Phylogeography of Falagoniamexicana Sharp, 1883 (Coleoptera, Staphylinidae, Aleocharinae).

Falagoniamexicana is an aleocharine distributed from northern Mexico to Guatemala and El Salvador. It is associated with Attamexicana ants and lives within their piles of waste or external debris. The phylogeography and historical demography of 18 populations from Mexico, Guatemala, and El Salvador were studied. The data set encompasses a 472 bp fragment of the COI. Results suggest that F.mexicana was originated during Middle Pliocene (ca. 0.5 Mya), starting its diversification at the Upper Pleistocene and Holocene. Populations were recovered forming at least four main lineages, with a significant phylogeographic structure. Evidence of contemporary restricted gene flow was found among populations. The historical demography suggests that the geographic structure is due to recent physical barriers (e.g., Isthmus of Tehuantepec) rather than ancient geological events. Also, recent geological and volcanic events in the east of the Trans-Mexican Volcanic Belt and the Sierra Madre Oriental might be responsible for the restricted gene flow among populations. Skyline-plot analyses suggested that a demographic expansion event took place at the end of the Late Quaternary glacial-interglacial cycles.

Evolution of Ceratozamia cycads: A proximate-ultimate approach.

Evidence suggests that past climatic fluctuations affected speciation of extant cycads. However, empirical genetic and morphological evidence explaining patterns and processes of species diversification are scarce. There are some explanations for the origin and evolution of the genus Ceratozamia, but with inconclusive results. To elucidate the evolution of Ceratozamia, we used genetic and phenotypic sources as empirical data, which were applied in a 'proximate-ultimate' framework (ecological and evolutionary scale, respectively). Our results suggested that the evolutionary mechanisms of speciation were shaped by deterministic (natural selection-adaptation) driven by climatic conditions associated to water stress, and probably enhanced by stochastic processes (gene drift and inbreeding). In general terms, punctuated evolution models were those that best explained the patterns of speciation throughout the phylogenetic history of the lineages encompassed in the genus Ceratozamia. Finally, we provide empirical evidence on the tempo and mode of the evolution of a 'living plant fossil'.

Combining morphological and molecular data to reconstruct the phylogeny of avian Haemosporida.

The traditional classification of avian Haemosporida is based mainly on morphology and life history traits. Recently, molecular hypotheses have challenged the traditional classification, leading to contradictory opinions on whether morphology is phylogenetically informative. However, the morphology has never been used to reconstruct the relationships within the group. We inferred the phylogeny of avian Haemosporida from 133 morphological characters present in blood stages. We included all species with at least one mitochondrial gene characterized (n = 93). The morphological hypothesis was compared with the one retrieved from mitochondrial DNA (mtDNA) nucleotide sequences and a hypothesis that used a combination of morphological and molecular data (i.e., total evidence). In order to recover the evolutionary history and identify phylogenetically and taxonomically informative characters, they were mapped on the total evidence phylogeny. The morphological hypothesis presented more polytomies than the other two, especially within Haemoproteus. In the molecular hypothesis, the two Haemoproteus subgenera are paraphyletic, and some relationships within Parahaemoproteus were resolved. By combining the morphological and molecular data, we were able to resolve the majority of polytomies and posterior probabilities increased. We identified a unique combination of morphological traits, clearly differentiating avian Haemosporida genera, sub-genera of Leucocytozoon and Haemoproteus, and some Plasmodium sub-genera. Plasmodium had the highest number of synapomorphies. Furthermore, 86% of the species presented a unique combination of taxonomically informative characters. A limiting factor was the mismatch of traits characterized in species descriptions, leading to a morphological matrix with a considerable amount of missing data, particularly for the stages of early young and young gametocytes (67% of all missing data). Characters lacking information for the majority of species included the colour of pigment granules, the cytoplasm appearance, and the presence and dimensions of vacuoles. According to our results, the combination of morphology and mtDNA proved to be a robust alternative to reconstruct the relationships among avian Haemosporida, obtaining a resolution and support similar to that obtained using full mitochondrial genome sequences for over 100 lineages.

Detection and prevalence of adenoviruses from free-ranging black howler monkeys (Alouatta pigra).

Adenoviruses are important pathogens known to infect vertebrate hosts, including a wide range of primates. Despite its importance, data on the diversity of these viruses in non-human primates living in their natural habitat remain scarce. In this study, we conducted a surveillance of adenoviral infection in wild black howler monkeys from two protected natural areas in Mexico. This was achieved by analyzing 67 fecal samples using a nested PCR that targets the adenovirus DNA polymerase gene. Adenoviral DNA was detected in 12 samples from both study sites, with an overall prevalence of 17.9%. The amplified DNA sequences shared 100% nucleotide identity and phylogenetic analyses revealed that the haplotype detected was novel, and clustered with Platyrrhini mastadenovirus A, which was previously described in captive New World monkeys. Our data, along with the previous evidence, confirm that monkeys native to the Americas are the original hosts of these adenoviruses.

Phylogeographic structure of Canthon cyanellus (Coleoptera: Scarabaeidae), a Neotropical dung beetle in the Mexican Transition Zone: Insights on its origin and the impacts of Pleistocene climatic fluctuations on population dynamics.

