California Academy of Sciences
  • San Francisco, United States
Recent publications
The epidermis is a constantly renewing stratified epithelial tissue that provides essential protective barrier functions. The major barrier is located at the outermost layers of the epidermis, formed by terminally differentiated keratinocytes reinforced by proteins of their cornified envelope (CE) and sequestered intercellular lipids. Disruptions to epidermal differentiation characterize various skin disorders. ZNF750 is an epithelial transcription factor essential for in vitro keratinocyte differentiation, whose truncating mutation in humans causes autosomal dominant psoriasis-like skin disease. Here, we utilized an epidermal-specific Znf750 conditional knockout mouse model to uncover the role ZNF750 plays in epidermal development. We show that deletion of Znf750 in the developing skin does not block epidermal differentiation completely, suggesting in vivo compensatory feedback mechanisms, although it does result in impaired barrier function and perinatal lethality. Molecular dissection revealed ultrastructural defects in the differentiated layers of the epidermis, accompanied by alterations in the expression of ZNF750-dependent genes encoding key CE precursor proteins and lipid processing enzymes, including gene subsets known to be mutated in human skin diseases involving impaired barrier function. Together, our findings provide molecular insights into the pathogenesis of human skin disease by linking ZNF750 to a subset of epidermal differentiation genes involved in barrier formation pathways.
The oscillating glacial–interglacial climate has had well-characterized effects on alpine species, driving rapid distributional and demographic shifts that have led to lineage diversification. It is unclear whether adaptive evolution has occurred during these rapid demographic changes, because strong genetic drift can overcome the force of selection. Here, using the alpine ground beetle Nebria vandykei, we test for evidence of adaptive evolution. Initially, we explore the genetic pathways induced during environmental stress responses through RNA sequencing, showing that cold, heat and desiccation stress activate a largely non-overlapping set of molecular pathways. Using additional transcriptome sequencing, we estimate the evolutionary relationship of N. vandykei to related species in the subgenus Catonebria and several outgroups. Phylogenetic analyses suggest that a history of admixture or very rapid diversification underlies the evolution of N. vandykei. Finally, using tests for selection polarized by high- and low-elevation relatives, we demonstrate selection acting on stress response pathways and on pathways known to function in tolerance to cold and hypoxic environments. These results support the role of environmental adaptation in alpine species despite rapid demographic change, while demonstrating that admixture might play a key role in facilitating adaptive diversification of alpine species.
In 2020, multiple lionfish (Pterois spp.) records along the equatorial Southwestern (SW) Atlantic revealed a new expansion of these potentially damaging invasive populations, which could impact over 3500 km of Brazilian coastline over the next few years, as well as unique ecosystems and marine protected areas in its path. To assess the taxonomic status, invasion route, and correlation with other centres of distribution, we investigated the genetic diversity patterns of lionfish caught in 2022 at the Amazonia, Northeastern Brazil, and Fernando de Noronha and Rocas Atoll ecoregions, using two molecular markers, the mitochondrial COI and the nuclear S7 RP1. The data indicate that all studied lionfish belong to what is generally accepted as P. volitans, and share the same genetic signature as lionfish present in the Caribbean Sea. The shared haplotypes and alleles indicate that the SW Atlantic invasion derives from an active movement of adult individuals from the Caribbean Sea into the Brazilian coast. The Amazon mesophotic reefs likely served as a stepping-stone to overcome the biogeographical barrier represented by the Amazon-Orinoco River plume. New alleles found for S7 RP1 suggest the onset of local genetic diversification, heightening the environmental risks as this bioinvasion heads towards other South Atlantic ecoregions.
