. A coordinated network of botanical gardens—with living collections serving as experimental gardens—could become a crucial hub for studying the impacts of climate change on cacti. A network of botanical gardens could open previously untapped funding avenues to support the research, education, and conservation of cacti and provide resources for underfunded botanical gardens in Latin America.
Disocactus heterodoxus is a poorly known species from Guatemala and Mexico. It has been treated in the taxonomic literature as a subspecies of D. speciosus or as a synonym of D. speciosus subsp. cinnabarinus. We present a detailed morphological description of this plant and synthesize the available data on its habitat and geographic distribution. In addition, we discuss its taxonomic affinities with other members of Disocactus. Based upon its unique combination of morphological characters (flat, 2-ribbed stems with few or no spines, and narrowly infundibuliform flowers with colors ranging from white to pink and red) and on published molecular data, we believe that there is sufficient evidence to recognize this plant as a distinct species.
Antecedentes y Objetivos:
En el sureste de México los estudios florísticos, y en particular los que tratan sobre las Hylocereeae, son escasos. Se presenta un estudio florístico taxonómico de las Cactaceae en Tabasco para conocer la riqueza y distribución de sus especies, se generó un listado de especies nativas y cultivadas y se presenta una clave de identificación de las especies para Tabasco.
Métodos:
Se consultaron los herbarios CSAT, MEXU, UJAT y XAL, así como literatura taxonómica pertinente para tener una aproximación de la diversidad de Cactaceae en Tabasco. Se realizó trabajo de campo en todos los tipos de vegetación del estado para obtener las muestras necesarias; éstas se depositaron en el herbario UJAT. Con el material colectado y los ejemplares revisados en los herbarios, se realizaron claves de identificación para los géneros y especies registrados.
Resultados clave:
En Tabasco se registran siete géneros y 14 especies de cactáceas, seis de las cuales representan nuevos registros para el estado. El género Selenicereus es el más diverso, mientras que el bosque tropical perennifolio y el municipio Tacotalpa presentaron la mayor riqueza de especies.
Conclusiones:
Las cactáceas en Tabasco se encuentran pobremente representadas en comparación con los estados del centro-norte de México; sin embargo, con los estados de Campeche y Yucatán se observa una notoria similitud en cuanto a la riqueza de especies.
The role of Pleistocene climate changes in promoting evolutionary diversification in global biota is well documented, but the great majority of data regarding this subject come from North America and Europe, which were greatly affected by glaciation. The effects of Pleistocene changes on cold- and/or dry-adapted species in tropical areas where glaciers were not present remain sparsely investigated. Many such species are restricted to small areas surrounded by unfavorable habitats, which may represent potential interglacial microrefugia. Here, we analyzed the phylogeographic structure and diversification history of seven cactus species in the Pilosocereus aurisetus complex that are restricted to rocky areas with high diversity and endemism within the Neotropical savannas of eastern South America. We combined paleodistributional estimates with standard phylogeographic approaches based on two chloroplast DNA regions (trnT-trnL and trnS-trnG), exon 1 of the nuclear gene PhyC, and 10 nuclear microsatellite loci. Our analyses revealed a phylogeographic history marked by multiple levels of distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages within the complex. Diversification and demographic events appear to have been affected by the Quaternary climatic cycles as a result of isolation in multiple patches of xerophytic vegetation. These small patches presently harboring P. aurisetus populations seem to operate as microrefugia, both at present and during Pleistocene interglacial periods; the role of such microrefugia should be explored and analyzed in greater detail.This article is protected by copyright. All rights reserved.
PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach.
METHODS: Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively.
KEY RESULTS: Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas.
CONCLUSIONS: Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity.
The cactus genus Harrisia contains 18 species, of which 11 are native to the Caribbean region. To evaluate species relationships, specimens of Harrisia were examined morphologically, sequenced for seven DNA regions (four nuclear, three plastid), and surveyed for additional polymorphisms using ten sets of AFLP primers. The analyses show that H. earlei is an isolated lineage, sister to the remaining ten species. The remaining ten species comprised three groups in the molecular analyses—a Cuba group, Florida group, and a southern/eastern Greater Antilles-Bahamas (SEGAB) group. Morphology suggests the Florida group is related to species of west Cuba and the SEGAB group is related to species of east Cuba. Harrisia likely first colonized west Cuba and then dispersed northeastward and southeastward.
