Unraveling Polyphyly in Flourensia (Asteraceae, Heliantheae, Enceliinae) and the Establishment of a New Genus Austroflourensia.

The monophyly of Flourensia was examined for the first time by sequencing the nuclear ITS and plastid psbA- trnH regions in 18 species of the genus, analyzing them along with representatives of the remaining genera of subtribe Enceliinae. Results showed strong evidence for the polyphyly of Flourensia identifying two well-supported groups: Flourensia, a clade from North America including the type F. laurifolia, and another clade, here designed as the new genus Austroflourensia, containing the South American species. Austroflourensia is related to the other four genera composing the subtribe Enceliinae, whereas Flourensia s.s. is sister to all of them. Austroflourensia can be mainly distinguished by having a shrubby or subshrubby habit, capitula always radiate usually arranged in weakly cymose-corymbose capitulescences, phyllaries 2-3-seriate, and disc corollas shortly dentate. This paper proposes twelve new combinations to accommodate species previously described in the genus Flourensia and provides emended descriptions of Flourensia and the new genus Austroflourensia. The illustration of the type of the new genus, a distribution map, and a key to the genera of Enceliinae are also provided.

Evolution of pollination by frugivorous birds in Neotropical Myrtaceae.

Bird pollination is relatively common in the tropics, and especially in the Americas. In the predominantly Neotropical tribe Myrteae (Myrtaceae), species of two genera, Acca and Myrrhinium, offer fleshy, sugary petals to the consumption of birds that otherwise eat fruits, thus pollinating the plants in an unusual plant-animal interaction. The phylogenetic position of these genera has been problematic, and therefore, so was the understanding of the evolution of this interaction. Here we include new sequences of Myrrhinium atropurpureum in a comprehensive molecular phylogeny based on a balanced sample of two plastid and two nuclear markers, with the aim of providing the historical framework of pollination by frugivorous birds in Myrteae. We developed 13 flower and inflorescence characters that comprehensively depict the macroscopic morphological components of this interaction. Bayesian and parsimony phylogenies concur in placing both Acca and Myrrhinium in a clade with Psidium species; with Myrrhinium sister to Psidium. Mapping of morphological characters indicated some degree of convergence (e.g., fleshy petals, purplish display) but also considerable divergence in key characters that point to rather opposing pollination strategies and also different degrees of specialization in Acca versus Myrrhinium. Pollination by frugivorous birds represents a special case of mutualism that highlights the evolutionary complexities of plant-animal interactions.

Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids.

Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level.

Phylogeny of the Paniceae (Poaceae: Panicoideae): integrating plastid DNA sequences and morphology into a new classification.

Included in the PACMAD clade of the family Poaceae (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae), the tribe Paniceae s.l. is one of the largest tribes of the subfamily Panicoideae, with more than 2000 species. This tribe comprises a huge morphological, cytological and physiological diversity represented by different inflorescence types, several basic chromosome numbers, and at least four major photosynthetic pathways. The tribe Paniceae has been the subject of molecular studies that have confirmed its paraphyly: two major clades were recognized based on their basic chromosome numbers (x = 9, x = 10). The x = 10 Paniceae clade is sister to the Andropogoneae-Arundinelleae s.s. clade (x = 10), while the combined x = 10 clade is sister to the x = 9 clade that contains the remaining genera of Paniceae. As a result of a recent realignment within the tribe in terms of the phylogenetic position of minor and major Paniceae genera, a reanalysis of the whole sampling is performed and new underrepresented taxa are discussed. A total of 155 genera, currently considered within subfamily Panicoideae, are represented here by almost all genera of Paniceae s.l., representatives of Andropogoneae and Arundinelleae s.s., and the endemic and small tribe Steyermarkochloeae; we also included specimens of subfamily Micrairoideae, tribes Isachneae and Eriachneae. The sampling includes as outgroups 18 genera of the PACMAD clade (excluding Panicoideae) and four genera from the BEP clade (Bambusoideae, Ehrhartoideae, Pooideae), rooting with Bromus inermis. A matrix with 265 taxa based on the combined evidence from ndhF plastid sequences (2074 bp) and 57 morphological characters was subjected to parsimony analyses. Jackknife resampling was used to calculate group support. Most clades are characterized by morphological, cytological, anatomical, and/or physiological characters. Major tribal changes are based on the basic chromosome number; the pantropical x = 9 clade is here recognized as Paniceae s.s., while the American x = 10 Paniceae s.l. is restricted to the reinstated tribe Paspaleae. The optimization of the photosynthetic pathway for the Paspaleae-Andropogoneae-Arundinelleae s.s. clade, including the monotypic Reynaudia, shows a plesiomorphic C4 state while the ancestral state for Paniceae s.s. is ambiguous. If Reynaudia were not included or placed elsewhere, the ancestral photosynthetic pathway for both the Paspaleae-Andropogoneae-Arundinelleae s.s. clade and the Paniceae s.s. would be unambiguously C3 . In order to explore character evolution further, the morphological characters were mapped onto one of the most parsimonious trees. A relationship between photosynthetic pathways and inflorescence morphology is suggested here for the first time. Based on the optimization of morphological characters and additional data, we propose names for almost all inner clades at the rank of subtribe with a few groups as incertae sedis. With this extensive sampling, we resolved the phylogenetic relationships and the assignation of synapomorphies, and improved the support in subtribe sorting; consequently a robust circumscription of the tribe Paniceae s.l. is proposed.

