Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Insights from ecological niche modeling on the taxonomic distinction and niche differentiation between the black‐spotted and red‐spotted tokay geckoes (Gekko gecko)

The black‐spotted tokay and the red‐spotted tokay are morphologically distinct and have largely allopatric distributions. The black‐spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red‐spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point‐based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black‐ and the red‐spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values (“black” = 0.982, SD = ± 0.002, “red” = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the “black” form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the “red” form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black‐ and the red‐spotted tokay.     

Macroanatomic,light microscopic,and scanning electron microscopic studies of the tongue in the seagull (Larus fuscus) and common buzzard (Buteo buteo)

The tongues of ten seagulls and six common buzzards were examined. In both species, papillae linguales caudales were shaped like a letter “V” between the corpus linguae and the radix linguae. From these papillae, the length of the laterally placed papillae was greater compared with others in both species. Two or three secondary papillae were detected on these papillae in the seagull. In scanning electron microscope (SEM) examinations, in the seagull, the apex linguae was composed of multilayered desquamated cells, while in the buzzard, scalelike simple projections on the surface of desquamated cells were observed. In the buzzard, glandula (gll). linguales, and gll. mandibulares caudales were seen, while in the seagull, gll. cricoarytenoideae and gll. mandibulares caudales were present. In the seagull, apex linguae were bifurcated, and there were desquamating multilayered cells, particularly at the apex linguae. The number and location of salivary gland orifices are specific to this species. The common buzzard had similarities to many characteristics of the long‐legged buzzard. An absence of long and curly threadlike projections at the two lateral sides of the corpus linguae and an excessive number of salivary gland orifices at the corpus linguae were the main differences from the long‐legged buzzard.     

Wilsonosiphonia gen. nov. (Rhodomelaceae,Rhodophyta) based on molecular and morpho‐anatomical characters

Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot‐shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts.     

Re‐evaluation of the ontogeny and reproductive biology of the Triassic fish Saurichthys (Actinopterygii,Saurichthyidae)

Viviparity has evolved independently at least 12 times in ray‐finned fishes. However, the fossil record of actinopterygian viviparity is poor, with only two documented occurrences. Both of these are from the non‐teleost actinopterygian Saurichthys, and include S. curionii and S. macrocephalus from the Middle Triassic Meride Limestone (Monte San Giorgio, Switzerland). Here, we present new data on the reproductive biology of these species, giving unprecedented insights into their life‐history. Based on positional and preservational criteria, six specimens were identified as unambiguously gravid. Embryos were positioned dorsal to the gastrointestinal tract, parallel to the axial skeleton and to each other, in the posterior two‐thirds of the abdominal region. A minimum of 16 embryos are preserved in the most fecund females and, based on the largest preserved embryos and smallest preserved neonates, birth must have occurred at 7–12% of maternal fork length. Embryonic crania and teeth are relatively well‐ossified, however ossification of the parietal region is delayed. In the postcranium, the median scale rows and lepidotrichia are ossified, but not the lateral scale rows. Ossified squamation and gradual allometric growth suggests that neonates did not undergo metamorphosis and were relatively precocial. When considered in a phylogenetic context, neither live birth nor internal fertilization appears to represent the primitive state for saurichthyid fishes.     

Adaptive morphology of the heart of Southern‐Fur‐Seal (Arctocephalus australis – Zimmermamm, 1783)

The Southern‐fur‐seal belongs to the order Carnivora, suborder Pinnipedia, and Otariidae family. This species inhabits aquatic and terrestrial environments, thus presenting important morphophysiological adaptive changes, especially in the cardiac system. For this purpose, Southern‐fur‐seal (Arctocephalus australis) hearts were used from animals that died from natural causes. Gross morphology observations were supported by light, scanning and transmission electron microscopy. The heart was long and flat; it was lined by pericardium and partly covered by lungs. Structurally, atrium and ventricle muscle fibers exhibit typical features of cardiac fibers revealing myofibrils bundles, mitochondria, plate‐shaped junctions, anastomosis between myofibrils bundles, and electron‐dense granule natriuretic around the nucleus and mitochondria of atrium muscle cells. The Southern‐fur‐seal heart was structurally similar to other mammals; however, it presented morphological changes that assist in their adaptation to their environment.     

