Publications

How morphological diversity arises from variations in biomechanical processes remains an open question. Although forces shape tissues, how force-generating systems differ across species to create diverse forms is unclear. Here, we combine comparative morphogenesis and active matter theory across six cnidarian species spanning 500 million years of divergence to identify the mechanical basis of larval shape diversity. We define species-specific configurations of mechanical modules-termed mechanotypes-that quantitatively predict larval shapes across taxa. We find that shape elongation is a simple trait at the mesoscale level, as its variation depends on one mechanical module, whereas shape polarity is a complex trait dependent on several modules. Perturbations mimicking interspecies regulatory differences reshape these modules, reprogramming larval morphology into forms resembling sister species. By establishing a mesoscale mechanical framework for cross-species comparison, this work reveals how variations in a limited set of tissue-scale parameters generate morphological diversity.

Since the discovery of Latimeria chalumnae, coelacanths have provided a critical comparative framework for reconstructing ancestral sarcopterygian anatomy. However, the function of several anatomical features in both extant and fossil coelacanths remains unresolved. Among these, the presence of large ossified chambers in the body cavity of fossil coelacanths has remained enigmatic, with different studies proposing respiratory or auditory functions. Here, we examine lung and inner ear anatomy based on new observations from synchrotron phase-contrast microCT scans of two 240-million-year-old latimerioid coelacanths, alongside multiple developmental stages of the extant L. chalumnae. These data, combined with archival histological sections of L. chalumnae and 3D reconstructions of a Devonian coelacanth, suggest that extinct coelacanths possessed an ossified lung capable of transmitting sound pressure to auditory sensory epithelia in the inner ear via a perilymphatic system. We propose that the lung of extinct coelacanths supported both respiratory and auditory functions.

Henderson (2023) gave informal descriptions of several soft-walled, monothalamid foraminifera from intertidal zones in the Lorne area of northwest Scotland based on morphology. In the present study, we use a combination of morphological and molecular data to formally establish one new genus and five new monothalamid species from the same area. Lorneia sphaerica gen. & sp. nov. (monothalamid Clade D) has a spherical, coarsely agglutinated test containing magnetic particles and minute aperture-like openings distributed around the test. Lorneia ovalis gen. & sp. nov. (Clade D) has similar characteristics, but the test is oval, and there is a terminal aperture situated at each end. Psammophaga owensi sp. nov. (Clade E) has an oval, finely agglutinated test with a simple terminal aperture and intracellular magnetic particles. In Hilla brevis sp. nov. (Clade Y), the test is broadly oval and finely agglutinated with a reflective sheen and a large terminal aperture with a pronounced collar. Flaviatella zaninettiae sp. nov. (Clade Y) has an elongate, finely agglutinated test with a reflective sheen, a tubular terminal apertural structure, and distinctive yellow cytoplasm. Two species, Flexammina islandica Voltski and Pawlowski, 2015 and Ovammina opaca Dahlgren, 1962, are reported for the first time in Scottish coastal waters. This study underlines the importance and diversity of monothalamid foraminifera in coastal settings.

Skin coloration is crucial for the survival of animals and ranges from spectacular colorful displays used to attract a mate to cryptic camouflage used to avoid predators. Among the 3 main types of chromatophores, melanophores are the most widespread in vertebrates and can set the skin tone by the amount of melanin they produce and store in dedicated vesicles, the melanosomes. Mutations associated with melanophore differentiation and maturation result in hypomelanistic and amelanistic phenotypes, both extensively studied in mammals but less so in snakes and lizards. Here, we characterize at the genomic, transcriptomic, and histological level, the Hypomelanistic corn snake morph and 3 hypomelanistic leopard gecko morphs. To minimize bias in studying leopard gecko color morphs, we first assembled a chromosome-level genome from a wild-type individual in terms of coloration. We propose that candidate mutations in 3 melanogenesis factors generate these phenotypes: (i) tyrosinase (TYR), an essential enzyme for melanin synthesis, (ii) NCKX5 (SLC24A5), an ion exchanger involved in melanosome maturation, and (iii) the P protein (OCA2), a transmembrane transporter for tyrosine. Our extended bulk RNA sequencing analyses show that additional pigmentation-related genes, affecting melanin production, melanosome motility, and melanophore migration, are dysregulated in the embryonic skin of the mutated animals. This observation highlights the likely associations among the corresponding pathways and is in line with our electron microscopy imaging results. Indeed, the subcellular structure of melanophores is uniquely altered at each of the 4 morphs and likely reflects a multigenic effect. These findings demonstrate that conserved pigmentation genes can produce species-specific effects, underscoring the modular nature of skin coloration in vertebrates. Our work establishes reptiles as comparative models for studying pigment cell biology and reveals evolutionary flexibility in the genetic regulation of melanogenesis.