This study aimed to test the phylogenetic relationships of the tribe Cacteae, the generic circumscription within the tribe, in particular, the monophyly of the genus Ferocactus, and to provide a biogeographical hypothesis about the origin of Cacteae. The analysis included 135 species from all of the 27 accepted genera and four outgroup species. Five chloroplast regions were sequenced, aligned, and coded postulating gaps, simple sequence repeats (SSRs), and inversions as potential synapomorphies, and their contributions to phylogenetic reconstruction were evaluated. The phylogenetic analyses recovered 63% of the genera as monophyletic. The contribution of rpl16, trnL-F and psbA to the phylogenetic signal was higher than in the two more slowly evolving genes (rbcL, matK), but the gaps and SSRs supported some of the genera. This result differs from those of previous phylogenetic studies in which less than 35% of the genera were recovered as monophyletic. In this work, Astrophytum and Echinocactus were re-circumscribed with five and four species, respectively. Turbinicarpus was found to be polyphyletic; 11 species correspond to Turbinicarpus s.str., whereas a highly supported clade corresponded to Rapicactus, and three species need further study. Contrary to its current circumscription, Ferocactus was not supported as monophyletic because it is polyphyletic concerning Glandulicactus, Leuchtenbergia, Stenocactus and Thelocactus. We recognize this group of genera as the Ferocactus clade in which the species share the presence of scales in the pericarpel and ribbed stems, whether tuberculated or not. The Cacteae seem to have originated in the Sierra Madre Oriental and then dispersed to the Mexican Plateau, where radiation and diversification occurred at the boundaries of the Miocene–Pliocene Epoch. The development of the Mexican Plateau and the Trans-Mexican Volcanic Belt may have favoured the isolation of the Cacteae. A taxonomic diagnosis is presented for the tribe Cacteae and 18 genera that we now recognize.
Allopolyploidy is common in angiosperms, but only rarely involves different genera. One hypothesized case of intergeneric allopolyploidy is Hylocereus megalanthus, a member of Cactaceae tribe Hylocereeae, a group of vine cactus species, some of which are known for their edible fruits ("pitahaya" or "dragon fruit"). This polyploid species has been interpreted as morphologically intermediate between Hylocereus and Selenicereus. Plastid and nuclear ribosomal DNA ITS sequences from all H. megalanthus individuals sampled are either identical (plastid), or form a monophyletic clade despite considerable intraindividual polymorphism (ITS). Plastid and ITS phylogenies both show H. megalanthus nested within a well-supported Hylocereus, which in turn is nested within a paraphyletic Selenicereus. The absence of more than one lineage of ITS in H. megalanthus is consistent with autopolyploidy, but could be due to inter-homoeologue concerted evolution. Numerous low-copy nuclear genes were tested for utility in these vine cacti, and two (phyC and Vatp1) were sampled from H. megalanthus and a subset of Hylocereus and Selenicereus species. In both cases, H. megalanthus haplotypes were more closely related to each other than to other Hylocereus or Selenicereus haplotypes. Thus, we found no evidence for allopolyploidy, let alone intergeneric allopolyploidy, in H. megalanthus.
This report is an investigation into the relationships among members of the genus Grusonia sensu Anderson (2001) with an emphasis on examining the relationship of Gru- sonia pulchella within Opuntioideae (Cactaceae). G. pulchella is morphologically and geographi- cally distinct from other Grusonia species, and nrITS DNA sequence data suggest that it may rep- resent an independent evolutionary lineage from other grusonioid cacti. With the morphological, geographical, and molecular evidence considered, I propose to resurrect the generic concepts Corynopuntia Knuth (1935), Grusonia Reichenbach ex Schumann (sensu Brit ton and Rose, 1919), and Micropuntia Daston (1946).
Unlabelled:
•
Premise of the study:
To increase the number of variable regions available for phylogenetic study in the Cactaceae, primers were developed for a portion of the plastid ycf1 gene and intron-spanning regions of two low-copy nuclear genes (isi1, nhx1). •
Methods and results:
Primers were tested on several families within Caryophyllales, focusing on the Cactaceae. Gel electrophoresis indicated positive amplification in most samples. Sequences of these three regions (isi1, nhx1, ycf1) from Harrisia exhibited variation similar to or greater than two plastid regions (atpB-rbcL intergenic spacer and rpl16 intron). •
Conclusions:
The isi, nhx, and ycf1 primers amplify phylogenetically useful information applicable to the Cactaceae and other families in the Caryophyllales.
