Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124–156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103–158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76–103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

A new subspecies in the Turdus nudigenis complex (Aves: Turdidae) from the Cauca River valley of Colombia

The taxonomy of the T. nudigenis complex has historically been challenging due to the uniformity in plumage among taxa, poorly known vocal variation, and allopatric distributions. Recent phylogenetic analyses have contributed to understanding relationships within the genus; however, much remains to be learned about the extent of phenotypic and genetic differentiation within taxa and its implications in species limits. Here, we analyze the taxonomic status of an enigmatic member of the T. nudigenis complex restricted to the Cauca River valley of Colombia. Our phylogenetic analyses suggest that the Cauca valley population is genetically distinctive from other members of the complex, although its sister relationships with respect to T. grayi and T. nudigenis could not be fully resolved due to paraphyly in the group. Based on similarity of plumage, calls, and biogeographic proximity we tentatively treat this taxon as a new subspecies of T. grayi. Populations from the northern Caribbean T. grayi casius/incomptus and the new taxon inhabit similar environmental conditions, being apparently isolated by the humid Nechí lowlands. A formal analysis of vocalizations coupled with a more robust genomic dataset are needed to resolve the systematic affinities and taxonomic status of several members of the T. nudigenis complex.

Mitochondrial Genome of Eleutheronema rhadinum With an Additional Non-coding Region and Novel Insights Into the Phylogenetics

The complete mitochondrial genome of Eleutheronema rhadinum was determined for the first time. The E. rhadinum mitogenome was 16,718 bp in length, comprising 13 protein coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 1 control region (CR), and 1 L-strand replication origin (OL). The genome organization, and base composition were similar to other teleosts. An additional non-coding region detected in the HSL cluster, was with significant similarity to the nearby tRNA-Leu (CUN), which could be a useful marker for identifying E. rhadinum and Eleutheronema tetradactylum. Furthermore, phylogenetic analysis showed species in the family Polynemidae were well clustered together. But sister relationships between Polynemidae and Sciaenidae, Menidae plus Lactariidae were refused by present study.

Molecular Characterization of Three B-1,4-Endoglucanase Genes in Pratylenchus loosi and Functional Analysis of Pl-eng-2 Gene

Pratylenchus loosi is an important root-lesion nematode that causes damage to tea plantations in Iran and all over the world. The present study reports on the characterization and evolution of three ß-1,4-endoglucanase genes: Pl-eng-2, Pl-eng-3 and Pl-eng-4. The gene structure of Pl-eng-2 was fully determined with the predicted signal peptide and devoid of the linker domain and carbohydrate-binding domain, while Pl-eng-3 and Pl-eng-4 were only partially sequenced. The transcription of Pl-eng-2 was localized in the secretory esophageal glands of all life stages, but it was upregulated in male and female stages. The exon/intron structures of Pl-eng-2, Pl-eng-3 and Pl-eng-4 confirmed that they resulted from gene duplication followed by sequence and gene structure diversification with loss of the linker domain and carbohydrate-binding domain during evolution. A phylogenetic analysis further confirmed that nematode endoglucanases resulted from the horizontal gene transfer of a bacterial gene, as Pl-eng-3 showed sister relationships with the CelB cellulase of Bacillus subtilis. Silencing Pl-eng-2 by in vitro RNA interference produced a 60% decrease of the transcript level. The reproductive ability of silenced P. loosi showed a 35% reduction of eggs and larval stages compared to untreated nematodes, suggesting that this gene is involved in the early steps of invasion.

Molecular Characterization of Three B-1,4-Endoglucanase Genes in Pratylenchus loosi and Functional Analysis of Pl-eng-2 Gene

Pratylenchus loosi is an important root-lesion nematode that cause damage to tea plantations in Iran and all over the world. The present study reports on the characterization and evolution of three ß-1,4-engoglucanase genes Pl-eng-2, Pl-eng-3 and Pl-eng-4. The gene structure of Pl-eng-2 was fully determined with the predicted signal peptide and devoid of the linker domain and carbohydrate-binding domain, while Pl-eng-3 and Pl-eng-4 were only partially sequenced. The transcription of Pl-eng-2 was localized in the secretory esophageal glands of all life stages, but it was upregulated in male and females stages. Exon/intron structures of Pl-eng-2, Pl-eng-3 and Pl-eng-4 confirmed that they resulted from gene duplication followed by sequence and gene structure diversification with loss of linker domain and carbohydrate-binding domain during evolution. Phylogenetic analysis further confirmed that nematode endoglucanases resulted from horizontal gene transfer of a bacterial gene as Pl-eng-3 showed sister relationships with CelB cellulase of Bacillus subtilis. Silencing Pl-eng-2 by in vitro RNA interference, produced a 60% decrease of the transcript level. The reproductive ability of silenced P. loosi showed a 35% reduction of eggs and larval stages compared to untreated nematodes suggesting that this gene is involved in the early steps of invasion.

