cpDNA Phylogeny Research Articles

Phylogeography of Pleurospermum foetens (Apiaceae) From the Sky Islands of Southwest China.

Sky islands provide insights on how glacial-interglacial cycles have shaped species distribution and help for predicting species' responses to climate warming. The alpine subnival belt of southwest China, especially in the Hengduan Mountains and adjacent areas, is sky island-like. Among them, the Yunnan-Kweichow Plateau harbors several isolated mountains with well-developed alpine subnival vegetation, sharing a similar species composition with the Hengduan Mountains. However, the relationship between the sky islands of the Hengduan Mountains and the Yunnan-Kweichow Plateau remains insufficiently explored. Pleurospermum foetens (Apiaceae) is a species endemic to the alpine screes of the Yunnan-Kweichow Plateau and the Hengduan Mountains. We used DNA sequence data from 59 individuals across 9 populations, combined with ecological niche modeling, to investigate the evolution history and future distribution of P. foetens within this sky island region. The results indicate the following: (1) P. foetens exhibits a significant phylogeographic structure and can be classified into three nrDNA clades and two cpDNA clades, respectively, (2) a nuclear-plastid discordance observed in P. foetens and its relatives based on phylogenetic analysis. P. foetens is monophyletic in the nrDNA phylogeny, while two major clades (HDM and YGP) are present in the cpDNA phylogeny, each forming a clade with other congeneric species. (3) Ecological niche modeling of P. foetens indicated that the species had the most extensive suitable habitat during the last glacial maximum (LGM). However, anticipated climate warming in the coming decades is expected to reduce the suitable range of P. foetens, posing a significant threat to isolated marginal populations (e.g., Shizi Mountain) with restricted alpine scree habitats. In conclusion, our study highlights the substantial effect of sky island and glacial-interglacial cycles on the population divergence of P. foetens. Conservation efforts for marginal populations of alpine plants in the Yunnan-Kweichow Plateau require increased attention and prioritization.

Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China

Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs.

Chloroplast genomes and ribosomal DNA provide insights into divergence and morphological evolution of alpine Tongoloa

AbstractTongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well‐resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC, ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high‐resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long‐obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.

Molecular phylogeny and genetic diversity of some Lepidagathis species (Acanthaceae) based on nuclear and chloroplast regions

Lepidagathis Wild., a pantropical genus belonging to the tribe Barlerieae, contains ∼147 species. Considerable morphological work has been done on Lepidagathis, but some taxonomical doubts and contrasting interpretations still persist. Molecular analysis is the best tool to resolve the taxonomic doubts, but few nucleotide sequence data are available to date on Lepidagathis. Recently, some phylogenetic and morphological studies have proposed the inclusion of Teliostachya and Lophostachys in Lepidagathis. This work constitutes the first phylogenetic analysis of some Lepidagathis species based on chloroplast and nuclear regions. Both Bayesian and Maximum Likelihood phylogenetic analyses divide studied Lepidagathis species into two main clades, i.e. Clade A and B and place the Indian endemic Lepidagathis in Clade A with strong support. Phylogeny based on combined data resolve Lepidagathis, Barleria, and Crabbea lineages with stronger support than nrITS and cpDNA phylogenies. This phylogenetic study supports previous systematic revisions about the inclusion of Lophostachys and Acanthura species in Lepidagathis as well as the inclusion of Golaea and Acanthostelma into Crabbea species. In conclusion, this study constitutes a baseline molecular phylogeny for Lepidagathis and, in particular, contributes to the knowledge of the genetic diversity of Indian representatives of the genus.

The Phylogeny ofErrazurizia(Fabaceae: Amorpheae) and Description of the New Monotypic GenusPictarena

Abstract—Errazurizia(Fabaceae) is a genus comprised of four species of New World desert shrubs with an ambiguous evolutionary history. Prior studies determined the North American species ofErrazuriziawere polyphyletic and the relationship ofE. rotundatawith other genera in the tribe Amorpheae remained undetermined. The sole South American species, which is also the type species, has never been included in a molecular study. We inferred the phylogenetic relationships ofErrazuriziaand six closely related genera using data from the cpDNA genome and nrDNA cistron from reference guided assemblies. Maximum likelihood and Bayesian analyses found two of the North American and the South American species were a monophyletic group, but thatE. rotundatawas sister to the monotypic genusParryella. Gland and pollen surface characters confirm the close relationship betweenP. filifoliaandE. rotundata. Cytonuclear discordance yielded partially incongruent tree topologies, and while the cpDNA phylogeny indicated a monophyleticAmorphawas sister to theE. rotundataandP. filifoliaclade, the nrDNA cistron phylogeny recovered a paraphyleticAmorpha, withA. californicasister to theE. rotundataandP. filifoliaclade. Molecular and morphological evidence support the elevation ofE. rotundatato its own monotypic genus,Pictarena. The new genusPictarenais defined by subsessile, suborbicular leaflets, mammiform leaflet glands, spicate inflorescences, and flowers with either all petals absent or rarely with a banner petal. ElevatingE. rotundatatoPictarenaresolves the confusing classification of the species, an imperiled endemic known only from four localities in northern Arizona and lends support for continued conservation.

Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species

Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium.

Revised Taxonomy of theArctotisAnnual Clade (Arctotideae, Asteraceae) from Southern Africa: Integration of Molecular Phylogenetic and Morphological Evidence

Abstract—Previous phylogenetic analysis of ITS nrDNA sequence data for Arctotidinae species resolved a strongly supported clade containing all but one of the showy annualArctotisspecies (informally designated theArctotisAnnual Clade). In the present study, phylogenetic relationships in theArctotisAnnual Clade were investigated by Bayesian inference and maximum parsimony analyses of cpDNA (trnT-trnL-trnFandtrnH-psbA) and nrDNA (ITS) sequence data. The cpDNA and nrDNA phylogenies were notably incongruent.Arctotis venustaand a putative unnamed species (A.‘sp. B’) were strongly supported as monophyletic by both data sets. The monophyly ofA. leiocarpawas strongly supported by the ITS data set, whereas the remaining accessions formed a poorly resolved complex (the ‘A. fastuosacomplex’). Within theA. fastuosacomplex,A. hirsutawas monophyletic with strong support in the ITS phylogeny. A statistical parsimony-derived cpDNA haplotype network resolved five broad groups of haplotypes and showed no consistent geographical structure, but species-specific haplotype lineages forA. venustaandA.sp. B were resolved.Arctotis fastuosaaccessions were distributed among four haplotype groups. Incongruence between the data sets and poor resolution within theA. fastuosacomplex may reflect reticulate evolution, ancestral polymorphism, and incomplete lineage sorting, in tandem with the low information content of the data sets. The greatest phenotypic diversification in the clade is in cypsela morphology. Comparison of cypsela morphology with the phylogenies suggests a general trend for reduction in the sizes of the cypsela, abaxial wings, pappus scales, and loss of pubescence during diversification. A revised taxonomy, integrating currently available evidence, accompanied by full descriptive accounts and a key to the taxa are presented. Eight species are recognized, including the nomenclatural noveltiesArctotis chrysantha(sp. nov.) andArctotis namibiensis(sp. nov.). The namesArctotis karasmontana,Venidium fugax, andVenidium macrocephalumare lectotypified.

Phylogeny, Biogeography, and Classification of the Elms (Ulmus)

Abstract— A RAD-seq phylogeny is presented for the genus Ulmus, and a revised infrageneric classification is given, with keys, descriptions, and range maps for the subgenera and sections. The previously accepted classification was based on a cpDNA phylogeny, but several well-marked clades in the chloroplast phylogeny are not recovered in the RAD-seq phylogeny and do not seem to represent valid clades in the organismal phylogeny. Ordination and STRUCTURE analysis support a broad species concept in Ulmus sect. Foliaceae and demonstrate interspecific hybridization in the section. Several sections of the genus are disjunct between Asia, Europe, and North America, indicating dispersals between the northern continents with inferred dates from ca. 20 Ma to ca. 3 Ma. Morphological variation is discussed, and some characters previously considered characteristic of Ulmus subg. Oreoptelea (narrowly winged achenes, ciliate achene margin) are shared with the unrelated U. villosa. A new subgenus, Ulmus subg. Indoptelea, is described. It can be recognized morphologically by its combination of compact inflorescences with very short pedicels, and samaras with narrow, strongly ciliate wings. It is sister to Ulmus subg. Ulmus, but has a smaller genome than either of the other subgenera.

Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics.

Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed. Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group. We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae. Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.

Genotyping-by-sequencing (GBS), ITS and cpDNA phylogenies reveal the existence of a distinct Pyrenean/Cantabrian lineage in the European high mountain genus Homogyne (Asteraceae) and imply dual westward migration of the genus

