Parsimony-informative Characters Research Articles

The Self-incompatibility Locus and Chloroplast DNA Regions of Prunus domestica Reflect the Origin and Genetic Diversity of Traditional Cultivars

A traditional cultivar, Besztercei Bt.2, and a clone of an autochthonous landrace (Nemtudom P3) of the hexaploid European plum (Prunus domestica) were studied to highlight their breeding perspectives. Five self-incompatibility ribonuclease (S-RNase) alleles were detected in both cultivars, with one allele shared. DNA sequence analysis confirmed it as a new, previously unidentified allele in P. domestica, which we labeled as S18. This allele was found to share ∼99% identity with the Prunus spinosa SB-RNase allele. Because Prunus species are readily hybridizing, sequence variations in 10 chloroplast DNA regions and nuclear internal transcribed spacers were studied to check if ‘Nemtudom P3’ and ‘Besztercei Bt.2’ are indeed P. domestica. The majority-rule consensus tree of maximum likelihood and Bayesian inferences confirmed it, and also indicated genetic differentiation with ‘Nemtudom P3’ and ‘Besztercei Bt.2’ forming a statistically supported subclade within the P. domestica germplasm. Our results pointed to some regions of the P. domestica chloroplast genome (trnS-trnG-trnG, trnC-ycf6, and trnD-trnT) that can be used to detect intraspecific variations. The proportion of parsimony informative characters compared with the total length of amplified regions was the highest in the case of nrITS with 12.1%. The S-genotyping of 68 wild-growing Nemtudom trees showed the genetic consequences of long-term vegetative propagation and occasional crossing between Besztercei and Nemtudom accessions. Controlled pollinations confirmed the self-compatibility of ‘Nemtudom P3’. By clarifying their phylogenetic position, and characterizing the S-locus, our results will help breeding P. domestica cultivars and pave the way to understanding how the S-locus works in a hexaploid Prunus species.

Reconstructing the phylogeny of the hornless rhinoceros Aceratheriinae

This study presents the first phylogenetic analysis focused on the subfamily Aceratheriinae to date, with 392 characters (361 parsimony-informative characters) coded from 50 taxa at the species level. We added 80 newly defined and 33 revised characteristics to an existing matrix, covering features of the skull, teeth, and postcranial bones. Based on the results of ordered and unordered analyses, combined with a diagnosis in accordance with traditional morphological taxonomy, we revised the diagnosis of Aceratheriinae and reconstructed the phylogeny of Aceratheriinae. The tribe Teleoceratini, as well as the tribe Aceratheriini, was reclassified within Aceratheriinae; however, the traditionally established contents of each tribe were changed somewhat. Aceratheriinae underwent evolutionary adaptation several times during the early stages of its evolution, and several genera are herein reconstructed as early-diverging taxa, such as Floridaceras, Chilotheridium, and Plesiaceratherium. Turkanatherium and Protaceratherium are excluded from Aceratheriinae in this study. We suggest another two subclades of Aceratheriinae, containing Hoploaceratherium and Aprotodon, respectively. Aceratheriini and Teleoceratini are redefined as two highly specialized groups of Aceratheriinae.

Phylogenetic placement of Trifolium kentuckiense (Fabaceae), a new member of the native eastern North American clover clade

In 2013, a new species of clover endemic to Kentucky was described. This species, Trifolium kentuckiense (Fabaceae), has yet to be placed in a phylogeny but is hypothesized to be most closely related to T. reflexum based on morphology. We present phylogenetic evidence from the nuclear (ITS) and plastid genomes (trnL and ndhA introns) that T. kentuckiense is a member of a clade of seven Trifolium species native to eastern North America. Within this clade, T. kentuckiense is strongly placed in a clade with three other annual/biennial Trifolium species (T. bejariense, T. carolinianum, and T. reflexum); it is sister to T. reflexum, although support for this relationship is weak. Our results support previous findings that suggest the ndhA intron is much more variable than the trnL intron in the Eurosid I clade. The ndhA intron contained over twice the number of parsimony informative characters when compared to the trnL intron, though ITS was more variable than either region. We also provide a dichotomous key to native and nonnative members of Trifolium for Kentucky and its surrounding states. We suggest determinations of historic specimens of Trifolium, particularly those identified as T. reflexum, be reassessed to obtain localities that may still support populations of this recently described species. We also provide guidance on when and in what habitats to search for new populations of this extremely rare taxon.

Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains.

Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts.

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.

PremiseHybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here.MethodsHyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.ResultsAlignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches.DiscussionThe approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.

Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)

BackgroundSaussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera.ResultsAll Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability.ConclusionsOur analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.

RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer).

We have identified 46 RNA editing sites located in 20 chloroplast (cp) genes of Borassus flabellifer (Asian Palmyra palm), family Arecaceae, and tested these genes for supporting phylogenetic study among the commelinids. Among the 46 sites, 43 sites were found to cause amino acid alterations, which were predicted to increase the hydrophobicity and transmembrane regions of the proteins, and one site was to cause a premature stop codon. Analysis of these editing sites with data obtained from seed plants showed that a number of shared-editing sites depend on the evolutionary relationship between plants. We reconstructed a deep phylogenetic relationship among the commelinids using seven RNA edited genes that are orthologous among monocots. This tree could represent the relationship among subfamilies of Arecaceae family, but was insufficient to represent the relationship among the orders of the commelinid. After adding eight gene sequences with high parsimony-informative characters (PICs), the tree topology was improved and could support the topology for the commelinid orders ((Arecales,Dasypogenaceae) (Zingiberales+Commelinales,Poales)). The result provides support for inherent RNA editing along the evolution of seed plants, and we provide an alternative set of loci for the phylogenetic tree reconstruction of Arecaceae’s subfamilies.

Phylogenetic positions of seven poorly known species of Ferula (Apiaceae) with remarks on the phylogenetic utility of the plastid trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers

Ferula L. is one of the most species-rich and taxonomically difficult genera of Apiaceae. In this study, we obtained nrDNA ITS sequences of seven poorly known species of Ferula (Ferula anatolica, Ferula sp. (tentatively identified as F. candelabrum by collectors), F. drudeana, F. huber-morathii, F. marmarica, F. talassica, and F. tunetana) and explored their phylogenetic positions using 148 ITS sequences of the subtribe Ferulinae from GenBank. Five of these newly sequenced species fall into three groups, corresponding to clades recognized in earlier molecular studies. Ferula sp. are added to clade, which is mostly composed of Central Asian species. This placement showed that identification as F. candelabrum was erroneous. The second clade, which is mostly composed of Mediterranean taxa, includes two species from North Africa: F. marmarica and F. tunetana. Despite the well-supported monophyly of this clade, the relationships inside this group need to be revised, as broadly distributed F. communis is paraphyletic with respect to other species. Ferula drudeana and F. huber-morathii, two narrow endemics from Turkey, are placed in the Central Asian clade. Two species, F. anatolica and F. talassica, do not fall into any of the recognized clades. In addition, we examined the sequence variation of three potentially highly variable pDNA regions, the trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers, for a subset of 18 specimens. The resulting pDNA and ITS based phylogenetic trees were incongruent, as supported by significant ILD tests. The cause of this incongruence can be manifold, including hybridization, a lack of a phylogenetic signal, and homoplastic substitutions. Our analyses suggest that only trnS-trnG can be added to the list of pDNA markers used for phylogenetic studies of Ferula, as it has the highest number of parsimony informative characters and is easy to amplify from degraded material.

Phylogeny and reclassification of the Caucasigenini radiation from the Caucasus region (Gastropoda, Hygromiidae)

The Caucasigenini is an endemic radiation of hygromiid land snails from the Caucasus region. A phylogenetic analysis of morphological characters of the genitalia and the shell showed that the morphological characters are insufficient for resolving the relationships within the Caucasigenini. Convergences of the few parsimony informative characters in other groups of the Hygromiidae demonstrate that these characters are not reliable indicators of phylogenetic relationships. Phylogenetic analyses of sequences of cox1, 16S rDNA, 5.8S rDNA, ITS2 and 28S rDNA revealed several well‐supported groups. The relationships among these groups could not be resolved. It is likely that these groups originated in a rapid radiation during the uplift of the Caucasus. Based on the molecular phylogeny, we propose a new classification of the species of the Caucasigenini and establish a new genus, Lazicana gen. n.

