New combinations in Pediomelum (Leguminosae: Psoraleeae)

Three new combinations includePediomelum pariense, P. megalanthum var.retrorsum, andP. megalanthum var.epipsilum.     

Lectotypifications of infrageneric taxa in Psoraleeae (Leguminosae: Papilionoidae)

Psoralea (Leguminosae: Papilionoidae) sectionsAxillariflorae, Capitatae, andSpicatae, andPsoralea subseriesSparsiflorae, Fasciculatae, Spicato-capitatae, andSpicato-racemosae are lectotypified.     

Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora). Based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, our analyses demonstrate that when the indels were not taken into consideration, the monophyly of Ursidae and Pinnipedia tree and the monophyly of Pinnipedia and Musteloidea tree were both recovered, whereas inclusion of indels by using three different indel coding schemes give identical phylogenetic tree topologies supporting the monophyly of Ursidae and Pinnipedia. Our work brings new perspectives on the previously controversial placements among Arctoidea families, and provides another example demonstrating the importance of identifying and incorporating indels in the phylogenetic analyses of introns. In addition, comparison of indel incorporation methods revealed that the three indel coding methods are all advantageous over treating indels as missing data, given that incorporating indels produces consistent results across methods. This is the first report of the impact of different indel coding schemes on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account in the future phylogenetic analyses.     

Divergence and diversification in North American Psoraleeae (Fabaceae) due to climate change

Background  

Past studies in the legume family (Fabaceae) have uncovered several evolutionary trends including differential mutation and diversification rates across varying taxonomic levels. The legume tribe Psoraleeae is shown herein to exemplify these trends at the generic and species levels. This group includes a sizable diversification within North America dated at approximately 6.3 million years ago with skewed species distribution to the most recently derived genus, Pediomelum, suggesting a diversification rate shift. We estimate divergence dates of North American (NAm) Psoraleeae using Bayesian MCMC sampling in BEAST based on eight DNA regions (ITS, waxy, matK, trnD-trnT, trnL-trnF, trnK, trnS-trnG, and rpoB-trnC). We also test the hypothesis of a diversification rate shift within NAm Psoraleeae using topological and temporal methods. We investigate the impact of climate change on diversification in this group by (1) testing the hypothesis that a shift from mesic to xeric habitats acted as a key innovation and (2) investigating diversification rate shifts along geologic time, discussing the impact of Quaternary climate oscillations on diversification.     

Chromosome numbers for native North American unifoliolate species of Crotalaria (Leguminosae)

Chromosome counts are reported for nine taxa of the genusCrotalaria. Previous reports ofn = 16 are confirmed forC. sagittalis L. andC. stipularia Desv. First counts ofn = 16 are reported forC. bupleurifolia var.bupleurifolia, C. nayaritensis, C. polyphylla,C. purshii, C. quercetorum, C. rotundifolia var.rotundifolia, andC. rotundifolia var.vulgaris.     

A phylogenetic analysis ofLeucaena (Leguminosae: Mimosoideae)

Chloroplast DNA restriction fragment length polymorphisms have been used to reconstruct the maternal phylogeny of all the known taxa in the small neotropical legume genusLeucaena. Three major plastome clades were recognized, but these did not conform with relationships between the taxa proposed on other characters from morphology, cytology or hybridization. The maternal parentage of tetraploids within the genus has been proposed. Evidence for introgression was found between diploidL. diversifolia and tetraploidL. diversifolia. The implications of these results for the origin of the cultivated taxa are discussed.     

Cladistic analysis of chloroplast DNA restriction site characters in Andira (Leguminosae: Dalbergieae)

Chloroplast DNA (cpDNA) restriction site variation was examined in 29 accessions, representing 29 populations of 17 species of Andira (Leguminosae, Papilionoideae, tribe Dalbergieae). This sample spans the morphological and geographical diversity of this poorly known, woody genus of approximately 30 species, which occurs throughout the neotropics, with one species in Africa. Cladistic analysis of 38 restriction site characters generated 182 equally most-parsimonious trees. The strict consensus tree preserved four well-supported clades, which are incongruent with previous infrageneric classifications of Andira. None of these clades has been recognized by previous workers, and three are not marked by any major morphological innovations. There were few restriction site differences between closely related species, but two (possibly three) species showed intraspecific cpDNA polymorphism, which probably reflects processes of hybridization with subsequent introgression, or lineage sorting.     

