Phylogeny and classification of the Phengaris–Maculinea clade (Lepidoptera: Lycaenidae): total evidence and phylogenetic species concepts

Abstract.  Total evidence analysis, based on a combination of morphological and ecological characters with two mitochondrial sequences (cytochrome c oxidase subunits I and II) and one nuclear (elongation factor-1α) sequence, provides a new phylogeny of the uniquely obligate ant parasitic Phengaris–Maculinea butterflies. The clade, including all species of Maculinea and Phengaris , is very stable and well supported. However, various analyses suggest that either Phengaris or Maculinea is not monophyletic with regard to the other, which necessitates generic reclassification of the clade. Application of the diagnostic and monophyletic 'phylogenetic' species concepts leads to species-level reclassification, including ten species ( P. alcon comb.n. including ' P. rebeli ', P. daitozana , P. albida , P. atroguttata , P. kurentzovi comb.n. , P. nausithous comb.n. , P. teleius comb.n. , P. arion comb.n. , P. arionides comb.n. , P. takamukui comb.n .) and one unresolved metaspecies (' P. cyanecula ' comb.n .) in four monophyletic species groups. The existence of further or additional cryptic species is possible within P. nausithous and P. teleius . Maculinea Van Eecke, 1915 syn.n. is considered a junior synonym of Phengaris Doherty, 1891.     

Cytochrome b-based phylogeny of the Praomys group (Rodentia,Murinae): a new African radiation?Phylogénie du groupe Praomys (Rodentia,Murinae) basée sur le cytochrome b : une nouvelle radiation africaine ?

Complete cytochrome b gene sequences allows, for the first time, establishing a nearly complete phylogeny among the Praomys group sensu lato. The genera Praomys, Mastomys and Stenocephalemys appear paraphyletic. Myomys is polyphyletic and this genus name probably needs to be restricted to its type species, M. verreauxii. The genera Zelotomys and Colomys appear as sister groups. Mastomys pernanus and Malacomys verschureni nest within the Praomys group, but their generic assignation must be further clarified. The genus Heimyscus appears closest to Praomys than to Hylomyscus. The different lineages probably result from an adaptive radiation at the end of the Miocene.     

Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event

According to recent taxonomic reclassification, the primate family Hylobatidae contains four genera (Hoolock, Nomascus, Symphalangus, and Hylobates) and between 14 and 18 species, making it by far the most species-rich group of extant hominoids. Known as the "small apes", these small arboreal primates are distributed throughout Southeast, South and East Asia. Considerable uncertainty surrounds the phylogeny of extant hylobatids, particularly the relationships among the genera and the species within the Hylobates genus. In this paper we use parsimony, likelihood, and Bayesian methods to analyze a dataset containing nearly 14 kilobase pairs, which includes newly collected sequences from X-linked, Y-linked, and mitochondrial loci together with data from previous mitochondrial studies. Parsimony, likelihood, and Bayesian analyses largely failed to find a significant difference among phylogenies with any of the four genera as the most basal taxon. All analyses, however, support a tree with Hylobates and Symphalangus as most closely related genera. One strongly supported phylogenetic result within the Hylobates genus is that Hylobates pileatus is the most basal taxon. Multiple analyses failed to find significant support for any singular genus-level phylogeny. While it is natural to suspect that there might not be sufficient data for phylogenetic resolution (whenever that situation occurs), an alternative hypothesis relating to the nature of gibbon speciation exists. This lack of resolution may be the result of a rapid radiation or a sudden vicariance event of the hylobatid genera, and it is likely that a similarly rapid radiation occurred within the Hylobates genus. Additional molecular and paleontological evidence are necessary to better test among these, and other, hypotheses of hylobatid evolution.     

