Diego Bogarín

A DNA barcode for land plants

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

DNA barcoding the floras of biodiversity hotspots

DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a “DNA barcoding gap” is present between intra- and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

Summary The Andean mountains of South America are the most species‐rich biodiversity hotspot worldwide with c. 15% of the worlds plant species, in only 1% of the worlds land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification. We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets. We find that the majority of Andean orchid lineages only originated in the last 20–15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones.

TESTING THE LINK BETWEEN POPULATION GENETIC DIFFERENTIATION AND CLADE DIVERSIFICATION IN COSTA RICAN ORCHIDS

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species‐level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach.

The Genus Campylocentrum (Orchidaceae: Angraecinae) in Costa Rica: A Revision

Abstract. A taxonomic revision of Campylocentrum (Orchidaceae) in Costa Rica is presented. The taxonomic history of the genus and its phylogenetic position are discussed. Characters of vegetative and floral morphology are treated, and their taxonomic significance is discussed. The genus is treated as comprising nine species in the country, and a key to species is provided. Each taxon is described on the basis of Costa Rican material, illustrated in a composite plate, and its distribution within the country is assessed. Distribution maps for all the taxa are given. Overall distribution, derivation of name, notes on species ecology, and diagnostic features are presented for each taxon. The names C. parvulum Schltr. and C. multiflorum Schltr. are neotypified. A new species from Costa Rica, C. generalense, is described and illustrated.

A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation.

Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy‐based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.

Two New Species of Lepanthes (Orchidaceae: Pleurothallidinae) from Costa Rica

Despite the monumental work by C. A. Luer, which disclosed the high diversity of Lepanthes Sw. in Costa Rica (Luer 1987, 1995, 2003), novelties in this species-rich genus of the Orchidaceae are continuously arising from botanical exploration in the country (Pupulin 2001, 2003; Blanco 2003). This may sound obvious for less known areas, relatively difficult to access, but it is also true for well-explored regions such as Monteverde. More than 3000 species of vascular plants were recorded there by Haber (2000), 400 of which are orchids according to Atwood (2000). The area of El Empalme, along the PanAmerican Highway is similar; botanists have made important collections here for at least the last 50 years. This paper describes two new species of Lepanthes from the continental divide of the Cordillera de Tilarin and the Talamanca range in central Costa Rica. All cited specimens have been seen by the authors. Descriptive terminology follows Luer (1996).

Phylogenetic Reassessment of Acianthera (Orchidaceae: Pleurothallidinae)

Abstract. The phylogenetic relationships within the Acianthera affinity are re-evaluated using Bayesian analyses of nrITS and chloroplast matK sequence data. Emphasis is made on species from the Antilles, Central America and the Andean South America as those have been less represented in previous studies. Acianthera is retrieved largely monophyletic, but is redefined to include the genera Aberrantia, Antilla, Apoda-prorepentia, Arthrosia, Brenesia, Cryptophoranthus, Didactylus, Dondodia, Kraenzlinella, Ogygia, Pleurobotryum, Proctoria, Sarracenella and Unguella. Four well-supported subgenera are proposed for Acianthera and characterized both geographically and morphologically. The species belonging to the three newly proposed subgenera are listed.

A new species of Trichosalpinx (Orchidaceae: Pleurothallidinae) from Costa Rica

Trichosalpinx sanctuarii, a new species of Orchidaceae, subtribe Pleurothallidinae, is described and illustrated. It most resembles T. ringens, from which it is distinguished in the text. The new species is endemic to Costa Rica.

Illustrations and studies in neotropical Orchidaceae - the Lepanthes jimenezii group (Pleurothallidinae).

Abstract. Recent advances in orchid DNA barcoding and molecular phylogeny have increased over the past few years. The need for rigorously delimited specific concepts and the development of an integrative taxonomic system intended to place molecular information within the context of morphological, ecological, and physiological knowledge are the main reasons for which traditional taxonomy should constitute the basis of future molecular works. This is the first in a series of manuscripts to focus on discrete groups of Neotropical orchid taxa, providing full and comparable species descriptions and illustrations for taxonomic discussion. Here, we revise the Lepanthes jimenezii group, in which Lepanthes caroli-lueri and Lepanthes pulcherrima are described. Lepanthes jimenezii is lectotypified and a key to the species is provided based on morphological characters.