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One fundamental project of biology is to determine which groups of organisms are “the same” and which are different, for taxonomic purposes but more fundamentally so that one can make general, meaningful claims about specific groups. Traditional bifurcating taxonomies have been and remain useful. However, what was designed to name unchanging “natural kinds” of relatively large organisms with distinct morphologies is not adequate for grouping and dividing very small organisms, reticulated histories, endosymbiosis, horizontal gene transfer, asexual reproduction, or ecosystems. Biological explanations need to be flexible enough to account for hierarchically embedded processes and structures at vastly different scales, from the molecular to the global. Modern biology has moved beyond naming things, and biological explanations now require more sophisticated ontologies.
The subfamily Polycerinae includes eight genera, from the monospecific Lamellana and Lecithophorus to the diverse Polycera and Gymnodoris, with 33 and 26 valid species, respectively. The monophyly of the subfamily has been tested by molecular data although not all genera were included. To date, relationships within the subfamily are not supported. In the present paper, three new species of polycerid nudibranchs are fully described based on specimens collected in Marshall Islands and Australia: one Palio species (Palio gaeli sp. nov.), one Polycera species (Polycera nimbsi sp. nov.) and a new genus (Paliota galactica gen. and sp. nov.). The new genus is described based on its peculiar radular teeth and genetic divergence.
The internal anatomy was studied by dissections and scanning electron microscope photographs. Partial sequences of mitochondrial cytochrome oxidase c subunit I (COI) and 16S ribosomal RNA (16S) as well as nuclear histone H3 (H3) were also obtained. A phylogenetic framework for two of these three species is proposed, also including for the first time the species Paliolla templadoi and Polycera melanosticta.
Combining the biogeography and phylogenetic patterns of parasite-host associations allows a better understanding of the history of parasite–host interactions, which can be achieved via biogeographic regionalization incorporating phylogenetic information. Recently, the concepts of evoregions (regions where a majority of species evolved from one or several ancestors inhabiting these regions) and evolutionary transition zones (regions of high phylogenetic turnover) have been proposed, coupled with a classification approach for these concepts. We applied this approach to 206 flea species and 265 host species of the Palearctic and aimed to identify evoregions and evolutionary transition zones for both fleas and hosts and to understand whether these evoregions and transition zones match each other. We identified 5 evoregions with 3 transition zones for either fleas or hosts, but neither the positions and boundaries of the flea and host evoregions nor the transition zones coincided. Indications of multiple geographic centres of diversification of the same flea lineages suggested that (a) the common evolutionary history of fleas and hosts was characterized by multiple events other than codiversification and that (b) dispersal played an important role in flea and host assemblies. Barriers to dispersal could be represented by landscape features (deserts and mountain ranges) and/or climate differences.
There is still a high diversity of lichen-forming fungi that remains undescribed, especially cryptic lineages at the species level. Integrating morphological, chemical, and DNA sequence data has proved useful in corroborating species descriptions and delimitations. Here we reviewed morphological features, secondary metabolites and the DNA sequences of ITS, mtSSU and nuLSU markers to study the diversity of Xanthoparmelia in southern Africa. A total of 37 species were recorded. Three of these appear undescribed, and we therefore describe them here as new: Xanthoparmelia nimisii, with a sorediate thallus and broad lobes, is well supported as a clade separate from X. annexa; X. pseudochalybaeizans with a white medulla is phylogenetically distinct from the otherwise similar X. chalybaeizans; and X. sipmaniana, well supported as a separate clade from the similar X. hypoprocetrarica. In addition, the separation of Xanthoparmelia capensis and X. tinctina requires further studies.
During a study of the incompletely known lichen flora of the Caucasus, we analyzed 237 specimens of corticolous Bacidia s. str. collected in the Northern and Southern Caucasus, including Armenia, Azerbaijan, Georgia, and Russia. Of these, 54 specimens belonging to 11 species of Bacidia s. str. were selected for molecular studies, representing the observed morphological variability of the genus. We obtained 142 sequences from three RNA-coding genes (nrITS, nrLSU, and mtSSU) and two protein-coding genes (RPB1 and RPB2). The single and concatenated datasets were complemented with Bacidia s. str. sequences from GenBank and subjected to Bayesian inference and two maximum likelihood analyses (RAxML and IQ-TREE). The resulting trees yielded highly concordant topologies of the groups and corresponded with previous results, supporting two main clades correlating with apothecia pigmentation. Our analyses are the first to reveal the presence of Bacidia heterochroa in the Caucasus. An exceptionally high degree of morphological plasticity was found in the Rubella and Suffusa groups. As a result of morphological examination and phylogenetic results, B. caucasica (Suffusa group) was described as new to science. Furthermore, two putative taxa in the Rubella group, Bacidia inconspicua ined. and B. maritima ined., were introduced. This study furthers our understanding and documentation of the understudied lichen flora of the Caucasus, bringing the total number of Bacidia species for the region to 13.