Detecting areas of endemism with a taxonomically diverse data set: plants, mammals, reptiles, amphibians, birds, and insects from Argentina.

The idea of an area of endemism implies that different groups of plants and animals should have largely coincident distributions. This paper analyses an area of 1152 000 km2 , between parallels 21 and 32°S and meridians 70 and 53°W to examine whether a large and taxonomically diverse data set actually displays areas supported by different groups. The data set includes the distribution of 805 species of plants (45 families), mammals (25 families), reptiles (six families), amphibians (five families), birds (18 families), and insects (30 families), and is analysed with the optimality criterion (based on the notion of endemism) implemented in the program NDM/VNDM. Almost 50% of the areas obtained are supported by three or more major groups; areas supported by fewer major groups generally contain species from different genera, families, or orders. © The Willi Hennig Society 2011.

When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae).

Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification. © The Willi Hennig Society 2011.

Phylogeny of New World Stipeae (Poaceae): an evaluation of the monophyly of Aciachne and Amelichloa.

© The Willi Hennig Society 2010. ABSTRACT: The tribe Stipeae, with nearly 550 species, includes 28 core genera, of which 13 occur in America: Achnatherum, Aciachne, Amelichloa, Anatherostipa, Hesperostipa, Jarava, Nassella, Ortachne, Oryzopsis, Pappostipa, Piptatherum, Piptochaetium and Ptilagrostis. Based on 37 species representing 14 Stipeae genera, and using four chloroplast markers and morphological characters, we provide a phylogenetic hypothesis of the New World Stipeae, with our focus on Amelichloa and Aciachne. Parsimony analyses included two approaches: (i) a multiple-sequence alignment where gaps were treated as missing or coded, (ii) using direct sequences by direct optimization as implemented by the program POY v.4.0.2870. Analyses under direct optimization were conducted using the molecular data sets independently and combined, and with morphological data. Different cost regimes were explored and the one producing the highest congruence between partitions was chosen. Among the genera considered, only Piptochaetium, Austrostipa, and Hesperostipa were resolved as monophyletic, while Achnatherum, Amelichloa s.l., Anatherostipa, Jarava and Nassella were polyphyletic, and Aciachne was polyphyletic or paraphyletic. As a result, Amelichloa can be restricted to a monophyletic group if including A. brachychaeta, A. ambigua, A. clandestina and A. caudata, or it should be considered within Nassella. The phylogenetic position of species of Aciachne suggests inbreeding and outbreeding events with species of Anatherostipa, Ortachne and Hesperostipa.

Quantitative biogeography in the South America highlands-recognizing the Altoandina, Puna and Prepuna through the study of Poaceae.