Pfeiffera is a genus of epiphytic, terrestrial and epilithic cacti. Its acceptance, circumscription and closest relatives have been debated. In the context of a phylogenetic survey of epiphytic cacti, we have studied relationships in Pfeiffera, sampling eight of nine species and using sequence data from three group II introns (trnK, rpl16, trnG) , four intergenic spacers (psbA-trnH, trnQ-rps16, rps3-rpl16, trnS-trnG) and the rapidly evolving gene matK of the plastid genome. Phylogenetic analyses revealed Pfeiffera to be polyphyletic, comprising two unrelated lineages, both highly supported. One clade includes the type species, P. ianthothele; the second contains two Pfeiffera and an erstwhile Lepismium species. Our results justify generic status for this newly found clade. Since it includes the type species of the earlier-proposed monotypic genus Lymanbensonia, we suggest the reinstatement of the latter in an amplified circumscription. The necessary new combinations for Pfeiffera brevispina and Lepismium incachacanum are provided. Our results further support the establishment of a separate tribe Lymanbensonieae, formally proposed here, to contain Lymanbensonia and Calymmanthium. The phylogenetic results imply that epiphytism evolved more frequently in Cactaceae than hitherto assumed and further show that morphological convergences in the family can be extreme. An integrated approach using morphology and sequence data is therefore needed to establish sound generic limits in the Cactaceae .
JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. Epiphytes represent an important element of the tropical flora and are widely distributed across vascular plants. Despite this diversity, however, little is yet known of the evolutionary history, habitat preference, morphological diversity, and biogeographical patterns of epiphytes as a whole. Approximately 10% of cacti are epiphytes inhabiting humid regions, and Rhipsalis represents the largest genus of these. Here we reconstruct relationships among species of the genus Rhipsalis on the basis of plastid and nuclear DNA markers (trnQ-rps16, rpl32-trnL, psbA-trnH, internal transcribed spacers, and malate synthase) and use them as a basis to study the evolution of habit, key morphological features, and the biogeographical history of the genus. Rhipsalis is highly supported as monophyletic, presenting three main lineages. Two lineages are marked by unique floral morphologies and one presents an exclusive stem-shape morphology. In spite of this, neither of these features seems to have been associated with small-scale habit transitions or large-scale transitions through different biogeographical regions. Several lineages of the genus seem to have originated in coastal Brazil and subsequently occupied other tropical forests in South America, North America, Africa, and Asia. These events occurred in relatively recent times, with most of them taking place on terminal branches, thus suggesting recent associations between South American epiphytic flora.
Introns and spacers are a rich and well-appreciated information source for evolutionary studies in plants. Compared to coding
sequences, the mutational dynamics of introns and spacers is very different, involving frequent microstructural changes in
addition to substitutions of individual nucleotides. An understanding of the biology of sequence change is required for correct
application of molecular characters in phylogenetic analyses, including homology assessment, alignment coding, and tree inference.
The widely used term “indel” is very general, and different kinds of microstructural mutations, such as simple sequence repeats,
short tandem repeats, homonucleotide repeats, inversions, inverted repeats, and deletions, need to be distinguished. Noncoding
DNA has been indispensable for analyses at the species level because coding sequences usually do not offer sufficient variability.
A variety of introns and spacers has been successfully applied for phylogeny inference at deeper levels (major lineages of
angiosperms and land plants) in past years, and phylogenetic structure R in intron and spacer data sets usually outperforms that of coding-sequence data sets. In order to fully utilize their potential,
the molecular evolution and applicability of the most important noncoding markers (the trnT–trnF region comprising two spacers and a group I intron; the trnS–G region comprising one spacer and a group II intron in trnG; the group II introns in petD, rpl16, rps16, and trnK; and the atpB–rbcL and psbA–trnG spacers) are reviewed. The study argues for the use of noncoding DNA in a spectrum of applications from deep-level phylogenetics
to speciation studies and barcoding, and aims at outlining molecular evolutionary principles needed for effective analysis.
