Article
Food Science & Technology
Madison Willy Silva Cordeiro, Diego Michel Matochi Mouro, Ingrid Duarte dos Santos, Roger Wagner
Summary: This study investigated the effect of gamma irradiation on the quality characteristics of yacare caiman meat under typical storage conditions. The overall quality characteristics of the irradiated samples were not significantly affected during frozen storage. However, the formation of volatile compounds from lipid oxidation was promoted in samples treated with high doses of irradiation after long-term frozen storage.
Article
Multidisciplinary Sciences
E. Martin Hechenleitner, Maria V. Fernandez Blanco, Segundo R. Nunez-Campero, Lucas E. Fiorelli, Paula Bona
Summary: Researchers used X-ray micro-CT scans to characterize crocodilian eggshells for the first time, revealing complex ornamentation and unique pore canal structures. These features may be related to nesting materials and nesting areas selected by different species.
SCIENTIFIC REPORTS
(2023)
Article
Biodiversity Conservation
Rodrigo Barban Zucoloto, Gilberto Cafezeiro Bomfim, Flora Maria de Campos Fernandes, Alessandra Selbach Schnadelbach, Carlos Ignacio Pina, Luciano M. Verdade
Summary: The study estimated the effective population size of broad-snouted caiman populations in Brazil using a single-sample estimator, revealing significant genetic and genotypic differentiation among wild populations. The effective population size of captive colonies was slightly larger than that of wild populations, with only a few adults effectively contributing to genetic variation in most wild populations.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Biochemistry & Molecular Biology
Richard Adams, Michael DeGiorgio
Summary: Likelihood-based tests of phylogenetic trees are crucial in modern systematics. While many such tests exist for gene trees, there is a lack of comparable frameworks for testing species tree hypotheses. To address this, we derive likelihood-based approaches for testing species tree topologies using gene tree topologies as input. These tests leverage the statistical procedures of their gene tree-based counterparts and have been demonstrated with simulated and empirical data sets. We also introduce an open-source R package for conducting formal likelihood-based tests of species topologies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Natalia B. C. Medeiros, Marcos Rodrigues, Drausio H. Morais, Marilia D. Nunes-Rodrigues
Summary: Research shows that caiman has a high carcass yield, with heavier animals resulting in more high-quality meat cuts, especially in the tail, back, and sirloin fillets.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2021)
Article
Multidisciplinary Sciences
Camilla B. Di-Nizo, Elkin Y. Suarez-Villota, Maria Jose J. Silva
Summary: This study examined the species limits and diversification patterns of Cerradomys, a genus of rodents, using cytogenetic and molecular analyses. The results identified eight species, with two potentially being species-complexes. The study suggests that the diversity of Cerradomys is underestimated and highlights the importance of interdisciplinary approaches in correctly identifying small rodent species and uncovering cryptic species.
Article
Environmental Sciences
Andres L. Rodriguez-Cordero, Sergio A. Balaguera-Reina, Juan C. Morales-Franco, Margaret Munn, Llewellyn D. Densmore
Summary: Climate change and habitat degradation pose serious threats to wildlife conservation, but their impacts on Neotropical crocodylians are poorly understood. This study used the Yacare Caiman as a model to explore the effects of climate change and habitat degradation on its distribution by 2050 and the effectiveness of protected areas. The results indicate that only a small portion of suitable habitat is currently protected, and a significant loss of species range is predicted. Therefore, the establishment of additional protected areas and sustainable management strategies are crucial for long-term species conservation.
CLIMATE RISK MANAGEMENT
(2022)
Article
Plant Sciences
Jie Wang, Chao-Nan Fu, Zhi-Qiong Mo, Michael Moeller, Jun-Bo Yang, Zhi-Rong Zhang, De-Zhu Li, Lian-Ming Gao
Summary: The taxonomy and phylogenetic relationships within the genus Cephalotaxus have been controversial. This study evaluated the efficiency of the complete plastome as a super-barcode in species discrimination and phylogenetic resolution in Cephalotaxus. A new taxonomic classification was proposed based on the plastome phylogeny, which also resolved all interspecific relationships. The rps16 gene was identified as a specific barcode for discriminating Cephalotaxus species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Sandrine Pavoine, Carlo Ricotta
Summary: Many unique species are the last survivors of a once diverse clade. However, the conservation actions for threatened unique species are limited. Researchers have developed a mathematical framework to connect different views on measuring a species' distinctiveness. The framework takes into consideration the risk of extinction for the target species and other species within a certain timeframe.