Development of the cymose inflorescence, cupulum and flower of Psoralea pinnata (Leguminosae: Papilionoideae: Psoraleeae)

The inflorescence of Psoralea pinnata sensu lato is composed of dichasial cymes of three to seven flowers in each bract axil. However, the main inflorescence terminal is indeterminate. Cymes are very unusual among legumes, occurring in perhaps six or seven genera. The 'cupulum' is a unique structure found only in Psoralea among legumes. While highly variable in form, it serves as a protective structure around the calyx during development. Developmentally the cupulum results from fusion by intercalary growth of three to four successive bracts on the pedicel. Paired bracteoles are also produced above the cupulum and below the calyx, but they are very reduced and easily overlooked. Their presence is evidence that the cupulum is not part of the flower proper. Organogeny in P. pinnata is unidirectional in each floral whorl, starting on the abaxia! side, except for a minor exception in precocity of the vexillary (adaxial) stamen arising with the two lateral stamens of the same inner whorl. There is no overlap between whorls. The carpel is initiated early, during or just after petal initiation and before stamen initiation.     

Examination of five nuclear markers for phylogenetic study of Hologalegina (Leguminosae)

Most legume phylogenies have relied heavily on plastid gene datasets, with or without nuclear ribosomal DNA ITS data, but the sequences of nuclear genes and gene-spanning regions offer certain advantages. We tested the phylogenetic utility of five nuclear loci across the species-rich legume clade Hologalegina: PGDH, TRPT, HRIP, RNAR, and CNGC4 (CNGC4-like protein). Our objective was to determine whether any of these nuclear loci could be beneficial at resolving lower-level phylogenetic relationships in this clade, with a particular interest in finding markers that might work at the species level. While the phylogenetic utility of these nuclear loci is unknown outside of Hologalegina, we determined that two of the loci, PGDH and TRPT, are useful for phylogenetic analyses within Hologalegina, depending upon the desired scale of resolution.     

A phylogenetic hypothesis for the Aizoaceae (Caryophyllales) based on four plastid DNA regions

The Aizoaceae is the largest family of leaf succulent plants, and most of its species are endemic to southern Africa. To evaluate subfamilial, generic, and tribal relationships, we produced two plastid DNA data sets for 91 species of Aizoaceae and four outgroups: rps16 intron and the trnL-F gene region (both the trnL intron and the trnL-F intergenic spacer). In addition, we generated two further plastid data sets for 56 taxa restricted to members of the Ruschioideae using the atpB-rbcL and the psbA-trnH intergenic spacers. In the combined tree of the rps16 intron and trnL-F gene region, three of the currently recognized subfamilies (Sesuvioideae, Mesembryanthemoideae, and Ruschioideae) are each strongly supported monophyletic groups. The subfamily Tetragonioideae is polyphyletic, with Tribulocarpus as sister to the Sesuvioideae and Tetragonia embedded in the Aizooideae. Our study showed that the group consisting of the Sesuvioideae, Aizooideae, and Tetragonioideae does not form a monophyletic entity. Therefore, it cannot be recognized as a separate family in order to accommodate the frequently used concept of the Mesembryanthemaceae or "Mesembryanthema," in which the subfamilies Mesembryanthemoideae and Ruschioideae are included. We also found that several genera within the Mesembryanthemoideae (Mesembryanthemum, Phyllobolus) are not monophyletic. Within the Ruschioideae, our study retrieved four major clades. However, even in the combined analysis of all four plastid gene regions, relationships within the largest of these four clades remain unresolved. The few nucleotide substitutions that exist among taxa of this clade point to a rapid and recent diversification within the arid winter rainfall area of southern Africa. We propose a revised classification for the Aizoaceae.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

