Senckenberg Ocean Species Alliance (SOSA)’s Post

学術研究院環境生命自然科学学域（農）の福田宏准教授の研究成果をEurekAlert!に掲載しました。 Three decades after its discovery, a snail species is officially named Xenassiminea nana following detailed morphological examinations https://lnkd.in/g4eFz26G #岡山大学 #OkayamaUniversity #EurekAlert #Lifesciences #Nativespecies #Biodiversityconservation #Marineconservation #Conservationbiology #Endangeredspecies #Environmentalsciences #Aquaticecology #Temperatezones #Ecologicalspeciation #Waterpollution #Animaltaxonomies

A landmark baseline paper to support the global community for species inventories and new species descriptions. Approximately 27 Phytophthora species were described or revalidated as the type or ex-type has been lost at international herbaria or culture collections. Types are important because they represent a materialization of the abstract concept of species, are objective references to compare newly discovered species, and, if conserved, make retrospective systematic revisions possible; thus, providing a sound backbone for a robust and long-lasting taxonomic system.

How to memorize taxonomic ranks \(mnemonic technique\) In biological classification, taxonomic rank is the relative level of a group of organisms \(a taxon\) in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, order, class, phylum, kingdom, domain, etc. A given rank subsumes under it less general categories, that is, more specific descriptions of life forms. Above it, each rank is classified within more general categories of organisms and groups of organisms related to each other through inheritance of traits or features from common ancestors. The rank of any species and the description of its genus is basic; which means that to identify a particular organism, it is usually not necessary to specify ranks other than these first two. Consider a particular species, the red fox, Vulpes vulpes: the next rank above, the genus Vulpes, comprises all the "true" foxes. Their closest relatives are in the immediately higher rank, the family Canidae, which includes dogs, wolves, jackals, and all foxes; the next higher rank, the order Carnivora, includes caniforms \(bears, seals, weasels, skunks, raccoons and all those mentioned above\), and feliforms \(cats, civets, hyenas, mongooses\). Carnivorans are one group of the hairy, warm-blooded, nursing members of the class Mammalia, which are classified among animals with backbones in the phylum Chordata, and with them among all animals in the kingdom Animalia. Finally, at the highest rank all of these are grouped together with all other organisms possessing cell nuclei in the domain Eukarya. The International Code of Zoological Nomenclature defines rank as: "The level, for nomenclatural purposes, of a taxon in a taxonomic hierarchy \(e.g. all families are for nomenclatural purposes at the same rank, which lies between superfamily and subfamily\) Problems: The correct sequence, from the most to the least comprehensive, of the taxonomic levels listed here is A\) family, phylum, class, kingdom, order, species, and genus. B\) kingdom, phylum, class, order, family, genus, and species. C\) kingdom, phylum, order, class, family, genus, and species. D\) phylum, kingdom, order, class, species, family, and genus. E\) phylum, family, class, order, kingdom, genus, and species. If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology? A\) A and B B\) A and C C\) BandD D\) C and F E\) D and F Youtube video: https://lnkd.in/dBaz2gtd \#nikolays_genetics_lessons

What defines a species? There is surprisingly a fundamental uncertainty over how we parse organisms, and it continues to rile biologists the world over. Arguments often hinge on decades-old definitions. In 1942, biologist Ernst Mayr coined what is perhaps the most enduring one: the biological species concept, which labels two organisms as different species if they cannot reproduce and create fertile offspring. Researchers have since established definitions on the basis of shared ancestry (the phylogenetic species concept), physical features (the morphological species concept), or shared ecology (the ecological species concept), wherein species diverge as they take over different niches in their environment. In all, there are at least 16 species definitions, and potentially as many as 32, circulating among scientists today. No definition seems to be without exception, however. There are species in which individuals look very different from one another, as well as "cryptic species" that appear identical but are genetically distinct. Hybridization is also common, leading to animals like the liger (a lion-tiger hybrid) and the beefalo (a cross between domestic cattle and the American bison). Evidence even suggests that humans once bred with two other ancient hominins that are usually considered separate species, the Neanderthals and the Denisovans, suggesting they might not have been so different from us after all. Groups are now coming together to establish guidelines for how species should be named and ordered across the tree of life and how to handle disputes when they arise. Indeed, coming up with a working list of agreed-upon rules is crucial, even if it's not perfect, biologists say. Today's scientists are tackling the species problem in different ways. Some are attempting to reconcile existing definitions with modern methods, such as by rebranding Mayr's biological species concept as the genetic species concept, which still suggests an inability to reproduce but links the mechanism specifically to genetic incompatibility. Others continue to develop new ideas. Jeannette Whitton, an evolutionary biologist , co-developed the retrospective reproductive community concept. Rather than adopting a strict definition, this concept encourages scientists to embrace uncertainty and acknowledge that speciation is a continuous process — that organisms we observe today were shaped by past forces. Taking this holistic view, which incorporates facets of several existing definitions, means that scientists can still make predictions or explain natural phenomena even in the absence of a clear definition. #Taxonomy #Biology #Species #Preservation https://lnkd.in/gPZRw7vj?

