Origin of African Physacanthus (Acanthaceae) via wide hybridization

Sequence Analysis of the Fusion Protein Gene of Human Respiratory Syncytial Virus Circulating in China from 2003 to 2014

The human respiratory syncytial virus (HRSV) fusion (F) protein is important for HRSV infection, but few studies have examined the genetic diversity of the F gene from Chinese samples. In this study, a total of 330 HRSV F sequences collected from different regions of China between 2003 and 2014 were analyzed to understand their genetic characteristics. In addition, these sequences were compared with 1150 HRSV F sequences in Genbank from 18 other countries. In phylogenetic analysis, Chinese HRSV F sequences sorted into a number of clusters containing sequences from China as well as other countries. F sequences from different genotypes (as determined based on the G gene sequences) within a HRSV subgroup could be found in the same clusters in phylogenetic trees generated based on F gene sequences. Amino acid analysis showed that HRSV F sequences from China and other countries were highly conserved. Of interest, F protein sequences from all Chinese samples were completely conserved at the palivizumab binding site, thus predicting the susceptibility of these strains to this neutralizing antibody. In conclusion, HRSV F sequences from China between 2003 and 2014, similar to those from other countries, were highly conserved.

Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.

Molecular evidence supports ancient long-distance dispersal for the amphi-Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides)

PREMISE OF THE STUDY

Barleria is a large, pantropical genus of ca. 265 species mainly distributed in the Old World with only one species, B. oenotheroides, extending to the neotropics. This amphi-Atlantic disjunction, frequently displayed by pantropical taxa, has been traditionally explained with vicariance or geodispersal hypotheses and increasingly with long-distance dispersal. The native status of this species in the New World is controversial.

METHODS

A molecular phylogeographic study based on the nuclear ribosomal ITS region and plastid trnL-F, rps16, and trnS-G sequences was done to clarify the origin of this tropical intercontinental disjunction. Divergence times were estimated with various analytical approaches, including different markers and primary calibration points.

KEY RESULTS

Divergence ages estimated for Barleria lineages disagree with vicariance or geodispersal hypotheses. Genetic differentiation of American vs. African populations of B. oenotheroides does not support a recent anthropogenic introduction to the New World. Our data suggest ancient long-distance dispersal from the Old to the New World probably during the Pliocene or Upper Miocene. The number of dispersal events remains unclear.

CONCLUSIONS

Our study demonstrates the native status of Barleria in the New World, resolving one of only three presumed natural Old World-New World disjunctions at the species level among Acanthaceae. This case constitutes a further documented example of the "out-of-Africa" pattern in the family, despite their lack of documented assisted-dispersal syndromes, and highlights the importance of long-distance dispersal to explain pantropical distributions in many families.