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Phylogeny of the major lineages of Membracoidea (Insecta: Hemiptera: Cicadomorpha) based on 28S rDNA sequences.

Analysis of sequences from a 3.5-kb region of the nuclear ribosomal 28S DNA gene spanning divergent domains D2-D10 supports the hypothesis, based on fossil, biogeographic, and behavioral evidence, that treehoppers (Aetalionidae and Membracidae) are derived from leafhoppers (Cicadellidae). Maximum-parsimony analysis indicated that treehoppers are the sister group of a lineage comprising the currently recognized cicadellid subfamilies Agalliinae, Megophthalminae, Adelungiinae, and Ulopinae. Based on this phylogenetic estimate, the derivation of treehoppers approximately coincided with shifts in physiology and behavior, including loss of brochosome production and a reversal from active, jumping nymphs to sessile, nonjumping nymphs. Myerslopiidae, traditionally placed as a tribe of the cicadellid subfamily Ulopinae, represented a basal lineage distinct from other extant membracoids. The analysis recovered a large leafhopper lineage comprising a polyphyletic Deltocephalinae (sensu stricto) and its apparent derivatives Koebeliinae, Eupelicinae (polyphyletic), Selenocephalinae, and Penthimiinae. Clades comprising Macropsinae, Neocoelidiinae, Scarinae, Iassinae, Coelidiinae, Eurymelinae + Idiocerinae, Evacanthini + Pagaroniini, Aphrodinae + Ledrinae (in part), Stenocotini + Tartessinae, and Cicadellini + Proconiini were also recovered with moderate to high branch support. Cicadellinae (sensu lato), Ledrinae, Typhlocybinae, and Xestocephalinae were consistently polyphyletic on the most-parsimonious topologies, but constraining these groups to be monophyletic did not significantly increase the length of the cladograms. Relationships among the major lineages received low branch support, suggesting that more data are needed to provide a robust phylogenetic estimate.

Animals↗

The different roles of MHC class recognition in thymocyte CD4 versus CD8 lineage commitment and positive selection.

Commitment to the CD4+ or CD8+ T cell lineages and positive selection for full maturation of precursor T cells take place in the thymus. A detailed phenotypic analysis of differentiating thymocytes in normal and MHC-deficient mice has led to the identification of previously unappreciated subpopulations whose characteristics and dependence on major histocompatibility complex (MHC) class I versus class II molecule expression seem incompatible with a CD4/CD8 coreceptor-dependent 'instructional' model of thymocyte development. We suggest here that these and other recent data are most consistent with a model in which the TCR-mediated decision to enter the CD4 versus the CD8 lineage is independent of the class of MHC molecule recognized and is distinct from positive selection. This latter event appears to involve already lineage-committed cells and to require a match of the MHC class specificity of the lineage-defining, highly expressed CD4 or CD8 coreceptor and the TCR.

Animals↗

Differential induction of apoptosis and MAP kinase signaling by mitochondrial toxicants in drug-sensitive compared to drug-resistant B-lineage lymphoid cell lines.

A panel of human B-lineage lymphoma cell lines differing in cancer drug-resistance status and Bcl-2/Bax expression were used to study the contribution of mitochondrial-based perturbations and regulation in differential induction of apoptosis. Mitochondrial dysfunction was induced in cells by the uncoupler carbonyl cyanide m-chlorophenylhydrazone (mClCCP) and the respiratory chain inhibitor antimycin A. Cells were then assayed for early changes in MAP kinase signaling and subsequent induction of apoptosis. The cancer drug-resistant cell lines EW36 and CA46, overexpressing Bcl-2 and deficient in Bax, respectively, were both resistant to mitochondrial toxicant-induced cleavage of poly(ADP-ribose) polymerase (PARP) and morphologically detectable apoptotic cell death. In contrast, cancer drug-sensitive ST486 cell line, with low Bcl-2 expression, was sensitive to PARP cleavage and apoptosis engagement. Interestingly, mClCCP induced twofold more apoptosis than antimycin A in the ST486 cells. Exposure to the mitochondrial toxicants resulted in the early and preferential activation of the ERK and p38 MAP kinase pathways in only the drug-sensitive ST486 cell line, with mClCCP more potent than antimycin A. Specific inhibition of the p38 pathway augmented baseline and mClCCP-induced apoptosis. These results show that multi-drug-resistant and -sensitive B-lineage cells are also resistant and sensitive to compounds inducing mitochondrial dysfunction. The differential sensitivity to mitochondrial toxicant effects involved regulation by MAP kinases, since ERK and p38 were found to be preferentially activated only in the drug-sensitive B-lineage cells. Modulation of the p38 signaling pathway altered the sensitivity of cells to mitochondrial stress and may play a more general role in regulating the sensitivity of B-lineage cells to drugs and environmental toxicants.

