Eduardo Ruiz-Sanchez

Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

BackgroundBambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.ResultsHere a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.ConclusionsPhylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos

BackgroundNext-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events.ResultsTranscriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers.ConclusionsInstances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.

A Multicriteria Analysis for Prioritizing Areas for Conservation of Oaks (Fagaceae: Quercus) in Oaxaca, Southern Mexico

Mexico has the fifth place among megadiverse countries, and the southern part of the country belongs to the Mesoamerican hotspot, where Oaxaca state has a very rich flora, related to its intricate topography. In this study, a multicriteria analysis (species richness, rareness, irreplaceability, turnover, and vulnerability) was used to prioritize conservation areas in Oaxaca, using as model system the genus Quercus (oaks), due to its high diversity and ecological importance. Our results indicate that the Sierra Madre de Oaxaca (SMOax) is the physiographic subprovince with the highest richness (38 species), rareness and irreplaceability of Quercus species, followed by the Montañas y Valles del Occidente (MVO; 29 species), the Sierra Madre del Sur (SMS; 25 species), and the Montañas y Valles del Centro (20 species). Areas that have retained most primary vegetation cover from 2000 to 2010 are mainly in the SMOax, in the Ixtlán district, and in the SMS, in the Miahuatlán district. On the other hand, MVO is the area with greater habitat disturbance, mainly in the Juxtlahuaca-Tlaxiaco districts. Oaxaca has numerous areas without official protection, named Indigenous Conservation and Community Areas, which play a central role as an alternative for conservation for 11 oak species. In conclusion, the priority conservation areas for the genus are mainly located in the SMOax and in the SMS. For white oaks, the semiarid area of Coixtlahuaca-Teposcolula-Nochitlán is important, while for the red oaks, the most important regions are the humid areas of Teotitlán, Sola de Vega, and Miahuatlán.

Species delimitation of the blue-spotted spiny lizard within a multilocus, multispecies coalescent framework, results in the recognition of a new Sceloporus species

Species delimitation is a major topic in systematics. Species delimitation methods based on molecular data have become more common since this approach provides insights about species identification via levels of gene flow, the degree of hybridization and phylogenetic relationships. Also, combining multilocus mitochondrial and nuclear DNA leads to more reliable conclusions about species limits. Coalescent-based species delimitation methods explicitly reveal separately evolving lineages using probabilistic approaches and testing the delimitation hypotheses for several species. Within a multispecies, multilocus, coalescent framework, we were able to clarify taxonomic uncertainties within S. cyanostictus, an endangered lizard that inhabits a narrow strip of the Chihuahuan Desert in Mexico. We included, for the first time in a phylogenetic analysis, lizards from the three populations of S. cyanostictus recognized so far (East Coahuila, West Coahuila and Nuevo León). Phylogenetic analysis corroborates the hypothesis of two separately evolving lineages, i.e. the East and West Coahuila populations, as proposed in a previous study. We also found a distant phylogenetic relationship between the lizards from Nuevo León and those of East and West Coahuila. Finally, based on the species delimitation results, we propose and describe a new species of Sceloporus: S. gadsdeni sp. nov.

A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica

The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.

Chusquea gibcooperi (Poaceae: Bambusoideae: Bambuseae: Chusqueinae), a new species endemic to Mexico

The Perote-Orizaba region in Veracruz and the Alto Soconusco in Chiapas encompass the highest diversity of Chusquea species in Mexico, followed by the Sierra de Juárez in Oaxaca. These three regions have a total of 15 known Chusquea species. With the description here of Chusquea gibcooperi the number of described Chusquea species in Mexico will increase to 21. Chusquea gibcooperi is here described as a new species endemic to Mexico, inhabiting neotropical cloud forest and the ecotone with pine forest in the Perote-Orizaba area, Veracruz, and the Sierra Madre Oriental in Hidalgo and Puebla. Chusquea gibcooperi is similar to C. enigmatica and C. glauca, but differs from the former in having taller and wider culms and longer and wider foliage leaf blades. Chusquea glauca has maculate culms, a ring of cilia at the base of the culm leaf, infravaginal branching, and abaxially pubescent foliage leaf blades. The culms of Chusquea gibcooperi are uniform in color (i.e., not maculate), the culm leaves lack the basal ring of cilia, branching is both intravaginal and extravaginal, and the foliage leaf blades are abaxially glabrous.ResumenLa región de Perote-Orizaba en Veracruz y la región del Alto Soconusco en Chiapas presentan la más alta diversidad de especies del género Chusquea Kunth, en México, seguido por la Sierra de Juárez en Oaxaca. Estas tres regiones tienen en total 15 especies conocidas de Chusquea. Con la descripción de Chusquea gibcooperi, el número de especies descritas de Chusquea en México, se incrementarán a 21. Chusquea gibcooperi es una especie nueva endémica de México y habita el bosque mesófilo de montaña y el ecotono con el bosque de pino en la región de Perote-Orizaba, Veracruz, y la Sierra Madre Oriental en Hidalgo y Puebla. Chusquea gibcooperi es similar a C. enigmatica y C. glauca, pero difiere de la primera por tener culmos más altos y anchos y hojas foliares más largas y anchas. Chusquea glauca tiene culmos maculados, un anillo de cilios en la base de las hojas del culmo, ramificación infravaginal, y pubescencia abaxial en las hojas foliares. Los culmos de Chusquea gibcooperi son uniformes en color (e.g., no presenta maculas), no tiene el anillo de cilios en las hojas del culmo, presenta ramificación intra y extravaginal y es glabra en la cara abaxial de las hojas foliares.