Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges.

To model distribution ranges, the most popular methods of phylogenetic biogeography divide Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates a plate motion model and a paleolandscape model directly derived from the models used by geologists in their tectonic and paleogeographic reconstructions.

Compound osteoderms preserved in amber reveal the oldest known skink.

Scincidae is one of the most species-rich and cosmopolitan clades of squamate reptiles. Abundant disarticulated fossil material has also been attributed to this group, however, no complete pre-Cenozoic crown-scincid specimens have been found. A specimen in Burmite (99 MYA) is the first fossil that can be unambiguously referred to this clade.

Historical biogeography of the Neotropical noctilionoid bats (Chiroptera: Noctilionoidea), revisited through a geographically explicit analysis.

Biogeographic studies have generally relied on methods that use a few, large predefined areas, which may overlook fine-scale patterns. Here we test previous hypotheses about the biogeographic history of a diverse bat clade regarding its association with major Neotropical geological formations, particularly the Antilles, the South American Dry Diagonal, the Andes and the Panamanian land bridge, by applying a recently available method that uses actual distributions instead of predefined areas. We compiled and curated spatially explicit, georeferenced data of 173 bat species (Mammalia: Chiroptera: Noctilionoidea) from the online database Global Biodiversity Information Facility.

Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae).

Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M.

Phylogenomics and Biogeography of the Mammilloid Clade Revealed an Intricate Evolutionary History Arose in the Mexican Plateau.

Mexico harbors ~45% of world's cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera , , , , , , and (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model.

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications.

Pilosocereus is one of the Cactaceae family's most relevant genera in terms of the number of species and its wide geographical range in the Americas. Within Pilosocereus, five informal taxonomic groups have been recognized, one of which is P. leucocephalus group s.

A new Early Cretaceous lizard in Myanmar amber with exceptionally preserved integument.

We here report on a well-preserved juvenile lizard specimen in Albian amber (ca. 110 mya) from the Hkamti site (Myanmar). This new taxon is represented by an articulated skull and the anterior portion of the trunk, including the pectoral girdle and forelimbs.

Blurring the Boundaries between a Branch and a Flower: Potential Developmental Venues in CACTACEAE.

Flowers are defined as short shoots that carry reproductive organs. In Cactaceae, this term acquires another meaning, since the flower is interpreted as a branch with a perianth at the tip, with all reproductive organs embedded within the branch, thus giving way to a structure that has been called a "flower shoot". These organs have long attracted the attention of botanists and cactologists; however, the understanding of the morphogenetic processes during the development of these structures is far from clear.

Unusual morphology in the mid-Cretaceous lizard Oculudentavis.

Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted narial openings, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement.

The importance of environmental conditions in maintaining lineage identity in (Cactaceae).

The use of environmental variables to explain the evolution of lineages has gained relevance in recent studies. Additionally, it has allowed the recognition of species by adding more characters to morphological and molecular information. This study focuses on identifying environmental and landscape variables that have acted as barriers that could have influenced the evolution of species and its close genera.

Evaluating the monophyly of series (Cactaceae).

(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.

Unraveling Reticulate Evolution in (Cactaceae) From Southern Mexico.

The process of hybridization occurs in approximately 40% of vascular plants, and this exchange of genetic material between non-conspecific individuals occurs unequally among plant lineages, being more frequent in certain groups such as (Cactaceae). This genus is known for multiple taxonomic controversies due to widespread polyploidy and probable hybrid origin of several of its species. Southern Mexico species of this genus have been poorly studied despite their great diversity in regions such as the Tehuacán-Cuicatlán Valley which contains around 12% of recognized Mexico's native species.

The chloroplast genome of the pincushion cactus subsp. , a Mexican endangered species.

The genus occupies diverse habitats and exhibits diverse growth patterns and a large range of morphologies. Most of the species of this genus are used as ornamental plants and are subject to mass habitat loss. Due to these factors, they are being submitted to selective pressure that might affect conservational efforts and management plans.

Enigmatic amphibians in mid-Cretaceous amber were chameleon-like ballistic feeders.

Albanerpetontids are tiny, enigmatic fossil amphibians with a distinctive suite of characteristics, including scales and specialized jaw and neck joints. Here we describe a new genus and species of albanerpetontid, represented by fully articulated and three-dimensional specimens preserved in amber. These specimens preserve skeletal and soft tissues, including an elongated median hyoid element, the tip of which remains embedded in a distal tongue pad.

Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of (Cactaceae, Caryophyllales).

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of .

Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion.

A likelihood method that approximates the behaviour of implied weighting is described. This approach provides a likelihood perspective on several aspects of implied weighting, such as guidance for the choice of concavity values, a justification to use different concavities for different numbers of taxa, and a natural basis for extended implied weighting. In this approach, the number of free parameters in the estimation depends on C, the number of characters (in contrast to the standard Mk model, which estimates 2T-3 parameters for T taxa).

De Novo Assembly Discovered Novel Structures in Genome of Plastids and Revealed Divergent Inverted Repeats in (Cactaceae, Caryophyllales).

The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.

Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology.

One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model-based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character-state reconstructions. Authors who favour model-based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference-such decision also requires considering the conditions of evolution that prevail in nature.

Effectiveness of systematic alphanumeric coded endoscopy for diagnosis of gastric intraepithelial neoplasia in a low socioeconomic population.

In the Western world, gastric cancer (GC) usually presents at an advanced stage, carrying a high mortality rate. Studies have reported that 14 % to 26 % of GCs are missed at endoscopy up to 3 years before diagnosis. Systematic Alphanumeric Coded Endoscopy (SACE) has been proposed to improve quality of esophagogastroduodenoscopy (EGD) by facilitating a complete examination of the upper gastrointestinal tract.