The dependence of leaf senescence on the balance between 1‐aminocyclopropane‐1‐carboxylate acid synthase 1 (ACS1)‐catalysed ACC generation and nitric oxide‐associated 1 (NOS1)‐dependent NO accumulation in Arabidopsis

• Ethylene and nitric oxide (NO) act as endogenous regulators during leaf senescence. Levels of ethylene or its precursor 1‐aminocyclopropane‐1‐carboxylate acid (ACC) depend on the activity of ACC synthases (ACS), and NO production is controlled by NO‐associated 1 (NOA1). However, the integration mechanisms of ACS and NOA1 activity still need to be explored during leaf senescence.
• Here, using experimental techniques, such as physiological and molecular detection, liquid chromatography‐tandem mass spectrometry and fluorescence measurement, we investigated the relevant mechanisms.
• Our observations showed that the loss‐of‐function acs1‐1 mutant ameliorated age‐ or dark‐induced leaf senescence syndrome, such as yellowing and loss of chlorophyll, that acs1‐1 reduced ACC accumulation mainly in mature leaves and that acs1‐1‐promoted NOA1 expression and NO accumulation mainly in juvenile leaves, when compared with the wild type (WT). But the leaf senescence promoted by the NO‐deficient noa1 mutant was not involved in ACS1 expression. There was a similar sharp reduction of ACS1 and NOA1 expression with the increase in WT leaf age, and this inflection point appeared in mature leaves and coincided with the onset of leaf senescence.
• These findings suggest that NOA1‐dependent NO accumulation blocked the ACS1‐induced onset of leaf senescence, and that ACS1 activity corresponds to the onset of leaf senescence in Arabidopsis.

     

Altered allocation to roots and shoots in the endophyte‐infected seedlings of Puccinellia distans (Poaceae)

Endophytes play an important role in ecological and evolutionary processes in plants and have marked economic value. Seed‐transmitted fungal endophytes are conventionally regarded as mutualistic symbionts, but their fitness consequences for the offspring of the host are not clear. Puccinellia distans infected with the fungus Epichloë typhina (E+) produces seeds that are several times smaller than normal (E?). This observation suggests that the E+ seedlings face a developmental disadvantage. Our growth chamber experiments compared the germination rates of the small E+ and large E? seeds of P. distans and examined the biomass allocation of seedlings to roots and shoots. The E+ seedlings germinated more slowly and maintained shorter shoots and a smaller root biomass for 30–50 days after sowing. Despite this disadvantage, the E+ plants more quickly increased their total size, attaining a larger shoot and whole‐plant biomass. The shoot:root biomass ratio increased more rapidly through time in the E+ seedlings, attaining a value nine times higher in the E+ than the E? group 50 days after sowing. Such differences between the E+ and E? seedlings were not explained by the growth allometry between shoots and roots. The seedlings of P. distans infected with the Epichloë endophyte were initially handicapped by their postponed emergence, but this disadvantage was quickly overcome by their superior growth capacity. The decrease in the relative allocation to roots may indicate that endophytes increase the performance of roots as resource‐acquiring organs and/or reduce the role of roots in protection against herbivores.     

Leaf morphology and anatomy of Camellia section Camellia (Theaceae)

The delimitations of species in Camellia section Camellia have been disputed for many years, resulting from uncertain relationships among species. Leaf morphological and anatomical characters for 54 species and three varieties in this section were investigated to reveal the relationships. Principal component analysis and cluster analysis were conducted using the transformed data for quantitative and qualitative characters from leaf morphology and anatomy. Combining the results of statistical analysis with comparative leaf characters of morphology and anatomy, we discussed the taxonomic treatment of section Camellia by Chang compared with that of Ming and we conclude that section Camellia consists of c. 50 species. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 456–476.     

Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae,Chlorophyta)

The monotypic genus Auxenochlorella with its type species A. protothecoides is so far only known from specific habitats such as the sap of several tree species. Several varieties were described according to physiological performances in culture on different organic substrates. However, two strains designated as Auxenochlorella were isolated from other habitats (an endosymbiont of Hydra viridis and an aquatic strain from an acidic volcano stream). We studied those isolates and compared them with six strains of Auxenochlorella belonging to different varieties. The integrative approach used in this study revealed that all strains showed similar morphology but differed in their SSU and ITS rDNA sequences. The Hydra endosymbiont formed a sister taxon to A. protothecoides, which included the varieties protothecoides, galactophila, and communis. The variety acidicola is not closely related to Auxenochlorella and represented its own lineage within the Trebouxiophyceae. In view of these results, we propose a new species of Auxenochlorella, A. symbiontica, for the Hydra symbiont, and a new genus Pumiliosphaera, with its type species, P. acidophila, for acidophilic strain. These results are supported by several compensatory base changes in the conserved region of ITS‐2 and ITS‐2 DNA barcodes.     

Leaf anatomy of Camellia sect. Oleifera and sect. Paracamellia (Theaceae) with reference to their taxonomic significance

Leaf anatomy of 21 species representing sect. Oleifera H. T. Chang and sect. Paracamellia Sealy in the genus Camellia was investigated using light microscopy. All the shapes of leaf epidermal cells were polygo-nal, and the patterns of anticlinal walls were sinuolate or sinuous, which were important to the classification of these two sections. The stomata were cyclocytic type and only present on the abaxial epidermis in both sampled sections. Seventeen leaf anatomical and cytologic characters were selected and used for the cluster analysis and principle components analyses performed by PAST program. Congruent results were obtained, with sect. Oleifera and sect. Paracamellia consistently grouping in two different clades, and some related species nesting together. This study provided leaf anatomical evidence for the merge of C. lanceoleosa H. T. Chang & J. S. Chiu and C. fluviatilis Hand.-Mazz.; of C. brevistyla Coh. St., C. obtusifolia H. T. Chang, and C. puniceiflora H. T. Chang; and of C. grijsii Hance and C. shensiensis H. T. Chang. In addition, it was also proved that C. tenii Sealy should be segregated from sect. Paracamellia and placed in the sect. Corallina Sealy. For further interest, we suggested that C. phaeoclada H. T. Chang be recognized as a subspecies of C. microphylla (Merr.) Chien. Overall, the results presented provided new insights into the relationships within a number of Camellia plants and sug-gested directions for future studies.     

A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, Phrynosoma cerroense and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The number of taxa recognized in the group has been reevaluated by herpetologists over 20 times during the last 180 years, and typically without the aid of explicit species delimitation methods, resulting in a turbulent taxonomy containing anywhere from one to seven taxa. In this study, we evaluate taxonomic trends through time by ranking 15 of these species delimitation models (SDMs) using coalescent analyses of nuclear loci and SNPs in a Bayesian model comparison framework. Species delimitation models containing more species were generally favoured by Bayesian model selection; however, several three‐species models outperformed some four‐ and five‐species SDMs, and the top‐ranked model, which contained five species, outperformed all SDMs containing six species. Model performance peaked in the 1950s based on marginal likelihoods estimated from nuclear loci and SNPs. Not surprisingly, SDMs based on genetic data outperformed morphological taxonomies when using genetic data alone to evaluate models. The de novo estimation of population structure favours a three‐population model that matches the currently recognized integrative taxonomy containing three species. We discuss why Bayesian model selection might favour models containing more species, and why recognizing more than three species might be warranted.     

Phylogenetic relationships within Adiaphanida (phylum Platyhelminthes) and the status of the crustacean‐parasitic genus Genostoma

The existence of the platyhelminth clade Adiaphanida—an assemblage comprising the well‐studied order Tricladida as well as two lesser known taxa, Prolecithophora and the obligate parasitic Fecampiida—is among the more surprising results of flatworm molecular systematics. Each of these three clades is itself largely well‐defined from a morphological point of view, although Adiaphanida at large, despite its strong support in molecular phylogenetic analyses, lacks known morphological synapomorphies. However, one taxon, the genus Genostoma, a parasite of the leptostracan crustacean Nebalia, rests uneasily within its current classification within the fecampiid family Genostomatidae; ultrastructural investigations on this taxon have uncovered a spermatogenesis reminiscent of Kalyptorhynchia, and a dorsal syncytium resembling the neodermatan tegument. Here, we provide molecular sequence data (nearly complete 18S and 28S rRNA) from a representative of Genostoma, with which we test hypotheses on the phylogenetic position of this taxon within Platyhelminthes, expanding upon a recently published phylum‐wide analysis, and applying novel alignment algorithms and substitution models. These analyses unequivocally position Genostoma as the sister group of Prolecithophora. However, even in taxon‐rich analyses, support for the position of the root of Adiaphanida is lacking, highlighting the need for new data types to study the phylogeny of this clade. Interestingly, our analyses also do not recover the monophyly of several taxa previously proposed, notably Continenticola within Tricladida and Protomonotresidae within Prolecithophora. In light of this phylogeny and the distinctive morphology (especially, spermatogenesis) of Genostoma, we advocate for a redefinition of the family Genostomatidae, outside of both Fecampiida and Prolecithophora, to encompass the members of this unique genus of parasites. Within Fecampiida, the family Piscinquilinidae fam. nov. is erected to accommodate the vertebrate‐parasitic Piscinquilinus, formerly Genostomatidae.     

