Sapindales: molecular delimitation and infraordinal groups

An analysis of rbcL sequence data for representatives of families of putative sapindalean/rutalean affinity identified a robust clade of core “sapindalean” taxa that is sister to representatives of Malvales. The constitution of this clade approximates the broad concept of Sapindales (sensu Cronquist). Five lineages within the order are recognized: a “rutaceae” clade (Rutaceae, Cneoraceae, Ptaeroxylaceae, Simaroubaceae sensu stricto, and Meliaceae); a “sapindaceae” clade (Sapindaceae, Aceraceae, and Hippocastenaceae); Anacardiaceae plus Burseraceae; Kirkiaceae; and Zygophyllaceae pro parte. Relationships among these groups were only weakly resolved, but there was no support for the recognition of the two more narrowly defined orders, Rutales and Sapindales sensu stricto. Several families that have previously been allied to Sapindales or Rutales show no affinity to the core sapindalean taxa identified with the molecular data, and are excluded from the order: viz. Akaniaceae, Bretschneideraceae, Conneraceae, Coriariaceae, Melianthaceae, Meliosmaceae, Physenaceae, Rhabdodrendraceae, Sabiaceae, Staphyleaceae, Stylobasiaceae, Surianaceae, and Zygophyllaceae sensu stricto.     

Phylogenetics and morphological evolution of coral‐dwelling barnacles (Balanomorpha: Pyrgomatidae)

Pyrgomatid barnacles are a family of balanomorphs uniquely adapted to symbiosis on corals. The evolution of the coral‐dwelling barnacles is explored using a multi‐gene phylogeny (COI, 16S, 12S, 18S, and H3) and phenotypic trait‐mapping. We found that the hydrocoral associate Wanella should be excluded, while some archaeobalanids in the genus Armatobalanus should be included in the Pyrgomatidae. Three well supported clades were recovered: clade I is the largest group and is exclusively Indo‐West Pacific, clade II contains two plesiomorphic Indo‐West Pacific genera, while clade III is comprised of East and West Atlantic taxa. Some genera did not form reciprocally monophyletic groups, while the genus Trevathana was found to be paraphyletic and to include members of three other apomorphic genera/tribes. The highly unusual coral‐parasitic hoekiines appear to be of recent origin and rapidly evolving from Trevathana sensu lato. Pyrgomatids include six‐, four‐, and one‐plated forms, and exhibit convergent evolutionary tendencies towards skeletal reduction and fusion, loss of cirral armature, and increased host specificity. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 162–179.     

Phylogenetic Relationships between some Members of the Subfamily Lamioideae (Family Labiatae) Inferred from Nucleotide Sequences of the rbcL Gene*

Total DNA was extracted from 25 species (8 genera) of the subfamily Lamioideae sensu Erdtman (family Labiatae). Using rbcL-specific primers, the rbcL gene was amplified by polymerase chain reaction (PCR) and 1420 bp were sequenced directly, or after cloning. RbcL sequences were evaluated with character-state (maximum parsimony; PAUP) and distance methods (neighbour-joining; MEGA). In agreement with classical systematics all taxa studied cluster outside the Nepetoideae. The following clades are apparent: I - Westringia/Prostanthera, II - Ajuga/Teucrium and III - Scutellaria, Stachys, Lamium and Marrubium. Lamium album, L. amplexicaule and L. garganicum appear as a sister clade to Marrubium. Both share a common ancestor with a second Lamium clade (including L. purpureum, L. maculatum and L. galeobdolon). The phylogenetic relationships are discussed with regard to the systematic classification of the subfamilies Lamioideae and Nepetoideae (sensu Erdtman).     

matK and rbcL gene sequence data indicate that Saxifraga (Saxifragaceae) is polyphyletic

