Preliminary Phylogenetic Analysis Research Articles

A new elasmosaurid (Sauropterygia, Plesiosauria) from the upper levels of the La Colonia Formation (upper Maastrichtian), Chubut Province, Argentina

A new elasmosaurid, Chubutinectes carmeloi gen. et sp. nov., from the Chubut Province, Argentina, is described. The holotype and only specimen of this species (MPEF-PV 5232) was collected from the La Colonia Formation. Chubutinectes carmeloi gen. et sp. nov. is among the few upper Maastrichtian elasmosaurids from the Southern Hemisphere whose postcranial anatomy is well known. It can be distinguished from other elasmosaurids by the following combination of characters: middle cervical centra longer than high with lateral keel and bilobate articular faces; pectoral and anterior dorsal centra with bilobate articular faces; coracoids with closed cordiform fenestra and long anterior coracoids process; high ratio coracoids/scapular length; ilium with angled shaft; pubis with small lateral cornua; humerus with posterior expansion ending in accessory facet and epipodial facets of humerus almost aligned; accessory ossification between tibia and tibial, and radius and radial. Preliminary phylogenetic analysis recovered Chubutinectes carmeloi gen. et sp. nov. within the Weddellonectia clade, including the Late Cretaceous Wedellian aristonectine elasmosaurids. The study of the associated microfossiliferous assemblages (micro- and nanofossils) suggests a marine inner neritic paleoenvironment, with restricted circulation and warm waters. The presence of Micula prinsii and Micula murus at this latitude indicates a latest Maastrichtian age, upper part of the UC20d sub-biozone and younger than ∼67,3 Ma.

On Procobus Khomenko, 1913 (Mammalia: Artiodactyla: Bovidae), with new evidence from the Late Miocene of Greece

Procobus is a rare and controversial Late Miocene bovid genus (Artiodactyla, Bovidae), originally known by a few cranial remains from the northern shores of the Black Sea. New material from Dytiko-1 fossil site in Axios Valley, northern Greece expands its geographic and chronological distribution and provides additional craniodental characters for its definition. A thorough description and comparison of all available specimens from Greece, Moldova and Ukraine highlight differences from the similar-sized and sympatric Palaeoryx and permit re-discussing its phylogenetic relationships. Our data reject previously proposed relations with Reduncini and suggests Procobus as a pan-Caprini, unique among Late Miocene bovid genera by the combination of large size and long, paedomorphic horns curving forward. A preliminary phylogenetic analysis indicates Procobus as the sister taxon of crown Caprini+Pantholops (Tibetan antelope) lineage.

A new species of the mud shrimp genus Naushonia Kingsley, 1897 (Decapoda: Gebiidea: Laomediidae) from the Ryukyu Islands, southwestern Japan, inhabiting burrows of an axiidean shrimp.

A new species of the laomediid mud shrimp genus Naushonia Kingsley, 1897 is described and illustrated based on seven specimens collected from Okinawa Island, Ryukyu Islands, southwestern Japan. All specimens of Naushonia karashimai n. sp. were collected from burrows of a large axiidean shrimp, Neaxius acanthus (A. Milne-Edwards, 1879), which inhabits seagrass beds in inner reef lagoons. The new species is easily distinguished from all 16 known congeners by its tridentate rostrum and relatively narrow pereopod 1 palm with a proximally located pollex. Sequences of the mitochondrial 16S rRNA and COI genes were newly generated for five species and two species of Naushonia, including the new species, respectively. Preliminary phylogenetic analysis using sequences of the 16S rRNA gene was performed.

A new species of planthopper in the genus Jamaha (Hemiptera: Fulgoroidea: Nogodinidae) from the Northeastern coast of Jamaica

A new species of Jamaha Gnezdilov & O'Brien, 2008, is described from Jamaica and compared with other species in the genus. A key to the species of Jamaha is provided. Molecular data for the five-prime region of the cytochrome c oxidase subunit I (COI) gene and 18S rRNA gene is provided and compared to available Colpopterini, with other Nogodinidae as the outgroup, for a preliminary phylogenetic analysis. While the Colpopterini grouped with high support, these data remain too sparse to draw firm conclusions.