Quaternary climatic oscillations have been a major factor in shaping plant diversity and distribution in the European Alpine System (EAS). Plants responded to these oscillations with repeated changes in their abundance and geographical distribution. However, oscillating shifts in geographical distribution have only rarely been reported in molecular analyses of genetic variation across the EAS. Homogyne, a genus endemic to the EAS, contains three species. While H. discolor and H. sylvestris are confined to the periphery of the Eastern Alps, H. alpina is widespread across the EAS. In phylogenetic reconstructions of a broad sample of Homogyne using DNA sequence data sets of the nuclear ribosomal internal transcribed spacer (ITS), plastid DNA (ndhF-rpl32, rpl32-trnL, psbA-trnH) and genotyping-by-sequencing (GBS), accessions of H. alpina from the Pyrenees and the Cantabrian Mts. form a clade which groups in conflicting positions. While the exact relationship of this Pyrenean/Cantabrian clade of H. alpina remains unclear, our data clearly imply that this clade is a lineage distinct from the remaining accessions of H. alpina (H. alpina s.str.). An ancestral area analysis unambiguously revealed the Eastern Alps as the ancestral area of the genus. Considering that relationships within H. alpina s.str. clearly illustrate East to West expansion, the identification of a Pyrenean/Cantabrian clade implies that westward expansion from an ancestral area in the Eastern Alps took place twice in the genus. Although the extant distributions of the Pyrenean/Cantabrian clade and H. alpina s.str. are mutually exclusive, plastid DNA evidence may imply past contact and hybridization between the two clades.

Phylogenetic analysis reveals the origins of tetraploid and hexaploid species in the Japanese Lepisorus thunbergianus (Polypodiaceae) complex.

The Japanese Lepisorus thunbergianus complex contains diploid and tetraploid races of L. thunbergianus and a hexaploid species, L. mikawanus. Here, we performed molecular phylogenetic analysis on this complex to delimit species and to elucidate the evolutionary origins of tetraploid and hexaploid species. Chloroplast DNA (cpDNA) phylogeny supported the monophyly of the complex. Based on a single-copy nuclear gene (PgiC) tree, the tetraploid L. thunbergianus samples could be classified into two variants: an allotetraploid of hybrid origin between diploid L. thunbergianus and Japanese L. angustus and another allotetraploid of hybrid origin between diploid L. thunbergianus and an unknown diploid race of L. tosaensis. These variants can be recognized morphologically and distinguished from their parent species. Hence, here we described these allopolyploids as new species, L. nigripes and L. kuratae, respectively. The hexaploid species L. mikawanus has three types of PgiC alleles, each of which was derived from diploid L. thunbergianus, L. tosaensis, and Japanese L. angustus, while cpDNA shows that it is included in Japanese L. thunbergianus clade. Based on the cpDNA phylogeny and PgiC nucleotide sequences, we therefore concluded that L. mikawanus is an allohexaploid that originated through hybridization between tetraploid species, L. nigripes and an unknown ancestral diploid race of L. tosaensis.

Two Species of "Entada" in Japan as Evidenced by cpDNA Phylogeny

Two Species of "Entada" in Japan as Evidenced by cpDNA Phylogeny

Quaternary climate change drives allo-peripatric speciation and refugial divergence in the Dysosma versipellis-pleiantha complex from different forest types in China

Subtropical China harbours the world’s most diverse temperate flora, but little is known about the roles of geographical and eco-climatic factors underlying the region’s exceptionally high levels of species diversity and endemism. Here we address this key question by investigating the spatio-temporal and ecological processes of divergence within the Dysosma versipellis-pleiantha species complex, endemic to subtropical China. Our cpDNA phylogeny showed that this monophyletic group of understory herbs is derived from a Late Pliocene ancestor of the Qinghai-Tibetan Plateau (QTP)/Southwest China. Genetic and ENM data in conjunction with niche differentiation analyses support that the early divergence of D. versipellis and D. pleiantha proceeded through allo-peripatric speciation, possibly triggered by Early Pleistocene climate change, while subsequent climate-induced cycles of range contractions/expansions enhanced the eco-geographical isolation of both taxa. Furthermore, modelling of population-genetic data indicated that major lineage divergences within D. versipellis likely resulted from long-term allopatric population isolation in multiple localized refugia over the last glacial/interglacial periods, and which in turn fostered endemic species formation (D. difformis, D. majoensis) from within D. versipellis in Southwest China. These findings point to an overriding role of Quaternary climate change in triggering essentially allopatric (incipient) speciation in this group of forest-restricted plant species in subtropical China.

Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

Supportive data related to the article “Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America” (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny.

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

BackgroundDuring adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.Methodology/Principal FindingsIn this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.ConclusionsThese findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.

A chloroplast phylogeny of Zieria (Rutaceae) in Australia and New Caledonia shows widespread incongruence with species-level taxonomy

This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.