The large genus Saxifraga, which consists of ≈400 morphologically and cytologically diverse species, has long been considered taxonomically complex. Phylogenetic analysis of over 2500 bp of chloroplast sequence data derived from matK and rbcL was employed to examine relationships among sections of Saxifraga, the segregate genera Zahlbrucknera, Saxifragopsis, and Cascadia, and the relationships of these taxa to other Saxifragaceae sensu stricto. Phylogenetic trees resulting from separate analyses of the matK and rbcL sequences were highly congruent; phylogenetic analysis of a combined matK–rbcL data matrix was therefore also conducted. Our analyses indicate that Saxifraga is polyphyletic, comprising two well-differentiated clades. One clade, Saxifraga sensu stricto, is the sister to the remainder of the family and consists of Saxifraga sections Irregulares, Heterisia, Trachyphyllum, Cymbalaria, Mesogyne, Xanthizoon, Porphyrion, Ciliatae, Cotylea, Ligulatae, Saxifraga, and Gymnopera. With the exception of Gymnopera, the species-rich sections of this clade are monophyletic. Also part of this clade is the problematic Zahlbrucknera paradoxa, which is allied with members of section Saxifraga. A second major clade of Saxifraga species, Micranthes sensu lato, comprises the large section Micranthes, as well as the segregate genus Cascadia, and S. tolmiei of section Merkianae. This clade is allied with the Heuchera, Darmera, and Chrysosplenium-Peltoboykinia groups of genera. The segregate genus Saxifragopsis is only distantly related to species of Saxifraga, and is instead the sister to Astilbe. The monotypic Oresitrophe is confirmed as a member of the Darmera group of genera. These results suggest that the floral features used to define Saxifraga may simply be symplesiomorphic in these well-separated Saxifraga lineages. Furthermore, the enormous cytological diversity encompassed by Saxifraga likely represents two independent instances of extensive aneuploidy and polyploidy in Saxifragaceae.     

A Molecular Phylogeny of Warbling-Finches (Poospiza): Paraphyly in a Neotropical Emberizid Genus

We investigated the phylogenetic relationships of 12 species within a single genus of neotropical passerine (Poospiza) using 849 bp (283 codons) of the cytochrome b mitochondrial gene. We further explored evolutionary affinities of these taxa using sequence from an additional 47 thraupine (tanagers) and 7 emberizine (sparrows and buntings) genera, members of the predominantly New World family Emberizidae. Poospiza have traditionally been considered part of the emberizine radiation. However, our analyses suggest that members of this genus are more closely related to some thraupine lineages than they are to the other neotropical emberizine genera included in our study (Atlapetes, Embernagra, Melopyrrha, Phrygilus, Saltatricula, Tiaris). Although member taxa are closely related, the genus Poospiza appears to be paraphyletic with representatives of 6 thraupine genera (Cnemoscopus, Cypsnagra, Hemispingus, Nephelornis, Pyrrhocoma, Thylpopsis) interspersed among four well-supported Poospiza clades. The majority of species within this Poospiza–thraupine clade have geographic ranges that are exclusive to, or partially overlap with, the Andes Mountains. It is probable that these mountains have played an important role in driving cladogenesis within this group. Sequence divergence (transversions only; mean 4.7 ± 1.3%) within the clade suggests that much of this diversification occurred within the late Miocene and Pliocene, a period coincident with major orogenic activity in central-western South America.     

The phylogeny of aglaspidid arthropods and the internal relationships within Artiopoda

The phylogenetic position of aglaspidids, a problematic group of Lower Palaeozoic arthropods of undetermined affinities, is re‐examined in the context of the major Cambrian and Ordovician lamellipedian arthropod groups. A cladistic analysis of ten genera of aglaspidids sensu stricto, six aglaspidid‐like arthropods and 42 Palaeozoic arthropod taxa indicates that Xenopoda, Cheloniellida, Aglaspidida sensu lato and Trilobitomorpha form a clade (Artiopoda Hou and Bergström, 1997 ) nested within the mandibulate stem‐lineage, thus discarding previous interpretations of these taxa as part 'of the chelicerate stem‐group (Arachnomorpha Heider, 1913 ). The results confirm an aglaspidid identity for several recently described arthropods, including Quasimodaspis brentsae, Tremaglaspis unite, Chlupacaris dubia, Australaglaspis stonyensis and an unnamed Ordovician Chinese arthropod. The problematic Bohemian arthropod Kodymirus vagans was recovered as sister taxon to Beckwithia typa, and both form a small clade that falls outside Aglaspidida sensu stricto, thus discarding eurypterid affinities for the former. The analysis does not support the phylogenetic position of Kwanyinaspis maotianshanensis at the base of Conciliterga as proposed in recent studies, but rather occupies a basal position within Aglaspidida sensu lato. The results indicate a close association of aglaspidid arthropods with xenopods (i.e. Emeraldella and Sidneyia) and cheloniellids (e.g. Cheloniellon, Duslia); the new clade “Vicissicaudata” is proposed to encompass these arthropods, which are characterized by a differentiated posterior region. The phylogenetic position of aglaspidid arthropods makes them good outgroup candidates for analysing the internal relationships within the groups that form Trilobitomorpha. This work provides a much clearer picture of the phylogenetic relationships among Lower Palaeozoic lamellipedians.     

