DSpace Repository :: Browsing by Author "Kocot, Kevin M."

Browsing by Author "Kocot, Kevin M."

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Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics
(BMC, 2021) Varney, Rebecca M.; Brenzinger, Bastian; Malaquias, Manuel Antonio E.; Meyer, Christopher P.; Schroedl, Michael; Kocot, Kevin M.; University of Alabama Tuscaloosa; University of Bergen; Smithsonian Institution; Smithsonian National Museum of Natural History; University of Munich
BackgroundHeterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the "lower heterobranchs". Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.ResultsTo assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of "lower heterobranchs". Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT+GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.ConclusionsAnalysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT+GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.
Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes
(Royal Society of London, 2021) Sun, Jin; Li, Runsheng; Chen, Chong; Sigwart, Julia D.; Kocot, Kevin M.; Ocean University of China; City University of Hong Kong; Japan Agency for Marine-Earth Science & Technology (JAMSTEC); Senckenberg Gesellschaft fur Naturforschung (SGN); Queens University Belfast; University of Alabama Tuscaloosa
Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Complete mitochondrial genomes of two scaphopod molluscs
(Taylor & Francis, 2019) Kocot, Kevin M.; Wollesen, Tim; Varney, Rebecca M.; Schwartz, Megan L.; Steiner, Gerhard; Wanninger, Andreas; University of Alabama Tuscaloosa; European Molecular Biology Laboratory (EMBL); University of Washington; University of Washington Tacoma; University of Vienna
Complete mitochondrial genomes were determined for two scaphopod molluscs: the dentaliid Antalis entalis and an unidentified Antarctic gadilid. Both genomes are complete except, in Gadilida sp. indet., a short stretch of nad5 was undetermined and trnR could not be annotated. Organization of the Gadilida sp. genome is nearly identical to that previously reported for the gadilid Siphonodentalium whereas trnK, nad5, trnD, nad4, and nad4l are transposed to the opposite strand in the previously published Graptacme genome relative to that of Antalis. Phylogenetic analysis of the 13 protein-coding and 2 rRNA genes recovered Scaphopoda, Gadilida, and Dentaliida monophyletic with maximal support.
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 Florida
Ctenophora, 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.
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 Hampshire
Dicyemids 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.
The embryology, metamorphosis, and muscle development of Schizocardium karankawa sp. nov. (Enteropneusta) from the Gulf of Mexico
(BMC, 2023) Jabr, Noura; Gonzalez, Paul; Kocot, Kevin M.; Cameron, Christopher B.; Universite de Montreal; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI); University of Alabama Tuscaloosa
Schizocardium karankawa sp. nov. has been collected from subtidal muds of the Laguna Madre, Texas, and the Mississippi coast, Gulf of Mexico. The Texas population is reproductive from early February to mid-April. Gametes are liberated by a small incision in a gonad. Oocyte germinal vesicle breakdown is increased in the presence of sperm, and the highest fertilization success was in the artificial seawater Jamarin U. Manually dechorionated embryos develop normally. Development was asynchronous via a tornaria larva, metamorphosis and maintained to the juvenile worm 6 gill-pore stage. Phalloidin-labeled late-stage tornaria revealed retractor muscles that connect the pericardial sac with the apical tuft anteriorly, the oesophagus ventrally, and muscle cells of the early mesocoels. The muscle development of early juvenile worms began with dorso-lateral trunk muscles, lateral trunk bands, and sphincters around the gill pores and anus. Adult worms are characterized by a stomochord that bifurcates anteriorly into paired vermiform processes, gill bars that extend almost the entire dorsal to ventral branchial region resulting in a narrow ventral hypobranchial ridge, and an elaborate epibranchial organ with six zones of discrete cell types. The trunk has up to three rows of liver sacs, and lateral gonads. The acorn worm evo-devo model species Saccoglossus kowalevskii, Ptychodera flava, and Schizocardium californicum are phylogenetically distant with disparate life histories. S. karnakawa from S. californicum are phylogenetically close, and differences between them that become apparent as adult worms include the number of gill pores and hepatic sacs, and elaborations of the heart-kidney-stomochord complex. An important challenge for evolutionary developmental biology is to form links from phylogenetically distant and large-scale differences to phylogenetically close and small-scale differences. This description of the embryology, development, and adult morphology of S. karankawa permits investigations into how acorn worm development evolves at fine scales.
