Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the ...Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene–Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences ...so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned ...fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
Abstract
High-risk human papillomaviruses (HPVs) 16 and 18 are responsible for more than 70% of cervical cancers and majority of other HPV-associated cancers world-wide. Current treatments for these ...cancers have limited efficacy, which in turn has resulted in disease recurrence and poor survival rates in advanced disease stages. Hence, there is a significant need for development of novel molecularly-targeted therapeutics. This can only be achieved through improved understanding of disease mechanism. Recently, we developed a Drosophila model of HPV18E6 plus human E3 ubiquitin ligase (hUBE3A) and demonstrated that the E6-induced cellular abnormalities are conserved between humans and flies. Subsequently, we demonstrated that reduced level and activity of IKKβ, a regulator of NF-κB, suppresses the cellular abnormalities induced by E6 oncoprotein and that the interaction of IKKβ and E6 is conserved in human cells. In this study, we performed transcriptomic analysis to identify differentially expressed genes that play a role in IKKβ-mediated suppression of E6-induced defects. Transcriptome analysis identified 215 genes whose expression was altered due to reduced levels of IKKβ. Of these 215 genes, 151 genes showed annotations. These analyses were followed by functional genetic interaction screen using RNAi, overexpression, and mutant fly strains for identified genes. The screen identified several genes including genes involved in Hippo and Toll pathways as well as junctional complexes whose downregulation or upregulation resulted in alterations of E6-induced defects. Subsequently, RT-PCR analysis was performed for validation of altered gene expression level for a few representative genes. Our results indicate an involvement for Hippo and Toll pathways in IKKβ-mediated suppression of E6 + hUBE3A-induced cellular abnormalities. Therefore, this study enhances our understanding of the mechanisms underlying HPV-induced cancer and can potentially lead to identification of novel drug targets for cancers associated with HPV.
ABSTRACT Characiformes is an order of freshwater fishes that includes many commercially important and emblematic species from South America and Africa, such as the popular piranhas, hatchetfishes, ...African tiger fishes and tetras. The order is split into two suborders with a total of 24 families, 282 genera and ca. 2,100 species. Here, we present an expanded phylogeny of characiform fishes, including data for 520 species and three genes (12S, 16S and RAG1), and the recently described family Tarumaniidae, which has not been examined by previous molecular analysis. Although our genetic coverage is limited to three gene fragments, the tree inferred based on maximum likelihood and Bayesian inference supports the monophyly of all characiform families and is largely congruent with results from recent studies that sampled less taxa but more genes. Also in agreement with a morphological hypothesis, our results strongly support the sister-group relationships between the family Tarumaniidae and Erythrinidae. Based on our results and that of the other molecular analyses, we propose a revised circumscription of the superfamily Erythrinoidea to include the families Tarumaniidae and Erythrinidae only.
RESUMEN Characiformes es un orden de peces de agua dulce que incluye un gran numero de especies emblemáticas y de importancia comercial en Sur América y África como lo son las populares pirañas, los peces voladores, los peces tigre de África y los tetras. El orden se divide en dos subórdenes con un total de 24 familias, 282 géneros y cerca de 2100 especies. Aquí, presentamos una filogenia expandida de Characiformes, que incluye datos de 520 especies, tres genes (12S, 16S y RAG1) y la recientemente descrita familia Tarumaniidae, la cual no ha sido examinada en previos análisis moleculares. Aunque nuestra cobertura genética esta limitada a tres genes, el árbol inferido basado en máxima verosimilitud e inferencia bayesiana apoya la monófila de todas las familias de Characiformes y es en gran medida congruente con los resultados de estudios recientes que examinaron menos especies pero más genes. También de acuerdo con una hipótesis morfológica, nuestros resultados apoyan firmemente las relaciones de grupos hermanos entre las familias Tarumaniidae y Erythrinidae. Con base en nuestros resultados y el de otros estudios moleculares, proponemos una circunscripción revisada de la superfamilia Erythrinoidea que incluye solo a las familias Tarumaniidae y Erythrinidae.