In biological taxonomy (the classification of organisms such as #insects), genus (plural: genera) is a category of ranking that comes after family and before species. This week, our #insectoftheweek series highlights about #Oodera, a genus of peculiar #wasps. This genus is a small one with 24 species described worldwide. It is among the easiest of #parasitoid genera to identify because of its greatly swollen fore femora (singular: femur). In fact, in the larger specimens, this feature can be seen with the naked eye. The fore tibiae are gently curved and together with the femur to possibly fit clamp-like on the body of a prospective host (little is known about this aspect of their biology). Oodera is sometimes found in association with the larvae of metallic wood-boring beetles (family Buprestidae). For such a small genus, Oodera has caused a bit of trouble taxonomically, sometimes placed in the family Eupelmidae, sometimes assigned to the Pteromalidae. Zdeněk Bouček (a Czech entomologist) transferred Oodera from Eupelmidae to Pteromalidae, assigning tribal status to it (Ooderini) within the pteromalid subfamily Cleonyminae (a note on suffixes in the classification of animals, going from higher to lower levels of organization; -oidea indicates a superfamily, -idae, a family, -inae a subfamily, and -ini, a tribe).    It is not only Oodera that creates problems within the superfamily Chalcidoidea. The family Pteromalidae itself has become the dumping ground for species that don’t fit neatly within any of the other 21 families of the Chalcidoidea. There are many such species and, not surprisingly, compared to other families the Pteromalidae had an outsized number of subfamilies (33). Unfortunately, despite the heroic attempts to separate the species into groups based largely on morphological features (i.e. using traditional taxonomic methods), no satisfactory method could be found until advances in molecular identification (first with DNA bar codes and subsequently with more sophisticated genetic methods) became a powerful tool in sorting out the problematic Pteromalidae. As a result of recent work combining biology (particularly feeding behaviour), molecular data and morphology, what had been a superfamily of 22 families became, almost overnight, one with 45 families. Our friend Oodera, with only one genus, has been elevated to family status (Ooderidae) along with 22 other new families, all formerly subfamilies or in some cases tribes of Pteromalidae. Read more: https://lnkd.in/dRiNrfXy Sida

Integrative taxonomy approach to detect spatial and temporal variability of the Mediterranean benthic communities through artificial substrate units (ASUs) - Frontiers in Marine Science: Monitoring spatial and temporal changes of marine benthic communities using standardized procedures is essential to take necessary steps towards conservation of marine ecosystems. In this study we combined Artificial Substrate Units (ASUs) for sampling of benthic communities, with integrative taxonomy approach that incorporated morphological identification of organisms and COI DNA metabarcoding, to characterize the diversity of communities at three locations across the Central Mediterranean Sea (Livorno and Palinuro, Italy; Rovinj, Croatia) in 2019 and 2020. Significant differences in the communities’ structure were observed both at large spatial scale between sampled locations, and at small spatial scale (less than ten kilometers) between sites. Moreover, significant temporal variability in species richness and structure of benthic assemblages was detected, with higher richness in 2020. Revealed variability can probably be attributed to the peculiar geomorphological, oceanographical, and ecological features of locations, but also to the influence of interplaying local chemical and physical factors and biological processes such as species settlement, competition, and migration that can act at small spatial and temporal scales. The similarity in the species composition and community structure accessed by morphological and metabarcoding approaches was low, with only 16% of the species (out of 133 species identified overall) commonly detected by both approaches. This is mostly both due to a lack of data on COI sequences of numerous benthic invertebrates in the public barcoding databases on the one hand, and difficulties in detecting small and cryptic taxa through morphological analyses on the other. This suggests that combining of two approaches is required to fully describe the biodiversity of benthic assemblages. Finally, comparison of the spatial variability of the benthic communities’ structure with two approaches at different taxonomic levels, indicated that genus and family levels give results that are consistent to those obtained by the species level. This suggests that family level might be satisfactory in monitoring the spatial-temporal variability of Mediterranean hard bottom benthic communities. https://lnkd.in/et2G2x6A