Diversity dynamics of Zosterophyllopsida

The Zosterophyllopsida were major contributors to the diversification of early land plants. We present the first detailed analysis of the diversity dynamics of these plants from an updated database of all currently recognized zosterophyllopsid species. A set of quantitative methods classically used in palaeodiversity studies was applied to two data sets. The first one, ‘Zosterophyllopsida sensu stricto’, corresponds to the clade identified by Hao & Xue (The Early Devonian Posongchong Flora of Yunnan. (2013), Science Press). In the second, called ‘Zosterophyllopsida sensu lato’, barinophytalean‐type plants and taxa for which zosterophyllopsid affinities are suspected are added. The number of localities is used to explore sampling bias. Results show that sampling effect is minimal for the Early Devonian. For this time interval, both data sets record consistent patterns of changes suggesting that, whatever their affinities, all taxa included in the Zosterophyllopsida sensu lato show similar evolutionary trends. The diversity dynamics of zosterophyllopsids are characterized by a radiation during the Lochkovian, maximal values in the Pragian and a decline starting in the Emsian. The proportion of zosterophyllalean taxa with terminal sporangia is high until the Late Lochkovian when gosslingialean taxa without terminal sporangia evolved. During the Middle and Late Devonian, when diversity patterns are strongly affected by sampling, zosterophyllopsid diversity is low and characterized by a high proportion of barinophytacean and gosslingialean taxa, the latter becoming extinct in the Early Frasnian.     

Comprehensive phylogeny of the Cleroidea (Coleoptera: Cucujiformia)

The first thorough molecular phylogeny of the superfamily Cleroidea, represented by 377 taxa, and the first with an emphasis on Trogossitidae, was undertaken. Maximum likelihood and Bayesian analyses were performed on a four‐gene dataset (18S, 28S, cox1, cytb) of 395 taxa (along with 18 outgroups), including all 16 currently recognized families of Cleroidea and all current and formerly recognized tribes of Trogossitidae. The superfamily as a whole received strong support in Bayesian analyses. On the basis of phylogenetic results, 18 families in Cleroidea are recognized, including three taxa elevated to family for the first time and two reinstated families. The former tribe Rentoniini (Trogossitidae: Peltinae) was strongly supported as a monophyletic group apart from the remainder of Trogossitidae, and is herein elevated to family status, Rentoniidae stat.n. Protopeltis was also found to be an isolated lineage and becomes Protopeltidae stat.n. Peltini + Larinotini were recovered as a weakly supported sister grouping; Peltini (including only Peltis) becomes Peltidae stat.rest. The trogossitid subfamily Lophocaterinae, to the exclusion of Decamerini, formed a clade which is here designated Lophocateridae stat.rest. and sensu n. The Trogossitinae tribes Calityini, Egoliini (represented by Egolia) and Larinotini were recovered apart from core Trogossitidae but showed no strong affinities to other taxa or congruence between analyses; they are here conservatively retained in Trogossitidae as Calityinae stat.rest. , Egoliinae stat.rest. and Larinotinae stat.rest. The genus Thymalus of the peltine tribe Thymalini was indicated with moderate to strong support as the sister group of the Decamerini (Trogossitidae: Lophocaterinae); together these represent Thymalidae stat.n. and sensu n. with subfamilies Decamerinae stat.rest. ( new placement ) and Thymalinae stat.n. The remainder of Trogossitinae, the tribes Trogossitini and Gymnochilini, formed a well‐supported clade which comprises the Trogossitidae: Trogossitinae sensu n. The tribe Gymnochilini syn.n. is synonymized with Trogossitini. The monotypic family Phloiophilidae was recovered, contradicting a recent placement within Trogossitidae. The melyrid lineage was recovered with moderate (maximum likelihood) to strong (Bayesian analyses) support and includes the families Phycosecidae, Rhadalidae, Mauroniscidae, Prionoceridae and Melyridae (including Dasytidae and Malachiidae). The genus Dasyrhadus is tentatively transferred from Rhadalidae to Mauroniscidae. The genus Gietella, once proposed as a distinct family but recently placed within Dasytidae, was recovered as strongly sister to Rhadalidae sensu n. , and we transfer it to that family as Gietellinae new placement . Attalomiminae (formerly Attalomimidae) syn.n. is synonymized with Melyridae: Malachiinae: Lemphini sensu n. Melyridae sensu n. includes only Dasytinae, Malachiinae and Melyrinae. Metaxina is returned to the Chaetosomatidae sensu n. , of which Metaxinidae syn.n. becomes a junior synonym. Resolution within Cleridae was generally poor, but a broadly defined Korynetinae stat rest. + Epiclininae received high support (Bayesian analyses). Outside of Trogossitidae, the main focus of this study, major rearrangements of the classification of Cleroidea were not undertaken, despite evidence indicating such changes are needed.     