Generic status, circumscription, and allopolyploid origin of Faberia (Asteraceae: Cichorieae) as revealed by ITS and chloroplast DNA sequence data

AbstractThe Chinese endemic Faberia (Asteraceae: Cichorieae) is imperfectly understood: its generic status, circumscription, and subtribal affiliation have long been in dispute. Here we present a molecular analysis to address these problems. Nuclear (ITS) and plastid (matK, psbA–trnH, rbcL, and trnL–F) sequence data were analyzed by means of Bayesian inference, maximum likelihood and maximum parsimony methods. Our results support the independent generic status of Faberia but not that of Faberiopsis, which should be re–submerged in the former. Dubyaea glaucescens is revealed as a member of Faberia, resulting in a new combination, F. glaucescens. The recent addition of Youngia racemifera to Faberia is refuted but the transfer of Prenanthes faberi to Faberia as F. faberi is corroborated. Consequently, Faberia is circumscribed here to include eight species (F. cavaleriei, F. ceterach, F. faberi, F. glaucescens, F. lancifolia, F. nanchuanensis, F. sinensis, F. thibetica). Most notably, phylogenies based on nrITS and cpDNA sequence data are highly incongruent with respect to the subtribal relationship of Faberia. The ITS phylogeny locates the genus in Lactucinae, whereas the cpDNA phylogeny places it in Crepidinae. This incongruence, together with karyological (Faberia has x = 17, a very rare number in Cichorieae) and palynological (Faberia has larger, 4–porate pollen grains, which are associated with polyploidy in Cichorieae) data, strongly favors the hypothesis that Faberia may have originated via hybridization between a member of Lactucinae with x = 9 (paternal parent or pollen donor) and a member of Crepidinae with x = 8 (maternal parent or ovule donor) and subsequent polyploidization. This work greatly increases our knowledge of Faberia and provides a convincing example of allopolyploid origin at the generic level within Cichorieae.

A New Vittarioid Fern Species, <I>Haplopteris heterophylla</I> (Pteridaceae)

Abstract A vittarioid fern (Pteridaceae) distributed in Eastern Asia is described here as a new species, Haplopteris heterophylla, which has long been included in H. hainanensis. A description, illustration, distribution, ecology, and a key to congeneric relatives of the new species are provided. Obovoid-shaped paraphyses and frond dimorphism are the diagnostic characteristics of H. heterophylla. In a trnL-F + matK + ndhF phylogeny of 14 Asian Haplopteris species, including H. hainanensis, both morphological observations and the cpDNA phylogeny support the systematic uniqueness of H. heterophylla.

Chloroplast DNA Intraspecific Phylogeography of Prairie Cordgrass (Spartina pectinata Bosc ex Link)

Chloroplast DNA (cpDNA) sequences are appropriate for studying intraspecific phylogeography. Comparing cpDNA phylogeny with different cytotypes provides insights into the origin and establishment of polyploid species. We have previously defined the geographic distribution of cytotypes in prairie cordgrass throughout the different regions of the United States. In this study, chloroplast haplotype variation is explored in 54 populations of prairie cordgrass, using nine noncoding chloroplast regions. These chloroplast analyses were combined with the cytotype surveys of prairie cordgrass to infer the phylogeography and to elucidate the origin of the different cytotypes. In this study, we identified three haplotypes, Prairie Cordgrass Group 1 (PCG1), Prairie Cordgrass Group 2 (PCG2), and Prairie Cordgrass Group 3 (PCG3). In general, related haplotypes were strongly associated with geographic distribution. Useful insertions–deletions (indels) were also found among prairie cordgrass populations. The PCG1 haplotypes collected inthe East North Central to the New England regions of the US, were polyploid (tetraploid, hexaploid, and octoploids), while the PCG2 haplotypes, found in southern South Dakota, Iowa, and Missouri, were primarily octoploids, but also included a small number of tetraploids. The PCG3 haplotypes were octoploids and were collected in North Dakota, South Dakota, and Minnesota.

Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa

Due to its unique geological history and isolated location, the Hawaiian Archipelago provides an ideal setting for studies on biogeography, phylogeny and population biology. Species richness in these islands has been attributed to unique colonization events. The Hawaiian mints comprising of three endemic genera represent one of the largest radiations in the island. Previous studies have shown the Hawaiian mints to be nested within the dry-fruited Stachys, probably resulting from one or more hybridization events. Stachydeae, the largest tribe in the subfamily Lamioideae (Lamiaceae), is a taxonomically complex and widespread lineage exhibiting remarkable chromosomal diversity. In this paper we attempted at untangling the relationships between the New World and Hawaiian mint taxa, as well as investigate the origin and diversification of the mints in the New World. There seem to have been at least two independent migration events of Stachys to the New World during the Middle to Late Miocene and towards the beginning of the Pliocene, respectively. Results indicate incongruence between the rDNA and cpDNA phylogenies suggesting a reticulate, New World origin for the Hawaiian mints, although dispersal to Hawaii appears to have happened only once during the Pliocene. South American Stachys diversified from their Mesoamerican relatives around Late Pliocene and may also have arisen from similar reticulate events indicated by their intercalating position among the Mesoamerican Stachys species. Further insights into the phylogenetic relationships between the New World mints may be gathered through the study of low copy nuclear loci.