The manna lichens, a group of vagrant species with subfruticose and subfoliose thalli in the genus Circinaria Link, have received attention for millennia. Here, a new manna lichen species, Circinaria nimisii sp. nov. (Megasporaceae), is described and illustrated. This vagrant lichen is found on Mount Olympus in Greece and is the fourth known manna lichen in Europe. The new taxon is characterized by its subfruticose, densely-branched thallus with a muddy, earthy colour, whitish pseudocyphellae on tips of branches, mature apothecia distinctly adnate to stipitate, and paraplectenchymatous cortex tissue. Molecular sequence data from the standard barcoding marker (nrITS) also corroborate the distinction of this species from closely related congeners. Finally, Agrestia zerovii, previously known only from its type locality in Ukraine, is proposed as a new synonym of Circinaria hispida.
Porina is a widely distributed, species-rich genus of crustose, lichen-forming fungi, some with thalline outgrowths that have been recognized as isidia. We studied three taxa with thalli consisting chiefly of ascending isidioid structures occurring on trunks and branches of Taxodium in southwestern Florida, and provide details of their structure with light and electron microscopy. Two of these taxa we describe as new species: P. microcoralloides and P. nanoarbuscula. Genetic sequences (mtSSU) suggest that they are closely related to each other, yet they differ markedly in the size, morphology and anatomical organization of their isidioid branches as well as in the length of their ascospores. In the three Floridian taxa studied, the crustose portion of the thallus is partly endophloeodic and partly superficial, the latter often patchy, evanescent or inconspicuous, and completely lacks the differentiated anatomical organization characteristic of the isidioid structures arising from it. In Porina microcoralloides, the ascendant thallus consists of branched, coralloid inflated structures with phycobiont (Trentepohlia) unicells arranged at the periphery of a loose central medulla. Sparse fungal cells are interspersed and overlie the algal layer in places, but no differentiated cortex is present, leaving phycobiont cells more or less exposed at the surface. In the closely related Porina nanoarbuscula, the isidioid structures are much finer, more densely branched, and composed of a single, central file of roughly spherical Trentepohlia cells surrounded by a jacket of subglobose fungal cells. The ascospores of P. microcoralloides are more than twice the length of those of P. nanoarbuscula. Although thalli of these two Porina species occur in the same habitats and are sometimes found growing alongside each other, phylogenetic analysis of rbcL sequences suggest that they partner with distinct clades of Trentepohlia phycobionts. A third taxon examined, Porina cf. scabrida, is morphologically rather similar to P. microcoralloides, but the ascendant branches are bright yellow-orange, more cylindrical, and corticated by a thin layer of agglutinated fungal hyphae; perithecia were not seen. Analysis of mtSSU sequences places it distant from P. microcoralloides and P. nanoarbuscula phylogenetically. None of the Floridian taxa studied was particularly close to the European isidiate species Porina hibernica and P. pseudohibernica, which appeared as sister to each other in the analysis. While a particular type of isidiose structure may be reliably characteristic of specific taxa, similarities or differences in these structures do not seem to be useful indicators of phylogenetic proximity or distances among taxa. The morphological trends evident in Porina suggest that multiple transitions from crustose to isidioid or microfruticose growth have arisen repeatedly and in quite different ways within this single genus. At least some of the diverse structures treated within the broad concept of isidia may be representative of the developmental pathways by which fruticose growth forms may arise.