BIOLOGICAL CONSERVATION
(2022)
Article
Biochemical Research Methods
Mahim Mahbub, Zahin Wahab, Rezwana Reaz, M. Saifur Rahman, Md Shamsuzzoha Bayzid
Summary: Estimating species trees from genes sampled from the whole genome is challenging due to gene tree-species tree discordance, with incomplete lineage sorting being a common cause. Quartet-based weighted methods offer a statistically consistent way for accurate species tree estimation in such cases. The proposed wQFM method extends the quartet FM algorithm to a weighted setting, providing highly accurate species tree estimation results on simulated and real biological datasets.
Article
Multidisciplinary Sciences
Marcele Laux, Renato R. M. Oliveira, Santelmo Vasconcelos, Eder S. Pires, Talvane G. L. Lima, Mayara Pastore, Gisele L. Nunes, Ronnie Alves, Guilherme Oliveira
Summary: Ipomoea is a widely distributed genus with importance beyond economic value. This study provides genetic data and insights into the systematic phylogenetic relationships of key Ipomoea species from Eastern Amazon. The results highlight the importance of new plastome assemblies in resolving inconsistencies and increasing statistical confidence, especially for South American clades of Ipomoea.
Review
Zoology
Marie L. Verheye, Cedric D'Udekem D'Acoz
Summary: The highly distinctive Glade of giant species among Antarctic amphipods of the genus Eusirus, named 'crested Eusirus', includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, as well as the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks were reconstructed, revealing that species diversity of crested Eusirus is underestimated, with DNA-based methods suggesting multiple putative species within the two complexes. The morphological analysis also identified a new species within the E. perdentatus complex, Eusirus pontomedon sp. nov.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Biology
Andrew Richards, Laura Kubatko
Summary: This paper introduces two new methods for species tree inference, Lily-T and Lily-Q, and compares them with two frequently used methods, SVDQuartets and ASTRAL. The results show that Lily-Q generally outperforms the other methods in most simulation settings.
BULLETIN OF MATHEMATICAL BIOLOGY
(2021)
Article
Zoology
Emmanouela Karameta, Petros Lymberakis, Heinz Grillitsch, Cetin Ilgaz, Aziz Avci, Yusuf Kumluta, Kamil Candan, Philipp Wagner, Spyros Sfenthourakis, Panayiotis Pafilis, Nikos Poulakakis
Summary: Situated in the Eastern Mediterranean, the region offers an ideal setting to study the effects of palaeogeography, ecology, and long human presence on animal evolution. The study on Laudakia stellio reveals its high morphological variation and suggests that it represents three distinct evolutionary entities. The research also highlights the role of humans in shaping the present distribution patterns and the importance of specific areas as refugia and diversity hotspots.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biology
Kristina Wicke, Mareike Fischer, Laura Kubatko
Summary: Phylogenetic diversity indices such as the FP index are commonly used in biodiversity conservation to prioritize species. However, due to discordance between gene trees and species trees, these indices may result in different rankings.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio M. G. Martins-Junior, Iracilda Sampaio, Artur Silva, Jean Boubli, Tomas Hrbek, Izeni Farias, Manuel Ruiz-Garcia, Horacio Schneider
Summary: Night monkeys, a widely distributed genus of Neotropical primates, have a poorly understood taxonomy and biogeography. This study used molecular markers to infer the phylogeny, divergence times, and biogeography of the genus. Nine taxa of Aotus were supported, rejecting the existence of monophyletic red-necked and grey-necked species groups. The study suggests a taxonomic reclassification of the genus and highlights the role of dispersal and geographic changes in the origin and diversification of Aotus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Antoine Fouquet, Josselin Cornuault, Miguel T. Rodrigues, Fernanda P. Werneck, Tomas Hrbek, Andres R. Acosta-Galvis, David Massemin, Philippe J. R. Kok, Raffael Ernst
Summary: The genus Pipa is a species-poor clade of Neotropical frogs that is known for its bizarre-looking anatomy. The diversity and phylogenetic relationships within Pipa are poorly understood, as are their historical biogeography and the evolution of certain striking features. This study used DNA sequencing to identify 15 main lineages within Pipa and found that the genus originated in the early Neogene period in the Amazon region. The different lineages of Pipa further diversified and spread to other regions, following patterns observed in other co-distributed groups. The study also suggests that certain features, such as the absence of teeth, were lost or acquired independently in different lineages.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Zoology
Cleuton Lima Miranda, Mario da Silva Nunes, Arielli Fabricio Machado, Izeni Pires Farias, Fernando Heberson Menezes, Natalia Carneiro Ardente, Manoel Dos Santos-Filho, Yennie Katarina Bredin, Maria Nazareth F. da Silva
Summary: This article describes a new species of Metachirus in the Brazilian Amazon, using multiple sources of evidence such as morphology, genetics, and geography. This new species is distinct from known species and is found in the Xingu river basin, which is under strong anthropogenic pressure. This highlights the need for conservation strategies in the region.