The Application of High-Resolution Melting Analysis to trnL (UAA) Intron Allowed a Qualitative Identification of Apple Juice Adulterations

Food authenticity plays a pivotal role in the modern age since an increased consumers awareness has led them to pay more attention to food commodities. For this reason, it is important to have reliable and fast techniques able to detect possible adulterations in food, which affect qualitative and economic value. Therefore, the aim of this study was to detect possible adulterations in apple juice from others fruit species (i.e., pear, peach, and kiwi) combining DNA barcoding approach, using trnL (UAA) intron, with high resolution melting analysis (HRMA). A preliminary phylogenetic analysis, using sequences retrieved by the GenBank, confirmed the discriminatory power of trnL (UAA) intron among the four fruit species examined. Moreover, the sequencing of the trnL (UAA) fragments obtained from apple, pear, peach, and kiwi, demonstrated the suitability of an inner shorter sequence, P6 loop, to differentiate the considered species. The HRMA coupled with trnL (UAA) intron allowed discrimination among the four fruits but provided incomplete results for juices. Whereas the HRMA targeting the P6 loop amplicons confirmed the suitability of the technique to qualitatively distinguish fruit juices composed by the combination of apple/pear and apple/peach. However, the impossibility of discriminating apple/kiwi juices from the pure kiwi sample highlighted limitations, most likely related to the DNA extraction process. This hypothesis was further confirmed by analyzing DNA blends obtained by combining nucleic acids extracted from pure matrixes (i.e., apple and kiwi fruits). In this specific case, the application of HRMA allowed both qualitative and quantitative assessment of the samples.

Degree of Dietary Specialization on Furanocoumarin-Containing Hostplants in a Newly Invasive Web Building Caterpillar.

The genus Depressaria (Lepidoptera: Depressariidae) mostly comprises specialist herbivores with varying capacity for detoxification of defensive phytochemistry. Depressaria depressana, a Eurasian moth recently introduced into North America, is a family-level specialist of the Apiaceae, whose hosts include more than a dozen species in multiple tribes; Depressaria radiella is a super-specialist of Eurasian origin that feeds exclusively on species in the genera Pastinaca and Heracleum throughout its native and introduced range. In eastern North America, it feeds upon Pastinaca sativa, an invasive European species, and Heracleum maximum, a native species. We determined whether differences in furanocoumarin metabolism exist between D. depressana and two isolated populations of D. radiella, feeding exclusively on either P. sativa or H. maximum. We also compared gravimetric estimates of feeding efficiency to assess D. depressana larval performance on different diets. Both populations of D. radiella metabolized furanocoumarins at a greater rate than D. depressana. Although there was no difference in rates of metabolism of linear furanocoumarins in the two populations of D. radiella, individuals collected from H. maximum metabolized angular furanocoumarins more rapidly. The gravimetric assessments of feeding efficiencies revealed that D. depressana exhibited highest efficiencies consuming Daucus carota; moreover, this species survived to pupation consuming fruits of Zizia aurea, an apiaceous species native to North America. Our preliminary phylogenetic analysis, building on an earlier morphological analysis, incorporates mitochondrial cytochrome oxidase subunit 1 data from the BOLD database and revealed that the presence or absence of furanocoumarins is not a strong predictor of species-level evolution in Depressaria.