Next‐generation sequencing (NGS)‐based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population

The identification of mutations in targeted genes has been significantly simplified by the advent of TILLING (Targeting Induced Local Lesions In Genomes), speeding up the functional genomic analysis of animals and plants. Next‐generation sequencing (NGS) is gradually replacing classical TILLING for mutation detection, as it allows the analysis of a large number of amplicons in short durations. The NGS approach was used to identify mutations in a population of Solanum lycopersicum (tomato) that was doubly mutagenized by ethylmethane sulphonate (EMS). Twenty‐five genes belonging to carotenoids and folate metabolism were PCR‐amplified and screened to identify potentially beneficial alleles. To augment efficiency, the 600‐bp amplicons were directly sequenced in a non‐overlapping manner in Illumina MiSeq, obviating the need for a fragmentation step before library preparation. A comparison of the different pooling depths revealed that heterozygous mutations could be identified up to 128‐fold pooling. An evaluation of six different software programs (camba , crisp , gatk unified genotyper , lofreq , snver and vipr ) revealed that no software program was robust enough to predict mutations with high fidelity. Among these, crisp and camba predicted mutations with lower false discovery rates. The false positives were largely eliminated by considering only mutations commonly predicted by two different software programs. The screening of 23.47 Mb of tomato genome yielded 75 predicted mutations, 64 of which were confirmed by Sanger sequencing with an average mutation density of 1/367 Kb. Our results indicate that NGS combined with multiple variant detection tools can reduce false positives and significantly speed up the mutation discovery rate.     

Morphological and anatomical analyses of rheophytic Rhododendron ripense Makino (Ericaceae)

The comparative morphology and anatomy of the leaves of the rheophytic Rhododendron ripense and the closely related inland species Rhododendron macrosepalum were examined. The leaf of R. ripense is thinner than that of R. macrosepalum, with leaf length to width ratios (leaf index) of 2.92 and 1.91, respectively. Moreover, the leaf of R. ripense consists of fewer cells than the leaf of R. macrosepalum, suggesting stenophyllization of R. ripense caused by the decreased number of cells. In addition, leaf thickness and the number of stomata per leaf of R. ripense were significantly greater than those of R. macrosepalum, but the density of the short glandular pilose hairs on the leaf of R. ripense was lower. The observed morphological differences between the two species may be explained by certain aspects of the riparian environment, such as high irradiation and frequent flooding after heavy rainfall, to which R. ripense is exposed.     

Remarkable leaf anatomical variations in Neurachne and its allies (Poaceae) in relation to G3 and G4 photosynthesis

The leaf blade anatomy of all species of Neurachne, Paraneurachne and Thyridolepis has been examined, with special reference to features reliably indicative of photosynthetic pathway. Neurachne alopecuroidea, N. queenslandica and N. tenuifolia exhibit C₃ anatomy, as do all three Thyridolepis species. Paraneurachne muelleri, N. munroi and N. minor all have C₄ anatomy, of the rare ' Alloteropsis-type'. However, all the species exhibit unusual anatomical features, and N. lanigera cannot be confidently assigned as C₃ or C, on anatomical grounds alone. Taxonomic considerations confirm that the three genera are closely related to one another in the context of the eu-panicoid assemblage as a whole, and that the genus Neurachne itself, although it exhibits variation in photosynthetic pathway, is not amenable to further taxonomic subdivision.     

Species‐delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis,including a new species from Brazil

Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI‐5P and rbcL) and performed several DNA‐based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods.