Vuruputoor V.S., A. Starovoitov, Y. Cai, Y. Liu, N. Rahmatpour, T. Hedderson, N. Wilding, J.L. Wegrzyn & B. Goffinet. 2024. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3: Genes, Genomes, Genetics 14(7): jkae104. pdf

Abstract reads: The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.

Muzio, F. M., & Rubega, M. A. 2024. What do we really know about the water repellency of feathers?. Journal of Avian Biology, 2024(11-12), e03259. pdf

Abstract reads: Feathers are complex integument structures that provide birds with many functions. They are vital to a bird’s survival, fundamental to their visual displays, and responsible for the evolutionary radiation of the avian class. Feathers provide a protective barrier for the body; their water repellency is a key feature. Despite hundreds of years of ornithological research, the available literature on how feathers repel water is both limited and puzzling. Most hypotheses from the early 1900s suggested uropygial gland oil provided feathers with a hydrophobic coating. Subsequent studies showed that the feather’s hierarchical structure creates a porous substrate that readily repels water with or without oil. Numerous studies and methods have been published attempting to explain, quantify, and compare the water repellency of feathers. Many overlook the role of barbules and the effect of their variation, which both likely play a crucial part in water repellency. The goal of this paper is to synthesize this research to better understand what has been done, what makes sense, and more importantly, what is missing. Previous reviews on this subject are mostly over 30 years old and did not use modern methods for systematic review. Here, we performed a systematic review to capture all relevant published papers on feather water repellency. We emphasize the crucial role of barbules in feather water repellency and why their morphological variation should not be ignored. We answer the question, what do we really know about the water repellency of feathers?

Drs. Caira, Menard and Goffinet were awarded $696,447 (DBI—2333910) from the national Science Foundation for a project: Lions and tiger sharks, and hares…oh my! Stabilizing and providing digital access to eight decades of parasites from vertebrates. 

Overview: This project focuses on nine historical collections of vertebrate metazoan parasites donated to UConn’s Department of Ecology & Evolutionary Biology’s Biodiversity Research Collection facility over the past two decades. These collections are the result of 80 years of fieldwork by expert parasitologists and students. The collections comprise 113,800 microscope slides, 13,850 vials, and 528 jars of fluid-preserved specimens complemented by 10,479 necropsy sheets and cards detailing host specimen data. Hosts include at least 716 species in 430 genera representing 74 vertebrate orders. The three most speciose phyla of vertebrate parasites (i.e., Platyhelminthes, Arthropoda, and Nematoda) are represented. We have focused our immediate efforts on stabilization and curation, which has revealed the scope of curatorial work needed to showcase these unique collections. Over 3,500 slides need remounting, 3,200 slides need their labels to be re-attached, and 9,520 vials must be replaced with archival vials and lids. We also now recognize the magnitude of manpower required to properly accession and digitize the approximately 128,000 specimens and containers. We are seeking funds to complete these tasks. The full curation of these unique collections and dissemination of all their data publicly through the Lawrence R. Penner Parasitology portal, iDigBio, and GBIF, will make it possible for these irreplaceable collections to achieve their full potential as a resource for discovering novelty and exploring a wide array of questions about the ecology and evolution of vertebrate parasites.

See 2024 NSF Collection grant for more info.

Two new publications on parasites, with vouchers in the BRC!

Herzog, K.S., J.N. Caira, P.Kumar Kar & K. Jensen. 2023. Novelty and phylogenetic affinities of a new family of tapeworms (Cestoda: Rhinebothriidea) from endangered sawfish and guitarfish. International Journal for Parasitology 53: 347–362.  pdf

Abstract reads: The parasites of hosts of conservation concern are often poorly known. This is the case with the iconic group of elasmobranchs known as the sawfish of the genus Pristis, all four species of which are considered as Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN, Switzerland). Examination of cestodes from three species of sawfish (Pristis pristis, Pristis clavata, and Pristis zijsron) in Australia and one of their close relatives, the also critically endangered widenose guitarfish, Glaucostegus obtusus, in India, collected over the past 25 years, yielded four new species of tapeworms which are described herein. All four belong to the previously monotypic Mixobothrium; the diagnosis of the genus is revised to accommodate the new species. Among the new taxa is a species that had been included in previous molecular phylogenies but whose identity and affinities within the order Rhinebothriidea, and thus also its familial placement, were unclear. This species exhibits the morphological features of Mixobothrium and thus its identity is, at long last, revealed. Sequence data generated for the 28S rDNA gene for three of the new species, as well as an additional new but yet undescribed species from Pristis pectinata from Florida (USA), confirms the uniqueness of this group among the rhinebothriideans. The new family Mixobothriidae is established to house these taxa. The members of this family differ from all but one of the five other families of rhinebothriideans in lacking apical suckers on their bothridia. They are also distinctive in that their bothridia are divided into three regions. The anterior and posterior regions have similar locular configurations to one another and differ from the locular configuration of the middle region. As a consequence, the bothridia are symmetrical along both their vertical and horizontal axes. We predict that a focus on species of guitarfish in the genus Glaucostegus will be the most productive approach for discovering additional diversity in this family of cestodes.