PHYLOGENY AND THE EVOLUTION OF HOST PLANT ASSOCIATIONS IN THE LEAF BEETLE GENUS OPHRAELLA (COLEOPTERA,CHRYSOMELIDAE)

Species of Ophraella, a North American genus of leaf beetles (Chrysomelidae), feed variously on eight genera in four tribes of Asteraceae. A phylogenetic analysis, based on morphological features and allozymes, was undertaken to deduce the history of host affiliation within the genus. The two data sets are combined to arrive at a provisional phylogeny of the species, onto which host associations are parsimoniously mapped. Among and within the 12 species studied, at least two shifts are postulated to have occurred among congeneric plant species, five between genera in the same tribe, and four between different tribes of Asteraceae. The phylogeny of Ophraella appears not to be congruent with that of its hosts. This and other evidence indicates that many host shifts in Ophraella postdate the divergence of the host plants, a conclusion that may apply commonly to phytophagous insects. A phenetic analysis of the plants' secondary compounds provides modest support for the hypothesis that host shifts are facilitated by commonalities in plant chemistry. A possible trend in host shifts is evident, from chemically simpler to chemically more forbidding plants. The chemical barriers to host shifts in Ophraella appear to require adaptation in both behavior and in physiological attributes. There is no evidence that the host associations of these insects or the divergence in secondary chemistry of their hosts can be attributed to coevolution.     

A phylogenetic analysis of the frog genera Vibrissaphora and Leptobrachium, and the correlated evolution of nuptial spine and reversed sexual size dimorphism

A phylogeny of the frog genus Vibrissaphora and seven Leptobrachium species was reconstructed based on 3808 base pairs of mitochondrial and nuclear DNA sequence data. Maximum parsimony, Bayesian, and statistical parsimony approaches were employed to reveal the historical relationships among the recovered haplotypes. The species of the genera Vibrissaphora and Leptobrachium failed to form their respective monophyletic groups. Therefore, Vibrissaphora should be part of the genus Leptobrachium. Our analysis also further delineated several species boundaries; Leptobrachium chapense is not a single species, rather, a species complex. On the other hand, although L. liui demonstrated substantial morphological variation, all populations belong to one species. The RAG-1 data revealed a case of species-level non-monophyly; when studying slowly evolving genes, population coalescence may not have been reached within species. The phylogenetic comparative analysis revealed a positive correlation between evolution of male nuptial spines and reversed sexual size dimorphism in this group. Resource defense polygyny and male parental care are possible explanations for the presence of large male size.     

Phylogenetic relationships of North American Gomphidae and their close relatives

Intrafamilial relationships among clubtail dragonflies (Gomphidae) have been the subject of many morphological studies, but have not yet been systematically evaluated using molecular data. Here we present the first molecular phylogeny of Gomphidae. We include six of the eight subfamilies previously suggested to be valid, and evaluate generic relationships within them. We have included examples of all genera reported from the Nearctic except Phyllocycla. This sample includes all North American species of Ophiogomphus, which has allowed us to explore intrageneric relationships in that genus. Our particular focus is on the closest relatives of the genus Gomphus, especially those North American species groups that have been commonly treated as subgenera of Gomphus. The Gomphus complex is split into additional genera, supported by molecular and morphological evidence: Phanogomphus, Stenogomphurus, Gomphurus and Hylogomphus are here considered to be valid genera. The genus Gomphus, in our restricted sense, does not occur in the western hemisphere; in addition, G. flavipes is transferred to Stylurus.     