Antimycin A↗

The tax gene sequences form two divergent monophyletic lineages corresponding to types I and II of simian and human T-cell leukemia/lymphotropic viruses.

Evolutionary associations of human and simian T-cell leukemia/lymphotropic viruses I and II (HTLV-I/II and STLV-I/II) are inferred from phylogenetic analysis of tax gene sequences. Samples studied consisted of a geographically diverse assemblage of viral strains obtained from 10 human subjects and 20 individuals representing 12 species of nonhuman primates. Sequence analyses identified distinct substitutions, which distinguished between viral types I and II, irrespective of host species. Phylogenetic reconstruction of nucleotide sequences strongly supported two major evolutionary groups corresponding to viral types I and II. With the type I lineage, clusters were composed of strains from multiple host species. A genetically diverse, monophyletic lineage consisting of eight new viral strains from several species of Asian macaques was identified. The second lineage consisted of a monophyletic assemblage of HTLV-II/STLV-II strains from Africa and the New World, including an isolate from a pygmy chimp (Pan paniscus) as an early divergence within the lineage. High levels of genetic variation among strains from Asian STLV-I macaque suggest the virus arose in Asia. Evidence of the origin of the type II virus is less clear, but diversity among HTLV-II variants from a single isolated population of Mbati villagers is suggestive but not proof of an African origin.

Amino Acid Sequence↗

Effects of neonatal transection on glial cell development in the rat optic nerve: evidence that the oligodendrocyte-type 2 astrocyte cell lineage depends on axons for its survival.

We have previously provided evidence that the rat optic nerve contains three types of macroglial cells that develop as two distinct lineages: one lineage comprises type 1 astrocytes, which develop before birth, while the other comprises oligodendrocytes and type 2 astrocytes, which develop after birth from a common, bipotential glial progenitor cell. In the present study we have examined the influence of axons on the development of these two glial cell lineages by cutting the optic nerve at birth so that the retinal ganglion cell axons in the nerve degenerate. Using antibodies to distinguish the different types of glial cells in suspensions and semithin frozen sections of cut and uncut optic nerves, we show that neonatal transection results in a striking decrease in the total number of oligodendrocytes, type 2 astrocytes and their progenitor cells but has much less effect on the number of type 1 astrocytes. Since the [3H]thymidine labelling indices of oligodendrocytes and their progenitor cells were not significantly decreased in cut nerves, our results suggest that the progenitor cells and/or their progeny die in large numbers following neonatal nerve transection. We conclude that axons are required for the survival of cells of the oligodendrocyte-type 2 astrocyte lineage, at least during postnatal development.

Animals↗

Origin and evolutionary pathways of the H1 hemagglutinin gene of avian, swine and human influenza viruses: cocirculation of two distinct lineages of swine virus.

The nucleotide sequences of the HA1 domain of the H1 hemagglutinin genes of A/duck/Hong Kong/36/76, A/duck/Hong Kong/196/77, A/sw/North Ireland/38, A/sw/Cambridge/39 and A/Yamagata/120/86 viruses were determined, and their evolutionary relationships were compared with those of previously sequenced hemagglutinin (H1) genes from avian, swine and human influenza viruses. A pairwise comparison of the nucleotide sequences revealed that the genes can be segregated into three groups, the avian, swine and human virus groups. With the exception of two swine strains isolated in the 1930s, a high degree of nucleotide sequence homology exists within the group. Two phylogenetic trees constructed from the substitutions at the synonymous site and the third codon position showed that the H1 hemagglutinin genes can be divided into three host-specific lineages. Examination of 21 hemagglutinin genes from the human and swine viruses revealed that two distinct lineages are present in the swine population. The swine strains, sw/North Ireland/38 and sw/Cambridge/39, are clearly on the human lineage, suggesting that they originate from a human A/WSN/33-like variant. However, the classic swine strain, sw/Iowa/15/30, and the contemporary human viruses are not direct descendants of the 1918 human pandemic strain, but did diverge from a common ancestral virus around 1905. Furthermore, previous to this the above mammalian viruses diverged from the lineage containing the avian viruses at about 1880.

