RESUMEN
We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology and Evolution journals, including methods to infer phylogenies, to test hypotheses in a phylogenetic framework, and to infer population genetic processes. We also mention many of the software implementations that make methods tractable for empiricists. In short, the Society for Molecular Biology and Evolution community has much to celebrate after four decades of publishing high-quality science including numerous important inferential methods.
Asunto(s)
Publicaciones Periódicas como Asunto , Filogenia , Biología Molecular , Evolución Molecular , Programas InformáticosRESUMEN
Evolution is both a fact and a theory. Evolution is widely observable in laboratory and natural populations as they change over time. The fact that we need annual flu vaccines is one example of observable evolution. At the same time, evolutionary theory explains more than observations, as the succession on the fossil record. Hence, evolution is also the scientific theory that embodies biology, including all organisms and their characteristics. In this paper, we emphasize why evolution is the most important theory in biology. Evolution explains every biological detail, similar to how history explains many aspects of a current political situation. Only evolution explains the patterns observed in the fossil record. Examples include the succession in the fossil record; we cannot find the easily fossilized mammals before 300 million years ago; after the extinction of the dinosaurs, the fossil record indicates that mammals and birds radiated throughout the planet. Additionally, the fact that we are able to construct fairly consistent phylogenetic trees using distinct genetic markers in the genome is only explained by evolutionary theory. Finally, we show that the processes that drive evolution, both on short and long time scales, are observable facts.
RESUMEN
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 â¼20% 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 â¼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.
Asunto(s)
Drosophila melanogaster/genética , Genes de Insecto/genética , Genes Ligados a Y/genética , Cromosoma Y/genética , Animales , Mapeo Cromosómico , Cromosomas de Insectos/genética , Proteínas de Drosophila/clasificación , Proteínas de Drosophila/genética , Femenino , Duplicación de Gen , Expresión Génica , Mutación INDEL , Masculino , Datos de Secuencia Molecular , Filogenia , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Cromosoma X/genéticaRESUMEN
Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.
Asunto(s)
Artrópodos , Animales , Filogenia , Funciones de Verosimilitud , Teorema de Bayes , InsectosRESUMEN
The CC chemokine receptor 5 (CCR5) gene of primates encodes a transmembrane protein involved in cellular signaling of some cell types of the immune system. Numerous studies have shown that this peptide is used by lentiviruses in conjunction with the CD4 receptor to mediate binding and entry in target cells of human and non-human primates. New World monkeys (NWM), differently from their African counterparts, have no description of in natura lentivirus infection. Some evidences suggest that a blockage occurs at the viral entry step of infection. To investigate this possibility, we have cloned and sequenced CCR5 genes from several representatives of Platyrrhini, and compared their sequences with those of other Platyrrhini and Catarrhini species available at public databases. Platyrrhini CCR5 genes were shown to be more genetically diverse than their Catarrhini correlates, and their phylogenetic relationships based on that locus were in agreement with previous studies. Comparison of Platyrrhini and Catarrhini CCR5 consensus sequences evidenced several amino acid residues that differ between both groups, some of which have been experimentally associated with lentiviral interaction. A codon-based positive selection analysis showed that some of these sites seem to be under strong selection for variation among the Platyrrhini but not among Catarrhini species. These results suggest the potential involvement of those sites in the apparent refraction of some NWM to lentiviruses. The high ccr5 genetic diversity observed in Platyrrhini, however, argues for a more extensive infection analysis of diverse NWM species to evaluate this resistance and the potential use of those primates as HIV/AIDS animal models.
Asunto(s)
Cebidae/genética , Evolución Molecular , Infecciones por Lentivirus/genética , Receptores CCR5/fisiología , Adaptación Fisiológica/genética , Secuencia de Aminoácidos , Animales , Predisposición Genética a la Enfermedad , Variación Genética , Lentivirus de los Primates/patogenicidad , Datos de Secuencia Molecular , Filogenia , Receptores CCR5/genética , Homología de Secuencia de AminoácidoRESUMEN
Penaeid shrimps are an important resource in crustacean fisheries, representing more than the half of the gross production of shrimp worldwide. In the present study, we used a sample of wide-ranging diversity (41 shrimp species) and two mitochondrial markers (758 bp) to clarify the evolutionary relationships among Penaeidae genera. Three different methodologies of tree reconstruction were employed in the study: maximum likelihood, neighbor joining and Bayesian analysis. Our results suggest that the old Penaeus genus is monophyletic and that the inclusion of the Solenocera genus within the Penaeidae family remains uncertain. With respect to Metapenaeopsis monophyly, species of this genus appeared clustered, but with a nonsignificant bootstrap value. These results elucidate some features of the unclear evolution of Penaeidae and may contribute to the taxonomic characterization of this family.
