Alan W. Meerow

Correction: Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

Background The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. Methodology/Principal Findings We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. Conclusions/Significance This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family.

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods

BACKGROUND AND AIMS Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera. METHODS DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree-species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted. KEY RESULTS Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia-Lepidozamia-Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia. CONCLUSIONS A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.

Plant Conservation in the Caribbean Island Biodiversity Hotspot

While the Caribbean is a recognized “biodiversity hotspot”, plant conservation has not received adequate attention; particularly, given the high levels of endemism in many plant groups. Besides establishing protected areas, there needs to be a sustained effort to study the taxonomy, systematics and ecology of the flora. Recent phylogenetic studies have shown high levels of endemism and conservation studies indicate a large propotion of the flora is threatened with extinction. Eight recommendations are given for plant conservation in the region.

Seed Plant Genera Endemic to the Caribbean Island Biodiversity Hotspot: A Review and a Molecular Phylogenetic Perspective

The Caribbean Island Biodiversity Hotspot is composed primarily of the Bahamas and Greater and Lesser Antilles. A total of 180 genera (727 spp., ca. 9% of the species endemic to the Antilles) are restricted to this hotspot. Most of these genera are unispecific (51%), a pattern that is also found on other islands of the world. The majority of the endemic genera belong to the “Core Eudicot” clade, and they were published in two time periods (1854–1878 and 1904–1928). There are molecular phylogenies available for 63 of the endemic genera. However, phylogenetic reconstructions of only 21 genera are based on more than one independent DNA region and have well-supported clades and good taxonomic sampling. Six of the endemic genera form part of early-branching groups. We could not infer biogeographical conclusions from the molecular phylogenies of most of the endemic genera (43: 68%). There is an urgent need for (1) additional field studies to learn the conservation status of these genera, (2) effective protection of the habitats where the most endangered genera occur, and (3) additional biological and systematic studies of the least understood genera.

Phylogenetic Relationships and Biogeography within the Eurasian Clade of Amaryllidaceae Based on Plastid ndhF and nrDNA ITS Sequences: Lineage Sorting in a Reticulate Area?

Abstract The monophyletic Eurasian clade of Amaryllidaceae was analyzed using plastid ndhF and rDNA ITS sequences for 33 and 29 taxa, respectively; all genera were represented by at least one species. Both maximum parsimony and Bayesian analysis were used on each data set and the combined data. Both sequence matrices resolve the Central and East Asian tribe Lycorideae as sister to the Mediterranean-centered genera of the clade, and recognize two large subclades within the greater Mediterranean region: Galantheae, consisting of Acis, Galanthus and Leucojum; and Narcisseae (Narcissus and Sternbergia)/Pancratium. However, there are areas of incongruence between the ndhF and ITS trees. When three predominantly monotypic genera, Hannonia, Lapiedra, and Vagaria, centered in North Africa, are removed from the alignments, the two sequence matrices produce fully congruent topologies with increased support at many of the nodes, with ILD between partitions rising from P = 0.07 to 0.96. We hypothesize that lineage sorting took place after the divergence of Galantheae and Narcisseae/Pancratium from a common genepool with Hannonia, Lapiedra, and Vagaria retaining a mosaic of the ancestral haplotypes. We also performed dispersal-vicariance analysis to reconstruct biogeographic scenarios on several of the generic level phylogenies found with and without these three genera included, as well as on a species-level phylogeny of Galantheae. After the vicariant divergence of the Asian Lycorideae, North Africa and the Iberian Peninsula are the most likely areas of origin for the rest of the clade. The results of the dispersal-vicariance analysis are discussed in the context of the complex biogeographic history of the Mediterranean basin.

What is the Conservation Value of a Plant in a Botanic Garden? Using Indicators to Improve Management of Ex Situ Collections

Living botanic garden plant collections are a fundamental and underutilized worldwide resource for plant conservation. A common goal in managing a botanical living collection is to maintain the greatest biodiversity at the greatest economic and logistic efficiency. However to date there is no unified strategy for managing living plants within and among botanic gardens. We propose a strategy that combines three indicators of the management priority of a collection: information on species imperilment, genetic representation, and the operational costs associated to maintaining genetic representation. In combination or alone, these indicators can be used to assay effectiveness and efficiency of living collections, and to assign a numeric conservation value to an accession. We illustrate this approach using endangered palms that have been studied to varying degrees. Management decisions can be readily extended to other species based on our indicators. Thus, the conservation value of a species can be shared through existing databases with other botanic gardens and provide a list of recommendations toward a combined management strategy for living collections. Our approach is easily implemented and well suited for decision-making by gardens and organizations interested in plant conservation.ResumenLas colecciones vivas en jardines botánicos son una parte fundamental y poco utilizada en la conservación de plantas a nivel mundial. Un objetivo común en el manejo de las colecciones botánicas vivas es mantener la mayor biodiversidad al menor costo económico y logístico. Sin embargo hasta ahora no existe una estrategia unificada para el manejo de plantas vivas dentro y entre jardines botánicos. Aquí proponemos una estrategia que combina tres indicadores para establecer prioridades de manejo de una colección: información acerca del riesgo en estado silvestre de la especie, representación genética, y los costos operativos asociados a mantener la representación genética. En combinación o solos, estos indicadores pueden ser utilizados para evaluar la efectividad y eficiencia de las colecciones vivas, y para asignar un valor numérico de conservación a un espécimen. Demostramos esta estrategia con palmas que tienen diversos tipos de estudios e información disponible. Decisiones de manejo basadas en nuestros indicadores se pueden extender y aplicar fácilmente a otras especies de manera similar a como lo demostramos aquí. Además, el valor de conservación de un especie puede ser compartido con otros jardines botánicos utilizando bases de datos pre-existentes y así proveer una serie de recomendaciones hacia el manejo integrado de las colecciones vivas. Nuestra estrategia se puede implementar fácilmente y es apropiada para la toma de decisiones en jardines y organizaciones interesadas en la conservación de recursos en plantas.