It is that day of the year again.... World Taxonomist Appreciation Day! And this day is enthousiastically celebrated by the World Register of Marine Species (WoRMS). And as for previous years, the World Register of Marine Species (WoRMS) has again released its annual list of the top-ten marine species described by researchers during the past year to coincide with this day. Every day in labs, museums, and out on fieldwork, taxonomists are busy collecting, cataloguing, identifying, comparing, describing, and naming species new to science. Over 300 taxonomists globally also contribute their valuable time to keeping the World Register of Marine Species up to date. Today is a chance for us at WoRMS to thank our taxonomic editors for this important task. We celebrate the work of taxonomists now with the WoRMS list of the top-ten marine species described in 2023 as nominated and voted for by taxonomists, journal editors and WoRMS users! This top-ten list is just a small highlight of about 2,000 fascinating new marine species discovered every year (there were almost 2000 marine species described in 2023 and added to WoRMS, including some 330 fossil species). Each of these marine species has a story. This year the chosen species cover the weird, the bewildering and the astonishing! We feature, amongst others, a beautifully colored nemertean, a carnivorous sponge, and a giant extinct penguin. Curious about the actual list? Quickly check out the full press release at https://lnkd.in/ey_nkRKU, or jump to our Top 10 of 2023 immediately at https://lnkd.in/eUB_jMa4. #marinespecies #VLIZ #LifeWatch #toptenmarinespecies #taxonomistappreciationday #OceanDecade #GenOcean #marinelife #oceancensus

Taxonomy, the science of naming and classifying organisms, is the foundation for conserving disappearing plants and animals. Yet the field — often viewed as an archaic, dusty tradition that harks back to intrepid 19th-century botanists describing the plants of newly colonized lands — is dying. Several decades after the taxonomic frenzy of 1830 to 1920, when Western scientists went deep into far-flung regions of the world, molecular genetics revolutionized our ability to classify species, and began vacuuming up funding while the analog field of taxonomy was left to languish. #sustainability #plants #flora #science #biology #environmental #nature #conservation #botany #climatechange #evolution

My first paper is out now in Review of Palaeobotany and Palynology!😁 "Optimisation of classification methods to differentiate morphologically-similar pollen grains from FT-IR spectra" https://lnkd.in/ezWvQmiR #pollen #palynology #ftir #classification #sporopollenin #randomforest

My first paper as a post-doc with Amro Zayed at York University 🐝🌿 https://lnkd.in/gcMJY3h6 Background: The mutualistic interaction between entomophilous plants and pollinators is fundamental to the structure of most terrestrial ecosystems. The sensitive nature of this relationship has been disrupted by anthropogenic modifications to natural landscapes, warranting development of new methods for exploring this trophic interaction. Characterizing the composition of pollen collected by pollinators, e.g. Apis mellifera, is a common means of exploring this relationship, but traditional methods of microscopic pollen assessment are laborious and limited in their scope. The development of pollen metabarcoding as a method of rapidly characterizing the abundance and diversity of pollen within mixed samples presents a new frontier for this type of work, but metabarcoding may have limitations, and validation is warranted before any suite of primers can be confidently used in a research program. We set out to evaluate the utility of an integrative approach, using a set of established primers (ITS2 and rbcL) versus melissopalynological analysis for characterizing 27 mixed-pollen samples from agricultural sites across Canada. Results: Both individual markers performed well relative to melissopalynology at the family level with decreases in the strength of correlation and linear model fits at the genus level. Integrating data from both markers together via a multi-locus approach provided the best rank-based correlation between metagenetic and melissopalynological data at both the genus (ρ = 0.659; p < 0.001) and family level (ρ = 0.830; p < 0.001). Species accumulation curves indicated that, after controlling for sampling effort, melissopalynological characterization provides similar or higher species richness estimates than either marker. The higher number of plant species discovered via the metabarcoding approach simply reflects the vastly greater sampling effort in comparison to melissopalynology. Conclusions: Pollen metabarcoding performed well at characterizing the composition of mixed pollen samples relative to a traditional melissopalynological approach. Limitations to the quantitative application of this method can be addressed by adopting a multi-locus approach that integrates information from multiple markers.