Morphology of larvae and pupae of the genus Autocrates (Coleoptera: Trictenotomidae) and its phylogenetic implications

The trictenotomid genus Autocrates Thomson, 1860 is remarkable for its large and robust adults, but its larval morphology and bionomics have been unknown over the last 160 years. Here, we describe and illustrate in detail the eggs, and also the first and last instar larva and the pupa of Autocrates maqueti Drumont, 2006, based on specimens reared from identified adults collected in South Korea. The first instar larva is very similar to the known trictenotomid larvae of the genus Trictenotoma Gray, 1832, sharing the following features: distinctly flattened and parallel-sided, well-sclerotized head and largely unpigmented postcephalic body, lyre-shaped frontal arms, very short coronal suture, five pairs of stemmata, asymmetrical and tridentate mandibles with mola, simple and apically upturned urogomphi, and absence of longitudinal ridges on the thorax and abdomen. Differences occur in the primary chaetotaxy. The last instar larva is almost identical with Trictenotoma in general appearance, but the longitudinal tergal ridges of Autocrates are much denser and more widely distributed than those of Trictenotoma. Our preliminary assessment of features of immature stages confirms a close relationship of Trictenotomidae with the “salpingid group”, i.e. Salpingidae, Boridae, Pyrochroidae and Pythidae. A sister group relationship with Pythidae is likely. The putative synapomorphy is the subdivision of the ventral element of tergites IX, even though this condition is not visible in the first instars of Autocrates, and quite indistinct (but recognizable) in the last larval stage. The complete mitochondrial genome of A. maqueti is provided. A preliminary phylogenetic analysis of trictenotomid species is presented using two mitochondrial genes (16S and COI). The morphology of eggs and biological information on feeding and oviposition behaviors are also provided with photographs of adults and eggs.

Additions to the genus Anthinus occurring in Minas Gerais and Goiás regions, Brazil, with description of five new species, one of them in the new related genus Catracca (Gastropoda, Eupulmonata, Strophocheilidae).

Four new species of the strophocheilid genus Anthinus are described from Brazil, being A. synchondrus from region of Unaí, Minas Gerais; A. vailanti from the region of Brasilândia de Minas, Minas Gerais; A. morenus from Paracatu region, Minas Gerais; and A. savanicus from Formosa region, Goiás. Another similar snail from Itacarambi, Minas Gerais, is described as a new genus and species: Catracca uhlei. All species are described conchologically and anatomically, with distinctions explored in almost all structures. For comparative purposes, a similar anatomical investigation on the Anthinus type species, A. multicolor, from Rio de Janeiro, is also performed. A detailed comparative analysis and discussion is provided, including taxonomic and initial phylogenetic inferences. The preliminary phylogenetic analysis is based on anatomically known species in the literature and in the presently study. A bulimulid, a simpulopsid and two dorcasiids are outgroups. The preliminary cladogram already shows a monophyletic Strophocheilidae (14 synapomorphies), divided into two also monophyletic subfamilies: Megalobuliminae (14 synapomorphies) and Strophocheilinae (5 synapomorphies). The new Catracca resulted as the most basal strophocheilid branch. Mirinaba and Anthinus were also supported as monophyletic (3 and 6 synapomorphies respectively. Register ZooBank: urn:lsid:zoobank.org:pub:FC4DD323-EF6A-404B-9755-F124F9DBB6D4.

A closer look reveals hidden diversity in the intertidal Caribbean Fortuyniidae (Acari, Oribatida).

A molecular genetic and morphometric investigation revealed the supposedly widespread Caribbean and Western Atlantic intertidal oribatid mite species Fortuynia atlantica to comprise at least two different species. Although there are no distinct morphological differences separating these taxa, COI and 18S sequence divergence data, as well as different species delimitation analyses, clearly identify the two species. Fortuynia atlantica is distributed in the northern Caribbean and the Western Atlantic and the new Fortuynia antillea sp. nov. is presently endemic to Barbados. Vicariance is supposed to be responsible for their genetic diversification and stabilizing selection caused by the extreme intertidal environment is suggested to be the reason for the found morphological stasis. The genetic structure of Fortuynia atlantica indicates that Bermudian populations are derived from the northern Caribbean and thus support the theory of dispersal by drifting on the Gulf Stream. Haplotype network data suggest that Bermudian and Bahamian populations were largely shaped by colonization, expansion and extinction events caused by dramatic sea level changes during the Pleistocene. A preliminary phylogenetic analysis based on 18S gene sequences indicates that the globally distributed genus Fortuynia may be a monophyletic group, whereas Caribbean and Western Atlantic members are distinctly separated from the Indo-Pacific and Western Pacific species.