KeywordsSpacers-Introns-Phylogenetic structure R
-Molecular evolution-SSRs-Inversions-Mutational hotspots-DNA barcoding
A molecular phylogenetic analysis of the Andean genus Tarasa (Malvaceae) and related genera yielded unexpected results regarding generic boundaries, the origins of polyploidy, and the morphological attributes of the polyploid taxa. The polyploid species of Tarasa are particularly unusual because they have life histories and floral morphologies that contradict two traditional polyploid dogmas: they are annuals and have smaller floral features (including pollen) than the diploid species. Typically, polyploids are perennial and larger than their parents. Nuclear (ITS1, 5.8S, and ITS2) and chloroplast (psbA-trnH and trnT-trnL spacers, matK-3′ trnK intron) sequence data were used to reconstruct independent phylogenies to test the monophyly of the genus, determine its sister group(s), and investigate the origin of the polyploid species. Neither the nuclear nor the chloroplast phylogeny supports monophyly of Tarasa as currently circumscribed. The high Andean genus Nototriche, the North/South American disjunct genus Sphaeralcea, and Malacothamnus chilensis are placed within the Tarasa clade. The polyploid species of Tarasa are not monophyletic and thus have been generated multiple times. These findings suggest that the unusual morphological features of the tetraploids are the result of convergent evolution and not shared ancestry.
Premise of the study:
The opuntias (nopales, prickly pears) are not only culturally, ecologically, economically, and medicinally important, but are renowned for their taxonomic difficulty due to interspecific hybridization, polyploidy, and morphological variability. Evolutionary relationships in these stem succulents have been insufficiently studied; thus, delimitation of Opuntia s.s. and major subclades, as well as the biogeographic history of this enigmatic group, remain unresolved.
Methods:
We sequenced the plastid intergenic spacers atpB-rbcL, ndhF-rpl32, psbJ-petA, and trnL-trnF, the plastid genes matK and ycf1, the nuclear gene ppc, and ITS to reconstruct the phylogeny of tribe Opuntieae, including Opuntia s.s. We used phylogenetic hypotheses to infer the biogeographic history, divergence times, and potential reticulate evolution of Opuntieae.
Key results:
Within Opuntieae, a clade of Tacinga, Opuntia lilae, Brasiliopuntia, and O. schickendantzii is sister to a well-supported Opuntia s.s., which includes Nopalea. Opuntia s.s. originated in southwestern South America (SA) and then expanded to the Central Andean Valleys and the desert region of western North America (NA). Two major clades evolved in NA, which subsequently diversified into eight subclades. These expanded north to Canada and south to Central America and the Caribbean, eventually returning back to SA primarily via allopolyploid taxa. Dating approaches suggest that most of the major subclades in Opuntia s.s. originated during the Pliocene.
Conclusions:
Opuntia s.s. is a well-supported clade that includes Nopalea. The clade originated in southwestern SA, but the NA radiation was the most extensive, resulting in broad morphological diversity and frequent species formation through reticulate evolution and polyploidy.
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
•
The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. •
We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. •
The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). •
The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.
The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information. The mat K coding region, evolving more rapidly than the trnL-trn F spacer and more slowly than the psb A-trn H spacer, produced the best resolved phylogenetic tree. The mat K phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.
Cacti are a large and diverse group of stem succulents predominantly occurring in warm and arid North and South America. Chloroplast DNA sequences of the trnK intron, including the matK gene, were sequenced for 70 ingroup taxa and two outgroups from the Portulacaceae. In order to improve resolution in three major groups of Cactoideae, trnL-trnF sequences from members of these clades were added to a combined analysis. The three exemplars of Pereskia did not form a monophyletic group but a basal grade. The well-supported subfamilies Cactoideae and Opuntioideae and the genus Maihuenia formed a weakly supported clade sister to Pereskia. The parsimony analysis supported a sister group relationship of Maihuenia and Opuntioideae, although the likelihood analysis did not. Blossfeldia, a monotypic genus of morphologically modified and ecologically specialized cacti, was identified as the sister group to all other Cactoideae. The tribe Cacteae was found to be sister to a largely unresolved clade comprising the genera Calymmanthium, Copiapoa, and Frailea, as well as two large and well-supported clades. Browningia sensu stricto (excluding Castellanosia), the two tribes Cereeae and Trichocereeae, and parts of the tribes Notocacteae and Rhipsalideae formed one clade. The distribution of this group is largely restricted to South America. The other clade consists of the columnar cacti of Notocacteae, various genera of Browningieae, Echinocereeae, and Leptocereeae, the tribes Hylocereeae and Pachycereeae, and Pfeiffera. A large portion of this latter group occurs in Central and North America and the Caribbean.
