Author: Bernard Goffinet

Publication on algae

Fučíková, K., M. Taylor, L.A. Lewis, B.K. Niece, A.S. Isaac & N. Pietrasiak. 2023. Johansenicoccus eremophilus gen. et sp. nov., a novel evolutionary lineage in Chlorophyceae with unusual genomic features. Plant Ecology and Evolution 156 (3): 311–325. pdf
Abstract reads:
Background – Green algae are a diverse group of photosynthetic eukaryotes, yet are still vastly understudied compared to land plants. For many years, green algae were characterized based on their morphology and life cycles. More recently, phylogenetic and genomic analyses have been added to the phycological toolkit for a better understanding of algal biodiversity and evolutionary history.
Material and methods – A desert strain of green algae was isolated from Joshua Tree National Park (JTNP) in southern California as part of a larger biodiversity survey. The alga’s nuclear rRNA genes as well as the chloroplast genome were sequenced, annotated, and analysed in addition to a morphological assessment.
Results – Morphologically this strain is especially similar to Pseudomuriella and Rotundella, and its lipid profile resembles that of other soil algae, but phylogenomic analyses demonstrate that it is a distinct evolutionary lineage in Chlorophyceae. The alga exhibits several unusual genomic features, the most remarkable being its highly derived yet apparently functional nuclear rRNA genes, 18S and 28S. Both genes are GC-rich and bear many compensatory base changes to maintain a similar secondary structure to that of other green algae. The chloroplast genome has a distinct gene order and repeat arrangement from other published green algal plastomes, but contains the expected genes and also provides phylogenetically informative data.
Conclusion – We conclude that the strain be placed into a new species and genus in the class Chlorophyceae, and
propose the name Johansenicoccus eremophilus for this new taxon. Johansenicoccus eremophilus exemplifies science’s
insufficient understanding of the range of genomic variations among inconspicuous soil algae.

New publication on bryophytes

Zhang L., Q. Zuo, W.Z. Ma, J. Shevock, N. Patel, M. Johnson, R. Medina, N. Wilding & B. Goffinet. 2023 Phylogenomics resolves the rediscovered Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), as a species of Entosthodon, prompting also the transfer of Clavitheca poeltii. Taxon 72: 1216–1227. pdf
Abstract reads: Traits of the spore-bearing generation have historically provided the basis for systematic concepts across the phylogenetic spectrum and depth of mosses. Whether taxa characterized by a simple sporophytic architecture are closely related or emerged from independent reduction is often ambiguous. Phylogenomic inferences in the Funariaceae, which hold the model taxon Physcomitrium patens, revealed that several such shifts in sporophyte complexity occurred, and mostly within the Entosthodon-Physcomitrium complex. Here, we report the rediscovery of the monospecific, Himalayan endemic genera Brachymeniopsis and Clavitheca, after nearly 100 years and 40 years since their respective descriptions. The genera are characterized by, among other traits, their short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal that Brachymeniopsis gymnostoma arose within the clade of Entosthodon s.str., a genus with typically long-exserted capsules. We therefore propose to transfer B. gymnostoma to the genus Entosthodon, as E. gymnostomus comb. nov. Furthermore, Clavitheca poeltii, the sole species of the genus, is morphologically highly similar to E. gymnostomus, and should also be transferred to Entosthodon, but is retained as a distinct taxon, E. poeltii comb. nov., until additional populations allow for testing the robustness of the observed divergence in costa and seta length between the Nepalese and Chinese populations.

New publications on parasites

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.

New publication on bryophytes

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.


New publication on new Hemiptera

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.

Publication on new Cicadas

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.



New publication on bryophytes

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.

BRC in UCONN today

UConn Biodiversity Research Collections Join an Effort to Combat Wildlife Trafficking

Or How jaguar skulls collected in the 1960s can help thwart wildlife poachers today

Globally, species extinction rates are accelerating and reaching unprecedented levels. Unfortunately for many species, this means they also become more valuable for animal traffickers.

UConn Ecology and Evolutionary Biology Professor Eric Schultz explains that wildlife trafficking – which the Wildlife Conservation Society estimates is worth as much as $10 billion per year – is often connected with other international crimes such as the drug and weapons trades, because when networks exist, it is relatively easy to add another valuable commodity.

To read more go to the article

New publications on lichenized fungi

A new publication on lichens lists many specimens deposited in the CONN herbarium, including various types.

Magain N., J. Miadlikowska, B. Goffinet, T. Goward, I. Juriado, A. Simon, C.J. Pardo De la Hoz, J. Mercado-Diaz, T. Barlow, B. Moncada, R. Lücking, A. Spielmann, L. Canez, L.S. Wang, P. Nelson, T. Wheeler, F. Lutzoni & E. Sérusiaux. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of sect. Polydactylon, including 23 new to science. Persoonia 51: 1–88. pdf GoogleScholar

Abstract readsApplying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification.

New publication on fish

Tellier, J.M., M. Humphreys, S. Minoudi, A. Triantafyllidis & E.T. Schultz. 2023. What are you doing here? Unexpected occurrences of Knobfin Sculpins (Cottus immaculatus) in Connecticut. Ichthyology and Herpetology 111: 1-7. pdf

Abstract reads: Reductions in cold-water habitat owing to anthropogenic stressors are focusing attention on indicator fish species. We investigated an apparent range expansion in Connecticut of a native cold-water fish, Slimy Sculpin (Cottus cognatus). Unexpectedly, genetic and morphological analyses identified the new population as a non-native cottid from the Ozark region, the Knobfin Sculpin (C. immaculatus). This is the first record of C. immaculatus outside of its native range. The new occurrences were not recognized for over a decade despite comprehensive watershed inventories by state natural resource managers. The mechanism by which the non-native Knobfin Sculpin first arrived in Connecticut is currently unknown. Our findings suggest that unintentional species introductions may occur more frequently than is currently recognized and highlight the need for more comprehensive assessments of non-native species distributions.