Brother-Sister Relationships in Early Modern Drama

This study aims to evaluate the commodified brother-sister relationship in Early Modern drama. It examines three different samples from three major playwrights of this time period: Isabella and Claudio in William Shakespeare’s Measure for Measure (1603), Charles and Susan in Thomas Heywood’s A Woman Killed with Kindness (1603), and Giovanni and Annabella in John Ford’s Tis Pity She’s a Whore (1632). The three aforementioned cases are closely evaluated through a Marxist-feminist lens. The study finds out that the brothers in the three examined plays are not very different since they all encourage their sisters to sacrifice their chastity to achieve some sort of personal interest. Interestingly enough, the sisters vary in their responses to their brothers’ requests of offering their bodies to help their brothers. Obviously, Shakespeare offers the ideal version of a sister who does everything in her power to save a brother. Yet, she refuses to offer her body in return to his freedom in spite of her brother’s desperate calls to offer her virginity to Angelo to save the former’s life. Susan of Heywood is also similar to Isabella of Shakespeare since she refuses to sell herself in return to the money needed to save her brother. However, Ford offers the ugliest version of a brother-sister relationship. The brother wants to have a love affair with his sister who yields to his sexual advances and eventually gets pregnant.

The global freshwater bivalve checklist’s extension: Freshwater occurrences and phylogenetic position of Galatea clams from West Africa (Venerida: Donacidae)

The bivalve genus Galatea Bruguière, 1797 (Venerida: Donacidae) was thought to contain exclusively brackish-water clams, the ranges of which are confined to estuaries and lower tidal parts of large rivers in West Africa. This genus was therefore included to the global freshwater bivalve checklists (Bogan 2013; Graf 2013) as a largely estuarine group. Conversely, a review of published data alongside our field surveys indicate that at least three populations of Galatea spp. largely occur in freshwater environment, i.e. those from the Sanaga (Cameroon), Niger (Nigeria), and Volta (Ghana) rivers. The systematic placement of these populations is unclear, as are the taxonomic status and validity of numerous nominal taxa described in this genus from a variety of localities throughout the Atlantic Coast of Africa (Angola to Senegal). We tentatively assign the populations from Niger and Volta to Galatea paradoxa (Born, 1778), while the Sanaga’s population is considered here as Galatea schwabi (Clench, 1929). However, these taxa do not share clear morphological differences and may belong to a single widespread species. In this study, we present the first DNA sequence data for a Galatea member, i.e. G. schwabi. Our COI phylogeny supports its placement within the family Donacidae suggesting sister relationships between Galatea and Donax Linnaeus, 1758. Most Galatea populations play a vital role for local riparian communities in West Africa as an intensively exploited food source. Furthermore, the clams are heavily threaten by anthropogenic impacts such as dam construction, riverbed substrate mining, and river pollution. The fishing loads and habitat degradation altogether lead to the rapid decreasing of Galatea populations in several water bodies, e.g. the Volta River in Ghana. It is impossible to develop conservation and management plans for these clams due to the lack of reliable species-level taxonomic concept of the genus. It is clear that the Galatea taxonomy and ecology need a thorough revision in the future based on DNA sequences of newly collected samples from all West African rivers, in which these remarkable clams occur.

Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples

The biotas of the Galápagos Islands are probably one of the best studied island systems and have provided a broad model of insular species’ origins and evolution. Nevertheless, some Galápagos species remain poorly characterized, such as the Galápagos Rail Laterallus spilonota. This bird species is one of the less explored groups of endemic vertebrates on these islands, due to its elusive behavior, cryptic plumage and restricted distribution. To date there is no genetic assessment of its origins and sister relationships to other taxa, and importantly, there is no data on its current genetic diversity. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multi-locus sequencing (mtDNA+nuDNA) from both modern and historical samples. We show that the Galápagos Rail is part of the ‘American black rail clade’, sister to Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 Mya. The separate analysis of cytb, ND2, and RAG-1 markers demonstrates shallow population structure across sampled islands, possibly due to elevated island connectivity. Additionally, birds sampled from Pinta possessed the lowest levels of genetic diversity, most likely reflecting the impact of past bottlenecks due to habitat loss caused by invasive goats grazing on sensitive habitat. The data presented here highlights the low genetic diversity in this endemic rail species and suggests the use of genetic data (both modern and historical) to guide conservation efforts.

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.