Phylogenetic classification of bony fishes

BMC Evolutionary Biology, Journal Year: 2017, Volume and Issue: 17(1)

Published: July 6, 2017

Fish classifications, as those of most other taxonomic groups, are being transformed drastically new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review the main criteria used ichthyologists to define their classifications during last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, trend has been rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with arbitrary groupings. Two leading sources ichthyology frequently fish (JS Nelson's volumes Fishes World W. Eschmeyer's Catalog Fishes) fail adopt a global framework despite much recent made resolution Tree Life. The first classification bony fishes was published 2013, based comprehensive phylogeny ( www.deepfin.org ). We here update version incorporating results. updated presented is inferred genomic data nearly 2000 fishes. total 72 orders (and 79 suborders) recognized this version, compared 66 1. resolves placement 410 families, or ~80% 514 families currently recognized. ordinal status 30 percomorph included study, remains uncertain (incertae sedis series Carangaria, Ovalentaria, Eupercaria). Comments decisions comparisons conflicting proposed others presented. also highlight cases morphological exist classified. This substantially improved, providing more than versions, densely sampled trees. study represents, unlike any other, up-to-date hypothesis Life

Language: Английский

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Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Aug. 2, 2018

Abstract Lake Tanganyika is the oldest and phenotypically most diverse of three East African cichlid fish adaptive radiations. It also cradle for younger parallel haplochromine radiations in Lakes Malawi Victoria. Despite its evolutionary significance, relationships among main lineages remained unresolved, as did general timescale evolution. Here, we disentangle deep phylogenetic structure radiation using anchored phylogenomics uncover hybridization at base, well early radiation. This suggests that might have facilitated these speciation bursts. Time-calibrated trees support cichlids coincided with lake formation Gondwanan vicariance concurred earliest splits family tree. Genes linked to key innovations show signals introgression or positive selection following colonization habitats species’ dietary adaptations are revealed major drivers colour vision These findings shed light onto processes shaping evolution

Language: Английский

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The joint evolution of the Myxozoa and their alternate hosts: A cnidarian recipe for success and vast biodiversity

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(7), P. 1651 - 1666

Published: March 25, 2018

The relationships between parasites and their hosts are intimate, dynamic complex; the evolution of one is inevitably linked to other. Despite multiple origins parasitism in Cnidaria, only belonging Myxozoa characterized by a complex life cycle, alternating fish invertebrate hosts, as well high species diversity. This inspired us examine history adaptive radiations myxozoans determining degree congruence phylogenies timing emergence myxozoan lineages relation hosts. Recent genomic analyses suggested common origin Polypodium hydriforme, cnidarian parasite acipenseriform fishes, Myxozoa, proposed original for both sister lineages. We demonstrate that emerged long before populated Earth phylogenetic with evident down most basal branches tree, indicating bryozoans annelids challenging previous evolutionary hypotheses. provide evidence that, following invasion, were acquired times, leading parallel cospeciation patterns all major identify acquisition vertebrate facilitate alternative transmission dispersion strategies reason distinct success massive host specification-linked diversification events. results this study transform our understanding metazoan known.

Language: Английский

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Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei)

Molecular Phylogenetics and Evolution, Journal Year: 2018, Volume and Issue: 127, P. 781 - 799

Published: June 18, 2018

Language: Английский

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Romanogobio skywalkeri, a new gudgeon (Teleostei: Gobionidae) from the upper Mur River, Austria

Zootaxa, Journal Year: 2018, Volume and Issue: 4403(2)

Published: April 4, 2018

Romanogobio skywalkeri, new species, is described from the upper Mur River in Austrian Danube drainage. It related to R. banarescui Mediterranean basin. skywalkeri distinguished by lacking epithelial crests on predorsal back, having 12–14 total pectoral-fin rays (vs. 10–11) and usually 8½ branched dorsal-fin 7½). other species drainage a very slender body; moderately long barbel, extending slightly beyond posterior eye margin; no back. minimum net divergence of 6.3% (uncorrected p-distance against banarescui) COI barcoding region European species. A key provided. Vardar carpathorossicus are treated as valid

Language: Английский

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Generic assignment of Leuciscus kurui Bogutskaya from the upper Tigris drainage, and a replacement name for Alburnus kurui Mangit & Yerli (Teleostei: Leuciscidae)