Premise of the study: Floral evolution in large clades is difficult to study not only because of the number of species involved, but also because they often are geographically widespread and include a diversity of outcrossing pollination systems. The cosmopolitan blueberry family (Ericaceae) is one such example, most notably pollinated by bees and multiple clades of nectarivorous birds. Methods: We combined data on floral traits, pollination ecology, and geography with a comprehensive phylogeny to examine the structuring of floral diversity across pollination systems and continents. We focused on ornithophilous systems to test the hypothesis that some Old World Ericaceae were pollinated by now-extinct hummingbirds. Key results: Despite some support for floral differentiation at a continental scale, we found a large amount of variability within and among landmasses, due to both phylogenetic conservatism and parallel evolution. We found support for floral differentiation in anther and corolla traits across pollination systems, including among different ornithophilous systems. Corolla traits show inconclusive evidence that some Old World Ericaceae were pollinated by hummingbirds, while anther traits show stronger evidence. Some major shifts in floral traits are associated with changes in pollination system, but shifts within bee systems are likely also important. Conclusions: Studying the floral evolution of large, morphologically diverse, and widespread clades is feasible. We demonstrate that continent-specific radiations have led to widespread parallel evolution of floral morphology. We show that traits outside of the perianth may hold important clues to the ecological history of lineages. This article is protected by copyright. All rights reserved.
Cleaning symbiosis is a cooperative interspecific interaction among reef fishes that helps to maintain healthy marine communities. Despite its importance, our knowledge on the cleaner role of many species, and on the costs and benefits of these interactions, is still scarce. Here, we report for the first time an adult Guinean angelfish Holacanthus africanus acting as cleaner of the smaller client blackbar soldierfish Myripristis jacobus in the remote Cabo Verde Archipelago, Eastern Atlantic. Adult angelfish cleaning behaviour is a rare juvenile trait retention, which based on our observations could have a negative effect on smaller clients. This negative effect can be associated with the fish’s extra lower jaw joint, adapted to extract sessile invertebrates from the substrate, which can remove the client’s tissues during the cleaning attempt. Thus, although cleaning interactions have been viewed as examples of marine mutualisms, the costs and benefits of cleaning for cleaners and clients require more studies. Our study also builds on the scarce information on cleaning behaviour of adult fishes and offers highlights on this symbiosis in isolated locations with low species richness and absence of dedicated cleaners.
The tribes Goniaderini Lacordaire, 1859 and Lupropini Lesne, 1926 within the tenebrionid subfamily Lagriinae Latreille, 1825 have previously been shown to be non-monophyletic by molecular phylogenetic analyses. The tribes and constituent genera are here reviewed and redefined morphologically. As part of tribal redefinitions, we establish Prateini New Tribe with type genus Prateus LeConte, 1862. We reestablish the subtribe Phobeliina Ardoin, 1961 Revised Status , which is transferred from Goniaderini and placed as a subtribe of Lagriini Latreille, 1825 where it is comprised of Phobelius Blanchard, 1842, and Rhosaces Champion, 1889 (previously in Lagriini: Statirina Blanchard, 1845). The fossil tribe Archaeolupropini Nabozhenko, Perkovsky, & Nazarenko, 2023 is transferred from Lagriinae to Tetratomidae: Tetratominae Billberg, 1820. Keys to extant tribes and subtribes of Lagriinae and genera of Goniaderini, Lupropini, and Prateini are provided. Generic and species-level changes from this work