Resolving evolutionary relationships in the lichen-forming genus Porpidia and related allies (Porpidiaceae, Ascomycota)

The lichen-forming genus Porpidia (Porpidiaceae, Ascomycota) provides excellent opportunities for evolutionary, reproductive, and ecological studies of crustose epilithic lichen symbioses. However, despite the fact that the genus itself seemed to be clearly delimited, the group was thought to be a hopeless case with regard to intrageneric relationships and species delimitations due to apparently rampant homoplasy throughout most character systems. Contrary to the situation for non-molecular data, a robust and generally well-resolved phylogeny was recovered based on DNA-sequence data. Separate and combined analyses of nuclear ribosomal RNA large subunit and nuclear beta-tubulin gene fragments were performed using maximum parsimony, maximum likelihood, and Bayesian approaches. Branch support was estimated using non-parametic bootstrapping and posterior probabilities, while monophyly of a priori defined groups was tested using posterior probabilities. The results reveal a highly supported "Porpidia sensu lato," however, Porpidia itself is not monophyletic. Several smaller genera of the Porpidiaceae and probably the large genus Lecidea (Lecideaceae) are nested within the group. Most taxa analyzed fall into one of four major subgroups within Porpidia s.l., though the basal relationships among these subgroups could not be supported. This phylogeny will make it possible to re-evaluate morphological and chemical characters in the group, and to conduct detailed studies of species delimitations within the monophyletic subgroups.     

The evolution of euhermaphroditism in caridean shrimps: a molecular perspective of sexual systems and systematics

Background  

The hippolytid genus Lysmata is characterized by simultaneous hermaphroditism, a very rare sexual system among Decapoda. Specialized cleaning behavior is reported in a few pair-living species; these life history traits vary within the genus. Unfortunately, the systematics of Lysmata and the Hippolytidae itself are in contention, making it difficult to examine these taxa for trends in life history traits. A phylogeny of Lysmata and related taxa is needed, to clarify their evolutionary relationships and the origin of their unique sexual pattern. In this study, we present a molecular phylogenetic analysis among species of Lysmata, related genera, and several putative hippolytids. The analysis is based upon DNA sequences of two genes, 16S mtDNA and nuclear 28S rRNA. Phylogenetic trees were estimated using Bayesian Inference, Maximum Likelihood, and Maximum Parsimony.     

REVIEW: Lycaenid-ant interactions of the Maculinea type: tracing their historical roots in a comparative framework

Parasitic relationships between lycaenid butterfly larvae and ants are contrasted with the more common, and ancestral, mutualistic butterfly-ant associations. Three types of lycaenid-ant parasitism can be recognized: (i) the Miletinae type (derived from predation on Homoptera); (ii) the Aphnaeini type (derived from obligate and specific mutualism or commensalism); and (iii) the Maculinea type (derived from facultative mutualism, only represented by the genera Maculinea and Lepidochrysops). Parasitic lycaenid-ant interactions are rare (37 confirmed recorded cases worldwide) and are mostly confined to single species, or small species-groups, in larger non-parasitic clades. Only the two genera representing the Maculinea type have undergone substantial radiation. Ant-parasitic lycaenids predominantly occur in highly seasonal habitats with an extended unfavourable dry or cold season. These observations suggest that (a) parasitic interactions are relatively unstable in evolutionary time, and (b) their evolution usually started with caterpillars seeking shelter in ant nests. Ecological and zoogeographical data for species of the Glaucopsychiti (of which Maculinea forms a part) are compiled and used to discuss the evolutionary origin of ant-parasitism in Maculinea butterflies in a comparative framework. These comparisons suggest that (a) Maculinea evolved from facultative unspecific ant-mutualists, (b) the loss of larval tentacle organs is primarily related to their endophytic feeding habits, (c) that Lamiaceae were the hostplants of ancestral Maculinea, and (d) that Maculinea evolved in eastern central Asia. Further phylogenetic and biogeographical analyses are required to quantitatively test these possibilities. © Rapid Science Ltd. 1998     