Female Genital Variation Far Exceeds that of Male Genitalia: A Review of Comparative Anatomy of Clitoris and the Female Lower Reproductive Tract in Theria.

SynopsisA review of the literature on the anatomy of the lower female genital tract in therian mammals reveals, contrary to the general perception, a large amount of inter-specific variation. Variation in females is anatomically more radical than that in the male genitalia. It includes the absence of whole anatomical units, like the cervix in many Xenarthra, or the absence of the urogenital sinus (UGS), as well as the complete spatial separation of the external clitoral parts from the genital canal (either vagina or UGS). A preliminary phylogenetic analysis shows two patterns. Some morphs are unique to early branching clades, like the absence of the cervix, while others arose multiple times independently, like the flattening out or loss of the UGS, or the extreme elongation of the clitoris. Based on available information, the ancestral eutherian configuration of the external female genitalia included a cervix, a single vaginal segment, a tubular UGS, and an unperforated clitoris close to the entrance of the genital canal. The evidence for either bilobed or unitary glandes clitorides is ambivalent. Despite the wealth of information available, many gaps in knowledge remain and will require a community-wide effort to come to a more robust model of female genital evolutionary patterns.

Revealing the Cryptic Diversity of Wood-Inhabiting Auricularia (Auriculariales, Basidiomycota) in Europe

Some unusual specimens of the wood-inhabiting fungus Auricularia auricula-judae have been studied using morphological and molecular methods. As expected from external features, we describe a new species Auricularia cerrina sp. nov. Sequencing of the ITS region confirms differences from other species of Auricularia, and preliminary phylogenetic analysis is presented. Auricularia cerrina is characterized by blackish fruitbodies in fresh conditions with the combined presence of the medulla layer and small spores compared with Auricularia auricula-judae. The new species is based on specimens from the Czech Republic (central Europe) of Quercus cerris. Colour photographs in situ of fruitbodies and some microscopic photos are provided.

Zapada (Plecoptera: Nemouridae), a stonefly genus new to the fauna of China.

A new species of Zapada Ricker, 1952, Zapada kondratieffi sp. nov. from central Sichuan Province of China is described and illustrated, which represents the first record of the genus in China. The new species is characterized mainly by the presence of five simple cervical gills, vestigial inner paraproct lobe, and absence of paraproct spines. The preliminary molecular phylogenetic analysis using COI sequences recovered the relationship among eight species of Zapada and supports the close relationship between Z. kondratieffi and Zapada frigida (Claassen, 1923).

El género Muellera L. f. en Mesoamérica y norte de Sudamérica

Se realizó un análisis filogenético preliminar, con secuencias de los espaciadores internos transcritos del rDNA (nrITS) nrITS, apoyando la ubicación de Muellera como entidad monofilética, hermana del género Dahlstedtia, siendo ambos grupos hermanos de Lonchocarpus. Se estudiaron 13 especies de Muellera de Mesoamérica y norte de Sudamérica; se hacen tres cambios nomenclaturales de Lonchocarpus a Muellera; se describen tres especies nuevas para la ciencia: Muellera amazonica, M. burkartii y M. chocoensis. Además se describen e ilustran a M. frutescens, M. tubicalyx y M. unifoliolata y se presenta una clave dicotómica para contrastar las diferencias entre los componentes reconocidos del género.