Molecular studies have shown that Neotropical fishes of the order Characiformes have undergone two independent events of cave colonization. Among these fishes are the Mexican blind cavefish (
...Astyanax mexicanus
), a well-studied model system for cave adaptation, and the lesser-known Brazilian blind characid (
Stygichthys typhlops
). Although various genomic and transcriptomic approaches have been used to identify genes responsible for cave adaptation in
A. mexicanus
, these genetic factors have not been explored in an evolutionary comparative framework in cave-adapted characiforms. To address this gap, we assembled a
de novo
transcriptome for the Brazilian blind characid, identifying 27,845 assembled unigenes, of which 22,580 were assigned as putative one-to-one orthologs to the Mexican cavefish. We then used the package RELAX to analyze 789 genes in cavefishes, identifying 311 genes under intensified or relaxed selection. Our analysis revealed 26 genes with signatures of convergent, relaxed selection linked to vision, circadian cycles, pigmentation, and hematopoiesis processes. Additionally, we conducted differential gene expression analyzes between the snout region and a control tissue sample (muscle), identifying 96 differentially expressed genes associated with cell-surface-bound and calcium-binding proteins. Our study offers insights into the genetic mechanisms underlying cave adaptation in characiform fishes, particularly the Brazilian blind characid. Moreover, our transcriptome dataset and list of genes under convergent, relaxed, and intensified selection serve as a valuable resource for future functional studies of genes involved in cave adaptation. Our work highlights the importance of examining genetic adaptations in multiple independent lineages to better understand the evolutionary processes underlying cave adaptation.
We conducted a revision of the Neotropical genus
Acrobrycon
. A previous study synonymized the species,
A. ipanquianus
, distributed from the western portion of the Amazon River to the north-western ...region of the La Plata River Basin, and
A. tarijae
, with type locality in the Lipeo River in Bolivia. We revisited this result by collecting new morphometric, meristic, and genetic data (
COI
mitochondrial gene) for 24 individuals distributed along La Plata River Basin in Argentina, and discussed our results in the context of multiple biogeographic processes of isolation in that basin. Our results revealed a more complex history of diversification and geographic distribution across
Acrobrycon
species than previously suspected, probably associated with multiple biogeographic processes of isolation in La Plata River Basin. We present new evidence that led us to reconsider the validity of
A. tarijae
, which is distinguishable from
A. ipanquianus
by the number of vertebrae (37–39 vs. 41–42) and pleural ribs (12–13 vs. 14). These results were also supported by our molecular analyses that revealed a genetic divergence >4% between
A. ipanquianus
and
A. tarijae
. We also identified two main genetic clusters within
A. tarijae
: the first cluster consisted of specimens from the Bermejo, Pilcomayo, Itiyuro and Juramento river basins (northern Argentina); and the second cluster included specimens from the southernmost basins, such as the Salí River in Tucumán, Cuarto River in the province of Cordoba and the Quinto River in the province of San Luis. Our results suggest that the genetic structure observed in
A. tarijae
is the result of the type of drainage (endorheic vs. exorheic) and geographical distance.
Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the ...Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene–Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.
Five new fish species of the genus Hemibrycon are described from the Río Magdalena basin, Colombia, using morphometric, meristic and osteological characters. Hemibrycon paez (n=40) differs in number ...of lateral line scales (39 to 42 vs. 43 to 54), by the number of scales between lateral line and anal-fin origin (6 to 7 vs. 4 to 5) and between lateral line and dorsal-fin origin (6 to 7 vs. 8); H. quindos (n=66) distinguished from its congeners by one autopomorphy: Males with cartilaginous protuberance, rounded on the anal fin ray branched, along all rays (vs. cartilaginous protuberance not present on anal-fin rays in males), by the maxilla without a fold on its anterior end (vs. maxilla with folding only at posterior end), by the number of pored scales in the lateral line (35 to 40 vs. 40 to 46); H. raqueliae (n=117) distinguished by a widened first tooth on the maxilla with the remaining teeth decreasing sharply in size (vs. first tooth of maxilla slender, remaining teeth gradually diminishing), by the first maxilla tooth pentacuspid and wider than the others (vs. first tooth on maxilla unicuspid or tricuspid and of same size as the others); H. virolinica (n=34) distinguished by the posterior end of the extrascapular spine surpassing the postemporal (vs. posterior end of extrascapular not exceeding postemporal spine), by having the posterior end of the first proximal pteryigiophores of dorsal fin of the same size as the anterior edge (vs. the posterior end of the first proximal pteryigiophores of dorsal fin more elongated than the anterior edge); and H. yacopiae (n=78) is distinguished by the following autopomorphic characters: first laterosensorial infraorbitals canal in contact with the posterior end of antorbital (vs. laterosensorial canal not reaching posterior end of antorbital), by the tip of the supraoccipital spine widened (vs. supraoccipital spine acute), by the posterior end of ectopterygoids failing to come in contact with the quadrate bone (vs. in contact); by the posterior edge of palatine more widened than the anterior edge of ectopterygoids (vs. posterior edge of the palatine approximately the same size, except for H. paez).
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent ...results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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