The genus Mammillaria is likely the most species-rich and morphologically variable genus in the Cactaceae. There is doubt as to whether the genus is monophyletic, and past infrageneric treatments differ regarding generic circumscription. Phylogenetic questions about Mammillaria were addressed using chloroplast DNA sequence data from the rpl16 intron and the psbA-trnH intergenic spacer for 125 taxa (113 Mammillaria, 10 Coryphantha, Escobaria, Neolloydia, Pelecyphora, Ortegocactus, and two outgroup taxa from Ferocactus and Stenocactus). Parsimony analyses were conducted using various heuristic search strategies. Bayesian analyses were conducted using the F81 and F81 + I + G models of sequence evolution. Tree topologies from the parsimony and Bayesian analyses were largely congruent. Hypothesis testing was undertaken using the parametric bootstrap to test the monophyly of the genus and the taxonomic status of Mammillaria candida. Phylogenies derived from the parsimony and Bayesian analyses indicate that Mammillaria is not monophyletic and that the genus Mammilloydia (synonym Mammillaria) is embedded within a "core" group of Mammillaria species. Both these results were corroborated by the parametric bootstrap tests. The entire rpl16 intron was deleted from species in the Mammillaria crinita group.
The cacti are well-known desert plants, widely recognized by their specialized growth form and essentially leafless condition. Pereskia, a group of 17 species with regular leaf development and function, is generally viewed as representing the "ancestral cactus," although its placement within Cactaceae has remained uncertain. Here we present a new hypothesis of phylogenetic relationships at the base of the Cactaceae, inferred from DNA sequence data from five gene regions representing all three plant genomes. Our data support a basal split in Cactaceae between a clade of eight Pereskia species, centered around the Caribbean basin, and all other cacti. Two other Pereskia clades, distributed mostly in the southern half of South America, are part of a major clade comprising Maihuenia plus Cactoideae, and Opuntioideae. This result highlights several events in the early evolution of the cacti. First, during the transition to stem-based photosynthesis, the evolution of stem stomata and delayed bark formation preceded the evolution of the stem cortex into a specialized photosynthetic tissue system. Second, the basal split in cacti separates a northern from an initially southern cactus clade, and the major cactus lineages probably originated in southern or west-central South America.
Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL((UAG)), trnQ((UUG))-5'rps16, 3'trnV((UAC))-ndhC, ndhF-rpl32, psbD-trnT((GGU)), psbJ-petA, 3'rps16-5'trnK((UUU)), atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.
Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55; 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided.
Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
Sequence analysis of the hypervariable internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) is commonly used to gain insights into plant and animal population structure and phylogeny. We characterized ITS1, ITS2, and the 5.8S coding region of 18 senita (Lophocereus) individuals from 12 different populations in Baja as well as from closely related cactus species. Analyses of multiple clones demonstrated extensive paralogy in the senita rDNA gene family. We identified at least two putatively non-recombining rDNA operons in senita as well as multiple paralogous sequences within each operon. Usage of PCR, reverse transcriptase (RT)-PCR, Southern blot, primary sequence analyses of the 18S rDNA gene, and secondary structure analyses of the 5.8S rRNA showed that one of the operons encodes rDNA pseudogenes in a low copy-number (Truncated), whereas the second operon encodes an expressed rRNA (Functional). Surprisingly, we found extensive paralogy not only in the ITS regions but also in the 5.8S coding regions in senita both within and between operons. Phylogenetic analyses suggest that the second rDNA operon originated prior to the divergence of Lophocereus. A significant (p < 0.05) divergence-rate acceleration was found in the Lophocereus 5.8S rDNA coding region in the Functional operon in comparison to Pereskiopsis porteri (Cactaceae) and Portulaca molokiniensis (Portulacaceae) with Silene dioica and Spinacia oleracea as the outgroups.
The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.