Amino Acid Sequence↗

A method of estimating from two aligned present-day DNA sequences their ancestral composition and subsequent rates of substitution, possibly different in the two lineages, corrected for multiple and parallel substitutions at the same site.

The course of evolutionary change in DNA sequences has been modeled as a Markov process. The Markov process was represented by discrete time matrix methods. The parameters of the Markov transition matrices were estimated by least-squares direct-search optimization of the fit of the calculated divergence matrix to that observed for two aligned sequences. The Markov process corrected for multiple and parallel substitutions of bases at the same site. The method avoided the incorrect assumption of all previously described methods that the divergence between two present-day sequences is twice the divergence of either from the common and unknown ancestral sequence. The three previous methods were shown to be equivalent. The present method also avoided the undesirable assumptions that sequence composition has not changed with time and that the substitution rates in the two descendant lineages were the same. It permitted simultaneous estimation of ancestral sequence composition and, if applicable, of different substitution rates for the two descendant lineages, provided the total number of estimated parameters was less than 16. Properties of the Markov chain were discussed. It was proved for symmetric substitution matrices that all elements of the equilibrium divergence matrix equal 1/16, and that the total difference in the divergence matrix at epoch k equals the total change in the common substitution matrix at epoch 2k for all values of k. It was shown how to resolve an ambiguity in the assignment of two different substitution rates to the two descendant lineages when four or more similar sequences are available. The method was applied to the divergence matrix for codon site 3 for the mouse and rabbit beta-globins. This observed divergence matrix was significantly asymmetric and required at least two different substitution rates. This result could be achieved only by using different asymmetric substitution matrices for the two lineages.

Animals↗

Lineage infidelity in chronic myeloid leukemia. Demonstration and significance of hybridoid leukocytes.

Blood smears from 13 cases of chronic myeloid leukemia (CML) were examined for bigranulated (basophil/eosinophil) cells. The cells were stained with May-Grünwald-Giemsa, toluidine blue, Biebrich scarlet, Adams' reaction, and were reacted for KCN-resistant peroxidase in two cases. A sequential stain (toluidine blue/Biebrich scarlet/Adams' reaction) was applied to 50 cells in each case. Hybridoid cells occurred in all cases with varying frequency. Double granulation was not only found in immature, non-segmented cells but often in mature segmented cells. The chimeric cells were difficult to detect with May-Grünwald-Giemsa. Biebrich scarlet and Adams' reaction being superior in this respect to Biebrich scarlet. Some granules that were positive by Adams' reaction did not stain with Biebrich scarlet. This is in sharp contrast to the normal and is, therefore, interpreted as a granule atypicality. Since under normal circumstances, eosinophilic and basophilic granules can be viewed as mutually exclusive markers of the respective granulocytic lineages, the simultaneous occurrence in CML cells of both markers demonstrates lineage infidelity. Until now lineage infidelity has been reported only in immature cells. However, our results show that lineage infidelity also occurs in mature segmented cells. This indicates that the progenitors of these chimeric granulocytes follow false genetic programs producing cells with profound irreversible neoplastic aberrations.

Basophils↗

The first sexual lineage and the relevance of facultative sex.

Models for the origin of the sex incorporate either obligate or facultative sexual cycles. The relevance of each assumption to the ancestral sexual population can be examined by surveying the sexual cycles of eukaryotes, and by determining the first lineage to diverge after sexuality evolved. Two protistan groups, the parabasalids and the oxymonads, have been suggested to be early-branching sexual lineages. A maximum-likelihood analysis of elongation factor-1alpha sequences shows that the parabasalids diverged prior to the oxymonads and thus represent the earliest sexual lineage of eukaryotes. Since both of these protist lineages and most other eukaryotes are facultatively sexual, it is likely that the common ancestor of all known eukaryotes was facultatively sexual as well. This finding has important implications for the "Best-Man hypothesis" and other models for the origin of sex.