Rolling into a ball: phylogeny of the Ceratocanthinae (Coleoptera: Hybosoridae) inferred from adult morphology and origin of a unique body enrollment coaptation in terrestrial arthropods

Results of a phylogenetic analysis of all but one of the 43 recognized extant genera of Ceratocanthinae scarab beetles (Coleoptera: Hybosoridae) are reported. The analysis is based on 97 parsimony informative adult morphological characters scored for 61 ingroup and 10 outgroup terminals. This pantropical subfamily of some 366 species is remarkable for the adults’ ability to pack their body into a tight sub-sphere using interlocking exoskeletal structures (= enrollment coaptations). An overview on known biological and fossil data on the subfamily is provided, as well as a list, an overview, a key and illustrations of adults of all Ceratocanthinae genera. The phylogenetic analysis supports a monophyletic Ceratocanthinae (bootstrap 76%) and a basal dichotomy between pantropical Ceratocanthini (97%) and the South American clade (98%) of Scarabatermitini. Ivieolini renders Scarabatermitini paraphyletic. Another well supported internal clade is the Philharmostes group of seven Afrotropical genera (85%). All other inclusive clades detected in the analysis have low bootstrap support (51–65%), likely indicative of limitations of the adult morphological dataset. We also provide a detailed distribution map of Ceratocanthinae and hypothesize about the South American origin of the subfamily, and that of its two subclades: Ceratocanthini and Scarabatermitini + Ivieolini. Overall this paper summarizes all existing information on Ceratocanthinae beetles in an evolutionary context in order to facilitate and stimulate further research on this subfamily.

Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence.

Background and Aims Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species.Methods Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices.Key Results The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species.Conclusions In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree because the total number of variable sites was much lower than in the entire plastid genome. The geographical clustering of the individuals against a background of overall low sequence divergence could indicate transfer of plastid genomes due to hybridization and introgression following secondary contact.

Development of chloroplast genomic resources for Cynara.

In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.

A modification to the SCAR (Sequence Characterized Amplified Region) method provides phylogenetic insights within Ceratozamia (Zamiaceae)

Phylogenetic relationships among closely related plant species is still problematic. DNA intergenic regions often are insufficiently variable to provide desired resolution or support. In this study, a modification to the Sequence Characterized Amplified Region (SCAR) method was used to find polymorphic loci for phylogenetic analyses within Ceratozamia. RAPD markers were first used to detect variation in five species. Then, equal length fragments in two or more species were excised from the gel, purified and digested with frequent cutter restriction enzymes for isolating both ends, which have the same primer site. Later, digested fragments were sequenced with the RAPD primer. Last, variable sequences were used to design specific primers for amplifying and sequencing all species for phylogenetic analyses. Our results confirmed the previously known high genome sequence resemblance within this genus that contrasts with its high morphological variation. Only six parsimony informative characters were generated with this approach. Nonetheless, the SCAR method provided some phylogenetic insights. Three main clades consistent with distribution ranges of the species were detected. The approach presented here was effective to solve some relationships within the genus and can be implemented in other organisms to find polymorphic loci for phylogenetic studies.

A modification to the SCAR (Sequence Characterized Amplified Region) method provides phylogenetic insights within Ceratozamia (Zamiaceae)

Phylogenetic relationships among closely related plant species is still problematic. DNA intergenic regions often are insufficiently variable to provide desired resolution or support. In this study, a modification to the Sequence Characterized Amplified Region (SCAR) method was used to find polymorphic loci for phylogenetic analyses within Ceratozamia . RAPD markers were first used to detect variation in five species. Then, equal length fragments in two or more species were excised from the gel, purified and digested with frequent cutter restriction enzymes for isolating both ends, which have the same primer site. Later, digested fragments were sequenced with the RAPD primer. Last, variable sequences were used to design specific primers for amplifying and sequencing all species for phylogenetic analyses. Our results confirmed the previously known high genome sequence resemblance within this genus that contrasts with its high morphological variation. Only six parsimony informative characters were generated with this approach. Nonetheless, the SCAR method provided some phylogenetic insights. Three main clades consistent with distribution ranges of the species were detected. The approach presented here was effective to solve some relationships within the genus and can be implemented in other organisms to find polymorphic loci for phylogenetic studies.

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

Comparative chloroplast genome analysis presents new opportunities for performing molecular phylogeny studies and revealing the significant evolutionary features in higher plants, which has been widely documented from conifers to grass family. However, a systematic analysis of chloroplast genomes in Asteraceae family has not been conducted up to now. In this study, we compared and analyzed the gene content, genomic organization, and RNA editing sites of eight representative Asteraceae chloroplast genomes. Results showed that Asteraceae chloroplast had relatively conservative gene content. No gain or loss events occurred in the protein-coding genes, while some differences were found to be present in the gene structure and transfer RNA (tRNA) abundance. Genome structure analysis found some Asteraceae-specific or species-specific structure variations, and sequence rearrangement events were present in these genomes, suggesting specific evolutionary processes have occurred in this family. Some DNA regions containing parsimony-informative characters higher than 5 % were also identified, which could be used as the new molecular markers for phylogenetic analysis and plant identification of Asteraceae species. Furthermore, RNA editing in these genomes was investigated through computational analysis, and some species-specific sites were identified. Finally, phylogenetic analysis of 81 genes from 70 species supported the monophyly of the Asteraceae. Our study for the first time compared the organization, structure, and sequence divergence of eight Asteraceae chloroplast genomes, which will provide the valuable resource for molecular phylogeny of Asteraceae species and also facilitate the genetic and evolutionary studies in this family.

