Phylogenetics of Eulophiinae (Orchidaceae: Epidendroideae): evolutionary patterns and implications for generic delimitation

Eulophiinae comprise c. 270 species divided into nine genera, with the species‐rich terrestrial genus Eulophia representing 60% of this diversity. Remarkable ecological and morphological variation, and an absence of clear diagnostic characters have led to uncertain generic delimitation in the subtribe. Using a combination of new and previously published DNA sequences, we created a dataset representing 122 taxa and all genera of Eulophiinae and inferred a complete generic‐level phylogeny for the subtribe for the first time. Our sampling focused on analysing Afro‐Madagascan taxa and therefore included representatives of the four mostly epiphytic Madagascan endemic genera, the near Madagascan endemic Oeceoclades and additional sampling of the predominantly African genera Eulophia and Orthochilus. In total, 104 new accessions were collected for this study in Zambia and Madagascar (88 of which represented 36 Eulophia spp. and 12 Oeceoclades spp.). Independent plastid and nuclear phylogenetic trees were inferred using Bayesian and maximum‐likelihood algorithms, which recovered strong support for a monophyletic Eulophiinae, the first‐branching position of the mostly epiphytic Madagascan endemic genera, and increased support for recognition of the terrestrial genera Oeceoclades and Orthochilus. Eulophia, the largest genus in the group, was recovered as polyphyletic, but with implications for its classification and that of Geodorum, that was nested in the main Eulophia clade. Although relationships among several genera were resolved with some confidence, the positions of the South African endemic genus Acrolophia and the epiphytic Madagascan endemic Paralophia require further work. Taxon sampling of Asian Eulophia is a priority for future work on the systematics of this group. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 43–56.     

The lace web spiders (Araneae,Phyxelididae) of Madagascar: phylogeny,biogeography and taxonomy

We briefly review the potential history of Madagascar as either a Darwinian or a Wallacean island, summarize the phylogenetic evidence regarding the biogeography of Madagascar spiders, examine the dispersal history of the Madagascar Phyxelididae, and monograph the family in Madagascar. Molecular phylogenetic analyses for 32 Malagasy phyxelidid exemplars, nine confamilial outgroup taxa, and seven other more distant outgroups are performed for three nuclear markers and one mitochondrial genetic marker (28S, 18S, H3 and COI) utilizing Bayesian, maximum‐likelihood and parsimony methods. These analyses suggest that there are 14 species of Phyxelididae that may be recognized from Madagascar, that these may be divided into three genera, and that the Malagasy phyxelidids form a monophyletic group, probably resulting from a single invasion of the island by an ancestor from Africa. Two new genera, ten new species, and two new combinations are proposed: Manampoka atsimo gen. nov., sp. nov. ; Rahavavy gen. nov. , including R. ida sp. nov. and R. fanivelona (Griswold, 1990) comb. nov. and R. malagasyana (Griswold, 1990) comb. nov. ; and Ambohima andrefana sp. nov. , A. antsinanana sp. nov. , A. avaratra sp. nov. , A. maizina sp. nov. , A. ranohira sp. nov. , A. vato sp. nov. , A. zandry sp. nov. and A. zoky sp. nov. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 728–810.     

Annotated checklist of Senegalia and Vachellia (Fabaceae: Mimosoideae) for the Indian subcontinent

