Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

Background: In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.Methods: We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared- change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.Results: Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony

Serological survey of post-campaign vaccination against the rabies in dogs of Santa Cruz de la Sierra, Bolivia

Durante la campaña de vacunación antirrábica masiva realizada en Santa Cruz, Bolivia, en agosto de 2007, 369.000 perros (82% de la población canina estimada) fueron vacunados durante 2 días con vacunas hechas en Cerebro de Ratón Lactante (CLR) Fuenzalida-Palacios. Desde entonces se han registrado 7 casos de rabia humana, además, el número de casos de rabia canina se ha reducido de 866 casos reportados el año 2006 a 516. Por esta razón, se realizó una encuesta serológica 3 meses después de la vacunación, colectando 320 muestras de sangre de perros con dueños seleccionados al azar, para determinar la respuesta inmune humoral. Tres meses después de la vacunación, el 20,94% de los perros tenían anticuerpos neutralizantes contra la rabia de > 0,5 Ul/ml. Al respecto se determinó que los animales mayores a un año estaban más protegidos que los menores (p0,05). De acuerdo con las recomendaciones de la Organización Panamericana de la Salud las campañas de vacunación deben contemplar coberturas no menores a 80 % para que tengan el efecto deseado. De nuestro estudio se desprende que existe una deficiente protección inmune contra la rabia en la población de canes vacunados de todas las zonas evaluadas, lo cual pone de manifiesto la susceptibilidad a aumentar los casos de rabia canina en la ciudad.During a 2 days massive anti-rabies vaccination campaign held in Santa Cruz, Bolivia in August 2007, 369,000 dogs (82% of the estimated canine population) were vac- cinated with vaccines made of suckling mouse brain (CLR) Fuenzalida-Palacios. Since then there have been 7 cases of human rabies, moreover, the number of canine rabies cases have been reduced from 866 cases reported in 2006 to 516. For this reason, a serological survey was performed 3 months after vaccination, collecting 320 samples from dogs with owners selected at random to determine the humoral immune response. Three months after vaccina- tion, 20.94% of the dogs had rabies neutralizing antibodies of > 0.5 IU / ml. We found that animals older than a year were more protected than younger ones (p <0.01), but when sex of the dogs was evaluated it showed no statistical association with protection (p> 0.05). Ac- cording to the recommendation of Panamerican Health Organization for rabies vaccination campaign, an effective coverage against the disease should be > 80%. Our results demonstrate a deficient immune protection against rabies in the population of dogs vaccinated in all areas evaluated, which shows increased susceptibility to canine rabies in the city.Facultad de Ciencias Veterinaria

Modelling carbon stock and carbon sequestration ecosystem services for policy design: a comprehensive approach using a dynamic vegetation model.

Ecosystem service (ES) models can only inform policy design adequately if they incorporate ecological processes. We used the Lund-Potsdam-Jena managed Land (LPJmL) model, to address following questions for Mexico, Bolivia and Brazilian Amazon: (i) How different are C stocks and C sequestration quantifications under standard (when soil and litter C and heterotrophic respiration are not considered) and comprehensive (including all C stock and heterotrophic respiration) approach? and (ii) How does the valuation of C stock and C sequestration differ in national payments for ES and global C funds or markets when comparing both approach? We found that up to 65% of C stocks have not been taken into account by neglecting to include C stored in soil and litter, resulting in gross underpayments (up to 500 times lower). Since emissions from heterotrophic respiration of organic material offset a large proportion of C gained through growth of living matter, we found that markets and decision-makers are inadvertently overestimating up to 100 times C sequestrated. New approaches for modelling C services relevant ecological process-based can help accounting for C in soil, litter and heterotrophic respiration and become important for the operationalization of agreements on climate change mitigation following the COP21 in 2015