A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex

The genus Ocotea (Lauraceae) includes about 450 species, of which about 90% are Neotropical, while the rest is from Macaronesia, Africa and Madagascar. In this study we present the first complete chloroplast genome sequences of seven Ocotea species, six Neotropical and one from Macaronesia. Genome sizes range from 152,630 (O. porosa) to 152,685 bp (O. aciphylla). All seven plastomes contain a total of 131 (114 unique) genes, among which 87 (80 unique) encode proteins. The order of genes (if present) is the same in all Lauraceae examined so far. Two hypervariable loci were found in the LSC region (psbA-trnH, ycf2), three in the SSC region (ycf1, ndhH, trnL(UAG)-ndhF). The pairwise cp genomic alignment between the taxa showed that the LSC and SSC regions are more variable compared to the IR regions. The protein coding regions comprise 25,503–25,520 codons in the Ocotea plastomes examined. The most frequent amino acids encoded in the plastomes were leucine, isoleucine, and serine. SSRs were found to be more frequent in the two dioecious Neotropical Ocotea species than in the four bisexual species and the gynodioecious species examined (87 vs. 75–84 SSRs). A preliminary phylogenetic analysis based on 69 complete plastomes of Lauraceae species shows the seven Ocotea species as sister group to Cinnamomum sensu lato. Sequence divergence among the Ocotea species appears to be much lower than among species of the most closely related, likewise species-rich genera Cinnamomum, Lindera and Litsea.

An integrative study of Pannaria hookeri (Ascomycota lichenized) from Argentina and the update of the taxon circumscription based on specimens from the Northern and Southern Hemispheres

Pannaria hookeri (Borrer ex Sm.) Nyl. is reported as a bipolar cyanolichen that occurs in more than twenty countries in both Hemispheres. In the Northern Hemisphere, a minor variation is attributed to the species, whereas larger morphological and chemical variations have been reported in specimens from the Southern Hemisphere. Six P. hookeri DNA sequences are available in GenBank, and only one (from Australia) is associated with a published morphological description. In this study, we performed a preliminary phylogenetic analysis including seven nuITS and mtSSU sequences from eight specimens collected in south Argentina. In addition, we provide an update of the taxon circumscription based on 50 specimens from 13 countries. Here, the molecular analyses revealed a well-supported monophyletic group formed by the P. hookeri sequences from Argentina, Australia, Norway and USA (Alaska). Regarding the morphological and anatomical characteristics, the Southern Hemisphere specimens did not present the historical reported variations, resulting in the proposition of a concise species description that accomplishes most of P. hookeri known geographical distribution.

DIVERSITY AND PHENETIC STUDY ON SYCONIUM OF FICUS L. (MORACEAE) FROM KERALA, INDIA REVEALING NATURAL CLASSIFICATION ALONG WITH AN IDENTIFICATION KEY

NAIR, S. S., BACHAN, K. H. A. & EBIN, P. J. 2021. Diversity and phenetic study on syconium of Ficus L. (Moraceae) from Kerala, India revealing natural classification along with an identification key. Reinwardtia 20(1): 27–36. — Ficus L. commonly called ‘figs’ is one of the most complex genera among the angiosperms with its specialised inflorescence called syconium that looks like a fruit. Syconium of 33 species of Ficus reported from Kerala were observed here to develop a novel key, solely based on syconium morphology. Numerical taxonomic methodology for syconium morphological characters were standardised, considering 22 characters with 104 character states and analysed using similarity clustering. The floral features of the genus are very much complex and all the existing keys for the species identification relays on both vegetative as well as floral features. Hence, the present key will be practical in use when syconium is the only available part. The numerical analysis of the syconium features well clustered and separated the trees with cauliflorous inflorescence, hemi epiphytic -epiphytic life forms and independent trees similar to the natural classification of the figs as “Atthi, Itthi and Aal”, indicating that phenetic analysis using the syconium characters alone provided a grouping similar to the natural grouping based on the habit. Preliminary phylogenetic analysis of figs also provided a similar clustering. This gives an insight into the fact that the separation of figs into these natural groups is reflecting phylogenetic trait. Detailed studies including more morphological traits and molecular analysis could establish the phylogenetic relation of figs in relation to the evolutionary history of climate and vegetation.

First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy).

The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.

