Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates

Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.Fil: Ferraz, Tiago. Universidade Federal do Rio Grande do Sul; Brasil. Universidade de Sao Paulo; BrasilFil: Rossoni, Daniela M.. Universidade de Sao Paulo; BrasilFil: Althoff, Sérgio L.. Universidade Regional de Blumenau; BrasilFil: Pissinatti, Alcides. Universidade Federal da Bahia; BrasilFil: Paixão Cortês, Vanessa R.. Centro de Primatologia do Rio de Janeiro; BrasilFil: Bortolini, María Cátira. Universidade Federal do Rio Grande do Sul; BrasilFil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Marroig, Gabriel. Universidade de Sao Paulo; BrasilFil: Salzano, Francisco M.. Universidade Federal do Rio Grande do Sul; BrasilFil: Gonçalves, Gislene L.. Universidad de Tarapacá de Arica; Chile. Universidade Federal do Rio Grande do Sul; BrasilFil: Hünemeier, Tábita. Universidade de Sao Paulo; Brasi

DNA Barcoding of Sigmodontine Rodents: Identifying Wildlife Reservoirs of Zoonoses

<div><p>Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome <i>c</i> oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus <i>Drymoreomys</i>. The data also indicated an expansion of the distribution of <i>Calomys tener</i>. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.</p> </div

Detail of misidentified specimens.

<p>Subtrees shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080282#pone-0080282-g002" target="_blank">Figure 2</a> from the Bayesian phylogeny inferred based on 648 bp of COI for sigmodontine rodents (posterior probability values on nodes) are shown in detail. Misidentified specimens are indicated with a light background. A: subtree for <i>Oligoryzomys nigripes</i> and <i>O. flavescens</i>; B: subtree for <i>Euryoryzomys russatus</i>; C: subtree for <i>Akodon</i> species.</p

Intra- (solid line) and interspecific (dotted line) pairwise genetic distance (K2P) distribution.

<p>Area overlap between distributions (< 0.01) is shaded. The 2% threshold is indicated as a vertical line. Distributions are estimated by kernel density estimation.</p

Box-and-whisker plot of evolutionary divergence among <i>Deltamys kempi</i>, <i>Deltamys</i> sp. n. and <i>Akodon</i> species.

<p>The box represents the median, first and third quartile, whiskers represent 1.5 times the interquantile range. Dots represent outliers. Distances were calculated based on Kimura 2-parameter model.</p

Mean intraspecific K2P pairwise distance after reclassification.

<p>First line indicates the 2% threshold of intraspecific variation. Twenty-three species are below this limit and nine are above. The second line indicates 5% genetic divergence. </p

Biomes and localities sampled in South America.

<p>Different shades of gray correspond to different biomes, as indicated in the legend. 1. Reserva de Santa Teresa, Rocha, UY (-34.36; -53.46); 2. Alegrete, RS, BR (-55.71; -29.57); 3. Margarida do Sul, RS, BR (-54.07; -30.37); 4. Rondinha, RS, BR (-53.75; -27.75); 5. Ronda Alta, RS, BR (-52.82; -27.79); 6. Passo Fundo, RS, BR (-52.48; -28.29); 7. Terra de Areia, RS, BR(-50.48; -29.39); 8. Derrubadas, RS, BR (-53.83; -27.17); 9. Erechim, RS, BR (-52.28; -27.60); 10. Barracão, RS, BR (-51.46; -27.67); 11. São Domingos, SC, BR (-52.54; -26.56) 12. São Francisco de Paula, RS, BR (-50.37; -29.40); 13. Blumenau, SC, BR (-49.07; -26.96) 14. São José dos Pinhais, PR, BR (-49.17; -25.58); 15. Capão Bonito, SP, BR (-24.06; -48.32); 16. Capitão Andrade, MG, BR (-19.06; -41.81) 17. Itinga, MG, BR (-41.82; -16.61) 18. Mimoso de Goiás, GO, BR (-15.06; -48.19); 19. Correntina, BA, BR (-44.16; -13.34); 20. Caetité, BA, BR (-42.50;-14.07); 21. Mucugê, BA, BR (-41.39; -13). BR: Brazil. UY: Uruguay. Brazilian States: RS-Rio Grande do Sul, SC-Santa Catarina, PR-Paraná, SP- São Paulo, MG-Minas Gerais, GO-Goiás, BA-Bahia. Coordinates in parentheses are given in decimal degrees. </p

ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

ATLANTIC BIRD TRAITS

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