Browsing by Author "Halanych, Kenneth M."
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Item Ctenophore relationships and their placement as the sister group to all other animals(Nature Portfolio, 2017) Whelan, Nathan V.; Kocot, Kevin M.; Moroz, Tatiana P.; Mukherjee, Krishanu; Williams, Peter; Paulay, Gustav; Moroz, Leonid L.; Halanych, Kenneth M.; Auburn University; United States Department of the Interior; US Fish & Wildlife Service; University of Alabama Tuscaloosa; University of FloridaCtenophora, comprising approximately 200 described species, is an important lineage for understanding metazoan evolution and is of great ecological and economic importance. Ctenophore diversity includes species with unique colloblasts used for prey capture, smooth and striated muscles, benthic and pelagic lifestyles, and locomotion with ciliated paddles or muscular propulsion. However, the ancestral states of traits are debated and relationships among many lineages are unresolved. Here, using 27 newly sequenced ctenophore transcriptomes, publicly available data and methods to control systematic error, we establish the placement of Ctenophora as the sister group to all other animals and refine the phylogenetic relationships within ctenophores. Molecular clock analyses suggest modern ctenophore diversity originated approximately 350 million years ago +/- 88 million years, conflicting with previous hypotheses, which suggest it originated approximately 65 million years ago. We recover Eupiokamis duniapae-a species with striated muscles-as the sister lineage to other sampled ctenophores. Ancestral state reconstruction shows that the most recent common ancestor of extant ctenophores was pelagic, possessed tentacles, was bio-luminescent and did not have separate sexes. Our results imply at least two transitions from a pelagic to benthic lifestyle within Ctenophora, suggesting that such transitions were more common in animal diversification than previously thought.Item Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida plus Orthonectida, Lophotrochozoa)(Royal Society of London, 2022) Drabkova, Marie; Kocot, Kevin M.; Halanych, Kenneth M.; Oakley, Todd H.; Moroz, Leonid L.; Cannon, Johanna T.; Kuris, Armand; Garcia-Vedrenne, Ana Elisa; Pankey, M. Sabrina; Ellis, Emily A.; Varney, Rebecca; Stefka, Jan; Zrzavy, Jan; University of South Bohemia Ceske Budejovice; Czech Academy of Sciences; Biology Centre of the Czech Academy of Sciences; University of Alabama Tuscaloosa; University of North Carolina; University of North Carolina Wilmington; University of California Santa Barbara; University of Florida; University of New HampshireDicyemids and orthonectids were traditionally classified in a group called Mesozoa, but their placement in a single clade has been contested and their position(s) within Metazoa is uncertain. Here, we assembled a comprehensive matrix of Lophotrochozoa (Metazoa) and investigated the position of Dicyemida (= Rhombozoa) and Orthonectida, employing multiple phylogenomic approaches. We sequenced seven new transcriptomes and one draft genome from dicyemids (Dicyema, Dicyemennea) and two transcriptomes from orthonectids (Rhopalura). Using these and published data, we assembled and analysed contamination-filtered datasets with up to 987 genes. Our results recover Mesozoa monophyletic and as a close relative of Platyhelminthes or Gnathifera. Because of the tendency of the long-branch mesozoans to group with other long-branch taxa in our analyses, we explored the impact of approaches purported to help alleviate long-branch attraction (e.g. taxon removal, coalescent inference, gene targeting). None of these were able to break the association of Orthonectida with Dicyemida in the maximum-likelihood trees. Contrastingly, the Bayesian analysis and site-specific frequency model in maximum-likelihood did not recover a monophyletic Mesozoa (but only when using a specific 50 gene matrix). The classic hypothesis on monophyletic Mesozoa is possibly reborn and should be further tested.Item Miscues misplace sponges(National Academy of the Sciences, 2016) Halanych, Kenneth M.; Whelan, Nathan V.; Kocot, Kevin M.; Kohn, Andrea B.; Moroz, Leonid L.; Auburn University; University of Alabama Tuscaloosa; University of FloridaItem Mitogenomics Reveals a Novel Genetic Code in Hemichordata(Oxford University Press, 2019) Li, Yuanning; Kocot, Kevin M.; Tassia, Michael G.; Cannon, Johanna T.; Bernt, Matthias; Halanych, Kenneth M.; Auburn University; University of Alabama Tuscaloosa; University of California