Canthon cyanellus is a roller dung beetle with a wide distribution range in the tropical forests of the New World. In Mexico, it inhabits the Pacific and the Gulf coasts, the Yucatan Peninsula and the south mainly in the State of Chiapas. This species shows a wide geographical variation in cuticle color, which has been used as defining trait for subspecies. In this study we analyzed the phylogeographic and demographic history of the Mexican populations of C. cyanellus using DNA sequences of the nuclear ITS2, and the mitochondrial COI and 16S genes. We found that not all the current valid subspecies are supported by the molecular analysis. The populations are genetically and geographically structured in five lineages. The diversification events that gave origin to the main lineages within this species complex occurred during the Pleistocine in a time range of 1.63-0.91Myr. The demographic history of these lineages suggests post-glacial expansions toward the middle and the end of the Pleistocene. The combined data of mitochondrial and nuclear DNA suggest that the phylogeographic structure and demographic history of the C. cyanellus populations are the result of: the geological and volcanic activity that occurred from the end of the Pliocene to the Pleistocene; and the contraction and expansion of tropical forests due to the glacial and inter-glacial cycles during the Pleistocene. Landscape changes derived from historical events have affected the demographic history of the populations of this species. The results presented here point to the need to review the taxonomic status and delimitation of the lineages encompassed in the Canthon cyanellus complex.

Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin.

Pluralistic approaches to taxonomy facilitate a more complete appraisal of biodiversity, especially the diversification of cryptic species. Although species delimitation has traditionally been based primarily on morphological differences, the integration of new methods allows diverse lines of evidence to solve the problem. Robber frogs (Pristimantis) are exemplary, as many of the species show high morphological variation within populations, but few traits that are diagnostic of species. We used a combination of DNA sequences from three mitochondrial genes, morphometric data, and comparisons of ecological niche models (ENMs) to infer a phylogenetic hypothesis for the Pristimantis acuminatus complex. Molecular phylogenetic analyses revealed a close relationship between three new species-Pristimantis enigmaticus sp. nov., P. limoncochensis sp. nov. and P. omeviridis sp. nov.-originally confused with Pristimantis acuminatus. In combination with morphometric data and geographic distributions, several morphological characters such as degree of tympanum exposure, skin texture, ulnar/tarsal tubercles and sexual secondary characters (vocal slits and nuptial pads in males) were found to be useful for diagnosing species in the complex. Multivariate discriminant analyses provided a successful classification rate for 83-100% of specimens. Discriminant analysis of localities in environmental niche space showed a successful classification rate of 75-98%. Identity tests of ENMs rejected hypotheses of niche equivalency, although not strongly because the high values on niche overlap. Pristimantis acuminatus and P. enigmaticus sp. nov. are distributed along the lowlands of central-southern Ecuador and northern Peru, in contrast with P. limoncochensis sp. nov. and P. omeviridis sp. nov., which are found in northern Ecuador and southern Colombia, up to 1200 m in the upper Amazon Basin. The methods used herein provide an integrated framework for inventorying the greatly underestimated biodiversity in Amazonia.

Using Range-Wide Abundance Modeling to Identify Key Conservation Areas for the Micro-Endemic Bolson Tortoise (Gopherus flavomarginatus).

A widespread biogeographic pattern in nature is that population abundance is not uniform across the geographic range of species: most occurrence sites have relatively low numbers, whereas a few places contain orders of magnitude more individuals. The Bolson tortoise Gopherus flavomarginatus is endemic to a small region of the Chihuahuan Desert in Mexico, where habitat deterioration threatens this species with extinction. In this study we combined field burrows counts and the approach for modeling species abundance based on calculating the distance to the niche centroid to obtain range-wide abundance estimates. For the Bolson tortoise, we found a robust, negative relationship between observed burrows abundance and distance to the niche centroid, with a predictive capacity of 71%. Based on these results we identified four priority areas for the conservation of this microendemic and threatened tortoise. We conclude that this approach may be a useful approximation for identifying key areas for sampling and conservation efforts in elusive and rare species.

Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma, Cerotoma, and Diabrotica).

Adaptive radiation is an aspect of evolutionary biology encompassing microevolution and macroevolution, for explaining the principles of lineage divergence. There are intrinsic as well as extrinsic factors that can be postulated to explain that adaptive radiation has taken place in specific lineages. The Diabroticina beetles are a prominent example of differential diversity that could be examined in detail to explain the diverse paradigms of adaptive radiation. Macroevolutionary analyses must present the differential diversity patterns in a chronological framework. The current study reviews the processes that shaped the differential diversity of some Diabroticina lineages (i.e. genera Acalymma, Cerotoma, and Diabrotica). These diversity patterns and the putative processes that produced them are discussed within a statistically reliable estimate of time. This was achieved by performing phylogenetic and coalescent analyses for 44 species of chrysomelid beetles. The data set encompassed a total of 2,718 nucleotide positions from three mitochondrial and two nuclear loci. Pharmacophagy, host plant coevolution, competitive exclusion, and geomorphological complexity are discussed as putative factors that might have influenced the observed diversity patterns. The coalescent analysis concluded that the main radiation within Diabroticina beetles occurred between middle Oligocene and middle Miocene. Therefore, the radiation observed in these beetles is not recent (i.e. post-Panamanian uplift, 4 Mya). Only a few speciation events in the genus Diabrotica might be the result of the Pleistocene climatic oscillations.

Models of the primary and secondary structure for the 12S rRNA of birds: a guideline for sequence alignment.

Models of the primary and secondary structure for the 12S ribosomal RNA (rRNA) gene of birds is presented based on a comparison of 100 species. Preliminary higher-order structures were delimited following the model for vertebrates. Paired regions were refined following a complementary base-pairing criterion and compensatory mutations were considered as a further confirmation of their existence. The model shows 40 stems, 20 internal loops and 17 external loops, arranged in the typical four domains suggested for the small subunit rRNA. The higher-order structures recovered in the model were used to build a multiple sequence alignment appropriate for phylogenetic analysis. The phylogeny recovered from this alignment was compared with trees inferred from alignments assembled using different alignment parameters in the program ClustalW. The alignment based on the secondary structure is sensitive to positional covariation of stems. Nonetheless, the phylogeny recovered with this method resulted in relationships that are more congruent with non-molecular data than those inferred from alternative alignments.