Our floristic work in British ancient forests resulted in a description of a frequently reported but misidentified species, Coenogonium nimisii. Its thallus is very similar to Porina rosei, but the apothecia and pycnidia correspond with C. luteum. Sterile collections are not easy to distinguish but the new species differs from P. rosei in several microscopic characters of the isidia. Coenogonium nimisii is so far known from bark and epiphytic bryophytes, rarely mossy rocks, in ancient humid forests of Great Britain and Ireland. The genus Coenogonium is poorly represented by molecular data in the GenBank database. Our preliminary results revealed distinct genetic lineages within two traditionally circumscribed species, C. luteum and C. pineti, which may represent cryptic species.
Furcocercariae of the genus Neodiplostomum Railliet, 1919 (Diplostomidae Poirier, 1886) were found in freshwater snails Helicorbis sujfunensis Starobogatov, 1957 (Planorbidae Rafinesque, 1815) collected from three localities in the Russian southern Far East. For the trematodes from each locality, frogs played the role of the second intermediate host, and rats were the definitive host. Chickens were insusceptible to infection. The morphological and molecular data obtained for these trematodes indicated they were representatives of the same species. The experimentally-derived adult individuals were morphometrically similar to the East Asian Neodiplostomum seoulense (Seo, Rim, Lee, 1964), Neodiplostomum oriolinum Oschmarin, 1963, Neodiplostomum leei Chai and Shin, 2002, and Neodiplostomum boryongense Shin et al., 2008. Analysis of available data on the life cycle, developmental stage morphology, and molecular genetic characteristics of East Asian Neodiplostomum revealed a lack of information for objective assessment of the species status of neodiplostomula found in the East Asia region. Based on the considerations above and the data for the cox1 marker, we named the trematode Neodiplostomum cf. seoulense (Seo, Rim, Lee, 1964) sensu Pyo et al., 2014. In a phylogenetic reconstruction based on nuclear and mitochondrial markers, neodiplostomulas clustered into geographically related groups: South American, North American, European, and East Asian, with the former occupying an external position in the tree, which may indicate South America as a center of Neodiplostomum speciation.
Cruznema velatum isolated from soil in a chestnut orchard located at Guangdong province, China, is redescribed with morphology, molecular barcoding sequences, and transcriptome data. The morphological comparison for C. velatum and six other valid species is provided. Phylogeny analysis suggests genus Cruznema is monophyletic. The species is amphimix, can be cultured with Escherichia coli in 7–9 days from egg to egg-laying adult, and has a lifespan of 11 to 14 days at 20°C. The transcription data generated 45,366 unigenes; 29.9%, 31.3%, 24.8%, and 18.6% of unigenes were annotated in KOG, SwissProt, GO, and KEGG, respectively. Further gene function analysis demonstrated that C. velatum share the same riboflavin, lipoic acid, and vitamin B6 metabolic pathways with Caenorhabditis elegans and Pristionchus pacificus.
During a survey of soil nematodes in Iran, a population of a species belonging to the order Mononchida was recovered. The new species, Paramylonchulus iranicus sp. n. is characterized by body length (1292–1535 μm in females and 1476–1670 μm in males), c (20.2–29.0 in females and 19.9–27.4 in males), buccal cavity length (23.0–26.0 μm), post vulval uterine sac length (135–162 μm), spicule length (46.0–50.0 μm), gubernaculum length (8.0–11.0 μm), and tail length (49.0–70.0 μm in females and 55.0–73.0 μm in males). Canonical discriminant analysis clearly separated P. iranicus sp. n. from the closely related species Paramylonchulus based on the important morphometric characters of females and males. A molecular study of the 18S rDNA region of P. iranicus sp. n. places this population in a well-supported clade with other species of the genus.
During a survey of soil nematodes in Kirstenbosch National Botanical Garden in Cape Town, a population of plectid nematodes belonging to the genus Anaplectus was recovered and proved to be a species new to science. Anaplectus deconincki n. sp. is characterized by female body length (612–932 μm), b = 4.6–5.2, c = 12.8–18.0, c’ = 2.6–3.1, V = 51–54, and tail length (43–63 μm). Males are characterized by body length (779–956 μm), b = 4.8–5.6, c = 13.9–16.7, c’ = 2.2–2.5, spicule length 33–39 μm, gubernaculum length 10–12 μm, and tail length (56–65 μm). Discriminant analysis clearly separated A. deconincki n. sp. from the other related species of Aanaplectus. The phylogenetic analysis placed Anaplectus deconincki n. sp. in a clade with 1.00 posterior probability values with other Anaplectus. Partial sequences of the 18S and 28S regions of the ribosomal DNA gene were amplified for Anaplectus deconincki n. sp., and 18S rDNA showed 99% similarity with an unidentified Anaplectus (AJ966473) and A. porosus (MF622934) from Belgium. In addition, 28S rDNA showed a 93% similarity with A. porosus from Belgium (MF622938) and a 98% similarity with A. granulosus from Germany (MF325171). Measurements, illustrations, and light microscopy pictures for Anaplectus deconincki n. sp. are given.
