Gabriel Johnson

DNA sequencing, anatomy, and calcification patterns support a monophyletic, subarctic, carbonate reef-forming Clathromorphum (Hapalidiaceae, Corallinales, Rhodophyta)

For the first time, morpho‐anatomical characters that were congruent with DNA sequence data were used to characterize several genera in Hapalidiaceae—the major eco‐engineers of Subarctic carbonate ecosystems. DNA sequencing of three genes (SSU, rbcL, ribulose‐1, 5‐bisphosphate carboxylase/oxygenase large subunit gene and psbA, photosystem II D1 protein gene), along with patterns of cell division, cell elongation, and calcification supported a monophyletic Clathromorphum. Two characters were diagnostic for this genus: (i) cell division, elongation, and primary calcification occurred only in intercalary meristematic cells and in a narrow vertical band (1–2 μm wide) resulting in a “meristem split” and (ii) a secondary calcification of interfilament crystals was also produced. Neopolyporolithon was resurrected for N. reclinatum, the generitype, and Clathromorphum loculosum was transferred to this genus. Like Clathromorphum, cell division, elongation, and calcification occurred only in intercalary meristematic cells, but in a wider vertical band (over 10–20 μm), and a “meristem split” was absent. Callilithophytum gen. nov. was proposed to accommodate Clathromorphum parcum, the obligate epiphyte of the northeast Pacific endemic geniculate coralline, Calliarthron. Diagnostic for this genus were epithallial cells terminating all cell filaments (no dorsi‐ventrality was present), and a distinct “foot” was embedded in the host. Leptophytum, based on its generitype, L. laeve, was shown to be a distinct genus more closely related to Clathromorphum than to Phymatolithon. All names of treated species were applied unequivocally by linking partial rbcL sequences from holotype, isotype, or epitype specimens with field‐collected material. Variation in rbcL and psbA sequences suggested that multiple species may be passing under each currently recognized species of Clathromorphum and Neopolyporolithon.

Sporolithon tenue sp. nov. (Sporolithales, Corallinophycidae, Rhodophyta) : A new rhodolith-forming species from the tropical southwestern Atlantic

A new species conforming to the generic description of Sporolithon was found forming small (1–3 cm in diameter) rhodoliths at 18–75 m depth on the eastern coast of Brazil. Sporolithon tenue Bahia, Amado‐Filho, Maneveldt et W.H. Adey, sp. nov. differs from other species of Sporolithon in having a thin, primary vegetative thallus of only 45–250 μm in thickness composed of up to 20 cell layers. Sporolithon tenue can build thicker crusts by overgrowths of thalli with new hypothallia. The absence of a layer of elongate cells at the base of the tetrasporangial chambers and the shedding of senescent tetrasporangial sori are also characters that separate the new species from all other currently recognized species within the genus. Observations from recently collected material and from herbarium specimens show that specimens previously designated as Sporolithon africanum (Foslie) J. Afonso‐Carillo in Brazil correspond to Sporolithon tenue. Molecular phylogenetic analyses of psbA sequence alignments show that the new species is phylogenetically distinct within the genus Sporolithon.

Generic Relationships and Classification of Tribe Paullinieae (Sapindaceae) with a New Concept of Supertribe Paulliniodae

Abstract The current study examines all genera of Sapindaceae tribe Paullinieae sensu Acevedo-Rodríguez et al. (2011). Based on molecular phylogenetic analyses of trnL intron and ITS sequence data along with critical evaluation of morphology, supertribe Paulliniodae is newly recognized and morphologically characterized by zygomorphic flowers, thyrses with lateral cincinni, corollas of 4 petals, and alternate leaves with a well-developed distal leaflet. Paulliniodae contains four successively nested subclades designated as tribes Athyaneae, Bridgesieae, Thouinieae, and Paullinieae. Athyaneae contains Athyana and Diatenopteryx, and is composed of trees with exstipulate pinnately compound leaves, and isopolar, spherical, colporate pollen grains. Bridgesieae contains the monospecific shrub genus Bridgesia with exstipulate, simple leaves, and isopolar, spherical, tricolporate pollen grains. Thouinieae is resurrected and amended to include three genera of trees or shrubs with exstipulate trifoliolate or unifoliolate leaves. Paullinieae is circumscribed to include only six genera (Thinouia, Lophostigma, Cardiospermum, Paullinia, Serjania and Urvillea) of climbers or climber-derived shrubs with stipulate leaves and a pair of inflorescence tendrils. Guindilia, previously considered a member of this clade, is shown to be more distantly related and not part of supertribe Paulliniodae. The following 14 new combinations are made to incorporate the results of our findings: Serjania biternata, Serjania cristobaliae, Serjania dissecta, Serjania guerrerensis, Serjania macrolopha, Serjania serjanioides, Serjania sonorensis, Serjania spinosa, Serjania tortuosa, Thinouia trifoliata, Urvillea cuchujaquense, Urvillea oliveirae, Urvillea procumbens, and Urvillea pterocarpa.

Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae): Chloroplast phylogenomics of Vitis

Vitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian clade of Vitis. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.