An annotated checklist of Senegalia Raf. and Vachellia Wight & Arn. taxa for the Indian subcontinent is presented, following the fragmentation and retypification of the former broadly defined genus Acacia Mill. The countries encompassed by this study include Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan and Sri Lanka. All indigenous species (and a few introductions) in this region previously referred to Acacia belong to Senegalia and Vachellia. All Acacia s.s. taxa are introduced (principally from Australia) and are not included in the study. There are 22 species of Senegalia (21 indigenous, 1 introduced; representing 23 taxa) and 21 species of Vachellia (12 indigenous, 9 introduced; representing 27 taxa) currently recognized for the subcontinent. The largest country, India, has most species. This checklist complements that which was recently provided for these genera in southeast Asia and China. Two names formerly recorded for the Indian subcontinent are excluded, namely, Senegalia intsia (L.) Maslin is a nomen confusum and Acacia pennata subsp. hainanensis (Hayata) I. C. Nielsen is now known to be restricted to southern China and Vietnam. Acacia eriantha Desv. is an unresolved name. The following new combinations are made herein: Senegalia tanjorensis (Ragup., Thoth. & A.Mahad.) A.S.Deshpande & Maslin, Vachellia campbellii (Arn.) A.S.Deshp., & Maslin and V. pseudowightii (Thoth.) A.S.Deshpande & Maslin. A lectotype has been selected for Acacia pennata var. canescens Graham ex Kurz (= Senegalia pennata (L.) Maslin).     

Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga section Porphyrion subsection Oppositifoliae)

The purple saxifrages, Saxifraga section Porphyrion subsection Oppositifoliae, comprise the closest relatives of the arctic–alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. Many taxa have been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting, we show that some taxa form strongly supported genetic entities best recognized at the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana and S. speciosa), whereas others (S. murithiana and S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s.s. is phylogenetically incoherent. Plastid DNA sequence data show limited congruence with the predominantly nuclear‐derived AFLPs. Several co‐distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s.s. and S. retusa) share the same set of haplotypes. In the widespread S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered which exhibit a geographical rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are probably responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, however, seems to be insufficient to break down species barriers. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 622–636.     

Comparative morphology,phylogeny, and classification of West African callopanchacine killifishes (Teleostei: Cyprinodontiformes: Nothobranchiidae)

A phylogenetic analysis combining 63 morphological characters and DNA sequences (3296 bp), comprising segments of the mitochondrial genes 16S and ND2, and the nuclear gene 28S, for 19 taxa of the West African killifish tribe Callopanchacini and 11 out‐group taxa, highly supported the monophyly of the tribe, and made it possible to provide the first unambiguous diagnoses for the included genera (Archiaphyosemion, Callopanchax, Nimbapanchax, and Scriptaphyosemion). The monophyly of the Callopanchacini is supported by six morphological synapomorphies: posterior portion of the mandibular channel consisting of a single open groove; basihyal pentagonal, as a result of a nearly rectangular basihyal cartilage and a triangular bony support; dorsal process of the urohyal usually absent, sometimes rudimentary; presence of a wide bony flap adjacent to the proximal portion of the fourth ceratobranchial; a broad bony flap adjacent to the proximal portion of the fifth ceratobranchial; and haemal prezygapophysis of the pre‐ural vertebra 2 ventrally directed. The analysis indicates that the medially continuous rostral neuromast channel, commonly used to diagnose the tribe, is plesiomorphic. This study also indicates that, among African aplocheiloids, the annual life cycle style developed once in Callopanchax, and then again independently in the clade containing Fundulopanchax and Nothobranchius. © 2015 The Linnean Society of London     

Comparative morphology,biology and phylogeny of terminal‐instar larvae of the European species of Toryminae (Hym., Chalcidoidea,Torymidae) parasitoids of gall wasps (Hym. Cynipidae)

We present a phylogenetic and taxonomic study of the morphology and biology of the terminal‐instar larval stage of 19 species representing all the genera of Torymidae parasitoids of gall wasps in Europe, with the single exception of Megastigmus. The genera studied include Adontomerus Nikol'skaya, Idiomacromerus Crawford, Chalcimerus Steffan & Andriescu, Glyphomerus Förster, Pseudotorymus Masi and Torymus Dalman. We primarily used chaetotaxy and some head structures. The terminal‐instar larvae of all studied species are thoroughly described for the first time and illustrated with SEM images. We provide diagnostic characters for the family and the genera studied, and keys to genera and species for the identification of torymid larvae associated with cynipid galls. The majority of the torymid larvae studied are solitary monophagous parasitoids. Finally, to assess the potential use of larval characters in systematic studies of the family, a phylogenetic analysis of the studied taxa based on 42 larval morphological characters is proposed and compared with the current taxonomy of Torymidae. Our results suggest that body chaetotaxy, and characters of the head and mouthparts could be used for genera and species discrimination. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 676–721.     