In this study, the mitochondrial genome of Eulaelaps silvestris, which parasitizes Apodemus chevrieri, was sequenced and assembled to fill the gap in understanding the molecular evolution of the genus Eulaelaps. The E. silvestris mitochondrial genome is a double-stranded DNA molecule with a length of 14 882 bp, with a distinct AT preference for base composition and a notably higher AT content than GC content. The arrangement between genes is relatively compact, with a total of 10 gene intergenic regions and 12 gene overlap regions. All protein-coding genes had a typical ATN initiation codon, and only 2 protein-coding genes had an incomplete termination codon T. Out of the 13 protein-coding genes, the 5 most frequently used codons ended in A/U, with only 1 codon ending in G/C had an relative synonymous codon usage value >1. Except for trnS1 and trnS2, which lacked the D arm, all other tRNAs were able to form a typical cloverleaf structure; and there were a total of 38 mismatches in the folding process of tRNA genes. Unlike the gene arrangement order of the arthropod hypothetical ancestor, the E. silvestris mitochondrial genome underwent fewer rearrangements, mainly near tRNA genes and control regions. Both the maximum likelihood tree and the Bayesian tree showed that the family Haemogamasidae is most closely related to the family Dermanyssidae. The results not only provide a theoretical basis for studying the phylogenetic relationships of the genus Eulaelaps, but also provide molecular evidence that the family Haemogamasidae does not belong to the subfamily Laelapidae.
Four species of Porpidia are newly reported from China, including one species new to science (Porpidia crystallina) and three records (Porpidia umbonifera, P. seakensis and P. cf. contraponenda) new to China. Porpidia crystallina is characterized by a macrocarpa-type exciple containing crystals, a Cinereorufa-green epihymenium, large ascospores and a lack of secondary metabolites. Morpho-anatomical, chemical and phylogenetic analyses were carried out to elucidate the placement of the species and to support the delimitation of the new taxon. Detailed taxonomic descriptions, ecological and chemical characters, and illustrations are provided for each species. A key to all known Chinese Porpidia species is also provided.
This is the first study reporting parasites from the freshwater cyprinid Oxynoemacheilus angorae (Steindachner 1897) caught in Nilüfer Stream, Bursa, in the Northwest Anatolian Region of Turkey. Allocreadium bursensis n. sp. was described from the intesine of O.angorae based on morphological and genetic characteristics. Allocreadium bursensis n. sp. was differentiated from other Allocreadium spp. in having a combination of external (ventral and oral suckers ratio; body length and width and its ratio to forebody) and internal (cirrus pouch position; uterus extension in hindbody; egg size; disposition of anterior border of vitellarium; esophagus length) features. Phylogenetic hypotheses based on maximum parsimony, maximum likelihood, Bayesian inferrence, and neighbor joining analyses of sequence data strongly supported the hypothesis that A. bursensis is nested within the clade of Allocreadium species hosted by cypriniform fish, and it is more closely related to the Far Eastern species A. pseudoisoporum (Primorsky region, Russia) than to the African A. apokryfi. According to genetic p-distances, the taxonomic status of trematodes collected in Turkey was established as independent relative to nine of the valid Allocreadium spp.: 1.8–5.8% in 28S gene and 18.8–22.6% in cox1 gene. The present study increases the number of Allocreadium species and their definitive hosts recorded in Turkey and raises the number of Palearctic representatives of Allocreadium spp. to 26.
