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Background Researchers conducting molecular phylogenetic studies are frequently faced with the decision of what to do when weak branch support is obtained for key nodes of importance. As one solution, the researcher may choose to sequence additional orthologous genes of appropriate evolutionary rate for the taxa in the study. However, generating large, complete data matrices can become increasingly difficult as the number of characters increases. A few empirical studies have shown that augmenting genes even for a subset of taxa can improve branch support. However, because each study differs in the number of characters and taxa, there is still a need for additional studies that examine whether incomplete sampling designs are likely to aid at increasing deep node resolution. We target Gracillariidae, a Cretaceous-age (~100 Ma) group of leaf-mining moths to test whether the strategy of adding genes for a subset of taxa can improve branch support for deep nodes. We initially sequenced ten genes (8,418 bp) for 57 taxa that represent the major lineages of Gracillariidae plus outgroups. After finding that many deep divergences remained weakly supported, we sequenced eleven additional genes (6,375 bp) for a 27-taxon subset. We then compared results from different data sets to assess whether one sampling design can be favored over another. The concatenated data set comprising all genes and all taxa and three other data sets of different taxon and gene sub-sampling design were analyzed with maximum likelihood. Each data set was subject to five different models and partitioning schemes of non-synonymous and synonymous changes. Statistical significance of non-monophyly was examined with the Approximately Unbiased (AU) test. Results Partial augmentation of genes led to high support for deep divergences, especially when non-synonymous changes were analyzed alone. Increasing the number of taxa without an increase in number of characters led to lower bootstrap support; increasing the number of characters without increasing the number of taxa generally increased bootstrap support. More than three-quarters of nodes were supported with bootstrap values greater than 80% when all taxa and genes were combined. Gracillariidae, Lithocolletinae + Leucanthiza , and Acrocercops and Parectopa groups were strongly supported in nearly every analysis. Gracillaria group was well supported in some analyses, but less so in others. We find strong evidence for the exclusion of Douglasiidae from Gracillarioidea sensu Davis and Robinson (1998). Our results strongly support the monophyly of a G.B.R.Y. clade, a group comprised of Gracillariidae + Bucculatricidae + Roeslerstammiidae + Yponomeutidae, when analyzed with non-synonymous changes only, but this group was frequently split when synonymous and non-synonymous substitutions were analyzed together. Conclusions 1) Partially or fully augmenting a data set with more characters increased bootstrap support for particular deep nodes, and this increase was dramatic when non-synonymous changes were analyzed alone. Thus, the addition of sites that have low levels of saturation and compositional heterogeneity can greatly improve results. 2) Gracillarioidea, as defined by Davis and Robinson (1998), clearly do not include Douglasiidae, and changes to current classification will be required. 3) Gracillariidae were monophyletic in all analyses conducted, and nearly all species can be placed into one of six strongly supported clades though relationships among these remain unclear. 4) The difficulty in determining the phylogenetic placement of Bucculatricidae is probably attributable to compositional heterogeneity at the third codon position. From our tests for compositional heterogeneity and strong bootstrap values obtained when synonymous changes are excluded, we tentatively conclude that Bucculatricidae is closely related to Gracillariidae + Roeslerstammiidae + Yponomeutidae.

The main motivation of this work is to study and obtain some reversible and DNA codes of length n with better parameters. Here, we first investigate the structure of cyclic and skew cyclic codes over the chain ring R:=F[sub.4] [v]/〈v[sup.3] 〉. We show an association between the codons and the elements of R using a Gray map. Under this Gray map, we study reversible and DNA codes of length n. Finally, several new DNA codes are obtained that have improved parameters than previously known codes. We also determine the Hamming and the Edit distances of these codes.

Small-spored Alternaria species are a taxonomically challenging group of fungi with few morphological or molecular characters that allow unambiguous discrimination among taxa. The protein-coding genes most commonly employed in fungal systematics are invariant among these taxa, so noncoding, anonymous regions of the genome were developed to assess evolutionary relationships among these organisms. Nineteen sequence-characterized amplified regions (SCAR) were screened for phylogenetic utility by comparing sequences among reference isolates of small-spored Alternaria species. Five of nineteen loci were consistently amplifiable and had sufficient phylogenetic signal. Phylogenetic analyses were performed with 150 small-spored Alternaria isolates using sequence data from an endopolygalacturonase gene and two anonymous loci. Associations among phylogenetic lineage, morphological classification, geography and host were evaluated for use as practical taxonomic characters. Samples included isolates from citrus in Florida, pistachio in California, desert plants in Arizona, walnuts in France/Italy and apples in South Africa. No associations were found between host or geographic associations and phylogenetic lineage, indicating that these characters were not useful for cladistic classification of small-spored Alternaria. Similarly strict congruence between morphology and phylogenetic lineage was not found among isolates grouped morphologically with A. alternata or A. tenuissima. In contrast 34 isolates grouped morphologically with A. arborescens fell into discrete clades for all datasets. Although 5-9 well supported clades were evident among isolates, it is currently unclear if these clades should be considered phylogenetic species or emerging evolutionary line-ages within the phylogenetically defined alternata species-group.

