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Creators/Authors contains: "Halanych, Kenneth M"

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  1. ; ; ; ( , Marine Biology)
    The Antarctic benthos is rich in biodiversity, with many species being endemic to the Southern Ocean. Multiple factors such as oceanic currents, glacial cycles and reproductive life stages have been attributed to the distribution of benthic dwelling invertebrates around the continent. The sea spider (Pycnogonida) Nymphon australe is a paternal brooder, which lacks a pelagic planktonic life stage. Typically brooding is assumed to suggest limited dispersal capabilities. Here we investigated the genetic structure of N. australe, a highly abundant pycnogonid species in the Southern Ocean to test assumptions of a documented circumpolar distribution. Previous studies with mitochondrial data have revealed that N. australe has high genetic diversity, limited gene flow, as well as distinct geographic structure. To resolve the phylogeographic structure of the circumpolar N. australe from the Antarctic continental shelf, we used 3RAD single nucleotide polymorphism (SNP) data from 111 individuals sampled from ten different, circumpolar geographic regions including the Western Antarctic Peninsula, Ross Sea, Weddell Sea, and Eastern Antarctica. Analyses revealed populations to have distinct regional populations with strong geographic structuring observed by locality and suggest the possibility that N. australe may be a species complex in the Southern Ocean. 
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    Free, publicly-accessible full text available September 1, 2025
  2. ; ; ; ; ; ( , F1000Research)
    Many molluscan genomes have been published to date, however only three are from representatives of the subphylum Aculifera (Polyplacophora, Caudofoveata, and Solenogastres), the sister taxon to all other molluscs. Currently, genomic resources are completely lacking for Solenogastres. This gap in knowledge hinders comparative and evolutionary studies. Here, we sequenced the genomes of the solenogaster aplacophoransEpimenia babaiSalvini-Plawen, 1997 andNeomenia megatrapezataSalvini-Plawen & Paar-Gausch, 2004 using a hybrid approach combining Oxford Nanopore and Illumina reads. ForE. babai, we produced a 628 Mbp haploid assembly (N50 = 413 Kbp, L50 = 370) that is rather complete with a BUSCO completeness score of 90.1% (82.0% single, 8.1% duplicated, 6.0% fragmented, and 3.9% missing). ForN. megatrapezata, we produced a 412 Mbp haploid assembly (N50 = 132 Kbp, L50 = 881) that is also rather complete with a BUSCO completeness score of 85.1% (81.7% single, 3.4% duplicated, 8.1% fragmented, and 6.8% missing). Our annotation pipeline predicted 25,393 gene models forE. babaiwith a BUSCO score of 92.4% (80.5% single, 11.9% duplicated, 4.9% fragmented, and 2.7% missing) and 22,463 gene models forN. megatrapezatawith a BUSCO score of 90.2% (81.0% single, 9.2% duplicated, 4.7% fragmented, and 5.1% missing). Phylogenomic analysis recovered Solenogastres as the sister taxon to Polyplacophora and Aculifera as the sister taxon to all other sampled molluscs with maximal support. These represent the first whole-genome resources for Solenogastres and will be valuable for future studies investigating this understudied group and molluscan evolution as a whole. 
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    Free, publicly-accessible full text available January 1, 2025
  3. ; ; ( , PLOS ONE)
    Shastry, Rajesh P. (Ed.)
    Symbiotic relationships are ubiquitous throughout the world’s oceans, yet for many marine organisms, including those in the high latitudes, little is understood about symbiotic associations and functional relationships. From a recently determined genome sequence of a filter-feeding basket star from Argentina, Gorgonocephalus chilensis , we discovered a novel Mycoplasma species with a 796Kb genome (CheckM completeness of 97.9%, G+C content = 30.1%). Similar to other Mycoplasma spp. within Mycoplasmatota, genomic analysis of the novel organism revealed reduced metabolic pathways including incomplete biosynthetic pathways, suggesting an obligate association with their basket star host. Results of 16S rRNA and multi-locus phylogenetic analyses revealed that this organism belonged to a recently characterized non-free-living lineage of Mycoplasma spp. specifically associated with marine invertebrate animals. Thus, the name “ Candidatus Mycoplasma mahonii” is proposed for this novel species. Based on 16S rRNA PCR-screening, we found that Ca . M. mahonii also occurs in Gorgonocephalus eucnemis from the Northwest Pacific and other Gorgonocephalus chilensis from Argentinian waters. The level of sequence conservation within Ca . M. mahonii is considerable between widely disparate high-latitude Gorgonocephalus species, suggesting that oceanic dispersal of this microbe may be greater than excepted. 
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  4. ; ; ; ; ; ( , Frontiers in Marine Science)
    The Southern Ocean’s continental shelf communities harbor high benthic biodiversity. However, most census methods have relied on trawling or dredging rather than direct observation. Benthic photographic and videographic transect surveys serve a key role in characterizing marine communities’ abundance and diversity, and they also provide information on the spatial arrangement of species within a community. To investigate diversity and abundance in Southern Ocean benthic communities, we employed photographic transects during cruises aboard the RVIB Nathanial B. Palmer (November 2012) and the ASRV Laurence M. Gould (February 2013). One kilometer long photographic transects were conducted at 8 sites along 6,000 km of Western Antarctica from the tip of the Antarctic Peninsula to the Ross Sea from which epifaunal echinoderms, tunicates, arthropods, cnidarians, poriferans, and annelids were identified and counted allowing estimations of biodiversity. Our results do not support a latitudinal trend in diversity, but rather a decrease in abundance of macrofaunal individuals at higher latitude sites. All communities sampled on the Western Antarctic shelf were primarily dominated by ophiuroids, pycnogonids, holothuroids, and demosponges. However, the most abundant taxon across all sites was Ophionotus victoriae , followed by the symbiotic partners Iophon sp. (demosponge) and Ophioplinthus spp. (ophiuroid). Data also confirm that the Southern Ocean is composed of discretely unique benthic communities. These results provide critical understanding of the current community structure and diversity serving as a baseline as the Antarctic continental shelf changes due to rising ocean temperatures, climate change, and collapse of large ice sheets. 
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  5. ; ; ; ; ; ; ; ( , Molecular Biology and Evolution)
    Leitner, Thomas (Ed.)
    Abstract Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Although their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes—the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral double-stranded RNA analog, poly(I:C), we show that S. kowalevskii responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., nuclear factor κB and interferon regulatory factor signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia. 
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  6. ; ; ; ( , Molecular Biology and Evolution)
    Rosenberg, Michael (Ed.)
    Abstract Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species. 
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  7. ; ; ; ; ; ; ; ; ; ; et al ( , Proceedings of the Royal Society B: Biological Sciences)
    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. 
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  8. ; ; ; ; ; ; ( , Molecular Phylogenetics and Evolution)
    null (Ed.)
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  9. ; ( , Journal of Biogeography)
    Abstract Aim