Zootaxa, Journal Year: 2018, Volume and Issue: 4410(1)

Published: April 16, 2018

The generic position of Leuciscus kurui Bogutskaya, 1995 is reviewed through a comparison morphological and molecular characters (COI). data place L. in Alburnus, close to Alburnus timarensis from the Lake Van basin. (Bogutskaya) distinguished this species by lacking ventral keel possessing both very low number gill rakers midlateral scales. selcuklui, upper Tigris drainage, cannot be widespread A. sellal therefore treated as synonym species. Mangit & Yerli, 2018 junior secondary homonym (Bogutskaya, 1995) carianorum proposed its replacement name. Several specimens caeruleus heckeli shared same haplotypes some these always mitochondrial characters. are valid Other individuals have different sellal, well having more rakers. basin separate freshwater ecoregion treatment several synonymy mento discussed.

Language: Английский

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Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

Systematic Biology, Journal Year: 2017, Volume and Issue: 66(6), P. 881 - 895

Published: Feb. 25, 2017

Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes sandfishes), Cypriniformes (carps minnows), Characiformes (tetras their allies), Siluriformes (catfishes), Gymnotiformes (electric knifefishes). Unambiguous resolution the relationships among these lineages remains elusive, with previous molecular morphological analyses failing to produce consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan compile one most data-rich phylogenies date. We data infer higher level (interordinal) fishes, focusing on monophyly Characiformes-one contentiously debated fish systematics. As studies, recover non-monophyletic two monophyletic suborders, Citharinoidei Characoidei, closely related other clades each other. also explore incongruence between results from different UCE sets, issues orthology, characters combination our data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation UCEs.].

Language: Английский

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Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2016, Volume and Issue: unknown

Published: Nov. 8, 2016

ABSTRACT An important goal of the angiosperm systematics community has been to develop a shared approach molecular data collection, such that phylogenomic sets from different focal clades can be combined for meta-studies across entire group. Although significant progress made through efforts as DNA barcoding, transcriptome sequencing, and whole-plastid current lacks cost efficient methodology collecting nuclear all angiosperms. Here, we leverage genomic resources 43 species enrichment probes useful ~500 loci non-model taxa diversity By taking an anchored phylogenomics approach, in which are designed represent sequence group, able efficiently target with sufficient phylogenetic signal resolve deep, intermediate, shallow relationships. After demonstrating utility this resource, present method generates heat map each node on phylogeny reveals sensitivity support analysis conditions, well locus, site, taxon schemes. Focusing effect locus site sampling, use statistically evaluate relative alternative relationships among eudicots, monocots, magnoliids. results supermatrix coalescent analyses largely consistent tree, find deep relationship more sensitive particular choice sites when employed. Averaged approaches subsampling schemes, our eudicot-monocot sister relationship, is supported by number recent studies.

Language: Английский

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Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera)

Systematic Entomology, Journal Year: 2018, Volume and Issue: 43(4), P. 762 - 776

Published: April 20, 2018

Abstract Understanding evolutionary relationships in the superfamily Psylloidea is challenging due to lack of clear morphological synapomorphies for many groups. Some families and genera, including two largest, Cacopsylla Ossiannilsson Trioza Foerster, have long been acknowledged as nonmonophyletic circumscription natural groups has remained fluid. We present best phylogenetic hypothesis date provide a working systematic framework better reflect relationships. A shotgun sequencing approach using mixed pool DNAs more than 400 species resulted recovery from de novo assemblies near‐complete mitogenomes (≥10 kb) 359 species, partial genomes (5–10 an additional 40 species. The resulting phylogeny improves clarifies family classification resolves some longstanding uncertainties within between genera. whole‐nuclear‐genome scan (yielding data estimated 373 nuclear genes) anchored hybrid enrichment method representative subset taxa confirms placement major groupings overall tree topology recovered with mitochondrial data. generated represent increase molecular resources this superfamily. In addition, we highlight areas remaining uncertainty that require further sampling and/or sources provides new insights both applied research, backbone constraint allows particular interest or concern (e.g. pest taxa) only small fragments sequence available DNA barcodes).

Language: Английский

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Unioverse: A phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida)

Molecular Phylogenetics and Evolution, Journal Year: 2019, Volume and Issue: 137, P. 114 - 126

Published: Feb. 22, 2019

Language: Английский

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