Bueno, V.M. & J.N. Caira. 2023. Phylogenetic relationships. host associations, and three new species of a poorly known group of “tetraphyllidean” tapeworms from elasmobranchs. Zootaxa 5254: 030–050. pdf

Abstract reads: This paper aims to expand understanding of a poorly known group of cestodes that parasitize an intriguingly diverse suite of elasmobranchs. The group’s three currently described members (i.e., Pentaloculum macrocephalum, Pentaloculum hoi, and Zyxibothrium kamienae) parasitize an electric ray, a carpet shark, and a skate, respectively. Pentaloculum grahami n. sp. is described from a second genus of carpet shark, specifically Parascyllium collare, in Australia. Zyxibothrium duffyi n. sp. and Zyxibothrium healyae n. sp. are described from the deep-sea skates Brochiraja asperula and Brochiraja spinifera, respectively off New Zealand. The three new species share distinctive bothridia that bear a small number of large, circular, facial loculi and lateral bands of vitelline follicles that converge posterior to the ovary—features which are found in all other members of these genera. Zyxibothrium healyae n. sp. is unique in possessing three, rather than four or five, facial loculi. Zyxibothrium duffyi n. sp. possesses a combination of five facial loculi and vitelline follicles that stop short of the anterior margin of the proglottid. Pentaloculum grahami n. sp. is the largest member of the group with the greatest number of proglottids. Based on striking similarities in scolex morphology, Pentaloculum and Zyxibothrium have been hypothesized to belong to a distinct subgroup of “tetraphyllideans” provisionally designated as Clade 1. Based on sequence data for the D1–D3 region of the 28S rDNA gene generated for species of Zyxibothrium for the first time, we confirm the reciprocal monophyly of both genera as well as the monophyly of Clade 1 and its status as a distinct lineage among the “Tetraphyllidea”. This work also suggests that the presence of five facial loculi is homoplasious given this character state is found in members of both genera. The new species expand the host associations of Clade 1 to include additional skate and carpet shark genera. Moving forward we would expect to find additional members of this group parasitizing other species of parascyliid carpet sharks as well as other species of the rajid genus Malacoraja and the arhynchobatid genus Brochiraja. Here we have doubled the number of described species in the taxon referred to as Clade 1 while simultaneously expanding our understanding of the morphology and anatomy of its members. This additional information will help inform the ultimate revision of the ordinal classification of the cestodes to address the highly polyphyletic nature of the order “Tetraphyllidea” as it is currently configured.

Patel N., R. Medina, L.D. Williams, O. Lemieux, B. Goffinet & M.G. Johnson. Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes. Evolution 77: 2561–2575. pdf

Abstract reads: Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. pyriforme, and P. sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

Menard, K.L. & M.D. Schwartz. 2023. Four new species of Phytocoris Fallén (Hemiptera, Miridae) from the Davis Mountains in Texas and further documentation of known species of Jeff Davis County. ZooKeys 1174: 97-139.

Abstract reads:  A recent survey of the entomofauna of the Davis Mountains in the state of Texas has revealed four new species in the genus Phytocoris Fallén (Miridae, Mirinae, Mirini): Phytocoris mcivor sp. nov. and Phytocoris schmitzi sp. nov. found on Quercus grisea Liebmann, and Phytocoris marqua sp. nov. and Phytocoris rileyi sp. nov. found attracted to lights. Descriptions, habitus, and genitalic images for the new species are included herein. Further, habitus and genitalic photographs of known Phytocoris species from the county are included to aid in identification.

Lee, Y.J., D.C. Marshall, A.B. Mohagan, K.B.R. Hill & D.P. Mohagan. 2023. Revised checklist of Cicadidae (Insecta: Hemiptera) of Mindanao, Philippines, with descriptions of a new genus and nine new species. Journal of Natural History 57: 193–242.

Abstract reads:  This paper provides a revised faunal checklist for the subfamilies, tribes, subtribes, genera and species of the family Cicadidae (Insecta: Hemiptera) from Mindanao, Philippines, comprising 31 species belonging to 19 genera. A new genus, Neopurana Lee and Marshall gen. nov., and nine new species, Platypleura bella Lee and A. Mohagan sp. nov., Platypleura minima Lee and Marshall sp. nov., Chremistica flavialata Lee and Marshall sp. nov., Oncotympana obesa Lee and Marshall sp. nov., Neopurana bouptera Lee and Marshall sp. nov., Purana mindanaoensis Lee and Marshall sp. nov., Mogannia tenebrosa Lee and Marshall sp. nov., Philipsalta exilis Lee and Marshall sp. nov. and Philipsalta lata Lee and Marshall sp. nov., are described. Platypleura transitiva Lee, 2021 is newly added to the list of cicadas from Mindanao. Male calling songs are illustrated and described for all new species. Information on the geographic distributions of the 31 Mindanao species is provided.

Bechteler J., G. Peñaloza-Bojacá, D. Bell, G. Burleigh, S. F. McDaniel, E. C. Davis, E. B. Sessa, A. Bippus, D. Christine Cargill, S. Chantanoarrapint, I. Draper, L. Endara, L. L. Forrest, R. Garilleti, S. W. Graham, S. Huttunen, J. Jauregui Lazo, F. Lara, J. Larraín, L. R. Lewis, D. G. Long, D. Quandt, K. Renzaglia, A. Schäfer-Verwimp, G. Ee Lee, A. S. Pinilla, M. von Konrat, C. E. Zartman, M. Regina Pereira, B. Goffinet & J. C. Villarreal. 2023. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. American Journal of Botany 110: e16249. pdf

Abstract reads: 
Premise: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns and processes of diversification across bryophytes remain unclear.

Methods: Using the GoFlag probe set we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.

Results: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology.

Conclusions: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.