Asunto(s)
Evolución Molecular , Variación Genética/genética , Mitocondrias/genética , Penaeidae/genética , Filogenia , Algoritmos , Animales , Teorema de Bayes , Complejo I de Transporte de Electrón/genética , Marcadores Genéticos , Funciones de Verosimilitud , Penaeidae/clasificación , ARN Ribosómico 16S/genética , Alineación de Secuencia/métodosRESUMEN
Mytella guyanensis Lamarck (1819) and Mytella charruana d'Orbigny (1846) are widespread euryhaline bivalves that have become commercially important in Brazil. Despite their importance, however, no genetic information that would be useful to orient governmental policies is available for these species. We analyzed, through allozyme electrophoresis, populations of M. guyanensis and M. charruana along 3,500 km of Brazilian coast. Pairwise comparisons among gene frequencies in M. guyanensis resulted in high levels of pairwise gene identity (I = 0.976 to 0.998). Conversely, significant levels of population structure were found in both M. guyanensis (FST = 0.089) and M. charruana (FST = 0.102). Heterozygosity levels for both species were high (H(e) = 0.090 to 0.134 in M. guyanensis and H(e) = 0.191 to 0.228 in M. charruana). The larger population size of M. charruana could explain, at least partially, the higher levels of genetic variability for this species. These levels of genetic variability yield an effective population size estimate of about 300,000 for M. guyanensis, and 540,000 for M. charruana, based on neutralist expectations. Remarkably, these numbers are much smaller than the estimated actual population sizes. This distortion might be explained by unstable population sizes and it suggests that long-term genetic variability studies are crucial to prevent artifactual viability analysis data for these commercially exploited species.
Asunto(s)
Variación Genética/genética , Mytilidae/genética , Animales , Brasil , Electroforesis en Gel de Almidón , Frecuencia de los Genes , Heterocigoto , Mytilidae/clasificación , Mytilidae/enzimología , Especificidad de la EspecieRESUMEN
The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.
Asunto(s)
Anopheles/genética , Evolución Molecular , Variación Genética , Filogenia , Animales , Anopheles/clasificación , Complejo IV de Transporte de Electrones/genética , Proteínas de Insectos/genética , Proteínas Mitocondriales/genética , Subunidades de Proteína/genética , ARN Ribosómico 5.8S/genética , Especificidad de la Especie , Factores de TiempoRESUMEN
BACKGROUND: The Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date. METHODS: The relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S. RESULTS: Our results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes. CONCLUSIONS: We propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera.
Asunto(s)
Filogenia , Triatominae/genética , Animales , ADN/genética , Variación Genética , Especificidad de la Especie , Triatominae/clasificaciónRESUMEN
BACKGROUND: The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily. METHODOLOGY: In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family. CONCLUSIONS: Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.
Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Zea mays/genética , Arabidopsis/química , Proteínas de Arabidopsis/química , Evolución Biológica , Eucariontes/genética , Evolución Molecular , Duplicación de Gen , Genes de Plantas , Datos de Secuencia Molecular , Familia de Multigenes , Filogenia , Fenómenos Fisiológicos de las Plantas , Proteínas de Plantas , Conformación Proteica , Estructura Terciaria de Proteína , Zea mays/químicaRESUMEN
Herbivorous insects are abundant and diverse and insect-host plant associations tend to be specialized and evolutionarily conserved. Some authors suggested that generalist insect lineages tend to become specialists, with host specialization leading to an evolutionary dead-end for the parasite species. In this paper, we have examined this tendency using a phylogenetic tree of Tomoplagia (Diptera: Tephritidae), a parasite of asteracean plants. We have tested the trend towards specialization in different hierarchical degrees of host specialization. The topology of the tree, the inference of ancestral hosts, and the lack of directional evolution indicated that specialization does not correspond to a phylogenetic dead-end. Although most Tomoplagia species are restricted to a single host genus, specialization does not seem to limit further host range evolution. This work emphasizes the advantages of the use of different levels of specialization and the inclusion of occasional hosts to establish a more detailed scenario for the evolution of this kind of ecological association.