Animals↗

Evolutionary relationships in the sand-dwelling cichlid lineage of lake tanganyika suggest multiple colonization of rocky habitats and convergent origin of biparental mouthbrooding.

The cichlid species flock of Lake Tanganyika is comprised of seven seeding lineages that evolved in step with changes of the lake environment. One seeding lineage diversified into at least six lineages within a short period of time. Our study focuses on the diversification of one of these lineages, the Ectodini, comprising highly specialized, sand- and rock-dwelling species. They display two distinct breeding styles: maternal and biparental mouthbrooding. By analyzing three mtDNA gene segments in 30 species representing all 13 described genera, we show that the Ectodini rapidly diversified into four clades at the onset of their radiation. The monotypic genus Grammatotria is likely to represent the most ancestral split, followed by the almost contemporary origin of three additional clades, the first comprising the benthic genus Callochromis, the second comprising the benthic genera Asprotilapia, Xenotilapia, Enantiopus, and Microdontochromis, and the third comprising the semi-pelagic genera Ophthalmotilapia, Cardiopharynx, Cyathopharynx, Ectodus, Aulonocranus, Lestradea, and Cunningtonia. Our study confirms the benthic and sand-dwelling life-style as ancestral. Rocky habitats were colonized independently in the Xenotilapia- and Ophthalmotilapia-clade. The Xenotilapia-clade comprises both maternal and biparental mouthbrooders. Their mode of breeding appears to be highly plastic: biparental mouthbrooding either evolved once in the common ancestor of the clade, to be reverted at least three times, or evolved at least five times independently from a maternally mouthbrooding ancestor. Furthermore, the genera Xenotilapia, Microdontochromis, Lestradea, and Ophthalmotilapia appeared paraphyletic in our analyses, suggesting the need of taxonomic revision.

Africa↗

Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages.

A phylogenetic-comparative approach was used to assess and refine existing secondary structure models for a frequently studied region of the mitochondrial encoded large subunit (16S) rRNA in two large lizard lineages within the Scincomorpha, namely the Scincidae and the Lacertidae. Potential pairings and mutual information were analyzed to identify site interactions present within each lineage and provide consensus secondary structures. Many of the interactions proposed by previous models were supported, but several refinements were possible. The consensus structures allowed a detailed analysis of rRNA sequence evolution. Phylogenetic trees were inferred from Bayesian analyses of all sites, and the topologies used for maximum likelihood estimation of sequence evolution parameters. Assigning gamma-distributed relative rate categories to all interacting sites that were homologous between lineages revealed substantial differences between helices. In both lineages, sites within helix G2 were mostly conserved, while those within helix E18 evolved rapidly. Clear evidence of substantial site-specific rate variation (covarion-like evolution) was also detected, although this was not strongly associated with specific helices. This study, in conjunction with comparable findings on different, higher-level taxa, supports the ubiquitous nature of site-specific rate variation in this gene and justifies the incorporation of covarion models in phylogenetic inference.

Animals↗

The nature of introns 4-7 largely reflects the lineage specificity of HLA-A alleles.

For most HLA-A alleles the phylogeny of the 3' non-coding regions has not yet been studied systematically. In this study, we have determined the sequences of introns 4-7 in 50 HLA-A variants, and have computed nucleotide substitution rates and phylogenetic relationships. The A2/A28, A9, and A10 groups were characterized by clear lineage specificity. For the A19 group, lineage specificity was weaker. A*3001 clustered together with the alleles of the A1/A3/A11/A36 serological family, but not with the A19 group alleles. Reduced lineage specificity was also observed for the alleles of the A1/A3/A11/A36groups. The 3' intron sequences of A*8001 were clearly distinct from all other alleles studied. In several cases two allelic groups shared identical intron sequences, whereby the patterns varied with the introns. A similar situation has been previously described for the 5' introns. Since recombination is the major mechanism of HLA diversification, the intronic lineage specificity corresponds to the comparatively lower recombination rate of the HLA-A 3' exons. The low level of recombination within the 3' region of HLA-A is supported by the low CpG content with a maximum of 3.0% in this region compared with up to 10.7% in the 5' region. Apart from phylogenetic studies of HLA diversity and diversification, the sequence data obtained in our study may prove valuable for the development of a haplotype-specific sequencing strategy for the HLA-A3' exons and for the explanation of recombination events in newly described HLA class I alleles.

