Phylogeny, character evolution, and classification of Sapotaceae (Ericales)

We present the first cladistic study of the largely tropical family Sapotaceae based on both morphological and molecular data. The data were analyzed with standard parsimony and parsimony jackknife algorithms using equally and successive weighted characters. Sapotaceae are confirmed to constitute two main evolutionary lineages corresponding to the tribes Isonandreae‐Mimusopeae‐Sideroxyleae and Chrysophylleae‐Omphalocarpeae. The Sideroxyleae are monophyletic, Isonandreae are polyphyletic as presently circumscribed, and as suggested by the analyses, the subtribe Mimusopeae‐Mimusopinae has evolved within the Mimusopeae‐Manilkarinae, which hence is also paraphyletic. Generic limits must be altered within Sideroxyleae with the current members Argania, Nesoluma and Sideroxylon. Argania cannot be maintained at a generic level unless a narrower generic concept is adopted for Sideroxylon. Nesoluma cannot be upheld in a narrow or broad generic concept of Sideroxylon. The large tribe Chrysophylleae circumscribes genera such as Chrysophyllum, Pouteria, Synsepalum, and Xantolis, but the tribe is monophyletic only if the taxa from Omphalocarpeae are also included. Neither Chrysophyllum nor Pouteria are monophyletic in their current definitions. The results indicate that the African taxa of Pouteria are monophyletic and distinguishable from the South American taxa. Resurrection of Planchonella, corresponding to Pouteria section Oligotheca, is proposed. The African genera Synsepalum and Englerophytum form a monophyletic group, but their generic limits are uncertain. Classification of the Asian genus Xantolis is particularly interesting. Morphology alone is indecisive regarding Xantolis relationships, the combined unweighted data of molecules and morphology indicates a sister position to Isonandreae‐Mimusopeae‐Sideroxyleae, whereas molecular data alone, as well as successive weighted combined data point to a sister position to Chrysophylleae‐Omphalocarpeae. An amended subfamily classification is proposed corresponding to the monophyletic groups: Sarcospermatoideae (Sarcosperma), Sapotoideae (Isonandreae‐Mimusopeae‐Sideroxyleae) and Chrysophylloideae (Chrysophylleae‐Omphalocarpeae), where Sapotoideae circumscribes the tribes Sapoteae and Sideroxyleae as well as two or three as yet unnamed lineages. Morphological characters are often highly homoplasious and unambiguous synapomorphies cannot be identified for subfamilies or tribes, which we believe are the reason for the variations seen between different classifications of Sapotaceae. © The Willi Hennig Society 2005.     

Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data

Phylogenetic analysis of noncoding trnL plastid DNA sequences and morphological data for 43 species of Zygophylloideae, representing most of the morphological and geographical variation in the subfamily, indicates that the currently recognised genera Augea (monotypic, southern Africa), Tetraena (monotypic, China), and Fagonia (c. 30 species, widespread), are embedded in Zygophyllum (c. 150 species, widespread). A generic classification based on six monophyletic and morphologically distinctive entities is proposed: Roepera with c. 60 species in Australia and southern Africa, Zygophyllum with c. 50 species in Asia, Tetraena with c. 40 species in Africa and Asia, Augea with a single species in southern Africa, Melocarpum with two species in the Horn of Africa region, and Fagonia with c. 30 species in both the Old and the New World. Scanning electron microscopy studies of testa structure provided important characters for the delimitation of some genera. New combinations (61) are made in Roepera, a resurrected genus originally described from Australia, one new name is proposed in Zygophyllum, 35 new combinations are made in Tetraena, and two new combinations are made in Melocarpum (previously Zygophyllum sect. Melocarpum).     