End-products of behaviour versus behavioural characters: a phylogenetic investigation of pupal cocoon construction and form in some North American black flies (Diptera: Simuliidae)

Cocoon spinning was analysed, using video recording and playback, in eighteen Nearctic black fly species, comparing nine Simulium species, six Eusimulium species, Stegopterna mutata, Cnephia dacotensis and Prosimulium mixtum. Fourteen behavioural characters were revealed that produced twenty-two equally parsimonious trees (CI = 0.93, RI = 0.96). Another tree was constructed on the basis of five characters relating to the cocoon structure (end-product characters). The goal of the study was to determine whether characters relating to behavioural components of black fly cocoon spinning or those based on end-products of the behaviour are superior for revealing phylogenetic relationships. This was accomplished by comparing both data sets to a phylogeny constructed with the use of cytological and morphological characters. If taxa are grouped according to end-products (the cocoons) there are some spurious groupings. The behavioural analysis only required one extra step to duplicate the morphological and cytological tree. In the case of black flies, it is more informative to use characters resulting from the analysis of the cocoon spinning behaviour than cocoon morphology.     

Pollen morphology and phylogenetic analysis of Eperua Aublet (Detarieae: Caesalpinioideae: Leguminosae)

The diverse pollen morphology of fourteen species of the genus Eperua is described and illustrated using light, scanning electron and transmission electron microscopy. Six pollen types are described and a key for their identification is provided. A cladistic analysis was carried out using macromorphological and palynological characters to form a hypothesis of relationships between taxa. The pollen morphology is discussed with regard to systematic relationships, function and phylogenetic significance of certain pollen morphological structures within the genus.     

A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies

We assessed the utility of eight DNA sequence markers (5.8S rDNA, 18S rDNA, 28S rDNA, ITS regions, long-wavelength opsin, elongation factor 1-alpha, cytochrome b, and cytochrome oxidase I) in reconstructing phylogenetic relationships at various levels of divergence in gallwasps (Hymenoptera: Cynipidae), using a set of eight exemplar taxa. We report sequence divergence values and saturation levels and compare phylogenetic results of these sequences analyzed both separately and combined to a well-corroborated morphological phylogeny. Likelihood ratio tests were used to find the best evolutionary model fitting each of the markers. The likelihood model best explaining the data is, for most loci, parameter rich, with strong A-T bias for mitochondrial loci and strong rate heterogeneity for the majority of loci. Our data suggest that 28S rDNA, elongation factor 1-alpha, and long-wavelength opsin may be potentially useful markers for the resolution of cynipid and other insect within-family-level divergences (circa 50-100 mya old), whereas mitochondrial loci and ITS regions are most useful for lower-level phylogenetics. In contrast, the 18S rDNA marker is likely to be useful for the resolution of above-family-level relationships.     

Chloroplast DNA restriction site polymorphism inGenisteae (Leguminosae) suggests a common origin for European and American lupines

Restriction site polymorphism in cpDNA of 35 legumes was studied in order to address natural relationships and geographic distribution within the tribeGenisteae. 386 sites were studied, 277 were polymorphic, 207 were informative. Phylogenetic inferences with distance and parsimony methods suggest that the American and MediterraneanLupinus species belong to a monophyletic group which arose from a single center of diversification. The data furthermore indicate thatLupinus should not be included in the tribeGenisteae since at the level of cpDNA polymorphismAnagyris foetida (tribeThermopsideae) appears more closely related to otherGenisteae thanLupinus does.     