A coadunation of biological and mathematical perspectives on the pandemic COVID-19: A Review

Background: Coronavirus disease 2019 (COVID-19) outbreak has created an emergency globally, and social distancing and isolation is the only solution to prevent its spread. Several countries have announced full lockdown to tackle this pandemic. The coronavirus family is inclusive of pathogens of both – animal species and humans, encapsulating the isolated severe acute respiratory syndrome coronavirus (SARS-CoV). Researchers round the globe have been dexterously working to decode this lethal virus. Many mathematical frameworks have also been depicted which have helped to understand the dynamics of the COVID-19. Methods: This systematic review highlights the virus genomic composition, preliminary phylogenetic analysis, pathogenesis, symptomatology, diagnosis, and prognosis along with mathematical models of disease transmission and dynamics. Results: Our preliminary phylogenetic analysis of the novel coronavirus sequence discerns that although shares its lineage with SARS, BAT-CoV, Beta-BAT-SARS,however, this protein is highly dissimilar to its ancestors. The widely prominent amino acid residues found in the protein are alanine (ALA), aspartic acid (ASP), phenylalanine (PHE), leucine (LEU), aspartic acid (ASP), threonine (THR), valine (VAL), tyrosine (TYR) and asparagine (ASN) that are responsible for its replication process. Conclusion: Research on coronaviruses continues towards developing a strong understanding of the rapidly evolving viral replication and its transmission between individuals.

Report of a giant titanosaur sauropod from the Upper Cretaceous of Neuquén Province, Argentina

One of the most fascinating research topics in the field of sauropod dinosaurs is the evolution of gigantism. In the particular case of Titanosauria, the record of multi-ton species (those exceeding 40 tons) comes mainly from Patagonia. The record of super-sized titanosaur sauropods has traditionally been extremely fragmentary, although recent discoveries of more complete taxa have revealed significant anatomical information previously unavailable due to preservation biases. In this contribution we present a giant titanosaur sauropod from the Candeleros Formation (Cenomanian, circa 98 Ma) of Neuquén Province, composed of an articulated sequence of 20 most anterior plus 4 posterior caudal vertebrae and several appendicular bones. This specimen clearly proves the presence of a second taxon from Candeleros Formation, in addition to Andesaurus, and is here considered one of the largest sauropods ever found, probably exceeding Patagotitan in size. While anatomical analysis does not currently allow us to regard it as a new species, the morphological disparity and the lack of equivalent elements with respect to coeval taxa also prevent us from assigning this new material to already known genera. A preliminary phylogenetic analysis places this new specimen at the base of the clade leading to Lognkosauria, in a polytomy with Bonitasaura. The specimen here reported strongly suggests the co-existence of the largest and middle-sized titanosaurs with small-sized rebbachisaurids at the beginning of the Late Cretaceous in Neuquén Province, indicating putative niche partitioning. This set of extremely large taxa from Patagonia has contributed to a better understanding of the phylogenetic relationships of titanosaurs, revealing the existence of a previously unknown lineage and shedding new light on body mass evolution.

Undressing Lophodoris danielsseni (Friele & Hansen, 1878) (Nudibranchia: Goniodorididae)

Lophodoris G. O. Sars, 1878 is a small genus of goniodoridid nudibranchs that includes only two species: the type species, Lophodoris danielsseni (Friele & Hansen, 1876), and Lophodoris scala Er. Marcus & Ev. Marcus, 1970. Sars (1878) erected Lophodoris in a footnote, without comment. Forty-four years later, Odhner (1922) finally described the type species and defined the diagnostic characteristics of Lophodoris. Lophodoris danielsseni is well differentiated among Goniodorididae species by a dorsal crest and jagged notum margin supported by spicules. However, the description of this species is still incomplete since information on the reproductive system or spicules pattern is not known. In the present work, we study freshly collected specimens of Lophodoris danielsseni (Friele & Hansen, 1876) from near the type locality. Morphological analyses are performed using micro-computed tomography as well as by dissections. We include the first scanning electron microscope photographs of the radula, labial cuticle, and penial spines. Moreover, we carry out a preliminary phylogenetic analysis using barcoding and including five out of eight genera belonging to the family Goniodorididae. Result shows for the first time its phylogenetic relationship within the family, separating each genus included. However, further species must be sequenced to clarify the evolutionary relationship among Goniodorididae species and genera.