The conquest of fresh water by the palaemonid shrimps: an evolutionary history scripted in the osmoregulatory epithelia of the gills and antennal glands

Extant Palaemonidae occupy aquatic environments that have generated physiological diversity during their evolutionary history. We analyze ultrastructural traits in gills and antennal glands of palaemonid species from distinct osmotic niches, and employ phylogenetic comparative methods to ascertain whether transformations in their osmoregulatory epithelia have evolved in tandem, driven by salinity. Gill pillar cells exhibit apical evaginations whose surface density (S_v, μm² plasma membrane area/μm³ cytoplasmic volume) ranges from 6.3–7.1 in Palaemon, and 0.7–38.4 in Macrobrachium. In the septal cells, S_v varies from 8.9–10.0 in Palaemon, and 3.3–21.6 in Macrobrachium; mitochondrial volumes (V_mit) range from 43.3–46.8% in Palaemon and 34.9–53.4% in Macrobrachium. In the renal proximal tubule cells, apical microvilli S_v varies from 27.0–34.3 in Palaemon, and 38.3–47.8 in Macrobrachium; basal invagination S_v ranges from 18.7–20.0 in Palaemon and 30.8–40.8 in Macrobrachium. Septal cell S_v shows phylogenetic signal; evagination height/density, apical S_v, and V_mit vary independently of species relatedness. Salt transport capability by the gill and renal epithelia has increased during palaemonid evolution, reflecting amplified membrane availability for ion transporter insertion. These traits underpin the increased osmotic gradients maintained against the external media. Gill ultrastructure and osmotic gradient have evolved in tandem, driven by salinity at the genus level. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 673–688.     

Systematic revision of Aluntiini Emeljanov, 1979 (Hemiptera: Fulgoromorpha: Dictyopharidae: Dictyopharinae): reclassification,phylogenetic analysis,and biogeography

The dictyopharid planthopper tribe Aluntiini s.l. is revised and reclassified into two tribes: Aluntiini s.s. and Arjunini Song & Szwedo trib. nov. The tribe Aluntiini s.s. includes five genera: Aluntia Stål, 1866; D endrophora Melichar, 1903 stat. rev. ; Dictyomorpha Melichar, 1912; Indodictyophara Liang & Song, 2012; and Madagascaritia Song & Liang gen. nov. The new tribe Arjunini comprises two genera – Arjuna Muir, 1934 and Pippax Emeljanov, 2008 – both moved from Aluntiini s.l. Four new species – A luntia longicephalica Song & Szwedo sp. nov. , Madagascaritia angusta Song & Liang sp. nov. , Arjuna maai Song & Wang sp. nov. , and Arjuna muiri Song & Wang sp. nov. – are described. A morphologically based phylogenetic analysis is undertaken for Aluntiini, Arjunini, and the representatives of Dictyopharini, Hastini, Orthopagini, and the fossil Worskaitini within Dictyopharinae, all distributed in the Old World. A matrix of 129 characters of the habitus, coloration, head, thorax, and male and female genitalia of the adults was used for the cladistic analysis. The phylogenetic results show that Aluntiini s.l. as placed in Dictyopharidae is well supported, but it is distinctly paraphyletic and should be separated into two unambiguous tribes. A palaeotropical distribution pattern displayed by Aluntiini is suggested. The origin and diversification of Aluntiini are discussed preliminarily. © 2015 The Linnean Society of London     

A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision,historical biogeography and evolution of leaf architecture

The thelypteroid fern genus Stegnogramma s.l. contains around 18–35 species and has a global, cross-continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive sampling to date and aim to pinpoint the phylogenetic positions of biogeographically and taxonomically important taxa. Based on the reconstructed historical biogeography and character evolution, we propose a new (infra)generic classification and discuss the diversification of Stegnogramma s.l. in a biogeographical context. New names or combinations are made for 12 (infra)species, including transferring the monotypic species of Craspedosorus to Leptogramma. Finally, we discuss a possible link between leaf architecture and ecological adaptation, and hypothesize that the increase in leaf dissection and free-vein proportion is an adaptive feature to cool climates in Stegnogramma s.l.     