Phylogenetic relationships in Saxifragaceae sensu lato: A comparison of topologies based on 18S rDNA and rbcL sequences

Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.     

PHYLOGENY OF LOBOCHARACIUM (CHLOROPHYCEAE) AND ALLIES: A STUDY OF 18S AND 26S rDNA DATA1

The phylogenetic affinities of Lobocharacium coloradoense were investigated by analysis of combined 18S and 26S rDNA data. Results from both parsimony and likelihood methods supported a close alliance among Lobocharacium, Characiosiphon, and Characiochloris. These three taxa formed a clade near the base of the “Dunaliella” group within the chlamydomonad lineage. Protosiphon, which exhibits a siphonous habit similar to Characiosiphon and Lobocharacium, was not resolved as a close ally of the latter two taxa. The Lobocharacium alliance was characterized by the presence of an attachment pad associated with the nonmotile vegetative stage and pyrenoids that possess cytoplasmic invaginations. The pyrenoid feature is an ultrastructural trait that has now been observed in five different chlorophycean lineages. The Lobocharacium–Characiosiphon–Characiochloris clade is not predicted by any classifications of green algae. Additional taxon and data sampling need to be completed to resolve inconsistencies between the molecular phylogenetic evidence and at least some of the current family‐level taxa.     

Comparative phytochemistry of Picramnia and Alvaradoa,genera of the newly established family Picramniaceae

The structures of the secondary metabolites, including fatty acids, of the genera Picramnia and Alvaradoa (Picramniaceae) are surveyed. Neither the fatty acid profiles nor the structures of the anthraquinones and sugar linked anthracenone derivatives characteristic of both genera indicate close relationships between the Picramniaceae and any other known families.     

Evolution of reproductive traits in the mahagony family (Meliaceae)

Meliaceae are a mostly pantropical family in the Sapindales, bearing flowers typically provided with a staminal tube, formed by filaments that are fused partially or totally. Nevertheless, several genera of subfamily Cedreloideae have free stamens, which may be adnate to an androgynophore in some taxa. The fact that the family exhibits a wide diversity of floral and fruit features, as well as of sexual systems and pollination syndromes, presents interesting questions on the evolutionary processes that might have taken place during its history. In this study, we analyzed the distribution of 20 reproductive morphological traits of Meliaceae, upon an available molecular phylogenetic framework, using 31 terminals from the family's two main clades (Cedreloideae and Melioideae), plus six Simaroubaceae taxa as outgroup. We aimed to identify and/or confirm synapomorphies for clades within the family and to develop hypotheses on floral evolution and sexual systems in the group. Our reconstruction suggests that the ancestor of Meliaceae was possibly provided with united stamens and unisexual flowers in dioecious individuals, with a subsequent change to free stamens and monoecy in the ancestor of Cedreloideae. Most characters studied show some degree of homoplasy, but some are unique synapomorphies of clades, such as the haplostemonous androecium. An androgynophore defines the Cedrela‐Toona clade. The comparative approach of our study and the evolutionary hypotheses generated herein reveal several aspects demanding further structural investigation, and possible evolutionary pathways of the reproductive structures along with the lineages' diversification, mostly related to the specialization of sexual systems, floral biology, and dispersal strategies.     