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human N-acetyltransferase 2 (NAT2) gene. NAT2 metabolizes several clinically used drugs including isoniazid, hydralazine, amifampridine, procainamide, and sulfonamides such as dapsone, and also some highly carcinogenic arylamines. Systematic nomenclature describing NAT2 variation is essential for pharmacogenetic testing, genotype interpretation, and translation to phenotype in research and clinical settings. This GeneFocus provides an overview of NAT2 variation and describes important changes to its star allele-based nomenclature that were made as it was transitioned to PharmVar in March 2024. We also highlight and discuss challenges regarding the characterization of allelic variation and determination of allele frequencies across world populations. The "new" NAT2 PharmVar nomenclature is utilized by ClinPGx (formerly PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).

Benthic foraminifera are one of the major groups of eukaryotes living at cold seeps on the Arctic seafloor. However, their distribution and endemicity in these habitats have been largely debated. It is still unclear whether foraminiferal species commonly found in cold seeps differ genetically from those in deep-sea environments, and to what extent the seep community is distinct. To address these questions, we analyzed sediment DNA metabarcoding data specifically targeting foraminifera in different deep-water cold seep microhabitats (microbial mats, siboglinid tubeworms field) and reference sites within and outside the seep. Our results revealed microhabitat specificity among benthic foraminifera species. Microbial mats were dominated by a unique type of rDNA sequences assigned to a new lineage of monothalamid (single-chambered) foraminifera not previously reported from any other Arctic location. Other foraminiferal species were found across both seeps and reference stations. This study shows the presence of an endemic benthic foraminiferal species at cold seeps and confirms the existence of many common opportunistic species.

The range over which a morphogen gradient provides reliable positional information is limited by intrinsic noise. We identify a regulatory circuit that counteracts this constraint for Dpp, a BMP that organizes the anterior/posterior axis of Drosophila wings. The transcriptional repressor Brinker (Brk), a Dpp target, enhances positional precision by repressing Dad, an inhibitory Smad, thereby extending Dpp's effective range. Thus, Brk mediates a feedback circuit that selectively amplifies low-level Dpp signals as would a logarithmic amplifier. This circuit also achieves temporal integration, mitigating the inevitable noise penalty associated with amplification. Although a core component of BMP signaling in flies, Brk is found exclusively in insects. Phylogenetic and expression analyses in the apterygote insect Thermobia domestica suggest that Brk originated in insects and was incorporated into the BMP network in pterygotes, possibly to permit long-range signaling in wing primordia. Brk exemplifies how gene regulatory network (GRN) evolution can enhance developmental precision, thus opening the door to increased morphological complexity.