Base Sequence↗

TNFB polymorphisms characterize three lineages of TNF region microsatellite haplotypes.

The human major histocompatibility complex (MHC) contains a variety of genes, many of which are highly polymorphic and of immunological importance. A database of MHC extended haplotypes was used to integrate experimental, cell line, and population data. Three alleles of the human TNF-beta (lymphotoxin-alpha) gene were identified, named TNFB*1SL, TNFB*2LL, and TNFB*1LS, each representing a different lineage in the evolution of TNF region haplotypes. Lower variability in the length of the associated microsatellite alleles indicates that *1SL characterizes the youngest of the three haplotype lineages. Microsatellite haplotypes in the two older lineages show evidence for a coevolution of alleles through concerted expansions. Genetic predispositions to high and low TNF-alpha (cachectin) responses seem to have evolved independently in more than one lineage. The literature data suggest different, or even opposite, associations concerning the regulation of TNF-alpha in macrophages and lymphoid cells. Microsatellite ud may be the most informative marker for studies of the associations of individual TNF region markers with secretion levels, immunity, and disease.

Alleles↗

Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers.

The Y-chromosome haplogroup composition of the population of the Cabo Verde Archipelago was profiled by using 32 single-nucleotide polymorphism markers and compared with potential source populations from Iberia, west Africa, and the Middle East. According to the traditional view, the major proportion of the founding population of Cabo Verde was of west African ancestry with the addition of a minor fraction of male colonizers from Europe. Unexpectedly, more than half of the paternal lineages (53.5%) of Cabo Verdeans clustered in haplogroups I, J, K, and R1, which are characteristic of populations of Europe and the Middle East, while being absent in the probable west African source population of Guiné-Bissau. Moreover, a high frequency of J* lineages in Cabo Verdeans relates them more closely to populations of the Middle East and probably provides the first genetic evidence of the legacy of the Jews. In addition, the considerable proportion (20.5%) of E3b(xM81) lineages indicates a possible gene flow from the Middle East or northeast Africa, which, at least partly, could be ascribed to the Sephardic Jews. In contrast to the predominance of west African mitochondrial DNA haplotypes in their maternal gene pool, the major west African Y-chromosome lineage E3a was observed only at a frequency of 15.9%. Overall, these results indicate that gene flow from multiple sources and various sex-specific patterns have been important in the formation of the genomic diversity in the Cabo Verde islands.

Chromosomes, Human, Y↗

Characterization of the rabbit gastric epithelial lineage progenitors in short-term culture.

Little is known about the mechanisms that establish and maintain the proliferation and differentiation programs of the gastric epithelium. This is largely due to the complexity of the gastric epithelial units and the presence of the different epithelial lineage progenitors among heterogeneous populations of various mature cell types. This study is undertaken to establish an in vitro system highly enriched for gastric epithelial lineage progenitors. By using adult male rabbits, a simple method of isolating gastric epithelial cell fractions enriched in lineage progenitors was applied. Cultured cells labeled with bromodeoxyuridine were characterized by using lectin and immunohistochemical studies at light- and electronmicroscopical levels. Analysis of primary cultures derived from the progenitor cell region of the epithelial units revealed that this system can support the proliferation and some of the differentiation programs of the progenitor cells. Cultured cells can be maintained for up to 5 days, while retaining most of the morphological features, molecular markers, and dynamic behavior of gastric epithelial progenitors. Differential cell counts at 1-day culture revealed that, while the undifferentiated progenitors formed about 30% of all attached cells, pre-pit, pit, and preparietal cells represented about 30%, 10%, and 2%, respectively. By 3 days, the increase in the percentage of pit and preparietal cells up to 25% and 9%, respectively, reflected their production in vitro. In conclusion, we have established a culture system enriched for gastric epithelial lineage progenitors that would hopefully allow the identification of factors and mechanisms involved in controlling their proliferative activity and differentiation pathways.

Animals↗

Lineage is an epigenetic modifier of QTL influencing behavioral coping with stress.

