Annual Review of Ecology, Evolution, and Systematics, Nov 2, 2021
The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century mar... more The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.
Results of a phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 base pai... more Results of a phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 base pairs) for all species of Catonotus are presented along with a synthesis and phylogenetic analysis of published morphological data. The two datasets are combined in a total evidence analysis, and results from the molecular, morphological, and total evidence datasets are compared with each other and with previously published hypotheses. Phylogenetic relationships suggested by morphological data are similar to those from ...
North America exhibits the most diverse freshwater fish fauna among temperate regions of the worl... more North America exhibits the most diverse freshwater fish fauna among temperate regions of the world. Species diversity is concentrated in the Central Highlands, drained by the Mississippi, Gulf Slope and Atlantic Slope river systems. Previous investigations of Central Highlands biogeography have led to conflicting hypotheses involving dispersal and vicariance to explain the diversity and distribution of the freshwater fish fauna. In this investigation predictions of the Central Highlands pre‐Pleistocene vicariance hypothesis are tested with a phylogeographic analysis of the percid species Percina evides, which is widely distributed in several disjunct areas of the Central Highlands. Phylogenetic analysis of complete gene sequences of mitochondrially encoded cytochrome b recover three phylogroups, with very low levels of sequence polymorphism within groups. The two western phylogroups are monophyletic with respect to the eastern phylogroup. The recovery of two monophyletic lineages with an eastern and western distribution in the disjunct highland areas is a pattern expected from vicariance, but is not predicted by the Central Highlands pre‐Pleistocene vicariance hypothesis. The recovery of very limited mitochondrial DNA polymorphism and lack of phylogeographic structuring across the entire range of the eastern clade, very shallow polymorphism between the disjunct Missouri River and upper Mississippi River populations, and lack of sequence polymorphism in the upper Mississippi River populations, support a hypothesis of dispersal during or following the Pleistocene. The present distribution of P. evides is best explained by both vicariant and dispersal events.
Application of genetic data to species delimitation often builds confidence in delimitations prev... more Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in the ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which the application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.[ddRADseq; multispecies coalescent; Notothenioidei; SNPs; Southern Ocean.]
Molecular Phylogenetics and Evolution, Dec 1, 1998
Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phy... more Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phylogenetic premises, the evolution of small benthic forms in Percidae has been interpreted as resulting from either convergence or common ancestry. In order to assess various phylogenetic hypotheses of Percidae we collected complete sequences (1140 bp) of mitochondrially encoded cytochrome b for 21 species of percids. Seven species representing four additional families of Perciformes were used as outgroups. Maximum parsimony and minimum evolution analyses both recovered single shortest trees, and the results of these analyses were generally congruent with one another. All analyses consistently recovered three monophyletic groups in Percidae: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Percinae (Perca and Gymnocephalus), and Luciopercinae (Stizostedion, Zingel, and Romanichthys). As a result of this analysis we present a revised classification of Percidae and discuss the phylogenetic evidence for the independent evolution of small benthic species within Etheostomatinae and Luciopercinae.
Understanding the history that underlies patterns of species richness across the Tree of Life req... more Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils."
Annual Review of Ecology, Evolution, and Systematics, Nov 2, 2021
The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century mar... more The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.
Results of a phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 base pai... more Results of a phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 base pairs) for all species of Catonotus are presented along with a synthesis and phylogenetic analysis of published morphological data. The two datasets are combined in a total evidence analysis, and results from the molecular, morphological, and total evidence datasets are compared with each other and with previously published hypotheses. Phylogenetic relationships suggested by morphological data are similar to those from ...
North America exhibits the most diverse freshwater fish fauna among temperate regions of the worl... more North America exhibits the most diverse freshwater fish fauna among temperate regions of the world. Species diversity is concentrated in the Central Highlands, drained by the Mississippi, Gulf Slope and Atlantic Slope river systems. Previous investigations of Central Highlands biogeography have led to conflicting hypotheses involving dispersal and vicariance to explain the diversity and distribution of the freshwater fish fauna. In this investigation predictions of the Central Highlands pre‐Pleistocene vicariance hypothesis are tested with a phylogeographic analysis of the percid species Percina evides, which is widely distributed in several disjunct areas of the Central Highlands. Phylogenetic analysis of complete gene sequences of mitochondrially encoded cytochrome b recover three phylogroups, with very low levels of sequence polymorphism within groups. The two western phylogroups are monophyletic with respect to the eastern phylogroup. The recovery of two monophyletic lineages with an eastern and western distribution in the disjunct highland areas is a pattern expected from vicariance, but is not predicted by the Central Highlands pre‐Pleistocene vicariance hypothesis. The recovery of very limited mitochondrial DNA polymorphism and lack of phylogeographic structuring across the entire range of the eastern clade, very shallow polymorphism between the disjunct Missouri River and upper Mississippi River populations, and lack of sequence polymorphism in the upper Mississippi River populations, support a hypothesis of dispersal during or following the Pleistocene. The present distribution of P. evides is best explained by both vicariant and dispersal events.
Application of genetic data to species delimitation often builds confidence in delimitations prev... more Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in the ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which the application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.[ddRADseq; multispecies coalescent; Notothenioidei; SNPs; Southern Ocean.]
Molecular Phylogenetics and Evolution, Dec 1, 1998
Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phy... more Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phylogenetic premises, the evolution of small benthic forms in Percidae has been interpreted as resulting from either convergence or common ancestry. In order to assess various phylogenetic hypotheses of Percidae we collected complete sequences (1140 bp) of mitochondrially encoded cytochrome b for 21 species of percids. Seven species representing four additional families of Perciformes were used as outgroups. Maximum parsimony and minimum evolution analyses both recovered single shortest trees, and the results of these analyses were generally congruent with one another. All analyses consistently recovered three monophyletic groups in Percidae: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Percinae (Perca and Gymnocephalus), and Luciopercinae (Stizostedion, Zingel, and Romanichthys). As a result of this analysis we present a revised classification of Percidae and discuss the phylogenetic evidence for the independent evolution of small benthic species within Etheostomatinae and Luciopercinae.
Understanding the history that underlies patterns of species richness across the Tree of Life req... more Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils."
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