Review
Multidisciplinary Sciences
Gerson Paulino Lopes, Fabio Rohe, Fabricio Bertuol, Erico Polo, Ivan Junqueira Lima, Joao Valsecchi, Tamily Carvalho Melo Santos, Stephen D. Nash, Maria Nazareth Ferreira da Silva, Jean P. Boubli, Izeni Pires Farias, Tomas Hrbek
Summary: In this study, a taxonomic revision of S. mystax was carried out using field surveys and genomic data testing, revealing the existence of three lineages/species. Saguinus mystax mystax from the left bank of the Jurua River was raised to species level, and a new species was discovered and described from the Jurua-Tefe interfluve previously attributed to S. mystax mystax. The subspecies S. m. pileatus and S. m. pluto were recognized as a single species under a new nomenclatural combination, but their phenotypic distinction and allopatric distribution suggest an early stage of speciation.
Article
Fisheries
Aline Mourao Ximenes, Valeria Nogueira Machado, Emil Jose Hernandez-Ruz, Fabio de Lima Muniz, Tomas Hrbek, Izeni Pires Farias
Summary: The discovery and characterization of cryptic diversity is important for conservation and management, especially for under-studied and underestimated ichthyofauna. In this study, the researchers investigated the existence of cryptic diversity in Pellona flavipinnis from the Amazon basin. Using genetic sequences and microsatellite loci, they found two spatially structured lineages of P. flavipinnis in the Amazon basin, differentiated from the population in the Parana River. Multiple methods of species delimitation confirmed the presence of these two lineages, and morphometric measurements showed no shape differences between them.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Hong Gao, Tobias Hamp, Jeffrey Ede, Joshua G. Schraiber, Jeremy McRae, Moriel Singer-Berk, Yanshen Yang, Anastasia S. D. Dietrich, Petko P. Fiziev, Lukas F. K. Kuderna, Laksshman Sundaram, Yibing Wu, Aashish Adhikari, Yair Field, Chen Chen, Serafim Batzoglou, Francois Aguet, Gabrielle Lemire, Rebecca Reimers, Daniel Balick, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idriss S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Fabiano R. de Melo, Fabricio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, Joao Valsecchi do Amaral, Mariluce Messias, Maria N. F. da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clement J. Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D. Keyyu, Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Thomas Bataillon, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut, Amanda Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli, Monkol Lek, Shamil Sunyaev, Anne O'Donnell-Luria, Heidi L. Rehm, Jinbo Xu, Jeffrey Rogers, Tomas Marques-Bonet, Kyle Kai-How Farh
Article
Multidisciplinary Sciences
Lukas F. K. Kuderna, Hong Gao, Mareike C. Janiak, Martin Kuhlwilm, Joseph D. Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries, Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idrissa S. Chuma, Julie E. Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Joshua G. Schraiber, Fabiano R. de Melo, Fabricio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, Joao Valsecchi, Malu Messias, Maria N. F. da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clement J. Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guoji Zhang, Julius D. Keyyu, Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut, Amanda D. Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli, Jeffrey Rogers, Kyle Kai-How Farh, Tomas Marques Bonet
Summary: The rich diversity of morphology and behavior displayed across primate species provides valuable insights into the impact of genomic diversity on biological processes. This study analyzed high-coverage whole-genome data from 233 primate species, representing a significant portion of the primate diversity, to create a phylogeny and reassess evolutionary divergence times. The study found associations between genetic diversity, climate, and sociality, but not extinction risk, and identified recurring missense mutations previously thought to be specific to humans. This research has significant implications for future primate genomic studies.
