DNA barcoding indicates multiple invasions of the freshwater snail Melanoides tuberculata sensu lato in Florida.

Melanoides tuberculata sensu lato (Thiaridae) are polymorphic female-clonal snails of Asian and African origins that have invaded freshwaters worldwide, including those in Florida. Although the snails have been documented in Florida for at least 70 years, no studies have investigated whether the observed distribution is due to a single introduction or multiple independent invasions. Here, cytochrome oxidase I was used to measure genetic diversity within and among sites in Florida and compare genetic diversity between Florida and other regions of the world. We also examined the relationship between shell morphology and haplotype diversity to determine if shell morphs can serve as a proxy for haplotypes. In total, we recovered 8 haplotypes randomly distributed across populations in Florida. Phylogenetic reconstruction supported the hypothesis of multiple invasions by diverse representatives of the M. tuberculata species complex. In contrast, shell morphology was not found to be a useful phylogeographic character, with divergent haplotypes represented by similar shell forms. These results suggest that the observed invasion patterns in Florida are best explained by serial introductions, and that shell morphology cannot be used to predict haplotypes or reconstruct invasion history of Melanoides tuberculata s.l. and that extensive taxonomic revisions are needed to investigate invasion dynamics.

Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos.

The objectives of the current study were to investigate the origin of polyploidy in the woody bamboos and examine putative hybrid relationships in one major lineage (the temperate woody bamboos, tribe Arundinarieae). Phylogenetic analyses were based on sequence data from three nuclear loci and 38 species in 27 genera. We identify six ancestral genome donors for contemporary bamboo lineages: temperate woody bamboos (tribe Arundinarieae) contain genomes A and B, tropical woody bamboos (tribe Bambuseae) contain genomes C and D, and herbaceous bamboos (tribe Olyreae) contain genome H; some hexaploid paleotropical bamboos contain genome E in addition to C and D. Molecular data indicate that allopolyploidy arose independently in temperate (AABB) and tropical woody lineages (CCDD and CCDDEE), and speciation occurred subsequent to polyploidization. Moreover, hybridization has played a surprising and recurrent role in bamboo evolution, generating allohexaploid species in the paleotropical clade and intergeneric hybrids among the allotetraploid temperate bamboos. We suggest this complex history of reticulate evolution is at least partially responsible for the taxonomic difficulty associated with the woody bamboos. This newly-resolved phylogenetic framework reflects a major step forward in our understanding of bamboo biodiversity and has important implications for the interpretation of bamboo phylogenomics.

Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited.

UNLABELLED: • PREMISE OF THE STUDY: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana, A. tecta, and Olyra latifolia, to refine our knowledge of their evolution and historical biogeography. A correction is noted regarding an error in an earlier report on the biogeography of Cryptochloa• METHODS: Single-end DNA libraries were prepared and sequenced on the Illumina platform. Complete plastomes were assembled and analyzed with 13 other Poaceae.• KEY RESULTS: Complete sampling in Arundinaria and an additional species of Olyreae gave a more detailed picture of their evolution/historical biogeography. Phylogenomic analyses indicated that the first major divergence in Arundinaria occurred around 2.3 to 3.2 mya and that Arundinaria tecta and A appalachiana diverged from their common ancestor around 0.57 to 0.82 mya. Estimates of the divergence of Olyra latifolia from Cryptochloa strictiflora ranged from 14.6 to 20.7 mya. The age of the stem node of Olyreae ranged from an estimated 26.9 to 38.2 mya.• CONCLUSIONS: Estimates of divergences in Arundinaria can be correlated with paleoclimatic events including an early Pliocene warming, subsequent cooling, and North American glaciations. Discriminating between alternate evolutionary/biogeographic scenarios in Olyreae is challenging.

Five nuclear loci resolve the polyploid history of switchgrass (Panicum virgatum L.) and relatives.

Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum) and common or Proso millet (P. miliaceum). Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels.

Reference genome sequence of the model plant Setaria.

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram.

BACKGROUND AND AIMS: Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa. METHODS: Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method. KEY RESULTS: The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica-E. tristachya clade, which is considered a source of maternal parents for allotetraploids. Two homoeologous loci are isolated from three tetraploid species in the Pepc4 phylogeny, and the maternal parents receive further support. The A-type EF-1α sequences possess three characters, i.e. a large number of variations of intron 2; clade E-A distantly diverged from clade E-B and other diploid species; and seven deletions in intron 2, implying a possible derivation through a gene duplication event. The crown age of Eleusine and the allotetraploid lineage are 3·89 million years ago (mya) and 1·40 mya, respectively. CONCLUSIONS: The molecular data support independent allotetraploid origins for E. kigeziensis and the E. africana-E. coracana clade. Both events may have involved diploids E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The habitat-specific hypothesis is proposed to explain the divergence of Eleusine and its allotetraploid lineage.

Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence.

The temperate bamboos (tribe Arundinarieae) are notorious for being taxonomically extremely difficult. China contains some of the world's greatest diversity of the tribe Arundinarieae, with most genera and species endemic. Previous investigation into phylogenetic relationships of the temperate bamboos revealed several major clades, but emphasis on the species-level relationships among taxa in North America and Japan. To further elucidate relationships among the temperate bamboos, a very broad sampling of Chinese representatives was examined. We produced 9463 bp of sequences from eight non-coding chloroplast regions for 146 species in 26 genera and 5 outgroups. The loci sequenced were atpI/H, psaA-ORF170, rpl32-trnL, rpoB-trnC, rps16-trnQ, trnD/T, trnS/G, and trnT/L. Phylogenetic analyses using maximum parsimony and Bayesian inference supported the monophyly of Arundinarieae. The two major subtribes, Arundinariinae and Shibataeinae, defined on the basis of different synflorescence types, were indicated to be polyphyletic. Most genera in this tribe were confirmed to be paraphyletic or polyphyletic. The cladograms suggest that Arundinarieae is divided into ten major lineages. In addition to six lineages suggested in a previous molecular study (Bergbamboes, the African alpine bamboos, Chimonocalamus, the Shibataea clade, the Phyllostachys clade, and the Arundinaria clade), four additional lineages were recovered in our results, each represented by a single species: Gaoligongshania megalothyrsa, Indocalamus sinicus, Indocalamus wilsonii, Thamnocalamus spathiflorus. Our analyses also indicate that (1) even more than 9000 bp of fast-evolving plastid sequence data cannot resolve the inter- and infra-relationships among and within the ten lineages of the tribe Arundinarieae; (2) an extensive sampling is indispensable for phylogeny reconstruction in this tribe, especially given that many genera appear to be paraphyletic or polyphyletic. Perhaps the ideal way to further illuminate relationships among the temperate bamboos is to sample multiple nuclear loci or whole chloroplast sequences in order to obtain sufficient variation.

Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria).

In spite of the ecological and economic importance of temperate bamboos, relatively little is known about their population biology or evolutionary history. Recently, hybridization has emerged as a potential source of diversity in this group, as well as an underlying cause of taxonomic problems. As part of a broader phylogenetic study of the temperate bamboos, we report the results of an analysis of the North American Arundinaria gigantea species complex, including estimates of genetic variation and molecular evidence of natural hybridization among A. gigantea, A. tecta, and A. appalachiana. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species plus individuals with intermediate or unusual morphological characteristics (putative hybrids). Molecular results support the recognition of three species previously defined on the basis of morphology, anatomy, and ecology, with most of the molecular variance accounted for by among-species variation. Molecular evidence also demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. The role of hybridization in the phylogenetic history of Arundinaria is discussed along with implications for the evolution and taxonomy of the temperate woody bamboos.