A revised generic classification of vittarioid ferns (Pteridaceae) based on molecular, micromorphological, and geographic data

In ferns, as in most branches of the tree of life, phylogenetic analyses of molecular data have greatly improved our ability to identify natural groupings that are subsequently reflected in classifications grounded in the principle of monophyly (Smith & al., 2006; Rothfels & al., 2012; Christenhusz & Chase, 2014). In some cases, the results of such analyses are consistent with earlier notions of relationships inferred from morphological features (Schneider & al., 2009). However, in many other instances, lineages are revealed that are morphologically confounding and we struggle to identify synapomorphies (Sundue & Rothfels, 2014). The pursuit of such defining characteristics is especially problematic when working within a group possessing very limited morphological disparity. The well-defined vittarioid fern clade consists of 100–130 (Lindsay, 2003) highly simplified and predominantly epiphytic species (Fig. 1). These plants, characterized by the presence of silica bodies (Sundue, 2009) but a lack of sclerenchyma (Bower 1928; Ruhfel & al., 2008), were long regarded as composing a distinct family—Vittariaceae (Ching, 1940; Tryon & Tryon, 1982; Kramer, 1990). However, phylogenetic analyses have demonstrated that these ferns nest well within the Pteridaceae (Crane & al., 1995; Hasebe & al., 1995; Prado & al., 2007; Schuettpelz & al., 2007), as sister to the genus Adiantum L. (Lu & al., 2012; Rothfels & Schuettpelz, 2014; Pryer & al., 2016). The vittarioids have been variously partitioned through time (Benedict, 1911; Williams, 1927; Copeland, 1947). In the years leading up to the first molecular phylogenetic analyses of these ferns, six genera were commonly recognized based primarily on leaf division, venation, and the distribution of A revised generic classification of vittarioid ferns (Pteridaceae) based on molecular, micromorphological, and geographic data

Analysis of whole chloroplast genomes from the genera of the Clauseneae, the curry tribe (Rutaceae, Citrus family)

The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied. Due to the recent significant taxonomic changes made to this tribe, a closer inspection of the genetic relationships among its genera has been warranted. Whole genome skimming was used to generate chloroplast genomes from six species, representing each of the four genera (Bergera, Clausena, Glycosmis, Micromelum) in the Clauseneae tribe plus one closely related outgroup (Merrillia), using the published plastome sequence of Citrus sinensis as a reference. Phylogenetically informative character (PIC) data were analyzed using a genome alignment of the seven species, and variability frequency among the species was recorded for each coding and non-coding region, with the regions of highest variability identified for future phylogenetic studies. Non-coding regions exhibited a higher percentage of variable characters as expected, and the phylogenetic markers ycf1, matK, rpoC2, ndhF, trnS-trnG spacer, and trnH-psbA spacer proved to be among the most variable regions. Other markers that are frequently used in phylogenetic studies, e.g. rps16, atpB-rbcL, rps4-trnT, and trnL-trnF, proved to be far less variable. Phylogenetic analyses of the aligned sequences were conducted using Bayesian inference (MrBayes) and Maximum Likelihood (RAxML), yielding highly supported divisions among the four genera.

Evolution of the Northern Rockweed, Fucus distichus, in a Regime of Glacial Cycling: Implications for Benthic Algal Phylogenetics.

Northern hemisphere rockweeds (Fucus) are thought to have evolved in the North Pacific and then spread to the North Atlantic following the opening of the Bering Strait. They have dispersed and widely speciated in the North Atlantic and its tributary seas. Fucus distichus is likely near the ancestral member of this genus, and studies have shown that there are several species/subspecies in this complex (i.e. F. evanescens and F. gardneri). We used phylogenetic and haplotype analyses to test the phylogenetic relationships and biogeography of F. distichus. Our data and subsequent analyses demonstrate that, unlike previous studies that lacked samples from an extensive geographical area of the Arctic and Subarctic, there is a distinct Arctic haplotype that is the source of subspecies in both the North Pacific and North Atlantic. Fucus distichus occupies a low tide zone habitat, and in Arctic/Subarctic regions it is adapted to the severe stress of sea ice coverage and disturbance during many months per year. We hypothesize that the very large geographic area of Arctic and Subarctic rocky shores available to this species during interglacials, supported by large Arctic/Subarctic fringe areas as well as unglaciated refugia during glacial cycles, provided a robust population and gene pool (described by the Thermogeographic Model). This gene pool dilutes that of the more fragmented and area-limited Temperate/Boreal area populations when they are brought together during glacial cycles. We suggest that similar subspecies complexes for a variety of Arctic/Subarctic shore biota should be examined further in this context, rather than arbitrarily being split up into numerous species.

Isoetes viridimontana: A Previously Unrecognized Quillwort from Vermont, USA

Abstract Isoëtes viridimontana is described and illustrated. Plants of this species are currently known only from Haystack Pond, a small, acidic, oligotrophic lake in south central Vermont. Isoëtes viridimontana is distinguished from other Isoëtes species in northeastern North America by its size (less than 5 cm high) and granulate to rugulate megaspore texture.

A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations

Abstract Based on sequence data of nuclear ITS and plastid matK, trnL-F and psbA-trnH markers, the phylogeny of the subtribes Caraganinae and Chesneyinae in tribe Caraganeae was inferred. The results support the monophyly of each of the subtribes. Within subtribes Caraganinae, Calophaca and Halimodendron are herein transferred into Caragana to ensure its generic monophyly. The subtribe Chesneyinae is composed of four well-supported genera: Chesneya, Chesniella, Gueldenstaedtia and Tibetia. Based on phylogenetic, morphological, distributional and habitat type evidence, the genus Chesneya was divided into three monophyletic sections: Chesneya sect. Chesneya, Chesneya sect. Pulvinatae and Chesneya sect. Spinosae. Chesneya macrantha is herein transferred into Chesniella. Spongiocarpella is polyphyletic and its generic rank is not maintained. The position of Chesneya was incongruent in the nuclear ITS and the plastid trees. A paternal chloroplast capture event via introgression is hypothesized for the origin of Chesneya, which is postulated to have involved the common ancestor of Chesniella (♂) and that of the Gueldenstaedtia – Tibetia (GUT) clade (♀) as the parents.

miRNAome expression profiles in the gonads of adult Melopsittacus undulatus

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.