CHLOROPLAST DNA VARIATION WITHIN AND AMONG GENERA OF THE HEUCHERA GROUP (SAXIFRAGACEAE): EVIDENCE FOR CHLOROPLAST TRANSFER AND PARAPHYLY

The Heuchera group (Saxifragaceae) comprises Bensoniella, Conimitella, Elmera, Heuchera, Lithophragma, Mitella, Tellima, Tiarella, and Totmiea. Earlier studies employing morphology, karyology, and flavonoid chemistry indicated that these genera form a natural group, but failed to resolve relationships among them. Restriction site analysis of chloroplast DNA (cpDNA) suggests that Bensoniella, Tolmiea, and Lithophragma are close allies and form the sister group of a large clade containing the remaining six genera. Mitella and Heuchera are both paraphyletic based on cpDNA data. cpDNA data, in conjunction with morphological and allozyme data, suggest at least four examples of intersectional hybridization and subsequent chloroplast capture in Heuchera. Several of these events may be explained via a stepping stone model in which the chloroplast genome of a species was captured by a second species, and then ultimately by a third taxon. Two well-differentiated groups of Tellima populations were detected: one group has a unique chloroplast genome characterized by nine autapomorphies, and the second group has a chloroplast genome identical to that found in M. trifida and M. diversifolia. cpDNA and allozyme data suggest that some Tellima populations probably obtained their chloroplast genome via intergeneric hybridization with M. trifida, M. diversifolia, or the ancestor of these taxa. The occurrence of intergeneric chloroplast transfer in some populations of Tellima, as well as extensive intersectional chloroplast capture in Heuchera, not only suggests caution in the use of cpDNA restriction site data in phylogenetic reconstruction, but also demonstrates again the importance of adequate sampling of conspecific populations. If the intergeneric relationships in the Heuchera group suggested by cpDNA analysis are accurate, fundamental questions arise regarding the validity of certain morphological traits as good taxonomic characters in Saxifragaceae. Furthermore, significant taxonomic changes at the generic level would be necessary.     

Phylogenetic relationships in the Marcetia alliance (Melastomeae,Melastomataceae) and implications for generic circumscription

The Marcetia alliance of Melastomataceae is an exclusively Neotropical group that includes at least 12 genera of mostly herbs and subshrubs, occurring in the cerrado of central Brazil and savannas of the Amazon region and Guayana highlands. This study aimed to test the monophyly of genera in the Marcetia alliance, evaluate their phylogenetic relationships and generic boundaries, and investigate morphological characters as potential synapomorphies for delimiting clades or genera. We used nuclear (ITS, ETS) and plastid (accD‐psaI, atpH‐atpF, trnS‐trnG) DNA sequences of 107 terminals in 12 genera from the alliance. Aciotis, Fritzschia, Marcetia and Siphanthera were shown to be monophyletic and supported by molecular and morphological characters. Other genera with variable morphology and wider distributions, such as Acisanthera, Comolia, Ernestia and Macairea, were recovered as paraphyletic or polyphyletic. Most morphological characters analysed were found to be homoplastic, but when combined they are potentially useful for the diagnosis of genera and infrageneric groups. This study represents a major step in understanding internal relationships and provides the basis for a revision of the generic classification in the Marcetia alliance.     

Bupleurum candollei var. paucefulcrans comb. nov. (Apiaceae) from Guizhou,China: comparison of allied species based on morphology,anatomy and molecular data

The new combination, Bupleurum candollei Wallich ex de Candolle var. paucefulcrans (C. Y. Wu) X. J. He & C. B. Wang, is proposed. The status of this taxon, endemic to Guizhou, China, has been confused since it was first described in 1963. Morphological and anatomical evidence, based primarily on bractlet number and length, umbel number and length, fruit size and shape, and stem structure indicated that B. hamiltonii N. P. Balakrishnan var. paucefulcrans C. Y. Wu is more closely related to B. candollei than to B. hamiltonii. To evaluate the credibility of the morphological similarity, the phylogenetic relationship of B. candollei var. candollei, B. hamiltonii var. hamiltonii and B. candollei var. paucefulcrans were inferred by Bayesian analysis of nrDNA ITS sequences. The molecular analysis is fully congruent with the morphological data and supports the transfer of the variety to B. candollei.     

First descriptions of Coelometopini pupae (Coleoptera: Tenebrionidae) from Australia,Southeast Asia and the Pacific region,with comments on phylogenetic relationships and antipredator adaptations

Abstract. The pupal stage of ten Coelometopini species occurring in Australia, New Guinea, Southeast Asia and the Pacific region are described and a key for their identification is provided. The species are Chrysopeplus expolitus Broun, Derosphaerus hirtipes Kaszab, Hypaulax crenata (Boisduval), Leprocaulus borneensis Kaszab, Metisopus purpureipennis Bates, Promethis carteri Kaszab, P. nigra (Blessig), P. quadraticollis (Gebien), P. quadricollis Pascoe and P. sulcigera (Boisduval). The gin trap structures of D. hirtipes and P. quadraticollis are described in detail using scanning electron micrographs. A summary of antipredator structures of all known Coelometopini pupae is given. The phylogenetic value of pupal characters is assessed at intra‐ and intergeneric levels within the tribe.     

中国茶渍属和石蕊属4新记录种

通过形态学及化学研究,结合nrDNA ITS序列的系统发育分析,该文报道了茶渍属(Lecanora Ach.)和石蕊属(Cladonia P. Browne)地衣4中国新记录种：莱氏茶渍(Lecanora layana Lendemer)、白头山茶渍(L. baekdudaeganensis B. G. Lee&Hur)、伪银茶渍(L. pseudargentata Lumbsch)和草皮石蕊[Cladonia caespiticia (Pers.) P. Gaertn., B. Mey&Scherb.]。该文对这些物种的分类学特征进行了详细描述,并与相似种进行了对比,同时提供了各种的地理分布图和形态图。这为中国茶渍属和石蕊属地衣物种多样性及资源利用提供了基础资料。     

Conflicting molecular and morphological evidence of evolution within the Bryaceae (Bryopsida) and its implications for generic taxonomy

Abstract

Phylogenetic analyses within the Bryaceae were performed based on DNA sequence data from three chloroplast genomic regions. Special emphasis was placed on sampling the small tuber-bearing species of Bryum ('Erythrocarpa') from Europe and those with axillary bulbils (B. dichotomum group). Multiple exemplars were studied for most of the species investigated. As in previous studies, the results demonstrate a pattern of evolutionary diversification that differs widely from that implied by traditional generic and subgeneric classifications. More recent generic arrangements based exclusively on morphological characters are also shown to seriously misrepresent phylogeny because of convergent evolution of morphology. Among the 'Erythrocarpa', for instance, the superficially similar B. rubens and B. subapiculatum emerge as only distant relatives, the former being close to B. capillare (treated in Ptychostomum here) whereas the latter is close to B. alpinum (placed in Imbribryum here). Likewise, using only morphological characters, B. dunense and B. versicolor [Bryum s.s.] may both be almost indistinguishable from some specimens of B. caespiticium [Ptychostomum]. On the other hand, rapid differentiation of morphology has occurred within some clades, notably of 'Plagiobryum' zieri from within Ptychostomum. Thus the argument is reiterated that 'classification of the Bryaceae based on morphological characters alone cannot be defended', since it leads to classifications which are incongruent with phylogeny and do not take account of all available information. Hence a generic classification is proposed here containing mainly those Bryaceae for which molecular data are available. Several nomenclatural questions that arise from this are resolved.     

First phylogenetic analysis of the subfamily Pachydeminae (Coleoptera,Scarabaeoidea, Melolonthidae): the Palearctic Pachydeminae*