Article
Genetics & Heredity
Jeferson Carneiro, Iracilda Sampaio, Jose de S. e Silva, Antonio Martins, Izeni Farias, Tomas Hrbek, Jean Boubli, Horacio Schneider
Summary: Pitheciines have unique dental adaptations that allow them to eat fruits with hard pericarps, making them important seed predators. A review of the Chiropotes genus reveals that there are five species which likely originated in the Rondonia and Tapajos regions of the Amazon. The speciation events within Chiropotes were likely influenced by the radiation and founder effects associated with the formation of the Amazonian basins.
Article
Multidisciplinary Sciences
Diana Sanchez-Bernal, Jose Gregorio Martinez, Izeni Pires Farias, Tomas Hrbek, Susana Caballero
Summary: The Neotropics are home to a diverse range of freshwater fish species, including the cardinal tetra, which is widely traded in the ornamental fish market. This study investigated the phylogeography and population structure of the cardinal tetra, as well as potential migration routes between the Orinoco and Negro basins. The results suggest that river capture, physical barriers, and ecological factors may have played a role in shaping the distribution and genetic patterns of the cardinal tetra.
Article
Multidisciplinary Sciences
Ingrid Nunes, Kelmer Passos, Aline Mourao Ximenes, Tomas Hrbek, Izeni Pires Farias
Summary: This study assessed the genetic diversity and spatial and temporal structure of Semaprochilodus insignis in the Brazilian Amazon basin using mtDNA control region sequencing (n=241) and eight microsatellite loci (n=180). The results showed homogeneous genetic diversity and the absence of spatial and temporal genetic structure, indicating a large panmictic population in the Brazilian Amazon.
Article
Zoology
Gerson Paulino Lopes, Roberta C. Oliveira, Tamily C. M. Santos, Paul M. Velazco, Paulo Estefano D. Bobrowiec, Maria Nazareth F. Silva, Tomas Hrbek, Izeni P. Farias
Summary: In this study, we report the discovery of Platyrrhinus guianensis in the Brazilian Amazon, extending its distribution range beyond Guyana and Suriname. This finding suggests the potential misidentification of Platyrrhinus guianensis as other similar species in scientific collections.
Article
Evolutionary Biology
Gerson Paulino Lopes, Fabio Rohe, Fabricio Bertuol, Erico Polo, Joao Valsecchi, Tamily Carvalho Melo Santos, Felipe Ennes Silva, Ivan Junqueira Lima, Ricardo Sampaio, Maria Nazareth Ferreira da Silva, Claudia Regina Silva, Jean Boubli, Rodrigo Costa-Araujo, Benoit de Thoisy, Manuel Ruiz-Garcia, Marcelo Gordo, Iracilda Sampaio, Izeni Pires Farias, Tomas Hrbek
Summary: This study presents a comprehensive dated genomic phylogeny of all known species and subspecies of Tamarinus based on double digest restriction associated DNA. The research confirms Tamarinus imperator and Tamarinus subgrisescens as distinct species and supports the taxonomic proposal of dividing Saguinus into three genera.
Article
Multidisciplinary Sciences
Aureo Banhos, Tania Margarete Sanaiotti, Renan Coser, Waleska Gravena, Francisca Helena Aguiar-Silva, Mylena Kaizer, Tomas Hrbek, Izeni Pires Farias
Summary: The Harpy Eagle, the largest eagle species with reversed sexual size dimorphism, exhibits a female-biased sex ratio at all life stages, indicating an evolutionary ecological pattern. An earlier sexual maturation age of males may compensate for the female bias.
ROYAL SOCIETY OPEN SCIENCE
(2023)