Phylogeny of Amaryllidaceae tribe Amaryllideae based on nrDNA ITS sequences and morphology

We present the results of cladistic analyses of morphology, nrDNA ITS sequences, and a combination of the two for tribe Amaryllideae of the Amaryllidaceae. The morphologically based analysis supports the recognition of Amaryllis as sister to two major clades, equivalent to Snijman and Linders (1996, Annals of the Missouri Botanical Garden 83: 362-386) Crininae and Amaryllidinae (less Amaryllis). A single tree is found with a successively weighted ITS sequence matrix. Amaryllis and Boophone form a grade at the base of the tree. All the other genera are included in two clades conforming to Snijman and Linders (1996) subtribes Amaryllidinae (less Amaryllis, thus now Strumariinae) and Crininae (less Boophone). Within Strumariinae, Strumaria sensu lato is resolved as polyphyletic. Strumaria subg. Gemmaria is sister to the rest of the subtribe. Hessea is monophyletic only if Namaquanula is excluded. The monotypic Carpolyza is embedded within Strumaria sensu stricto. The consensus of the combined analysis is highly resolved, and most similar to the sequence topology. Based on the results of the combined analyses, the major clades are recognized as subtribes, and Carpolyza is placed into synonymy under Strumaria.

Can a Botanic Garden Cycad Collection Capture the Genetic Diversity in a Wild Population

Premise of research. Conservation of plant species often requires ex situ (off-site) cultivation of living collections. Cycads constitute the most imperiled major group of plants, and ex situ collections are an important part of conservation planning for this group, given seed recalcitrance, difficulties with tissue culture, and ongoing in situ threats. Very little is known about the genetics of ex situ conservation collections of cycads. Thus, this study seeks to illuminate how well an ex situ collection of a cycad can capture the diversity in a wild population. Methodology. A model species, Zamia decumbens, was chosen on the basis of geographic isolation and detailed census knowledge, which allowed near-total sampling of in situ plants. Overall, 375 in situ plants were compared to 205 ex situ plants via 10 microsatellite markers. Pivotal results. Genetic-distance analysis shows high fidelity of the ex situ collections to their in situ source populations as well as clustering of ex situ progeny by accession and strong identity with their respective mother plants. Structured resampling of allele capture from the in situ populations by the ex situ collections shows that allele capture increases as number of ex situ plants maintained increases, but with a diminishing rate of increase. Conclusions. These data demonstrate that botanic garden collections can better conserve the genetic diversity of in situ cycad populations if four recommendations are followed: (1) use the species biology to inform the collecting strategy; (2) manage each population separately; (3) collect and maintain multiple accessions; and (4) collect over multiple years.

Development of single nucleotide polymorphism markers in Theobroma cacao and comparison to simple sequence repeat markers for genotyping of Cameroon clones

Single nucleotide polymorphism (SNP) markers are increasingly being used in crop breeding programs, slowly replacing simple sequence repeats (SSR) and other markers. SNPs provide many benefits over SSRs, including ease of analysis and unambiguous results across various platforms. We have identified and mapped SNP markers in the tropical tree crop Theobroma cacao, and here we compare SNPs to SSRs for the purpose of determining off-types in clonal collections. Clones are used as parents in breeding programs and the presence of mislabeled clones (off-types) can lead to the propagation of undesired traits and limit genetic gain from selection. Screening was performed on 186 trees representing 19 Theobroma cacao clones from the Institute of Agricultural Research for Development (IRAD) breeding program in Cameroon. Our objectives were to determine the correct clone genotypes and off-types using both SSR and SNP markers. SSR markers that amplify 11 highly polymorphic loci from six linkage groups and 13 SNP markers that amplify eight loci from seven linkage groups were used to genotype the 186 trees and the results from the two different marker types were compared. The SNP assay identified 98% of the off-types found via SSR screening. SNP markers spread across multiple linkage groups may serve as a more cost-effective and reliable method for off-type identification, especially in cacao-producing countries where the equipment necessary for SSR analysis may not be available.

Cycad biodiversity in the Bahamas Archipelago and conservation genetics of the threatened Zamia lucayana (Zamiaceae)

A conservation assessment for the three cycad species native to the Bahamas Islands is presented. Results are based on field surveys on all islands where these species occur. Zamia angustifolia is native to Eleuthera, Zamia integrifolia is native to Abaco, Andros, Eleuthera, Grand Bahama and New Providence, and Zamia lucayana is endemic to Long Island. Z. angustifolia is of the highest conservation concern because of the small number of adult plants, its restricted distribution and the extensive development occurring within its habitat. Z. integrifolia also has a restricted distribution on Eleuthera and Grand Bahama and, although threatened by urban development in New Providence, it is relatively common on Abaco and Andros. Z. lucayana comprises three populations within a narrow strip of land of c. 1 km 2 ; we propose a reassignment of its current conservation status from Endangered to Critically Endangered. We assessed the genetic structure of Z. lucayana based on 15 polymorphic microsatellite DNA loci; this indicated that the three known populations should be considered a single management unit. However, the high number of private alleles suggests that genetic drift, indicative of recent fragmentation, is progressing. We propose in situ conservation strategies, and we also collected germplasm from a total of 24 populations of these three cycad species, for ex situ conservation.