Phylogenomics of the carrot genus (Daucus, Apiaceae).

• We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species.• We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach.• Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of many different species as monophyletic with strong support, but failed to support other species. The single allele analysis gave slightly better topological resolution; trimming homopolymers failed to increase taxonomic resolution; the exonic data had a smaller proportion of parsimony-informative characters. Similar results demonstrating the same dominant topology can be obtained with many fewer markers. A Bayesian concordance analysis provided an overall similar phylogeny, but the coalescent analysis provided drastic changes in topology to all the above.• Our research highlights some difficult species groups in Daucus and misidentifications in germplasm collections. It highlights a useful subset of markers and approaches for future studies of dominant topologies in Daucus.

Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species

Praxelis (Eupatorium catarium Veldkamp) is a new hazardous invasive plant species that has caused serious economic losses and environmental damage in the Northern hemisphere tropical and subtropical regions. Although previous studies focused on detecting the biological characteristics of this plant to prevent its expansion, little effort has been made to understand the impact of Praxelis on the ecosystem in an evolutionary process. The genetic information of Praxelis is required for further phylogenetic identification and evolutionary studies. Here, we report the complete Praxelis chloroplast (cp) genome sequence. The Praxelis chloroplast genome is 151,410bp in length including a small single-copy region (18,547bp) and a large single-copy region (85,311bp) separated by a pair of inverted repeats (IRs; 23,776bp). The genome contains 85 unique and 18 duplicated genes in the IR region. The gene content and organization are similar to other Asteraceae tribe cp genomes. We also analyzed the whole cp genome sequence, repeat structure, codon usage, contraction of the IR and gene structure/organization features between native and invasive Asteraceae plants, in order to understand the evolution of organelle genomes between native and invasive Asteraceae. Comparative analysis identified the 14 markers containing greater than 2% parsimony-informative characters, indicating that they are potential informative markers for barcoding and phylogenetic analysis. Moreover, a sister relationship between Praxelis and seven other species in Asteraceae was found based on phylogenetic analysis of 28 protein-coding sequences. Complete cp genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade.

Molecular Phylogeny of the Bamboo Sharks (Chiloscylliumspp.)

Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.

Novel nuclear markers inform the systematics and the evolution of serpentine use in Streptanthus and allies (Thelypodieae, Brassicaceae)

Streptanthus is a genus of ca. 35 species in the tribe Thelypodieae (Brassicaceae) that has remarkable morphological and ecological diversity, a large number of species in the group being edaphic specialists endemic to unusual soils such as serpentine. While ecological research has shed some light on adaptation to serpentine in Streptanthus, there have been few insights on the origins and evolution of serpentine tolerance in this group, largely due to limited success in resolving the phylogenetic relationships among Streptanthus and allied genera of the Thelypodieae (Streptanthoid complex).We present a well-resolved phylogenetic hypothesis for the Streptanthoid complex, based on three newly identified and highly variable single copy nuclear regions (AT4G34700, AT1G61620, and AT1G56590, and three others that are widely used (ITS, phyA, and PEPC). We also include data for two chloroplast regions (trnL and trnH-psbA). Collectively, our new markers provide 75% of the nuclear parsimony informative characters in our data. Taxonomically, our sampling is the most inclusive of any study of the Streptanthoid Complex to date, including 46 out of the 53 species of Streptanthus and Caulanthus, as well as representatives of several closely allied genera in the Thelypodieae.Our results reveal that Streptanthus, Caulanthus, and Thelypodium are not reciprocally monophyletic as currently defined. The species of Streptanthus form two rather distantly related clades. One clade (SC-I) is comprised of species with bilateral flowers and urn-shaped calyces that occur mainly within the California Floristic Province (CFP) hotspot; the other clade (SC-II) is composed of species with extant ranges mainly outside the CFP. Our data indicate that serpentine tolerance has evolved between eight and ten times in this group, of which between four and five have resulted in endemism. While serpentine endemism has been rarely lost, large and diverse clades composed mainly of serpentine endemics indicate that serpentine endemics in this group are more than mere ‘dead-ends’.