Small snails in a big place: a radiation in the semi‐arid rangelands in northern Australia (Eupulmonata,Camaenidae, Nanotrachia gen. nov.)

Continuing the revision of the Camaenidae in the Australian Monsoon Tropics, we employed comparative analyses of morphological features (with a focus on shell and penial anatomy) and genetic markers (with a focus on mitochondrial COI and 16S sequences) to address the systematic relationships of land snails from the Victoria River District, Northern Territory, and adjacent East Kimberley (Western Australia). These analyses revealed that the species under study represented the previously undescribed genus Nanotrachia. This genus differs from all other camaenid genera known from north‐western Australia most conspicuously by its small, flat, and ribbed shell. Six species are identified as members of the new genus, four of them new species ( Nanotrachia costulata sp. nov. , Nanotrachia carinata sp. nov. , Nanotrachia coronata sp. nov. , Nanotrachia levis sp. nov. ). Two further species have already been described previously but assigned to different genera. These species, Ordtrachia intermedia (as the type species of Nanotrachia) and Mouldingia orientalis, are here transferred to Nanotrachia. Like other camaenids from the Australian Monsoon Tropics, species of Nanotrachia are characterized by essentially allopatric distributions, regional endemism, and a patchy distribution across their range. © 2013 The Linnean Society of London     

Re‐evaluation of the generic status of Athenaea and Aureliana (Withaniinae,Solanaceae) based on molecular phylogeny and morphology of the calyx

Subtribe Withaniinae (Solanaceae) comprises seven genera and c. 40 species, with an almost cosmopolitan distribution. Athenaea and Aureliana are exclusively South American, with diversity centres in the Brazilian Atlantic Rainforest. The generic status of Athenaea and Aureliana was investigated using molecular phylogenetic analysis of five plastid regions (ndhF gene, trnL intron and trnL‐trnF, psaI‐accD and trnC‐ycf6 intergenic spacers), nuclear internal transcribed spacers (ITS) and morphometric analysis of the calyx. Divergence time estimates were also performed. Withaniinae was recovered as monophyletic. The diversification time estimated for Withaniinae was 6.3 Myr, and the estimated diversification time for the Athenaea and Aureliana clades was 2.3 Myr. Athenaea and Aureliana species formed a strongly supported clade. However, the genera were not monophyletic, and support for internal relationships was moderate to weak. The morphometric analysis of the increasing size of the fruit calyx that included all species of the genera showed a cline that did not allow us to conclude that the species could be separated into two genera. Because the accrescent calyx is the only morphological character that distinguishes them, we recognize Athenaea as a synonym of Aureliana and propose five new combinations. The list of accepted species is presented. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00 , 000–000.     

Molecular phylogenetics of Vanda and related genera (Orchidaceae)

The genus Vanda and its affiliated taxa are a diverse group of horticulturally important species of orchids occurring mainly in South‐East Asia, for which generic limits are poorly defined. Here, we present a molecular study using sequence data from three plastid DNA regions. It is shown that Vanda s.l. forms a clade containing approximately 73 species, including the previously accepted genera Ascocentrum, Euanthe, Christensonia, Neofinetia and Trudelia, and the species Aerides flabellata. Resolution of the phylogenetic relationships of species in Vanda s.l. is relatively poor, but existing morphological classifications for Vanda are incongruent with the results produced. Some novel species relationships are revealed, and a new morphological sectional classification is proposed based on support for these groupings and corresponding morphological characters shared by taxa and their geographical distributions. The putative occurrence of multiple pollination syndromes in this group of taxa, combined with complex biogeographical history of the South‐East Asian region, is discussed in the context of these results. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 549–572.     