A new species of the genus Stephanostomum is described for the southeastern Gulf of Mexico based on morphological and nucleotide evidence. Stephanostomum minankisi n. sp. infects the intestine of the dusky flounder Syacium papillosum in the Yucatan Continental Shelf, Mexico (Yucatan Peninsula). Sequences of the 28S ribosomal gene were obtained and compared with available sequences of the other species and genera of the families Acanthocolpidae and Brachycladiidae from GenBank. A phylogenetic analysis was conducted, including 39 sequences, 26 of which represented 21 species and six genera of the family Acanthocolpidae. The new species is characterized by the absence of circumoral spines and spines on the tegument. Nonetheless, scanning electron microscopy consistently revealed the pits of 52 circumoral spines distributed in a double row with 26 spines each, and forebody spined. Other distinctive features of this species are testes in contact (sometimes overlapping), the vitellaria running along the body lateral fields to the mid-level of the cirrus-sac, pars prostatica and ejaculatory duct similar in length, and uroproct present. The phylogenetic tree showed that the three species found as parasites of dusky flounder (the new adult species and two in metacercaria stages) were grouped into two different clades. S. minankisi n. sp. was the sister species of Stephanostomum sp. 1 (Bt = 56) and formed a clade with S. tantabiddii, supported by high bootstrap values (100).
A new lichen species, Lecanora zeorina Li J. Li & Printzen is described here from the south-west of China. Lecanora zeorina is characterized by its somewhat areolate-squamulose thallus, zeorine to lecanorine apothecia, an epihymenium without crystals around expanded paraphyses tips, an amphithecium with large calcium oxalate crystals and the production of atranorin. A new combination, Lecanora crystalliniformis (B.G. Lee & Hur) Li J. Li & Printzen, is based on Protoparmeliopsis crystalliniformis B.G. Lee & Hur, which was described as a new species from South Korea. Collections from China are almost identical in morphology and chemistry, and are phylogenetically closely related. Phylogenetic reconstructions based on ITS and mtSSU suggest that these two lecanoroid species belong in Lecanora s. str. where they form a sister group to sorediate species such as L. barkmaniana Aptroot & Herk and L. variolascens Nyl. Detailed descriptions, discussions, distributions and phylogenetic trees, based on multiple collections, are presented.
Parasitic nematodes of millipedes from Nigeria are molecularly characterized for the first time. During nematode surveys on live giant African millipedes from several localities in Nigeria, 4 species of rhigonematids were identified by application of integrative taxonomical approaches (morpho-anatomy and molecular markers), including Brumptaemilius sp., Gilsonema gabonensis, Obainia pachnephorus, and Rhigonema disparovis. The results of morphometric and molecular analyses of D2-D3 28S, ITS, partial 18S rRNA, and cytochrome oxidase c subunit 1 (COI) gene sequences further characterized the rhigonematid species, and clearly separated them from other related species. Phylogenetic relationships based on 28S and 18S rRNA genes suggest that genera within Ransomnematoidea (Ransomnema, Heth, Carnoya, Brumptaemilius, Cattiena, Insulanema, Gilsonema) and Rhigonematoidea (Rhigonema, Obainia, Xystrognathus, Trachyglossoides, Ichthyocephaloides) clustered rather closer than could be expected in view of their morphological differences. Phylogenetic relationships based on ITS and COI are congruent with those of other ribosomal genes; however, they are not conclusive due to the scarcity of available sequences of these genes for these genera in NCBI.
The evolutionary relationships of the nematode genus Loofilaimus are explored with an integrative approach, combining morphological and molecular (28S-rDNA) data. Never recorded since its original description in 1998, the finding of fresh specimens of its type and only species, L. phialistoma, allowed us to obtain SEM observations and sequencing, both for the first time, resulting in relevant aspects to elucidate its phylogeny. Morphologically, the genus is characterized by two autapomorphies affecting its lip region and pharynx. Molecular study revealed that it represents a very restricted evolutionary trend within Dorylaimida. The clade (Nygolaimina + (Loofilaimus + Dorylaimina)) is well supported. Loofilaimidae is accepted as a separate and valid family, which should also include Bertzuckermania.
Every textbook of biology will supply a number of ‘modes of speciation’, the ways in which new species evolve. But the issues in dispute among the biologists themselves are rather odd. The adoption of evolutionary theory by biologists has had a great impact on how species are understood. From the idea that kinds of living beings were created and at best had devolved to localised varieties, now species were the target of a ‘mechanical’ or ‘physiological’ explanation: they came into being. And under Darwin’s version of the evolutionary account (initially known as the ‘development theory’, since the Latin word evolutio means ‘development’), species were made from other, allied (which means ‘closely related’), species. The processes and causes of new species set up the ‘species question’ that Darwin and other naturalists were seeking to answer.