Asunto(s)
Adaptación Biológica/genética , Asteraceae/parasitología , Filogenia , Tephritidae/genética , Tephritidae/fisiología , Animales , Secuencia de Bases , Brasil , Cartilla de ADN , ADN Mitocondrial/genética , Interacciones Huésped-Parásitos , Funciones de Verosimilitud , Modelos Genéticos , Datos de Secuencia Molecular , Análisis de Secuencia de ADNRESUMEN
UNLABELLED: MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. AVAILABILITY: MamMiBase is available at http://www.mammibase.lncc.br
Asunto(s)
Mapeo Cromosómico/métodos , ADN Mitocondrial/clasificación , ADN Mitocondrial/genética , Bases de Datos de Ácidos Nucleicos , Filogenia , Alineación de Secuencia/métodos , Análisis de Secuencia de ADN/métodos , Interfaz Usuario-Computador , InternetRESUMEN
The origin of New World monkeys (Infraorder Platyrrhini) has been an extensively debated issue. In this study, we analyzed mitochondrial genomes from Cebus (Platyrrhini), Homo, Hylobates, Pan, Pongo (Hominoids), Macaca, Papio (Cercopithecoids), and Tarsius (outgroup) to investigate this matter. Two distinct methodologies were employed on mitochondrial genes to estimate divergence times: the traditional likelihood ratio test performed in ML analyses of individual and concatenated gene sequences and the recent multigene Bayesian approach. Using the Cercopithecoid-Hominoid split as calibration point (25 MYA), our results show consistently that Platyrrhines split from Catarrhines at around 35 MYA. Although the main focus of the study is New World monkey origins, we have also estimated other primate divergence times: Homo-Pan at 5-7 MYA; Pongo-(Homo/Pan) at 13-16 MYA; Hylobates-(Pongo/Homo/Pan) at 15-19 MYA; and Macaca-Papio at 10-12 MYA. Our estimate for the origin of New World monkeys is in agreement with the hypothesis of a transatlantic journey from Africa to South America, as suggested by the fossil record.
Asunto(s)
Cebidae/genética , Cercopithecidae/genética , Evolución Molecular , Animales , ADN Mitocondrial , Hominidae/genética , Humanos , Mitocondrias/genética , Datos de Secuencia MolecularRESUMEN
The sponge species Chondrilla nucula has a simple morphology and a very wide geographical distribution. To verify whether the latter might be an artifact of the former, samples of this species were collected across 10,000 km of its range, in the Mediterranean, the Caribbean, and the southwestern atlantic. The classical (spicule morphology) and molecular (allozymes) systematic approaches were compared, to try to define the geographic limits between populations and detect possible cryptic species. We found five distinct genetic forms within C. nucula that sometimes showed morphological homogeneity and other times plasticity. The difference in size of spicules could not be related to the clear-cut genetic differences, suggesting that the use of spicule sizes for sponge systematics should be reappraised. The population of one of the genetic forms along 3000 km of the Brazilian coast was highly structured (FST = 0.21; Ne m = 0.96). Our results reject the null hypothesis of cosmopolitanism of C. nucula and indicate that the putative worldwide distribution of some marine sponges, and possibly many other benthic invertebrates, may be the result of overly conservative systematics. Cryptic species appear to be particularly prevalent when genera are well defined but species are characterized by only a few morphological characters.
RESUMEN
MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root to flower and fruit development. Members of the MADS-box gene family share a highly conserved sequence of approximately 180 nucleotides that encodes a DNA-binding domain. We used bioinformatics tools to investigate the information generated by the Eucalyptus Expressed Sequence Tag (FORESTs) genome project in order to identify and annotate MADS-box genes. The comparative phylogenetic analysis of the Eucalyptus MADS-box genes with Arabidopsis homologues allowed us to group them into one of the well-known subfamilies. Trends in gene expression of these putative Eucalyptus MADS-box genes were investigated by hierarchical clustering analysis. Among 24 MADS-box genes identified by our analysis, 12 are expressed in vegetative organs. Out of these, five are expressed predominately in wood. Understanding of the molecular mechanisms performed by MADS-box proteins underlying Eucalyptus growth, development and stress reactions would provide important insights into tree development and could reveal means by which tree characteristics could be modified for the improvement of industrial properties