Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to de... more Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to demonstrate the task of character coding and its importance in phylogenetic systematics. This exercise is appropriate for undergraduate students in life sciences and related courses. The teacher must provide a single group of masks in which color patterns, textures, and formats provide the characters to fill the data matrix. (The masks could be replaced by a set of other complex objects.) In this case, because there is no actual phylogeny, students will not be concerned with recovering the correct topology. Character coding is the aim of the exercise. After the character matrix is completed, a phylogenetic tree is drawn and the students interpret the evolution of a single character, starting from the common ancestor, based on the topological pattern of the tree and on the data matrix. In sequence, the students name and provide a full diagnosis for the group of masks as revealed by the topo...
This study is the first report on the mammalian fauna of the Quaternary of Serra da Bodoquena sec... more This study is the first report on the mammalian fauna of the Quaternary of Serra da Bodoquena section, Mato Grosso do Sul, Brazil. We investigated three limestone caves for the occurrence of fossils: Nossa Senhora Aparecida, Japonês, and Nascente do Formoso, the two latter being underwater caves. For underwater caving, we developed an airlift system in order to collect small fossil fragments. We also attempted to retrieve specimens of the recent mammalian fauna. We recovered about 1650 fragments from the caves, and identified 74 species for the region (of which 34 are fossils). The paleontological results suggest that the Bodoquena region was probably characterized by an open savannah vegetation habitat rich in water patches.
This study aims to clarify the taxonomic status of Monodelphis dimidiata and M. sorex, using mole... more This study aims to clarify the taxonomic status of Monodelphis dimidiata and M. sorex, using molecular and morphometric data. Cytochrome-b sequences were obtained from specimens morphologically assignable to those taxa from the vicinity of type localities, but also representing their presumptive area of sympatry and extremes in their known distributions. These sequences were compared to GenBank downloaded sequences of select Monodelphis spp. and also of Marmosa lepida, Micoureus demerarae, and Didelphis albiventris, used as outgroups. Genetic distances and maximum likelihood analyses were performed to recover phylogenetic affinities among taxa. To access morphometric variation, univariate and multivariate statistical methods (Principal Component Analysis and Canonical Variate Analysis) were applied to the covariance matrix of 25 craniometric measurements obtained from a total of 108 specimens sampled across the geographic ranges of the species. The molecular analyses revealed a clad...
The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand ex... more The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2015
Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linke... more Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FD...
Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to de... more Phylogenetics has a central role in the biological sciences. We suggest a hands-on exercise to demonstrate the task of character coding and its importance in phylogenetic systematics. This exercise is appropriate for undergraduate students in life sciences and related courses. The teacher must provide a single group of masks in which color patterns, textures, and formats provide the characters to fill the data matrix. (The masks could be replaced by a set of other complex objects.) In this case, because there is no actual phylogeny, students will not be concerned with recovering the correct topology. Character coding is the aim of the exercise. After the character matrix is completed, a phylogenetic tree is drawn and the students interpret the evolution of a single character, starting from the common ancestor, based on the topological pattern of the tree and on the data matrix. In sequence, the students name and provide a full diagnosis for the group of masks as revealed by the topo...
This study is the first report on the mammalian fauna of the Quaternary of Serra da Bodoquena sec... more This study is the first report on the mammalian fauna of the Quaternary of Serra da Bodoquena section, Mato Grosso do Sul, Brazil. We investigated three limestone caves for the occurrence of fossils: Nossa Senhora Aparecida, Japonês, and Nascente do Formoso, the two latter being underwater caves. For underwater caving, we developed an airlift system in order to collect small fossil fragments. We also attempted to retrieve specimens of the recent mammalian fauna. We recovered about 1650 fragments from the caves, and identified 74 species for the region (of which 34 are fossils). The paleontological results suggest that the Bodoquena region was probably characterized by an open savannah vegetation habitat rich in water patches.
This study aims to clarify the taxonomic status of Monodelphis dimidiata and M. sorex, using mole... more This study aims to clarify the taxonomic status of Monodelphis dimidiata and M. sorex, using molecular and morphometric data. Cytochrome-b sequences were obtained from specimens morphologically assignable to those taxa from the vicinity of type localities, but also representing their presumptive area of sympatry and extremes in their known distributions. These sequences were compared to GenBank downloaded sequences of select Monodelphis spp. and also of Marmosa lepida, Micoureus demerarae, and Didelphis albiventris, used as outgroups. Genetic distances and maximum likelihood analyses were performed to recover phylogenetic affinities among taxa. To access morphometric variation, univariate and multivariate statistical methods (Principal Component Analysis and Canonical Variate Analysis) were applied to the covariance matrix of 25 craniometric measurements obtained from a total of 108 specimens sampled across the geographic ranges of the species. The molecular analyses revealed a clad...
The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand ex... more The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2015
Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linke... more Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FD...
Uploads
Papers by Claudia Russo