Santa Barbara; Helmholtz Association; Helmholtz Center for Environmental Research (UFZ)The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this Clade.Item Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution(Royal Society of London, 2017) Tanner, Alastair R.; Fuchs, Dirk; Winkelmann, Inger E.; Gilbert, M. Thomas P.; Pankey, M. Sabrina; Ribeiro, Angela M.; Kocot, Kevin M.; Halanych, Kenneth M.; Oakley, Todd H.; da Fonseca, Rute R.; Pisani, Davide; Vinther, Jakob; University of Bristol; Hokkaido University; Curtin University; Norwegian University of Science & Technology (NTNU); University of New Hampshire; University of Copenhagen; University of Alabama Tuscaloosa; Auburn University; University of California Santa BarbaraColeoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 +/- 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.Item New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships(Nature Portfolio, 2020) Kocot, Kevin M.; Poustka, Albert J.; Stoeger, Isabella; Halanych, Kenneth M.; Schroedl, Michael; University of Alabama Tuscaloosa; Max Planck Society; University of Munich; Auburn UniversityRelationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (Tryblidia) to have several plesiomorphic molluscan traits. The phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of Conchifera whereas earlier molecular studies supported a clade of Monoplacophora +Polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora +Cephalopoda. Phylogenomic studies have also strongly supported a clade including Gastropoda, Bivalvia, and Scaphopoda, but relationships among these taxa have been inconsistent. In order to resolve conchiferan relationships and improve understanding of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phylogenomic analyses with broad taxon sampling including newly sequenced genomic data from the monoplacophoran Laevipilina antarctica. Whereas a partitioned maximum likelihood (ML) analysis using site-homogeneous models recovered Monoplacophora sister to Cephalopoda with moderate support, both ML and Bayesian inference (BI) analyses using mixture models recovered Monoplacophora sister to all other conchiferans with strong support. A supertree approach also recovered Monoplacophora as the sister taxon of a clade composed of the rest of Conchifera. Gastropoda was recovered as the sister taxon of Scaphopoda in most analyses, which was strongly supported when mixture models were used. A molecular clock based on our BI topology dates diversification of Mollusca to similar to 546 MYA (+/- 6 MYA) and Conchifera to similar to 540 MYA (+/- 9 MYA), generally consistent with previous work employing nuclear housekeeping genes. These results provide important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral character states of major mollusc clades.Item Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot(Royal Society of London, 2019) Kocot, Kevin M.; Todt, Christiane; Mikkelsen, Nina T.; Halanych, Kenneth M.; University of Alabama Tuscaloosa; University of Bergen; Auburn UniversityRecent molecular phylogenetic investigations strongly supported the placement of the shell-less, worm-shaped aplacophoran molluscs (Solenogastres and Caudofoveata) and chitons (Polyplacophora) in a Glade called Aculifera, which is the sister taxon of all other molluscs. Thus, understanding the evolutionary history of aculiferan molluscs is important for understanding early molluscan evolution. In particular, fundamental questions about evolutionary relationships within Aplacophora have long been unanswered. Here, we supplemented the paucity of available data with transcriptomes from 25 aculiferans and conducted phylogenomic analyses on datasets with up to 525 genes and 75 914 amino acid positions. Our results indicate that aplacophoran taxonomy requires revision as several traditionally recognized groups are non-monophyletic. Most notably, Cavibelonia, the solenogaster taxon defined by hollow sclerites, is polyphyletic, suggesting parallel evolution of hollow sclerites in multiple lineages. Moreover, we describe Apodomenia enigmatica sp. nov., a bizarre new species that appears to be a morphological intermediate between Solenogastres and Caudofoveata. This animal is not a missing link, however; molecular and morphological studies show that it is a derived solenogaster that lacks a foot, mantle cavity and radula. Taken together, these results shed light on the evolutionary history of Aplacophora and reveal a surprising degree of morphological plasticity within the group.