The cactus genus Harrisia contains 18 species, of which 11 are native to the Caribbean region. To evaluate species relationships, specimens of Harrisia were examined morphologically, sequenced for seven DNA regions (four nuclear, three plastid), and surveyed for additional polymorphisms using ten sets of AFLP primers. The analyses show that H. earlei is an isolated lineage, sister to the remaining ten species. The remaining ten species comprised three groups in the molecular analyses—a Cuba group, Florida group, and a southern/eastern Greater Antilles‐Bahamas (SEGAB) group. Morphology suggests the Florida group is related to species of west Cuba and the SEGAB group is related to species of east Cuba. Harrisia likely first colonized west Cuba and then dispersed northeastward and southeastward.
The phylogenetic relationships of Pachycereus (Cactaceae) species and relatives from subtribe Pachycereinae were studied using DNA sequence data. The plastid rpl16 intron, trnL intron, trnL-F intergenic spacer, and nuclear rDNA internal transcribed spacer region (ITS) were sequenced for 30 species, representing the four genera of subtribe Pachycereinae (Carnegiea, Cephalocereus, Neobuxbaumia, and Pachycereus) as well as three additional outgroup genera from subtribe Stenocereinae. Phylogenetic analyses support neither the monophyly of Pachycereus as currently circumscribed nor Pachycereinae unless Stenocereus aragonii and S. eichlamii are included within it. However, these results suggest that the subtribe can be divided into three major clades. The first includes Pachycereus hollianus and P. lepidanthus, which is sister to a large clade combining species from the Pachycereus and Cephalocereus groups. Within this large clade Cephalocereus and Neobuxbaumia together with Pachycereus fulviceps are sister to the remaining species of Pachycereus as well as Stenocereus aragonii, S. eichlamii, and Carnegiea gigantea. Our results suggest that Pachycereus is paraphyletic and that several other genera (Backebergia, Lemaireocereus, Lophocereus, and Pseudomitrocereus) may be resurrected to accommodate these new phylogenetic insights. A number of morphological and anatomical characters support these relationships, indicating that future analyses combining both molecular and morphological characters will be particularly useful in resolving relationships within this group of columnar cacti.
Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles. Availability: SeqState runs on all major computer platforms and is downloadable for free from http:// www. nees. uni-bonn. de/ downloads/ SeqState, together with documentation and sample data files, or can be requested from the author.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing
methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform
(FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid
residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy
of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented
in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark
tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over
100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Premise of the study:
In its current circumscription, Echinopsis with 100-150 species is one of the largest and morphologically most diverse genera of Cactaceae. This diversity and an absence of correlated characters have resulted in numerous attempts to subdivide Echinopsis into more homogeneous subgroups. To infer natural species groups in this alliance, we here provide a plastid phylogeny and use it to infer changes in growth form, pollination mode, and ploidy level.
Methods:
We sequenced 3800 nucleotides of chloroplast DNA from 162 plants representing 144 species and subspecies. The sample includes the type species of all genera close to, or included in, Echinopsis as well as a dense sample of other genera of the Trichocereeae and further outgroups. New and published chromosome counts were compiled and traced on the phylogeny, as were pollination modes and growth habits.
Key results:
A maximum likelihood phylogeny confirms that Echinopsis s.l. is not monophyletic nor are any of the previously recognized genera that have more than one species. Pollination mode and, to a lesser extent, growth habit are evolutionarily labile, and diploidy is the rule in Echinopsis s.l., with the few polyploids clustered in just a few clades.
Conclusions:
The use of evolutionary labile floral traits and growth habit has led to nonnatural classifications. Taxonomic realignments are required, but further study of less evolutionary labile traits suitable for circumscribing genera are needed. Surprisingly, polyploidy seems infrequent in the Echinopsis alliance and hybridization may thus be of minor relevance in the evolution of this clade.
Bayesian, maximum-likelihood, and maximum-parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK-matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum-likelihood analyses, not in the maximum-parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera. © The Willi Hennig Society 2011.