This paper presents the first phylogenetic analysis of Pachydeminae Reitter, 1902 ; one of the least known subfamilies of Melolonthidae, `leaf‐chafers' (Scarabaeoidea, Coleoptera). Some species of Pachydeminae have recently become agricultural pests in southern Spain. We analysed the phylogenetic relationships among 49 species belonging to 16 genera in the Palearctic region, based on a set of 63 morphological characters from the adult external morphology, wing anatomy, mouthparts and male and female genitalia. The last three sets of characters are described here for the first time. The phylogeny shows that the Palearctic Pachydeminae are monophyletic within the subfamily. Mouthparts and male and female genitalia provide the best synapomorphies for intergeneric relationships. In contrast, most of the external morphological characters used in the taxonomy of Pachydeminae are highly homoplastic. The phylogeny shows a basal split between the genera Hemictenius Reitter, 1897; Pachydema Castelnau, 1832, and the monospecific Peritryssus Reitter, 1918; and a second clade including the rest of genera. The remarkable Peritryssus is confirmed as a Pachydeminae, being the sister group to the monophyletic Hemictenius . Except for the position of P. rubripennis (Lucas, 1848) and P. zhora Normand, 1951, the phylogeny supports the monophyly of Pachydema but rejects the traditional division into species groups and the monophyly of the endemic Canarian species. In contrast, Tanyproctus Faldermann, 1835, must be rejected as polyphyletic. Otoclinius Brenske, 1896, is also probably polyphyletic (two new species synonymies), whereas Leptochristina Baraud and Branco, 1991 , is either mono‐ or paraphyletic. The two Mediterranean genera Ceramida Baraud, 1897, and Elaphocera Gené, 1836, form a monophyletic group, this clade being the best supported by the data set. Ceramida is clearly monophyletic, whereas Elaphocera is probably monophyletic except for E. barbara Rambur, 1843, which shares with Ceramida the character state for numerous mouthpart and genitalic characters. The phylogeny questions the generic status of the small and monospecific genera of Pachydeminae. The monotypic Alaia Petrovitz, 1980 , and Brenskiella Berg, 1898, are merged with Europtron Marseul, 1867, into one clade, whereas Atanyproctus Petrovitz, 1954, is grouped with some species of Tanyproctus , and the monotypic Pachydemocera Reitter, 1902 , is proposed as a junior synonym of Elaphocera .     

Phylogenetic relationships of Italian Bellevalia species (Asparagaceae), inferred from morphology,karyology and molecular systematics

The seven Bellevalia species and subspecies known from Italy, representing about 10% of the genus and three out of six sections, were studied. An integrated morphological, karyological and molecular approach was used to infer phylogenetic and systematic relationships among them. B. romana (the generitype) is the most distinctive species on karyotype asymmetry grounds. B. boissieri and B.dubia, usually considered as subspecies of one species (the latter endemic to Sicily), deserve specific status based on biparental nrDNA markers (internal transcribed spacer, ITS), since they do not form a single clade. The allotetraploid endemic B. pelagica, morphologically similar to B. romana, is sister to the latter under parsimony, both in morphological and ITS trees; it is also related with B. dubia, based on karyotype asymmetry and a uniparental cpDNA marker (trnL^(UAA)–trnF^(GAA) IGS (intergenic spacer)). A second allotetraploid endemic, B. webbiana, is closely related, on morphological, karyological and molecular grounds, with B. boissieri and B. ciliata, and also with B. trifoliata, three species that might all involved in its origin. B. sect. Conicae Feinbr. and sect. Nutantes Feinbr. are here typified, the former (type: B. ciliata) is most likely a synonym of the latter (type: B. trifoliata).     

Relationships and divergence of some taxa of the subfamily Lycodinae (Zoarcidae,Pisces) based on molecular-genetic and morphological data

An integrated molecular-genetic and morphological study of 14 species of 6 genera of Zoarcidae of the subfamily Lycodinae was performed. A high coincidence of study results obtained using both methods was found. The generic independence of the genus Petroschmidtia that includes species P. albonotata and P. toyamensis was justified. It was shown that species L. schmidti and L. nigrocaudatus belong to the genus Lycogrammoides; and the generic status of the genus Bothrocarichthys with species B. microcephalus and of the genus Allolepis with species A. hollandi was restored. The studied taxa fall into three large monophyletic groups that include species of the genus Petroschmidtia, species of the genus Lycodes, and species of the genera Bothrocara, Allolepis, Bothrocarichthys, and Lycogrammoides. Taxa of the last group are characterized by a large complex of morphological differences from the first two groups, including the absence of ventral fins. A key to species and genera of Lycogrammoides and Bothrocarichthys was compiled. The problem of determination of the time of divergence of the studied zoarcid-like fish using the concept of “molecular clock” and its calibration according to paleontological and paleogeographic data is discussed.     