(Blanford, 1878), a rarely encountered species of Asian snake, is characterized by ambiguous systematics and biology. Based on a sole specimen of rediscovered in southeastern Xizang, China, we conduct a detailed morphological examination and description, and investigate the systematic position of this species. Morphologically, the newly collected specimen is closely aligned with specimens previously described. Mitochondrial DNA-based phylogenetic analyses reveal that constitutes an independent evolutionary lineage, forming a clade with (Anderson, 1879), Vogel & Luo, 2011, Boulenger, 1900, and Grismer, Quah, Anuar, Muin, Wood & Nor, 2014. The closest genetic distance between and its congeners was 10.2%. The discovery of in Medog County, China, signifies an eastward expansion of its known geographical distribution.

Diatrypaceae is a diverse family with a worldwide distribution, occurring on a wide range of hosts in terrestrial and marine environments, some of which are important plant pathogens. During a survey of ascomycete diversity in Guizhou Province, China, three new taxa within are proposed based on morphological comparisons and phylogenetic analyses of combined ITS and sequences data. The newly proposed species are , and . In addition, was recorded for the first time from China, with an updated description. Detailed morphological descriptions, illustrations, comparative analyses, and a tabular comparison of the new species with related and similar taxa are provided.

Species of the anamorph genus Phoma are commonly isolated from a wide range of ecological niches. They are notoriously difficult to identify due to the paucity of morphological features and the plasticity of these when cultivated on agar media. Species linked to Phoma section Peyronellaea are typified by the production of dictyochlamydospores and thus have additional characters to use in taxon delineation. However, the taxonomy of this section is still not fully understood. Furthermore the production of such chlamydospores also is known in some other sections of Phoma. DNA sequences were generated from three loci, namely ITS, actin, and β-tubulin, to clarify the phylogeny of Phoma taxa that produce dictyochlamydospores. Results were unable to support section Peyronellaea as a taxonomic entity. Dictyochlamydospore formation appears to be a feature that developed, or was lost, many times during the evolution of Phoma. Furthermore, based on the multigene analyses, five new Phoma species could be delineated while a further five required taxonomic revision to be consistent with the genetic variation observed.

The family Macrothricidae (Branchiopoda: Anomopoda) remains one of the least studied groups of water fleas (Cladocera). One of macrothricids with an unclear phylogenetic status is Lilljeborg, 1853 comprising a single universally accepted valid species, (O.F. Müller, 1785). Despite its wide distribution in the Northern Hemisphere, no studies were conducted to prove conspecificity of from different regions and properly describe its gamogenetic stages. Here, the morphological and genetic diversity of in the Holarctic is revised. Our results show that in East Eurasia and Alaska a separate species of the genus occurs, , which differs from s. str. by the posteroventral valve armature, structure of antenna I, and ephippium ornamentation. Mitochondrial DNA barcoding supports separation of and reveals a deeply divergent clade of s. l. in Canada, for which parthenogenetic females are morphologically indistinct from those of s. str. distribution fits well to the known patterns of Anomopoda biogeography. Males of possess two additional setae at antenna II basipodite, P1 with a subdistal lobe lacking setae, P1 IDL with a hook and an additional seta, and an unmodified postabdomen. As noted in some previous studies, likely represents a phylogenetic lineage distinct from the subfamily Macrothricinae, differing from most macrothricines by the absence of Fryer's fork at P1 inner endite anterior setae and presence of P1 accessory seta. However, the phylogenetic position of the genus and its diversity in South Eurasia, Africa, and North America requires further studies.

(Chace, 1966) was originally described from three specimens collected from Saint Helena Island, South Atlantic, and assigned to Leach, 1814. It is a poorly known species, and until now, no new records have been reported. Recently, this species was transferred to a new genus, Muñoz, García-Raso, González, Lopes, dos Santos & Cuesta, 2023, based exclusively on morphology. Nearly 60 years on from the original description, another eight specimens of have been made available for further study and sequencing. Mitochondrial 16S rRNA and cytochrome c oxidase subunit I sequences confirm the assignment of this Chace species to . Photographs of the male holotype and female paratype confirmed the presence of additional characters; consequently, the present work provides a redescription of this species.

Botryosphaeria dothidea is one of the most commonly reported species in a genus of important pathogens of woody plants. This taxon generally is accepted to represent a species complex, and hence its identity remains unclear. Previous studies either have treated B. dothidea as the valid name for B. ribis and B. berengeriana or argued for them to be separate entities. To add to the confusion, no ex-type cultures are available for either B. dothidea or B. ribis. The aim of the present study, therefore, was to recollect and characterize these fungi and designate a set of reference cultures that can be used in future studies. To this end, morphological, cultural and multi-allelic DNA sequence datasets from the rDNA (ITS 1, 5.8S, and ITS 2), β-tubulin and EF1-α genes were used to fully characterize these species. Botryosphaeria dothidea was found to be distinct from B. ribis, while B. berengeriana was retained as synonym of the former name. Furthermore, Fusicoccum aesculi is accepted as anamorph of B. dothidea, while the anamorph of B. ribis is newly described as F. ribis sp. nov. Botryosphaeria ribis could be distinguished from B. parva based on β-tubulin and EF1-α sequence data. A combined phylogeny of the three gene regions used in this study also showed that the genus Botryosphaeria represents two distinct phylogenetic assemblages that correspond to species with Diplodia and Fusicoccum anamorphs.