Evidence of introgressive hybridization between the morphologically divergent land snails Ainohelix and Ezohelix

Hybridization between different taxa is likely to take place when adaptive morphological differences evolve more rapidly than reproductive isolation. When studying the phylogenetic relationship between two land snails of different nominal genera, Ainohelix editha and Ezohelix gainesi, from Hokkaido, Japan, using nuclear internal transcribed spacer and mitochondrial 16S ribosomal DNA, we found a marked incongruence in the topology between nuclear and mitochondrial phylogenies. Furthermore, no clear association was found between shell morphology (which defines the taxonomy) and nuclear or mitochondrial trees and morphology of reproductive system. These patterns are most likely explained by historical introgressive hybridization between A. editha and E. gainesi. Because the shell morphologies of the two species are quite distinct, even when they coexist, the implication is that natural selection is able to maintain (or has recreated) distinct morphologies in the face of gene flow. Future studies may be able to reveal the regions of the genome that maintain the morphological differences between these species. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 77–95.     

Molecular phylogenetics and complementary geographical distributions of species of the Western Australian land snail genera Plectorhagada Iredale, 1933 and Strepsitaurus Solem, 1997 (Gastropoda: Camaenidae)

The Western Australian camaenid genera Plectorhagada and Strepsitaurus have morphological similarities and mutually exclusive ranges near Cape Range. Sequences of ctyochrome c oxidase subunit I (COI) and 16S mitochondrial DNA (mtDNA) genes confirmed that the two genera are genetically close sister clades. Targeted sampling showed that Strepsitaurus, which is confined to Cape Range, lies within a hole in the distribution of the more broadly distributed Plectorhagada that occurs on the coastal strip surrounding Cape Range. Species of the two genera meet at the transition between the rocky Cape Range and the sandier coastal areas, providing a rare example of the close replacement of genera. Within each genus, mtDNA sequences confirmed the monophyly and genetic distinctness of species, with few exceptions that show the need for additional work, and with the addition of three new species in the Cape Range area. As is typical of Australian camaenids, distributions of congeneric species are mutually exclusive, but in some cases close proximity is associated with contrasting habitats, such as gorge endemics versus the species on top of Cape Range. In sympatry, Strepsitaurus rugus (Cotton, 1951) and Strepsitaurus williami Solem, 1997 are separated by microhabitat. These local associations with habitat indicate that ecological differences, and not simply allopatric divergence, contribute to the lack of sympatry between closely related Australian camaenids. © 2015 The Linnean Society of London     

Molecular phylogenetic analysis of Arenaria (Caryophyllaceae: tribe Arenarieae) and its allies inferred from nuclear DNA internal transcribed spacer and plastid DNA rps16 sequences

The systematics and phylogeny of the genus Arenaria and allied genera are unresolved. The use of morphological data has resulted in contradictory taxonomic concepts in the past due to their homoplastic nature. We present a phylogenetic analysis based on internal transcribed spacer (ITS) and rps16 sequence data of 140 (132 taxa) and 131 (120 taxa) accessions, respectively. Maximum parsimony and Bayesian analyses of each marker produced nearly congruent trees. Monophyly of Arenaria s.s. and Eremogone is confirmed here. Our results corroborate earlier results indicating that Arenaria subgenus Odontostemma is monophyletic, but outside the core group of Arenaria. Arenaria subgenus Solitaria is sister to Odontostemma and also not closely related to the latter; both of these subgenera are excluded from Arenaria and treated as distinct genera. The molecular data indicate that the ‘Arenaria s.s. clade’ consists of a few well‐supported subgroups and that the current subgeneric classification of the genus does not reflect evolutionary history. Arenaria subgenus Leiosperma is clearly monophyletic, but we reduce it to sectional level. Our molecular data show that the monotypic Arenaria subgenera Porphyrantha and Arenariastrum are nested in A. subgenus Arenaria, whereas subgenus Eremogoneastrum is included in Eremogone. None of the species‐rich sections in subgenus Arenaria is monophyletic. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 648–669.     