A genome-wide scan was carried out on a segregating F2 population of rats derived from reciprocal intercrosses between two inbred strains of rats, Fisher 344 (F344) and Wistar Kyoto (WKY) that differ significantly in their behavioral coping responses to stress measured by the defensive burying (DB) test. The DB test measures differences in coping strategies by assaying an animal's behavioral response to an immediate threat. We have previously identified three X-linked loci contributing to the phenotypic variance in behavioral coping. Here we report on six significant autosomal quantitative trait loci (QTL) related to different behaviors in the DB test:one for the number of shocks received, three for number of prod approaches, one for latency to bury, and one pleiotropic locus affecting both approach and latency. These QTL contributing to different aspects of coping behaviors show that the effect of genotype on phenotype is highly dependent on lineage. The WKY lineage was particularly influential, with five out of the six QTL affecting coping behavior only in rats of the WKY lineage, and one locus affecting only those in the F344 lineage. Thus, epigenetic factors, primarily of WKY origin, may significantly modulate the genetic contribution to variance in behavioral responses to stress in the DB test.

Adaptation, Psychological↗

The gynogenetic reproduction of diploid and triploid hybrid spined loaches (Cobitis: Teleostei), and their ability to establish successful clonal lineages--on the evolution of polyploidy in asexual vertebrates.

Polyploidisation is assumed to have played a significant role in the evolution of hybrid asexual lineages. The virtual absence of natural asexual systems in which more than a single ploidy level successfully establishes successful independent clonal lineages is generally explained by the strong effects of polyploidisation on fitness. Experimental crosses were made between diploid and triploid asexual Cobitis elongatoides x C. taenia hybrids (female) and both parental spined loach species (male). Genotyping of the progeny using allozymes and multilocus DNA fingerprinting, along with flow cytometric measurement of ploidy level, demonstrated the occurrence of gynogenetic reproduction in both female biotypes. The incorporation of the sperm genome occurred in some progeny, giving rise to a higher ploidy level, but the rate of polyploidisation differed significantly between the diploid and triploid females. These outcomes are consistent with the existence of developmental constraints on tetraploidy, which determine the rarity of tetraploids in natural populations. No cases of ploidy level reduction were observed. Since diploid and triploid hybrid populations occur where the lack of potential progenitor excludes the possibility of de novo origin, it is probable that both diploid and triploid females can establish successful clonal lineages. Spined loaches represent a unique example, among asexual vertebrates, where more than one ploidy level can establish persistent clonal lineages, which are reproductively independent of one another.

Animals↗

Mitogenomic and phylogenomic analyses identify a cohesive Western Atlantic lineage within the Narcine complex (Torpediniformes: Narcinidae).

BACKGROUND: Accurate species delimitation within electric rays of the genus Narcine has been hindered by overlapping morphological characters and limited molecular resolution in previous single-locus studies. This study aims to evaluate phylogenetic relationships and species boundaries within the Narcine species complex across the Western Atlantic using complete mitochondrial genomes. METHODS AND RESULTS: Seven complete mitogenomes were newly assembled from individuals representing distinct morphotypes sampled across geographically widespread Western Atlantic localities and analyzed together with publicly available reference sequences. Mitochondrial protein-coding genes (PCGs) were examined using concatenated nucleotide and amino acid datasets under partitioned maximum-likelihood frameworks. Both approaches recovered highly congruent topologies, consistently supporting a single, well-defined western Atlantic mitochondrial lineage with low internal divergence (0.04-2.13%). Species delimitation analyses based on multiple methods yielded partially congruent results but consistently identified a dominant lineage encompassing all Atlantic samples. In contrast, two Colombian reference mitogenomes formed a separate and highly divergent lineage relative to the Atlantic group, despite showing moderate divergence between them. Comparative mitogenomic analyses revealed conserved genome organization, nucleotide composition bias, codon usage, and transfer RNA (tRNA) structures. All PCGs evolved under strong purifying selection, with Ka/Ks ratios well below unity. CONCLUSIONS: These results support mitochondrial genetic continuity across the Western Atlantic Narcine populations and do not provide mitochondrial evidence for multiple evolutionary lineages within the Western Atlantic. The marked mitochondrial divergence of Colombian reference mitogenomes highlights potential issues in sequence attribution and underscores the importance of data curation. Overall, complete mitochondrial genomes provide a robust framework for species delimitation and future integrative taxonomic assessments within Narcine.

Animals↗