The tropical Andes harbor a major part of the world's plant biodiversity. The montane cacti of the tribes Browningieae, Cereeae, and Trichocereeae underwent extensive radiation and thus are well suited as a model group to study the diversification of Andean plants. We reconstructed their phylogeny employing three noncoding chloroplast regions and explained it in the context of the geological history of South America. We found that the clade of cephalia-bearing cacti with naked pericarpels is centered in northeastern Brazil, whereas almost all other clades comprise Andean species. The spatial split between the clades was probably caused by the Andean uplift and the concurrent formation of intracontinental marine basins in the Tertiary. The phylogenetic reconstructions based on parsimony and Bayesian approaches do not reflect the traditional delimitation of the tribes and of the large genera. Our results suggest that Rebutia s.l. and Echinopsis s.l. are not monophyletic and that Sulcorebutia, Weingartia, and Cintia should be united into one genus. Even though this "Weingartia-complex" and the genus Gymnocalycium are similar in size and morphological diversity, Gymnocalycium has a very high molecular divergence suggesting a comparably older radiation.
Cactaceae is one of the most charismatic plant families because of the extreme succulence and outstanding diversity of growth forms of its members. Although cacti are conspicuous elements of arid ecosystems in the New World and are model systems for ecological and anatomical studies, the high morphological convergence and scarcity of phenotypic synapomorphies make the evolutionary relationships and trends among lineages difficult to understand.
We performed phylogenetic analyses implementing parsimony ratchet and likelihood methods, using a concatenated matrix with 6148 bp of plastid and nuclear markers (trnK/matK, matK, trnL-trnF, rpl16, and ppc). We included 224 species representing approximately 85% of the family's genera. Likelihood methods were used to perform an ancestral character reconstruction within Cactoideae, the richest subfamily in terms of morphological diversity and species number, to evaluate possible growth form evolutionary trends.
Our phylogenetic results support previous studies showing the paraphyly of subfamily Pereskioideae and the monophyly of subfamilies Opuntioideae and Cactoideae. After the early divergence of Blossfeldia, Cactoideae splits into two clades: Cacteae, including North American globose and barrel-shaped members, and core Cactoideae, including the largest diversity of growth forms distributed throughout the American continent. Para- or polyphyly is persistent in different parts of the phylogeny. Main Cactoideae clades were found to have different ancestral growth forms, and convergence toward globose, arborescent, or columnar forms occurred in different lineages.
Our study enabled us to provide a detailed hypothesis of relationships among cacti lineages and represents the most complete general phylogenetic framework available to understand evolutionary trends within Cactaceae.
Choosing and designing primers based on available DNA sequence data and statistical contrasting of domains or structural features is a common routine among molecular biologists. Currently available, free software tools were found to lack desirable features related to these tasks. This was the motivation for developing a new program, SeqState. SeqState locates regions that remain to be sequenced in phylogenetic DNA datasets, evaluates user-provided primers and selects primers best suited to fill gaps in the sequences. If the primers provided by the user are unsuitable, new primers are designed. Primers can be loaded from a primer database, be supplied as part of the alignment or be entered manually. The position of internal primers is automatically localised in the loaded data file. Primers can be edited, and changes and new primers can be saved to the database. Primer sheets allow the user to view internal dimers, complements to a second primer, mismatches to all loaded sequences, and other primer characteristics. Calculation of various sequence statistics can be requested for the whole dataset or parts thereof (character sets), with standard errors estimated by bootstrapping. Insertion-deletion events can be evaluated statistically and encoded for subsequent phylogenetic analysis according to several published coding principles.
Molecular studies of 21 species of the large Cactaceae genus Mammillaria representing a variety of intrageneric taxonomic levels revealed a high degree of intra-individual polymorphism of the internal transcribed spacer region (ITS1, 5.8S rDNA, ITS2). Only a few of these ITS copies belong to apparently functional genes, whereas most are probably non-functional (pseudogenes). As a multiple gene family, the ITS region is subjected to concerted evolution. However, the high degree of intra-individual polymorphism of up to 36% in ITS1 and up to 35% in ITS2 suggests a non-concerted evolution of these loci in Mammillaria. Conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of Mammillaria. Some of these motifs (e.g., ITS1 motif 1, 'TGGT' within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the identification of pseudogene rDNA regions.
Nopalxochia conzattianum new species" in MacDougall in Cact
- Cactaceae Syst
- Init
Cactaceae Syst. Init. 16: 17. 2003. -Lectotype (designated by Bauer in Cactaceae Syst. Init. 17: 17.
2003): [illustration] "Nopalxochia conzattianum new
species" in MacDougall in Cact. Succ. J. (Los Angeles) 19: 22, fig. 15. 1947.