Genomics of Diploidization in Palms and Grasses
(University of Alabama Libraries, 2024) Deb, Sontosh Kumar; McKain, Michael R.
Polyploidy refers to a state in which organisms have more than two complete sets of chromosomes. Following polyploidy, short and long-term cytological and genomic changes lead polyploids to restore a diploid-like state--the process known as diploidization. The diploidization rate and mechanisms show lineage-specific differences, and there is insufficient evidence to define a clear paradigm of how different polyploid species respond to post-polyploidy changes. Here, I investigated the consequences of whole genome duplication (WGD) following an ancient event in palms and another recent event in grass species Zea mays. I generated a chromosome-level genome assembly of a mangrove palm species Nypa fruticans, characterized its variation in the structural features compared to other palm genomes, and investigated the retention of duplicated genes. I found that the N. fruticans genome differs in chromosomal rearrangements and in accumulation of transposable elements with other palm species following WGD. I also identified high retention of duplicated genes in N. fruticans. Functional enrichment analysis showed that the dosage balance hypothesis and selective pressures of adapting to a harsh intertidal environment could primarily explain the retention of the duplicated genes. Further exploration of salt-tolerant orthologous genes also supports the hypothesis. To study maize, I generated a chromosome-level monoploid genome assembly of a parental relative Vossia cuspidata and used phylogenomic approaches to detect signals of homoeologous exchange, exploring its impact on the evolutionary history of maize subgenomes following WGD. The study found that V. cuspidata is closely related to one of the maize diploid progenitors, with homoeologous exchanges potentially obscuring the ancestry of maize subgenomes. Further, through transcriptomic profiling of maize and its wild relatives, I investigated the functional differences in the flooding tolerance of these species. I identified evolutionarily conserved and species-specific genes in response to flooding stress. The findings suggest that extensive rewiring of the gene regulatory circuitry and the outcome of phenotypic plasticity resulting from the interaction with their environment might underlie the variation in flooding response in maize and its relatives. Altogether, my dissertation provides important insights into the dynamics and complexity of diploidization and suggests that understanding the lineage-specific differences requires further investigations.
Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny
(BMC, 2019) Smythe, Ashleigh B.; Holovachov, Oleksandr; Kocot, Kevin M.; Swedish Museum of Natural History; University of Alabama Tuscaloosa
BackgroundNematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum.ResultsWe supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with ahigh proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA.ConclusionsExpanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment.
The Iron-Responsive Genome of the Chiton Acanthopleura granulata
(Oxford University Press, 2021) Varney, Rebecca M.; Speiser, Daniel, I; McDougall, Carmel; Degnan, Bernard M.; Kocot, Kevin M.; University of Alabama Tuscaloosa; University of South Carolina Columbia; Griffith University; University of Queensland
Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.
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 Florida
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.
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 Barbara
Coleoid 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.
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 University
Relationships 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.
Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing
(Royal Society of London, 2022) Krug, Patrick J.; Caplins, Serena A.; Algoso, Krisha; Thomas, Kanique; Valdes, Angel A.; Wade, Rachael; Wong, Nur Leena W. S.; Eernisse, Douglas J.; Kocot, Kevin M.; California State University Los Angeles; University of California Davis; California State Polytechnic University Pomona; University of British Columbia; Universiti Putra Malaysia; California State University Fullerton; University of Alabama Tuscaloosa
Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20 000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs, and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modelling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.
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 University
Recent 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.