The distribution data of 340 grass species sampled in a region of 53.219 km2 in the northwestern corner of Argentina (between ∼21°S and ∼24°S) were analyzed to search for concordance in species distributions by using the program NDM/VNDM. Here, the traditional biogeographic hypothesis proposed for the region is evaluated for the first time by using a quantitative method and an optimal criterion specifically developed within the context of areas of endemism. Three different grid sizes (0.5° × 0.5°, 0.35° × 0.35 ° and 0.2° × 0.2°) were used to analyze three nested data sets: species found in the Andes of Argentina, Bolivia and/or Chile; Andean distributed species; and all grass species found in the study region. The main areas supported by the analyses correspond generally to the traditional biogeographic hypothesis proposed for the region. Local distribution patterns defined by species restricted to the study region were best supported under the small grid sizes, while the bigger grid sizes recovered areas defined by species with a broader distribution. The local distribution patterns emerged in all the analyses even when widespread species were added to the data set. © The Willi Hennig Society 2009.

Molecular phylogenetics of an aquatic plant lineage, Potamogetonaceae.

Like most aquatic plants, the pondweeds (Potamogetonaceae) are among the most phenotypically reduced and plastic of all angiosperms. As such, hypotheses of structural homology present difficulties for morphological phylogenetic reconstruction. We used non-coding nuclear and plastid DNA data to address Potamogetonaceae relationships and accompanying issues in character evolution and biogeography. Genera currently assigned to Potamogetonaceae, plus Zannichellia, formed a strongly supported monophyletic group. Potamogeton and Stuckenia (Potamogeton subg. Coleogeton) were both resolved as monophyletic. Within Potamogeton proper, two major clades followed the traditional split between broad- and narrow-leaved species, with the latter condition optimized as basal. Heterophylly (submerged plus floating leaves) has evolved several times, and the ancestral distribution for Potamogeton appears to be Northern Hemispheric. Our phylogenetic results have provided a useful genetic framework from which to interpret morphological, cytological and biogeographical evolution.

Direct optimization, affine gap costs, and node stability.

The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions. Robustness to changes in cost sets is measured as number of successive changes that can be made in a given cost set before a specific clade is lost. The changes are in all cases base change cost, gap penalties, and adding/removing/changing affine gap costs. When combining data partitions, the number of clades that appear in the entire parameter space is not remarkably increased, in some cases this number even decreased. However, when combining data partitions the trees from cost sets including affine gap costs were always more similar than the trees were from cost sets without affine gap costs. This was not the case when the data partitions were analyzed independently. When data sets were combined approximately 80% of the clades found under cost sets including affine gap costs resisted at least one change to the cost set.

Sequence length variation, indel costs, and congruence in sensitivity analysis.

The behavior of two topological and four character-based congruence measures was explored using different indel treatments in three empirical data sets, each with different alignment difficulties. The analyses were done using direct optimization within a sensitivity analysis framework in which the cost of indels was varied. Indels were treated either as a fifth character state, or strings of contiguous gaps were considered single events by using linear affine gap cost. Congruence consistently improved when indels were treated as single events, but no congruence measure appeared as the obviously preferable one. However, when combining enough data, all congruence measures clearly tended to select the same alignment cost set as the optimal one. Disagreement among congruence measures was mostly caused by a dominant fragment or a data partition that included all or most of the length variation in the data set. Dominance was easily detected, as the character-based congruence measures approached their optimal value when indel costs were incremented. Dominance of a fragment or data partition was overwhelmed when new sequence length-variable fragments or data partitions were added.

An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae).

The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adh1 sequences. The Adh1 sequences used span exon 2-4. Nearly all variation is found in intron 2 and intron 3, which form the basis for the phylogenetic analyses. Both in some ingroup and outgroup taxa intron 3 has a major duplication. Previous phylogenetic analyses have repeatedly confirmed monophyly of both Secale and Hordeum, the latter being part of the outgroup. However, optimization alignment only recovers both genera as monophyletic when knowledge of the duplication is incorporated in the analysis. The phylogenetic relationships within Secale are not clearly resolved. Subspecific taxa of Secale strictum have identical sequences and they are confined to a monophyletic group. However, the two subspecific taxa of Secale cereale do not form a monophyletic group, and the position of Secale sylvestre is uncertain.