are as follows: Prateini is comprised of the following 15 genera: Antennoluprops Schawaller, 2007, Ardoiniellus Schawaller, 2013, Bolitrium Gebien, 1914, Enicmosoma Gebien, 1922, Indenicmosoma Ardoin, 1964, Iscanus Fauvel, 1904, Kuschelus Kaszab, 1982, Lorelopsis Champion, 1896, Mesotretis Bates, 1872, Microcalcar Pic, 1925, Micropedinus Lewis, 1894, Paratenetus Spinola, 1845, Prateus , Terametus Motschulsky, 1869, and Tithassa Pascoe, 1860. Lorelus Sharp, 1876 is Returned to Synonymy with Prateus , resulting in the following 49 New Combinations : Prateus angulatus (Doyen & Poinar, 1994), P. angustulus (Champion, 1913), P. armatus (Montrouzier, 1860), P. biroi (Kaszab, 1956), P. blairi (Kaszab, 1955), P. brevicornis (Champion, 1896), P. breviusculus (Champion, 1913), P. caledonicus (Kaszab, 1982), P. carolinensis (Blair, 1940), P. chinensis (Kaszab, 1940), P. clarkei (Kulzer, 1957), P. crassicornis (Broun, 1880), P. crassepunctatus (Kaszab, 1982), P. cribricollis (Kaszab, 1940), P. curvipes (Champion, 1913), P. dybasi (Kulzer, 1957), P. fijianus (Kaszab, 1982), P. fumatus (Lea, 1929), P. glabriventris (Kaszab, 1982), P. greensladei (Kaszab, 1982), P. guadeloupensis (Kaszab, 1940), P. hirtus (Kaszab, 1982), P. ivoirensis (Ardoin, 1969), P. kanak (Kaszab, 1986), P. kaszabi (Watt, 1992), P. laticornis (Watt, 1992), P. latulus (Broun, 1910), P. longicornis (Kaszab, 1982), P. mareensis (Kaszab, 1982), P. marginalis (Broun, 1910), P. niger (Kaszab, 1982), P. norfolkianus (Kaszab, 1982), P. obtusus (Watt, 1992), P. ocularis (Fauvel, 1904), P. opacus (Watt, 1992), P. palauensis (Kulzer, 1957), P. politus (Watt, 1992), P. priscus (Sharp, 1876), P. prosternalis (Kaszab, 1982), P. pubescens (Broun, 1880), P. pubipennis (Lea, 1929), P. punctatus (Watt, 1992), P. quadricollis (Broun, 1886), P. queenslandicus (Kaszab, 1986), P. rugifrons (Champion, 1913), P. solomonis (Kaszab, 1982), P. tarsalis (Broun, 1910), P. unicornis (Kaszab, 1982), and P. watti (Kaszab, 1982). Microlyprops Kaszab, 1939 is placed as a New Synonym of Micropedinus resulting in the following New Combinations : Micropedinus ceylonicus (Kaszab, 1939) and M. maderi (Kaszab, 1940). Lorelopsis Revised Status is revalidated as a genus and eight species formerly in Lorelus are transferred to it resulting in the following six New Combinations : Lorelopsis bicolor (Doyen, 1993), L. glabrata (Doyen, 1993), L. exilis (Champion, 1913), L. foraminosa (Doyen & Poinar, 1994), L. minutulis (Doyen & Poinar, 1994), L. trapezidera (Champion, 1913), and L. wolcotti (Doyen, 1993). Lorelopsis pilosa Champion, 1896 becomes a Restored Combination . In Goniaderini, Aemymone Bates, 1868 Revised Status and Opatresthes Gebien, 1928 Revised Status , which were recently considered as subgenera of Goniadera Perty, 1832, are restored as valid genera based on new character analysis resulting in the following New Combinations : Aemymone hansfranzi (Ferrer & Delatour, 2007), A. simplex (Fairmaire, 1889), A. striatipennis (Pic, 1934) and Restored Combinations : Aemymone cariosa (Bates, 1868), A. crenata Champion, 1893, and A. semirufa Pic, 1917. Gamaxus Bates, 1868 is Returned to Synonymy with Phymatestes Pascoe, 1866, and the type species Gamaxus hauxwelli Bates, 1868 is placed as a New Synonym of Phymatestes brevicornis (Lacordaire, 1859). The following seven genera are placed as New Synonyms of Anaedus Blanchard, 1842: Microanaedus Pic, 1923, Pengaleganus Pic, 1917, Pseudanaedus Gebien, 1921, Pseudolyprops Fairmaire, 1882, Spinolyprops Pic, 1917, Spinadaenus Pic, 1921, and Sphingocorse Gebien, 1921. Fourteen species described by Pic in Aspisoma Duponchel & Chevrolat, 1841 (not Aspisoma Laporte, 1833) are returned to Tenebrionidae as valid species of Anaedus . These synonymies necessitate the following 51 New Combinations : Anaedus albipes (Gebien, 1921), A. amboinensis (Kaszab, 1964), A. amplicollis (Fairmaire, 1896), A. anaedoides (Gebien, 1921), A. angulicollis (Gebien, 1921), A. angustatus (Pic, 1921), A. australiae (Carter, 1930), A. bartolozzii (Ferrer, 2002), A. beloni Fairmaire, 1888), A. biangulatus (Gebien, 1921), A. borneensis (Pic, 1917), A. carinicollis (Gebien, 1921), A. conradti (Gebien, 1921), A. cribricollis (Schawaller, 2012), A. gabonicus (Pic, 1917), A. himalayicus (Kaszab, 1965), A. inaequalis (Pic, 1917), A. jacobsoni (Gebien, 1927), A. lateralis (Pic, 1917), A. latus (Pic, 1917), A. longeplicatus (Gebien, 1921) , A. maculipennis (Schawaller, 2011), A. major (Pic, 1917), A. nepalicus (Kaszab, 1975), A. nigrita (Gebien, 1927), A. notatus (Pic, 1923), A. pakistanicus (Schawaller, 1996), A. pinguis (Gebien, 1927), A. punctatus (Carter, 1914), A. raffrayi (Pic, 1917), A. rufithorax (Pic, 1917), A. rufus (Pic, 1917), A. serrimargo (Gebien, 1914), A. sumatrensis (Pic, 1917), A. terminatus (Gebien, 1921), A. testaceicornis (Pic, 1921), A. testaceipes (Pic, 1917), A. thailandicus (Schawaller, 2012), A. trautneri (Schawaller, 1994); and 13 restored combinations: Anaedus boliviensis (Pic, 1934), A. claveri (Pic, 1917), A. diversicollis (Pic, 1917), A. elongatus (Pic, 1934), A. guyanensis (Pic, 1917), A. holtzi (Pic, 1934), A. inangulatus (Pic, 1934), A. inhumeralis (Pic, 1917), A. mendesensis (Pic, 1917), A. minutus (Pic, 1917), A. rufimembris (Pic, 1932), A. rufipennis (Pic, 1917), A. subelongatus (Pic, 1932). The new synonymies with Anaedus necessitate the following six New Replacement Names Anaedus maculipennis (for Spinolyprops maculatus Kulzer, 1954), A. grimmi (for Aspisoma forticornis Pic, 1917), A. minimus (for Anaedus minutus Pic, 1938), A. merkli (for Anaedus diversicollis Pic, 1938), A. ottomerkli (for Anaedus lateralis Pic, 1923), A. schawalleri (for Anaedus nepalicus Schawaller, 1994). Capeluprops Schawaller, 2011 is removed from Lupropini and provisionally placed in Laenini Seidlitz, 1895. Plastica Waterhouse, 1903 is transferred from Apocryphini Lacordaire, 1859 to Laenini. Paralorelopsis Marcuzzi, 1994 is removed from Lupropini and provisionally placed in Lagriinae incertae sedis. Pseudesarcus Champion, 1913 is transferred from Lagriinae incertae sedis to Diaperinae incertae sedis. Falsotithassa Pic, 1934 is transferred from Lupropini to Leiochrinini Lewis, 1894 (Diaperinae). Mimocellus Wasmann, 1904 is transferred from Lupropini to Tenebrionidae incertae sedis, and likely belongs in either Diaperinae or Stenochiinae.
With ca. 375 species worldwide, Ruellia is a morphologically diverse and geographically widespread lineage of flowering plants. The majority of these species (ca. 275 of 375) occur in the New World (NW), with most of these occurring in the tropics and only about 65 occurring in temperate regions. In the NW, the genus spans some 77° of latitude, ranging from the northern United States (Wisconsin) to northeastern Argentina (Córdoba) and southern Uruguay (Canelones). In this study, we generated ddRAD molecular sequence data for 187 of 275 species of NW Ruellia (ca. 68% of NW species) to reconstruct phylogenetic relationships within this lineage. Coupled with morphological and ecological information, we used this well‐resolved and strongly supported molecular phylogeny to delimit 15 sections of NW Ruellia . Representing the first comprehensive attempt in ca. 125 years, we present a revised classification for NW Ruellia , which places a total of 205 species in the following sections: Ruellia sect. Aphragmia , sect. Blechum , sect. Boreosilva , sect. Brasilia , sect. Cerradicola , sect. Chiropterophilae , sect. Chromatoruellia , sect. Eurychanes , sect. Gymnacanthus , sect. Mexicanae , sect. Physiruellia , sect. Ruellia , sect. Siphonacanthus , sect. Stephanophysum , and sect. Strobiliformes . Nomenclatural innovations in this study include the description of several new sections, new combinations, and new names proposed. Our study complements an earlier reclassification of Old World species to provide a globally unique perspective on the taxonomy and phylogeny of a geographically widespread lineage of flowering plants.