- G Don
G. Don, Encycl. Pl., ed. 3: 1380. 1855. – Lectotype
(designated by Bauer in Cactaceae Syst. Init. 17: 26.
2003): [illustration] " Phyllocactus anguliger Ch. L. "
in Lemaire in Jard. Fleur. 1: t. 92. 1851.
Los Angeles) 46: 67. 1974 ≡ Disocactus speciosus subsp. aurantiacus (Kimnach) Ralf Bauer in Cactaceae Syst
Disocactus aurantiacus (Kimnach) Barthlott in Bradleya 9: 87. 1991 ≡ Heliocereus aurantiacus Kimnach
in Cact. Succ. J. (Los Angeles) 46: 67. 1974 ≡ Disocactus speciosus subsp. aurantiacus (Kimnach) Ralf
Bauer in Cactaceae Syst. Init. 17: 16. 2003. -Holotype: Nicaragua, Jinotega, Potter's Folly, between
Santa Maria Ostumes and Jinotega, 4500 feet, 1959,
A. H. Heller s.n. (UC barcode 1229424!; isotypes:
HNT barcode 0000028!, US barcode 00115677!).
16: 17 – Lectotype (designated here): [illustration] " fig. 1 Epiphyllum crenatum var. kimnachii
- Cactaceae Guzmán In
- Syst
- Init
Guzmán in Cactaceae Syst. Init. 16: 17. 2003. – Lectotype (designated here): [illustration] " fig. 1 Epiphyllum crenatum var. kimnachii " in Bravo in Anales Inst.
Biol. Univ. Nac. México 35: 78. 1964.
16: 259. 1913 ≡ Phyllocactus eichlamii Weing 21: 5. 1911 ≡ Trochilocactus eichlamii (Weing.) Linding. in Beih
- Disocactus
- Weing
Disocactus eichlamii (Weing.) Britton & Rose in
Contr. U.S. Natl. Herb. 16: 259. 1913 ≡ Phyllocactus eichlamii Weing. in Monatsschr. Kakteenk. 21: 5.
1911 ≡ Trochilocactus eichlamii (Weing.) Linding.
in Beih. Bot. Centralbl. 61: 383. 1942 ≡ Epiphyllum
eichlamii (Weing.) L. O. Williams in Fieldiana, Bot.
29: 378. 1962. – Lectotype (designated by Kimnach
& Hutchison in Cact. Succ. J. (Los Angeles) 29: 78.
1957): Guatemala, locality unknown, 13 Nov 1910,
F. Eichlam s.n. (US!)
Barthlott in Brad leya 9: 88. 1991 ≡ Lobeira macdougallii Alexander in CactLos Angeles) 16: 178. 1944 ≡ Nopal xochia macdougallii (Alexander) W. T. Marshall in Cactus 4: 6. 1946 ≡ Heliocereus macdougallii
*9. Disocactus macdougallii (Alexander) Barthlott in
Brad leya 9: 88. 1991 ≡ Lobeira macdougallii Alexander in Cact. Succ. J. (Los Angeles) 16: 178. 1944
≡ Nopal xochia macdougallii (Alexander) W. T. Marshall in Cactus 4: 6. 1946 ≡ Heliocereus macdougallii
(Alexander) Doweld in Sukkulenty 4(1 – 2): 42. 2002.
– Lectotype (designated by Bauer in Cactaceae Syst.
Init. 17: 17. 2003): [illustration] " fig. 162. Lobeira
macdougallii sp. nov., natural size " in Alexander in
Cact. Succ. J. (Los Angeles) 16: 176. 1944.
Molecular phylogeny and taxonomy of Disocactus *11a – 2): 41. 2002 ≡ Diso cactus nelsonii var
- Cruz
Cruz & al.: Molecular phylogeny and taxonomy of Disocactus
*11a. Disocactus nelsonii subsp. hondurensis (Kimnach)
Doweld in Sukkulenty 4 (1 – 2): 41. 2002 ≡ Diso cactus
nelsonii var. hondurensis Kimnach in Cact. Succ. J.
(Los Angeles) 37: 33. 1965. – Holotype: Honduras,
Comayagua, 4 miles beyond El Rincon, on way from
Siguatepeque, in canyon along road, 11 Aug 1962, M.
Kimnach 394 (UC; isotype: HNT barcode 0000082!).