Latin America's Nitrogen Challenge

Latin America (LA) has many social indicators similar to those of highly developed economies but most frequently falls midway between least developed countries and industrialized regions. To move forward, LA must address uncontrolled urbanization, agricultural production, social inequity, and destruction of natural resources. We discuss these interrelated challenges in terms of human impact on the nitrogen (N) cycle. Human activity has caused unprecedented changes to the global N cycle; in the past century; total global fixation of reactive N (Nr) has at least doubled (1). Excess Nr leaked into the environment negatively affects soils, atmosphere, and water resources in temperate zones (1). In addition to N excess from human impact, mining of natural soil N creates N deficits in some regions (2, 3).Fil: Austin, Amy Theresa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Bustamante, M. M. C.. Universidade Do Brasilia; BrasilFil: Nardoto, G. B.. Universidade Do Brasilia; BrasilFil: Mitre, S. K.. Universidade Do Brasilia; BrasilFil: Pérez, T.. Instituto Venezolano de Investigaciones Cientificas; VenezuelaFil: Ometto, J. P. H. B.. Centro de Previsao de Tempo e Estudos Climaticos. Instituto Nacional de Pesquisas Espaciais; BrasilFil: Ascarrunz, N. L.. Instituto Boliviano de Investigación Forestal; BoliviaFil: Forti, M. C.. Centro de Previsao de Tempo e Estudos Climaticos. Instituto Nacional de Pesquisas Espaciais; BrasilFil: Longo, K.. Centro de Previsao de Tempo e Estudos Climaticos. Instituto Nacional de Pesquisas Espaciais; BrasilFil: Gavito, M. E.. Universidad Nacional Autónoma de México; MéxicoFil: Enrich Prast, A.. Universidade Federal do Rio de Janeiro; BrasilFil: Martinelli, L. A.. Universidade de Sao Paulo; Brasi

Antibody seroprevalences against rabies in dogs vaccinated under field conditions in Bolivia

Bolivia currently has one of the highest numbers of cases for human and canine rabies and is thus clue to the elimination process. The objective of the present study was to assess antibody seroprevalences against rabies in dogs vaccinated under field conditions and other factors that might influence the success of the on-going rabies control programmes in an endemic area of the disease, Santa Cruz de la Sierra, Bolivia. All 240 study animals, selected using area-stratified random sampling, were investigated in April 2007. Test prevalences were adjusted for the imperfect test characteristics using the Rogan-Gladen estimator (deterministic and stochastic functions) and Bayesian inference. Ninety-four of the tested 240 vaccinated dogs were classified as test-positive for rabies-specific antibodies. With regard to adjusted overall antibody seroprevalence, Bayesian true prevalence estimates (41%, 95% CI: 37-46%) were lower than both of the Rogan-Gladen estimates. The effect of various epidemiological factors on post-vaccination response was also assessed.Facultad de Ciencias Veterinaria

Modelling carbon stock and carbon sequestration ecosystem services for policy design: a comprehensive approach using a dynamic vegetation model

Ecosystem service (ES) models can only inform policy design adequately if they incorporate ecological processes. We used the Lund-Potsdam-Jena managed Land (LPJmL) model, to address following questions for Mexico, Bolivia and Brazilian Amazon: (i) How different are C stocks and C sequestration quantifications under standard (when soil and litter C and heterotrophic respiration are not considered) and comprehensive (including all C stock and heterotrophic respiration) approach? and (ii) How does the valuation of C stock and C sequestration differ in national payments for ES and global C funds or markets when comparing both approach? We found that up to 65% of C stocks have not been taken into account by neglecting to include C stored in soil and litter, resulting in gross underpayments (up to 500 times lower). Since emissions from heterotrophic respiration of organic material offset a large proportion of C gained through growth of living matter, we found that markets and decision-makers are inadvertently overestimating up to 100 times C sequestrated. New approaches for modelling C services relevant ecological process-based can help accounting for C in soil, litter and heterotrophic respiration and become important for the operationalization of agreements on climate change mitigation following the COP21 in 2015

Biodiversity recovery of Neotropical secondary forests

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes. Copyright © 2019 The Authors, some rights reserved

Polymorphic characters in the reconstruction of the phylogeny of geoemydid turtles

Several attempts to resolve the phylogeny of turtles in the clade Geoemydidae using morphology have been unsuccessful, in part because of unusually high levels of polymorphism. This has hindered the integration of the geoemydid fossil record into a phylogenetic framework. Many methods, shown to improve phylogenetic inference, allow the incorporation of different amounts of state frequency information from polymorphic characters into a phylogenetic analysis. Here, we present a new character matrix for the shell of geoemydids and assess the performance of polymorphism coding methods (‘majority', ‘generalized frequency coding', ‘polymorphic' and ‘missing') in a phylogenetic analysis by comparing the result topology of each method with a reference molecular phylogeny. The four coding methods failed to recover trees that were both well resolved and highly congruent with the reference phylogeny. Moreover, contrary to previous studies, the coding methods that made more use of character states frequencies did not perform better. However, a leave-one-out subsampling analysis suggested that despite these problems, the new matrix can still be used to place fossils in the geoemydid phylogeny with some reliability. Finally, we provide a list of characters that diagnose the major clades in our molecular reference tree

Foth-et-al-Turtle-Skull-disparity-S1 from Still slow, but even steadier: an update on the evolution of turtle cranial disparity interpolating shapes along branches

Addtional tables showing main results and information on material and method