In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.
Coral reefs are losing the capacity to sustain their biological functions¹. In addition to other well-known stressors, such as climatic change and overfishing¹, plastic pollution is an emerging threat to coral reefs, spreading throughout reef food webs², and increasing disease transmission and structural damage to reef organisms³. Although recognized as a global concern⁴, the distribution and quantity of plastics trapped in the world’s coral reefs remains uncertain³. Here we survey 84 shallow and deep coral ecosystems at 25 locations across the Pacific, Atlantic and Indian ocean basins for anthropogenic macrodebris (pollution by human-generated objects larger than 5 centimetres, including plastics), performing 1,231 transects. Our results show anthropogenic debris in 77 out of the 84 reefs surveyed, including in some of Earth’s most remote and near-pristine reefs, such as in uninhabited central Pacific atolls. Macroplastics represent 88% of the anthropogenic debris, and, like other debris types, peak in deeper reefs (mesophotic zones at 30–150 metres depth), with fishing activities as the main source of plastics in most areas. These findings contrast with the global pattern observed in other nearshore marine ecosystems, where macroplastic densities decrease with depth and are dominated by consumer items⁵. As the world moves towards a global treaty to tackle plastic pollution⁶, understanding its distribution and drivers provides key information to help to design the strategies needed to address this ubiquitous threat.
The richness of marine teleost fishes from the tropical northeastern Brazilian coast was compiled through an extensive search of published species records and of voucher specimens in collections. Results are presented in a systematic listthat includes 571 marine species across 98 families considered as valid records in coastal and estuarine environments.516 species (90.4%) are represented by voucher specimens in collections. Species reported in the literature with pending confirmation, or known only from vouchers, may add 72 species to the list, 18 of them without previous mention in theliterature representing new records for the study region. Brazilian endemic species are also reported, seven of which are exclusive to the northeastern coast. Additionally, 91 species belonging to 41 families are treated as erroneous or doubtful records for the region, and their geographic distribution or taxonomic status commented upon. Among the validspecies recorded, 21 are listed as threatened according to the IUCN Red List and 24 by the Brazilian official list of threatened species. At least four species introduced in the Western Atlantic are now considered invasive in northeastern Brazil. The data presented herein result from the most comprehensive survey of the coastal marine ichthyofauna of northeastern Brazil. It adds 154 species records when compared to the maximum species richness previously reported for the study region in a single publication and serves as a baseline to promote future studies in fish systematics, biogeography, ecology and conservation. Notwithstanding, the species richness of this region remains an underestimate pending additional taxonomic research and the availability of online data for regional collections
A coral reef system at the Steinhart Aquarium in San Francisco, CA, USA experienced a population explosion of pycnogonid sea spiders (Arthropoda: Class Pycnogonida) with subsequent deleterious health effects on the corals in the system. Sixteen coral colonies across three species (Stylophora pistillata, Pocillopora damicornis, and Acropora tenuis) were chosen from this system for milbemycin oxime immersion therapy trials, with the goal of decreasing or eradicating the sea spider population with minimal detrimental effect to the corals. Corals underwent two milbemycin immersion treatments, administered 1 wk apart, at the previously published aquatic invertebrate dose of 0.016 parts per million (ppm; mg/L), but therapy did not reduce the number of sea spiders. Doubling the dose to 0.032 ppm milbemycin and repeating this immersion therapy 1/wk for three treatments successfully reduced the sea spiders. Histopathology was used to assess the health of the corals and tolerance to therapy, and posttreatment biopsies confirmed that there were no adverse effects to any of the three species of coral. Repeated 1/ wk treatments of milbemycin oxime immersion therapy at 0.032 ppm appears to be both safe and effective for reducing the numbers of pycnogonid sea spiders in the stony corals S. pistillata, P. damicornis, and A. tenuis.