Morphological and molecular evidence for phylogeny and classification of South American pitvipers,genera Bothrops,Bothriopsis, and Bothrocophias (Serpentes: Viperidae)

Species in the genus Bothrops s. l. are extraordinarily variable in ecology and geography, compared with other genera in the subfamily Crotalinae. In contrast to the trend of splitting large and variable groups into smaller, more ecologically and phenotypically cohesive genera, the genus Bothrops has remained speciose. In addition, previous phylogenetic analyses have found Bothrops to be paraphyletic with respect to the genus Bothriopsis. Taxonomic arguments exist for synonymizing Bothriopsis with Bothrops, and for splitting Bothrops into smaller genera, but the greatest hindrance to taxonomic revision has been incomplete phylogenetic information. We present a phylogeny of Bothrops, Bothriopsis, and Bothrocophias based on 85 characters of morphology and 2343 bp of four mitochondrial gene regions, and with significantly greater taxonomic coverage than previous studies. The combined data provide improved support over independent datasets, and support the existence of discrete species groups within Bothrops. The monophyly and distinctness of these groups warrant recognition at the generic level, and we propose a new taxonomic arrangement to reflect these findings. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 617–640.     

Checklist of Commelinaceae of Equatorial Guinea (Annobón,Bioko and Río Muni)

A checklist of Commelinaceae of Equatorial Guinea, comprising 46 taxa in 12 genera, is presented. The best represented genus is Palisota, with 11 species. Bibliographical references for Commelinaceae from Equatorial Guinea have been gathered and checked. Eleven species of Commelinaceae are recorded for the first time in the country. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 106–122.     

Systematic revision of the freshwater snail Margarya Nevill, 1877 (Mollusca: Viviparidae) endemic to the ancient lakes of Yunnan,China, with description of new taxa

The systematics of the viviparid freshwater snail genus Margarya endemic to the ancient lakes of Yunnan, China, is revised based on comparative analyses of morphological features, including shell, operculum, radula, and genital anatomy, and molecular phylogenetic analyses of partial sequences of the mitochondrial 16S rDNA (16S) and cytochrome c oxidase subunit I (COI) genes, as well as the nuclear Internal Transcribed Spacer 2 (ITS2). The taxonomic utility of key anatomical and morphological features in this group is evaluated. The genus Margarya as delimited previously is split into three genera in order to retain monophyletic taxa: (1) Margarya s.s., consisting of four species, i.e. the type species Margarya melanioides plus Margarya francheti, Margarya oxytropoides, and Margarya monodi; (2) the previously introduced subgenus Tchangmargarya is elevated to an independent genus containing two species, Tchangmargarya yangtsunghaiensis and the new species T changmargarya multilabiata sp. nov. ; and (3) a new genus, A nularya gen. nov. , is described, also containing two species, i.e. Anularya mansuyi and Anularya bicostata. Molecular phylogenies based on analyses of three gene fragments have identical topologies, supporting the monophyly of these genera. The sister group of Margarya s.s. is Cipangopaludina, whereas the sister group of Anularya is Sinotaia; Tchangmargarya is sister to a clade containing all the aforementioned groups. Features of the operculum and the right male tentacle (penis) are particularly informative on the generic level, whereas shell and radular characters are especially useful to differentiate species. The phylogenetic relationships recovered here are consistent with orogenic patterns of the Yunnan Mountains. Changes in the river system and water area of ancient lakes caused by tectonic activities probably play an important role in speciation and shaping the current pattern of species distribution in Yunnan. © 2015 The Linnean Society of London