Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae)

Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation].

Subtle environmental variation affects phenotypic differentiation of shallow divergent treefrog lineages in Amazonia

Amazonia harbours a vast biotic and ecological diversity, enabling investigation of the effects of microevolutionary processes and environmental variation on species diversification. Integrative approaches combining phenotypic and genetic variation can improve our knowledge on diversification processes in megadiverse regions. Here, we investigate the influence of environmental and geographic variation on the genetic and morphological differentiation in the Amazonian Boana calcarata-fasciata (Anura: Hylidae) species complex. We analysed the variation of one mtDNA gene from individuals of different forest environments, and assessed their phylogenetic relationships and species limits to define the lineages to perform a phenotypic-environmental approach. We collected morphological data (head shape and size) using 3D models and investigated the phylogenetic signal, evolutionary model and influence of environmental variables on morphology. We verified associations between environmental and geographical distances with morphological and genetic variation using distance-based redundancy analyses and Mantel tests. We found an even higher cryptic diversity than already recognized within the species complex. Body size and head shape varied among specimens, but did not present phylogenetic signal, diverging under a selective evolutionary model. Our results show that diverse factors have influenced morphological and genetic variation, but environmental conditions such as vegetation cover, precipitation and climate change velocity influenced morphological diversification. Possible population-level mechanisms such as parallel morphological evolution or plastic responses to similar environments could account for such patterns in these typical Amazonian treefrogs.

Curatorial guidelines and standards of the American Society of Mammalogists for collections of genetic resources

The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial standards for managing a collection-accreditation program under the auspices of the American Society of Mammalogists. To date, the Systematic Collections Committee has provided guidance for the more traditional specimen collections (skin, skeletal, fluid, etc.) and specimen data management. Given the rapidly expanding role of genetic resources in biological research, the Systematic Collections Committee herein presents a series of formal guidelines and standards designed to assist collections professionals in the current best practices for curation and maintenance of collections of genetic resources, to ensure long-term integrity of the archived material, and to address personnel safety and guidelines for researchers and curatorial staff. These guidelines and standards are intended to provide constructive guidance and a mechanism of accreditation for collections that vary in scale and infrastructure.

El Comité de Colecciones Sistemáticas de la Sociedad Americana de Mastozoólogos asesora a curadores y demás personal afiliado a colecciones de historia natural en asuntos relacionados a la administración, curación y acreditación de especímenes de mamíferos y su información pertinente. El Comité de Colecciones Sistemáticas mantiene también una lista de normas curatoriales para la gestión de un programa de acreditación de colecciones auspiciados por la Sociedad Americana de Mastozoólogos. A la fecha, el Comité de Colecciones Sistemáticas ha proporcionado una guía para las colecciones de muestras tradicionales (piel, esqueleto, líquido, etc.) y el manejo de datos asociados a estos especímenes. Dado el rápido crecimiento del papel que desempeñan los recursos genéticos en investigaciones biológicas, el Comité de Colecciones Sistemáticas presenta en esta publicación una serie de pautas y estándares formales diseñados para ayudar a los profesionales de colecciones científicas en las mejores prácticas actuales para la conservación y mantenimiento de colecciones de recursos genéticos, a modo de garantizar la integridad a largo plazo del material archivado, y tratar sobre la seguridad del personal y directrices para investigadores y personal curatorial. Estas pautas y estándares tienen como objetivo proporcionar una orientación constructiva y un mecanismo de acreditación para colecciones que varían en escala e infraestructura.

In the wake of invasion: tracing the historical biogeography of the South American cricetid radiation (Rodentia, Sigmodontinae)

The Great American Biotic Interchange (GABI) was greatly influenced by the completion of the Isthmus of Panama and impacted the composition of modern faunal assemblages in the Americas. However, the contribution of preceding events has been comparatively less explored, even though early immigrants in the fossil records are evidence for waif dispersals. The cricetid rodents of the subfamily Sigmodontinae are a classic example of a species-rich South American radiation resulting from an early episode of North American invasion. Here, we provide a temporal and spatial framework to address key aspects of the historical biogeography and diversification of this diverse mammal group by using mitochondrial and nuclear DNA datasets coupled with methods of divergence time estimation, ancestral area reconstruction and comparative phylogenetics. Relaxed-clock time estimates indicate that divergence of the Sigmodontinae began in the middle-late Miocene (ca. 12-9 Ma). Dispersal-vicariance analyses point to the arrival of a single lineage of northern invaders with a widespread ancestral distribution and imply that the initial differentiation between Central and South America gave rise to the most basal groups within the subfamily. These two major clades diversified in the late Miocene followed by the radiation of main tribes until the early Pliocene. Within the Oryzomyalia, tribes diverged initially in eastern South America whereas multiple dispersals into the Andes promoted further diversification of the majority of modern genera. A comparatively uniform background tempo of diversification explains the species richness of sigmodontines across most nodes, except for two akodontine genera with recent increases in diversification rates. The bridging of the Central American seaway and episodes of low sea levels likely facilitated the invasion of South America long before the onset of the post-Isthmian phase of the GABI.

The cost-effectiveness of biodiversity surveys in tropical forests

The identification of high-performance indicator taxa that combine practical feasibility and ecological value requires an understanding of the costs and benefits of surveying different taxa. We present a generic and novel framework for identifying such taxa, and illustrate our approach using a large-scale assessment of 14 different higher taxa across three forest types in the Brazilian Amazon, estimating both the standardized survey cost and the ecological and biodiversity indicator value for each taxon. Survey costs varied by three orders of magnitude, and dung beetles and birds were identified as especially suitable for evaluating and monitoring the ecological consequences of habitat change in our study region. However, an exclusive focus on such taxa occurs at the expense of understanding patterns of diversity in other groups. To improve the cost-effectiveness of biodiversity research we encourage a combination of clearer research goals and the use of an objective evidence-based approach to selecting study taxa.

Sampling Rhodnius neglectus in Mauritia flexuosa palm trees: a field study in the Brazilian savanna

Two sampling methods (manual capture and live-baited adhesive traps) were compared for collecting the bug Rhodnius neglectus Lent (Hemiptera: Reduviidae: Triatominae) from palm trees, Mauritia flexuosa L. (Arecaceae), in the savanna of Brasília DF. R. neglectus was found in 19/50 (38%) of palm trees sampled. The detection rate was much higher by visual inspection and manual capture (18/50=36%) than by our trapping method (5/50=10%), although one tree was found to be positive by trapping but not by manual capture. Bugs collected manually were mostly (146/154=95%) found among the dead organic material in palm crowns. In combination, these sampling techniques are useful for quick detection of triatomine bug infestation in palm trees, especially in areas of high ecological value where the palms should not be cut and dissected, but arboreal Rhodnius are suspected to transmit enzootic Trypanosoma cruzi that might represent a risk of causing human cases of Chagas disease.