Phylogenomics reveals deep relationships and diversification within phylactolaemate bryozoans
(Royal Society of London, 2022) Saadi, Ahmed J.; Bibermair, Julian; Kocot, Kevin M.; Roberts, Nickellaus G.; Hirose, Masato; Calcino, Andrew; Baranyi, Christian; Chaichana, Ratcha; Wood, Timothy S.; Schwaha, Thomas; University of Vienna; University of Alabama Tuscaloosa; Kitasato University; Kasetsart University; Wright State University Dayton
Bryozoans are mostly sessile colonial invertebrates that inhabit all kinds of aquatic ecosystems. Extant bryozoan species fall into two clades with one of them, Phylactolaemata, being the only exclusively freshwater clade. Phylogenetic relationships within the class Phylactolaemata have long been controversial owing to their limited distinguishable characteristics that reflect evolutionary relationships. Here, we present the first phylogenomic analysis of Phylactolaemata using transcriptomic data combined with dense taxon sampling of six families to better resolve the interrelationships and to estimate divergence time. Using maximum-likelihood and Bayesian inference approaches, we recovered a robust phylogeny for Phylactolaemata in which the interfamilial relationships are fully resolved. We show Stephanellidae is the sister taxon of all other phylactolaemates and confirm that Lophopodidae represents the second offshoot within the phylactolaemate tree. Plumatella fruticosa clearly falls outside Plumatellidae as previous investigations have suggested, and instead clusters with Pectinatellidae and Cristatellidae as the sister taxon of Fredericellidae. Our results demonstrate that cryptic speciation is very likely in F. sultana and in two species of Plumatella (P. repens and P. casmiana). Divergence time estimates show that Phylactolaemata appeared at the end of the Ediacaran and started to diverge in the Silurian, although confidence intervals were large for most nodes. The radiation of most extant phylactolaemate families occurred mainly in the Palaeogene and Neogene highlighting post-extinction diversification.
Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization
(BMC, 2016) Kocot, Kevin M.; Aguilera, Felipe; McDougall, Carmel; Jackson, Daniel J.; Degnan, Bernard M.; University of Queensland; University of Alabama Tuscaloosa; University of Bergen; University of Gottingen
An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.
Spider phylogenomics: untangling the Spider Tree of Life
(PeerJ, 2016) Garrison, Nicole L.; Rodriguez, Juanita; Agnarsson, Ingi; Coddington, Jonathan A.; Griswold, Charles E.; Hamilton, Christopher A.; Hedin, Marshal; Kocot, Kevin M.; Ledford, Joel M.; Bond, Jason E.; Auburn University System; Auburn University; University of Vermont; Smithsonian Institution; Smithsonian National Museum of Natural History; California Academy of Sciences; California State University System; San Diego State University; University of Alabama Tuscaloosa; University of California System; University of California Davis
Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the "usual suspect" genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.
Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach
(Nature Portfolio, 2018) Rodriguez, Juanita; Jones, Tappey H.; Sierwald, Petra; Marek, Paul E.; Shear, William A.; Brewer, Michael S.; Kocot, Kevin M.; Bond, Jason E.; Auburn University; Commonwealth Scientific & Industrial Research Organisation (CSIRO); Field Museum of Natural History (Chicago); Virginia Polytechnic Institute & State University; University of North Carolina; East Carolina University; University of Alabama Tuscaloosa
With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth's biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing through intermediate "stepping stone" states. Here we present the first phylogenetic-based study of the evolution of complex chemical defenses in millipedes by generating the largest genomic-based phylogenetic dataset ever assembled for the group. Our phylogenomic results demonstrate that chemical complexity shows a clear pattern of escalation through time. New pathways are added in a stepwise pattern, leading to greater chemical complexity, independently in a number of derived lineages. This complexity gradually increased through time, leading to the advent of three distantly related chemically complex evolutionary lineages, each uniquely characteristic of each of the respective millipede groups.
The time is right for an Antarctic biorepository network
(National Academy of the Sciences, 2022) O'Brien, Kristin M.; Crockett, Elizabeth L.; Adams, Byron J.; Amsler, Charles D.; Appiah-Madson, Hannah J.; Collins, Allen; Desvignes, Thomas; Detrich, H. William; Distel, Daniel L.; Eppley, Sarah M.; Frable, Benjamin W.; Franz, Nico M.; Grim, Jeffrey M.; Kocot, Kevin M.; Mahon, Andrew R.; Mayfield-Meyer, Teresa J.; Mikucki, Jill A.; Moser, William E.; Schmull, Michaela; Seid, Charlotte A.; Smith, Craig R.; Todgham, Anne E.; Watkins-Colwell, Gregory J.; University of Alaska Fairbanks; Ohio University; Brigham Young University; University of Alabama Birmingham; Northeastern University; Smithsonian Institution; Smithsonian National Museum of Natural History; University of Oregon; Portland State University; University of California San Diego; Scripps Institution of Oceanography; Arizona State University; Arizona State University-Tempe; University of Tampa; University of Alabama Tuscaloosa; Central Michigan University; University of New Mexico; University of Tennessee Knoxville; Harvard University; University of Hawaii Manoa; University of California Davis; Yale University

Browsing by Author "Kocot, Kevin M."

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