中国松毛虫属八个种和亚种亲缘关系的DNA指纹证据

利用DNA指纹谱方法探讨了中国松毛虫属8个种和亚种〔马尾松毛虫Dendrolimus punctatus punctatus (Walker),德昌松毛虫D. punctatus tehchangensis Tsai et Liu,文山松毛虫D. punctatus wenshanensis Tsai et Liu,思茅松毛虫D. kikuchii Matsumura,赤松毛虫D. spectabilis Butler,油松毛虫D. tabulaeformis Tsai et Liu,落叶松毛虫D. superans (Butler),云南松毛虫D. houi Lajonquiere之间的亲缘关系。13个随机引物在8种松毛虫中共检测到168个多态分子标记。分析表明,这8个种间的遗传距离的变化范围为0.3780～0.7360;马尾松毛虫与其亚种德昌松毛虫的遗传距离最近,为0.3780,与其另一亚种文山松毛虫以及油松毛虫的遗传距离次之,皆为0.5233;赤松毛虫、落叶松毛虫、云南松毛虫与马尾松毛虫的遗传距离则再次之,分别为0.6362,0.6770和0.6944;与马尾松毛虫遗传距离最远的是思茅松毛虫,为0.7360。8种松毛虫间具体的亲缘关系为: (D. superans (D. tabulaeformis (D. p. wenshanensis (D. p. tehchangensis, D. p. punctatus)(D. Kikuchii (D. spectabilis, D. houi))。     

Nuclear DNA variability withinPisum sativum (Leguminosae): Cytophotometric analyses

The cultivars or experimental lines ofPisum sativum were analyzed cytophotometrically for nuclear DNA content of early prophases after ethanol-acetic acid fixation. Wide variability was found (from 3.93 to 5.07pg per haploid nucleus). This result was confirmed by the cytophotometric analysis of interphase nuclei isolated from leaf tissues fixed in formalin. Analysis of interphase nuclei at different thresholds of optical density showed that certain chromatin fractions are involved in the variations.     

Amazonian lowland, white sand areas as ancestral regions for South American biodiversity: Biogeographic and phylogenetic patterns in Potalia (Angiospermae: Gentianaceae)

Present-day white sand areas in South America are thought to be relictual areas of earlier, widespread habitats now covered by more recent sediments mainly from the Andean orogeny. These ancient, nutrient-poor areas have been suggested to be possible ancestral regions for neotropical plant diversity. Members of the genus Potalia of the Gentianaceae grow in the New World tropics from Costa Rica in the north to southern Bolivia. Until recently, only one Potalia species was accepted, but a new revision identifies eight others. Three species are endemic to lowland, white sand areas in the Amazon and Orinoco basins and share morphological characteristics with Anthocleista, the African – Malagasy sister group to Potalia. To resolve phylogenetic and biogeographic patterns in Potalia, morphological characters and sequences of the internal transcribed spacer (ITS) and the 5S non-transcribed spacer (5S-NTS) of the ribosomal nuclear DNA were collected and used for phylogenetic reconstruction using Bayesian and parsimony-based methods. Potalia species restricted to ancient, nutrient-poor white sand areas of the Amazon Basin and Guayana Shield were placed basal to other Potalia taxa from finer, lateritic, and younger soils, further suggesting that lowland white sand areas may be ancestral seats of neotropical diversity.     

Systematic anatomical characters of the leaves of Dimorphandra and Mora (Leguminosae: Caesalpinioideae)

A systematic study of the leaf anatomy of Dimorphandra and Mora showed that the leaf epidermis provides taxonomic characters for the separation of the two sections of Dimorphandra, Pocillum and Dimorphandra , viz. the structure of the guard cells and the degree of sunkenness of the stomata. The diverse arrangements of the neighbouring cells around the stomata do not provide a clear distinction between the sections: in section Pocillum the stomata are paracytic but in section Dimorphandra several types are found. Papillae of diverse shape, size and disposition are present in the different species of Dimorphandra , and with all these variations in the epidermal characters it is possible to establish series of increasing complexity in the two sections.
Mora presents several characters which distinguish it from Dimorphandra (e.g. thickenings in the walls of the stomata and other epidermal cells, granular silica in the lumen of some epidermal cells, and sinuous anticlinal walls in the cells of both epidermides), thus supporting its recognition as a separate genus.