Systematics of Serinus canaries and the status of Cape and Yellow-crowned Canaries inferred from mtDNA and morphology

The taxonomy of, and phylogenetic relationships among, African canaries typically assigned to the genus Serinus sensu lato (including the putative genera Alario, Pseudochloroptila, Serinops, Ochrospiza, Dendrospiza and Crithagra) were investigated, based on 823bp of the mitochondrial cytochrome b gene. Two clades emerged: (1) Palaearctic and Afrotropical taxa, including Serinus serinus, S. canaria, A. alario and the S. canicollis complex (S. c. canicollis, thompsonae and flavivertex), and (2) taxa endemic to the Afrotropics comprising Pseudochloroptila, Serinops, Ochrospiza, Poliospiza, Dendrospiza, Poliospiza and Crithagra spp. However, only clade one has jackknife and bootstrap support values above 50. The two clades were separated by Carduelis taxa, suggesting that Serinus sensu lato is not monophyletic. As it stands, the phylogeny does not support the recognition of Alario and Serinops and possibly Ochrospiza, Dendrospiza and Pseudochloroptila (Cape siskins) as distinct genera. Alario is sister to Serinus canicollis whereas the others are intermingled in a clade comprised primarily by Crithagra spp. The use of Serinus is confined to the Palaearctic canaries and allied species, and Crithagra for the strictly Afrotropical clade. Since the cytochrome b sequence divergence between the allopatric Cape (S. [c.] canicollis) and Yellow-crowned (S. [c.] flavivertex) canaries (2.8%) was similar to differences between other closely-related species and there are marked plumage differences between these taxa, we suggest that they be elevated to full species rank.     

Determination of the evolutionary relationships in Rattus sensu lato (Rodentia : Muridae) using L1 (LINE-1) amplification events

We determined ∼215 bp of DNA sequence from the 3′-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from 22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study of mammalian evolution. Received: 8 November 1996 / Accepted: 11 April 1997     

Floral Developmental Evidence for the Systematic Relationships of Tropaeolum(Tropaeolaceae)

The floral ontogeny of three species of Tropaeolum was studiedusing scanning electron microscopy to find morphological evidencefor discussing the systematic position of the family. The initiationof the androecium is highly unusual: there are always eightstamens which arise (1) either in a spiral sequence startingwith the stamen opposite sepal four, running in a directionopposite to the sequence of the sepals, and with reversals inthe direction of the spiral, or (2) as a sequence of pairedand unpaired stamens. The floral symmetry changes twice duringthe development of the flower, from polysymmetrical at sepaland petal initiation, through oblique monosymmetry at stameninitiation, and ending with median monosymmetry in later developmentalstages. The occurrence of median monosymmetry is a late-developmentalevent and is caused by the initiation of a hypanthial spur,and the unequal growth of the petals and styles. The originfor the unusual sequence of stamen initiation reflects a trendaffecting the whole flower which is linked with the changingpatterns of floral symmetry. Octandry is enhanced by multiplecauses, such as the loss of two stamens in an originally diplostemonousandroecium and the regulating pressure of the gynoecium. Thechange in symmetry during ontogeny is significant for discussingthe systematic position of Tropaeolaceae in comparison withthe glucosinolate-producing taxa and the Sapindales. The combinationof an androecium with eight stamens and oblique monosymmetryis either a single event in evolution and links Tropaeolum withthe Sapindales, or it has evolved at least twice, once in theSapindales, and once in a clade comprising Tropaeolaceae, Akaniaceaeand Bretschneideraceae. Morphological data support a sistergroup relationship of the three latter families, which is inline with macromolecular studies. Copyright 2001 Annals of BotanyCompany Tropaeolum, Tropaeolaceae, Glucosinolate clade, Sapindales, oblique monosymmetry, androecium, octandry, floral development, phylogeny