    Polyploids have been theorized to occur more frequently in environments that are subjected to severe conditions or sudden disruptions. Here we test the expectation that polyploid taxa occur more frequently in extreme or disrupted environments than their diploid counterparts, whether due to increased adaptive potential, environmental resilience or cross‐ploidy competition.

     Location

    South America.

     Taxon

    All frog genera in the area with both polyploid and diploid member species (Ceratophrys, Chiasmocleis, Odontophrynus, PhyllomedusaandPleurodema).

     Methods

    In all, 13,556 occurrence records of 82 frog species were collected from the Global Biodiversity Information Facility. Species distribution models, range overlap estimates, statistical tests and principal component analyses were used to estimate and compare environments between diploid and polyploid species within and across genera using several categorical and quantitative variables taken from multiple publicly available sources.

     Results

    Almost all polyploid occurrences are found within southeastern South America, largely to the exclusion of diploids. Polyploid species occur more closely with intergeneric polyploids than they do with congeneric diploids. Southeastern South America is more temperate, seasonal and less forested when compared to the tropical environments more commonly inhabited by diploids. The habitat ranges of polyploid species are subject to greater temperature fluctuations than diploid species. This region has also experienced major transformations in the modern era, owing to an agriculture boom over the last century. Polyploid occurrences are more likely to be found in areas with greater cropland usage, fertilizer application and pesticide application than diploids.

     Main Conclusions

    Across species, temperature seasonality was the only variable with strong statistical differences between diploids and polyploids. Greater annual fluctuations in temperature may lead to more established polyploid species due to reasons mentioned above; however, extreme temperature differences are also known to contribute to polyploid gamete formation, providing a possible non‐selective explanation. Polyploid occurrences are also more likely to be found in areas of high agricultural impact, providing support for the hypothesis that polyploids are more resilient to environmental disruptions than diploids.

     
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  10. ; ; ; ; ; ; ; ; ( , Geobiology)
    Abstract

    Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635–560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low‐oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia‐inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low‐oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957–1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole‐genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre‐Tonian emergence of metazoans under low‐oxygen conditions, and an increase in oxygen response elements during animal evolution.

     
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