A phylogenetic analysis of Pisum based on morphological characters, and allozyme and RAPD markers

Cladistic analyses of 17 wild and cultivated pea taxa were performed using morphological characters, and allozyme and RAPD (random amplified polymorphic DNA) markers. Both branch-and-bound and bootstrap searches produced cladograms that confirmed the close relationships among the wild species and cultivars of Pisum proposed by a variety of systematic studies. Intraspecific rankings were supported for northern P. humile, southern P. humile, P. elatius and P. sativum, which together comprise a single-species complex. P. fulvum, while clearly the most divergent of the pea taxa, could also be assigned to the same species complex without violating the hierarchial logic of the cladogram. Its inclusion or exclusion depends on whether the level of interfertility it displays with other pea taxa or its overall morphological and chromosomal distinction are emphasized. As suggested by previous studies, northern P. humile was the most likely sister taxon to cultivated P. sativum; although, rigorous phylogenetic evaluation revealed a close genealogical affinity among P. elatius, northern P. humile and P. sativum. Despite their limited number, the 16 morphological characters and allozyme markers used precisely organized the pea taxa into established taxonomic groupings, perhaps in part reflecting the role morphology has played historically in pea classification. The RAPD data also generally supported these same groupings and provided additional information regarding the relationships among the taxa. Given that RAPDs are relatively quick and easy to use, are refractory to many environmental influences, can be generated in large numbers, and can complement traditional characters that may be limited in availability, they provide a valuable new resource for phylogenetic studies.     

Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)

Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and the hybrid origin hypothesis of Photinia bodinieri. This study employs complete plastomes and the entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae, especially Maleae. Based on three datasets, including the whole plastome, coding sequence, and nrDNA repeats, the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non‐monophyletic. Six clades have been recovered herein within Photinia and its allied genera: Aronia, Heteromeles, Photinia s.s., Pourthiaea, Stranvaesia, and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia. The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events, while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri. We provide 12 new combinations, to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia.     

A high frequency of intergenomic mitochondrial recombination and an overall biased segregation of B. campestris or recombined B. campestris mitochondria were found in somatic hybrids made within Brassicaceae

Mitochondrial segregation and rearrangements were studied in regenerated somatic hybrids from seven different species combinations produced using reproducible and uniform methods. The interspecific hybridizations were made between closely or more distantly related species within the Brassicaceae and were exemplified by three intrageneric, two intergeneric and two intertribal species combinations. The intrageneric combinations were represented by Brassica campestris (+) B. oleracea, B. napus (+) B. nigra and B. napus (+) B. juncea (tournefortii) hybrids, the intergeneric combinations by B. napus (+) Raphanus sativus and B. napus (+) Eruca sativa hybrids, and the intertribal combinations by B. napus (+) Thlaspi perfoliatum and B. napus (+) Arabidopsis thaliana hybrids. In each species combination, one of the two mitochondrial genotypes was B. campestris since the B. napus cultivar used in the fusions contained this cytoplasm. Mitochondrial DNA (mtDNA) analyses were performed using DNA hybridization with nine different mitochondrial genes as probes. Among the various species combinations, 43–95% of the hybrids demonstrated mtDNA rearrangements. All examined B. campestris mtDNA regions could undergo intergenomic recombination since hybrid-specific fragments were found for all of the mtDNA probes analysed. Furthermore, hybrids with identical hybrid-specific fragments were found for all probes except cox II and rrn18/rrn5, supporting the suggestion that intergenomic recombination can involve specific sequences. A strong bias of hybrids having new atp A-or atp9-associated fragments observed in the intra- and intergeneric combinations could imply that these regions contain sequences that have a high reiteration number, which gives them a higher probability of recombining. A biased segregation of B. campestris-or B. campestris-like mitochondria was found in all combinations. A different degree of phylogenetic relatedness between the fusion partners did not have a significant influence on mitochondrial segregation in the hybrids in this study.     

Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae,Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae‐zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3‐rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3‐rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3‐rpl16 spacer, shows greater variation between ssp. fragile and novae‐zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae‐zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re‐evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.