In this global review we recognise, describe and figure 205 morphospecies of living elphidiids (Cribroelphidiidae, Elphidiellidae, Elphidiidae, Haynesinidae) from around the world and summarise their biogeography. Fifty-eight phylospecies (S1–58) are recognised by DNA sequencing grouping in eight clades and almost all are shown to be morphologically distinguishable. A further 148 morphospecies, that have not yet been sequenced, have sufficiently distinct morphology to be recognised and we hypothesise there could be at least another 100 rather cryptic and less common species that we have not been able to distinguish confidently to include in this review. We recognise the following families and genera: Family Cribroelphidiidae (clade F), containing the genera Cribroelphidium and Protelphidium; Family Elphidiellidae containing the genera Cryptoelphidiella (clades D and E), Elphidiella (clade B), Emayerella (replacement name for Mayerella junior homonym), and Rectoelphidiella; Family Elphidiidae s.l. (clades A, B, H and I), containing the genera Australononion (n. gen.) (clade I), Elphidium (clades A and H), Epistomaroides, Hispidoelphidium (n. gen.), Millettoelphidium (n. gen.) (clade H), Stomoloculina, and Toddinella (clade B); Family Haynesinidae (clade C), containing genera Aubignyna and Haynesina; Family Notorotaliidae, which molecular analyses confirm branches among these “elphidiids” has been reviewed previously and contains genera Buccella, Cristatavultus, Notorotalia, Parrellina and Porosorotalia. The families Elphidiidae and Elphidiellidae are based on morphological characters, as molecular analysis shows them to be polyphyletic but for the moment a clear morphological distinction is not possible for the obtained molecular clades. Seven molecular species and 34 morphospecies are described and named as new: Cribroelphidium calvomarcileseae, C. inflatogunteri, C. knudsenae (S3), C. revetsi (S41), Cryptoelphidiella daisyana, C. schweizerae, Elphidium altenbachi (S49), E. apthorpae, E. canni, E. davidhaigi, E. fajemilai, E. feylinghansseni, E. gischleri, E. goldsteinae, E. hanseni, E. hollisi, “E.” hulmei (S39, S57), E. kawagatai (S33), E. korsuni, E. larsi, E. lobulatum, E. lunatum, E. mouangaae, E. pereirai, E. pilleti (S18), E. poagi, E. sabaaae, E. scottorum, E. thisseni, E. yankoae, Epistomaroides fordererae, Haynesina lecozei, Millettoelphidium culveri (S51), M. yassinii, Protelphidium hottingeri, Toddinella akandaensis, T. crundwelli, T. darlingae, T. grenfelli, T. lutzei, and T. spezzaferriae. Two genotypes of “Elphidium” hulmei are genetically distinct but morphologically cryptic and unable to be separated using morphology. A further 16 unnamed morphospecies are described but not formally named because of insufficient material to do so. A neotype is proposed for Epistomaroides punctulatus (d’Orbigny) and a lectotype for Elphidium owenianum (d’Orbigny). Elphidiids live in mostly shallow seas (hyposaline to hypersaline) and occur throughout the world except for around the coast of the bulk of Antarctica. No species is cosmopolitan but a few (e.g., Australononion simplex, Cribroelphidium clavatum, C. decipiens, C. gunteri, C. knudsenae, C. lidoense, Elphidium advena, E. alvarezianum, E. articulatum, E. fax, “E.” formosum, E. gerthi, E. hanseni, E. jenseni, E. longipontis, Haynesina germanica, Hispidoelphidium hispidulum, Preotelphidium schmitti and Toddinella incerta) are widespread in two or more ocean regions, whereas the majority are endemic to smaller areas. Twenty biogeographic “provinces” are recognised by cluster analysis of presence/absence records with the highest diversities in the northwest Pacific and tropical East Indies-North Australia provinces with 74 and 49 species each. At the highest level of clustering their world biogeography can be divided into three large regions – Arctic and Atlantic; Indian and Pacific; and Southern Ocean. Levels of endemism in our “provinces” range between 0 (five provinces) and 33% (Southern Ocean). This review identifies at least 33 non-indigenous species (2 genotypes, 31 morphospecies) presumably introduced by accidental anthropogenic transfer in the last several centuries, probably in ship’s ballast, across large oceanic barriers to establish disjunct distribution patterns.

Non-marine foraminifera are among the least-studied groups of protists due to their low population densities, patchy distribution, and spatiotemporal variability. This study investigated foraminifera from four caves within the Dinaric karst region of southeastern Europe, using both morphological and molecular methods. Our results confirm the presence of foraminifera in all examined caves. A new monothalamous foraminifer, Lacogromia cepelaki sp. nov., is described based on morphological and molecular data from Jopićeva Cave (Croatia). Three additional Lacogromia taxa are informally described from different caves. However, due to the lack of distinct morphological characteristics, their formal taxonomic description will require molecular analyses of live specimens. A further important outcome of this study is the morphological description of Spirolocammina petrae sp. nov., discovered in Miljacka II Cave (Croatia). This represents the first discovery of an agglutinated tubothalamid foraminifer adapted to a freshwater environment. As no molecular data could be obtained, its phylogenetic position remains undetermined, and further research will be necessary.

A new genus and species of a monothalamid foraminifera, Adhaerentella dendrocorona, has been identified through phylogenetic and morphological assessment from the Pacific Ocean abyssal plain at Station M, off California. After at least 1 year of colonization time on the seafloor at 4000 m, 141 specimens belonging to the new species were observed attached to plastic substrate deposited on the bottom as a part of the Seafloor Epibenthic Attachment Cube (SEA3) experiments. Adhaerentella dendrocorona is characterized by agglutinated hemispherical tests connected with dendritic tubes. The delicate phyllosilicate branches collapse when not immersed, but embedding in agar or resin facilitates imaging. MicroCT images reveal compositional differences between the agglutinated base and branching tube structures, consisting of phyllosilicates. Despite sharing some morphological similarities with other attached agglutinated genera, such as Capsammina, Crithionina, and Hemisphaerammina, Adhaerentella dendrocorona is genetically different from the latter genera and branches in the monothalamid Clade M. Adhaerentella dendrocorona has a close relationship with undescribed monothalamids from Antarctica, suggesting the possible global distribution of the genus. This study indicates that monothalamid foraminifera are important components of attached abyssal meiofauna, which have evolved morphologies that are likely adapted for suspension feeding in oligotrophic environments that feature hard substrates.