Background Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Results Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. Conclusions The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.
Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.
Premise: Plants with stiff, leathery leaves pose a challenge for standard DNA extraction protocols. These tissues are recalcitrant to mechanical disruption via TissueLyser (or analogous devices) and are often high in secondary metabolites. These compounding factors result in low yields, which may be sufficient for PCR amplification but are generally inadequate for genomic applications that require large quantities of high-quality DNA. Cycads in the genus Encephalartos exemplify these challenges, as this group of plants is fortified for life in harsh, dry habitats with notoriously thick and rigid leaves. Methods and results: Using a DNA extraction kit, we tested three methods of mechanical disruption and examined the differences between stored vs. freshly collected samples and mature vs. senescing leaflets. We found that the manual method of pulverizing tissue yields the highest concentrations of DNA, and that both senescing leaflets and leaflet tissue that has been stored for extended periods yield sufficient DNA for genomic analyses. Conclusions: These findings shed light on the feasibility of using senescing leaves and/or tissue that has been stored on silica for long periods of time when attempting to extract large amounts of DNA. We provide here an optimized DNA extraction protocol that can be applied to cycads and other plant groups with tough or rigid leaves.
Background Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. Results We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. Conclusions Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo. 8entVVL2Hhkfc-ejj4sDuQVideo Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
Modern scleractinian corals can display high phenotypic plasticity, which reflects an interplay among various environmental controls, such as sediment input, water hydrodynamics or light intensity. In particular, the latter can strongly influence the morphology of coral species living across broad depth gradients. Light intensity was also a factor shaping the colonies of extinct Palaeozoic tabulate corals (Anthozoa: Tabulata). Based on gradual transitions in morphology observed in corals from the Middle Devonian (Givetian stage, ~ 385 Ma) mesophotic coral ecosystems (MCE) of the Aferdou el Mrakib reef (Anti-Atlas mountains , Morocco) and comparative material originating from different palaeobathymetric and biogeographical settings, we show that Devonian tabulate corals, such as Roseoporella and Alveolites, were characterised by high phenotypic plasticity and the ability to dramatically change their morphology depending on the inferred light conditions. Such a mechanism is similar to that observed in modern scleractin-ians, e.g. Porites sillimaniana. This recurring morphological theme suggests that Palaeozoic tabulate corals shared many functional characteristics of modern scleractinians.
Parabasalid protists recently emerged as keystone members of the mammalian microbiota with important effects on their host’s health. However, the prevalence and diversity of parabasalids in wild reptiles and the consequences of captivity and other environmental factors on these symbiotic protists are unknown. Reptiles are ectothermic, and their microbiomes are subject to temperature fluctuations, such as those driven by climate change. Thus, conservation efforts for threatened reptile species may benefit from understanding how shifts in temperature and captive breeding influence the microbiota, including parabasalids, to impact host fitness and disease susceptibility. Here, we surveyed intestinal parabasalids in a cohort of wild reptiles across three continents and compared these to captive animals. Reptiles harbor surprisingly few species of parabasalids compared to mammals, but these protists exhibited a flexible host-range, suggesting specific adaptations to reptilian social structures and microbiota transmission. Furthermore, reptile-associated parabasalids are adapted to wide temperature ranges, although colder temperatures significantly altered the protist transcriptomes, with increased expression of genes associated with detrimental interactions with the host. Our findings establish that parabasalids are widely distributed in the microbiota of wild and captive reptiles and highlight how these protists respond to temperature swings encountered in their ectothermic hosts.
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197 members
Gopinathan Menon
  • Ornithology & Mammology
Robert Drewes
  • Department of Herpetology
John Philip Dumbacher
  • Institute for Biodiversity Science and Sustainability
Matthew R Lewin
  • Center for Exploration and Travel Health
Iria Fernandez-Silva
  • Department of Ichthyology
San Francisco, United States