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon 1 of the IRBP gene (approximately 1.3 kb) and first intron of the TTR gene (approximately 1 kb). These data were used to analyze carnivoran phylogeny at the family and generic level as well as the interspecific relationships within recently derived Felidae. Phylogenetic results using a combined IRBP+TTR dataset strongly supported within the superfamily Califormia, the red panda as the closest lineage to procyonid-mustelid (i.e., Musteloidea) clade followed by pinnipeds (Otariidae and Phocidae), Ursidae (including the giant panda), and Canidae. Four feliform families, namely the monophyletic Herpestidae, Hyaenidae, and Felidae, as well as the paraphyletic Viverridae were consistently recovered convincingly. The utilities of these two gene segments for the phylogenetic analyses were extensively explored and both were found to be fairly informative for higher-group associations within the order Carnivora, but not for those of low level divergence at the species level. Therefore, there is a need to find additional genetic markers with more rapid mutation rates that would be diagnostic at deciphering relatively recent relationships within the Carnivora.     

Phylogenetic relationships among New Caledonian Sapotaceae (Ericales): molecular evidence for generic polyphyly and repeated dispersal

The phylogeny of a representative group of genera and species from the Sapotaceae tribe Chrysophylleae, mainly from Australia and New Caledonia, was studied by jackknife analyses of sequences of nuclear ribosomal DNA. The phylogeny conflicts with current opinions on generic delimitation in Sapotaceae. Pouteria and Niemeyera, as presently circumscribed, are both shown to be nonmonophyletic. In contrast, all species currently assigned to these and other segregate genera confined to Australia, New Caledonia, or neighboring islands, form a supported clade. Earlier classifications in which more genera are recognized may better reflect relationships among New Caledonian taxa. Hence, there is need for a revision of generic boundaries in Chrysophylleae, and particularly within the Pouteria complex, including Leptostylis, Niemeyera, Pichonia, Pouteria pro parte (the main part of section Oligotheca), and Pycnandra. Section Oligotheca have been recognized as the separate genus Planchonella, a monophyletic group that needs to be resurrected. Three clades with strong support in our jackknife analysis have one Australian species that is sister to a relatively large group of New Caledonian endemics, suggesting multiple dispersal events between this small and isolated tropical island and Australia. The phylogeny also suggests an interesting case of a relatively recent and rapid radiation of several lineages of Sapotaceae within New Caledonia.     

Genomic fingerprints in the tribe Triticeae produced by PCR using a tRNA consensus primer

Forty-one accessions belonging to ten genera of the tribe Triticeae representing both wild and cultivated species were analyzed by polymerase chain reaction (PCR). Of two consensus tRNA primers tested, one primer revealed characteristic amplification products for all of the species. A total of 35 tRNA markers were scored across all accessions. Five genus-specific and three species-specific markers were obtained. Genomic fingerprints were largely conserved within a genus. The phylogram obtained using parsimony has separated most of the accessions into their prevailing taxonomic species and genus groups. The phylogram showed close association among the three genera Secale, Triticum and Hordeum as expected. The Triticum-Secale relationship was closer than the Triticum-Hordeum or the Secale-Hordeum relationships. The tree also reflected the close associations among the forage grass species belonging to Leymus and Elymus. Thus tDNA-PCR helped to identify species and genera. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evolution of host specialization in the Adelgidae (Insecta: Hemiptera) inferred from molecular phylogenetics

The Adelgidae form a small group of insects in the Aphidoidea. They are cyclically parthenogenetic with host alternating, multiple-generation complex life cycles and are restricted to certain host genera in the Pinaceae. Species that host alternate always have Picea as the primary host where sexual reproduction and gall formation occur, and another genus in the Pinaceae as the secondary host where a series of parthenogenetic generations are produced. Other species that do not host alternate complete their entire life cycle on one host and only reproduce parthenogenetically. We studied relationships within Adelgidae using DNA sequences from the mitochondrial COI, COII, and cytb genes, and the nuclear EF1alpha gene. Analysis of the combined data resulted in a well-resolved phylogeny in which the major adelgid clades correspond neatly to their association with secondary host genera. Specialization on each secondary host genus occurred only once and was followed by diversification on the host genus. Molecular dating of divergence times in the Adelgidae suggest that diversification among host genera occurred in the Late Cretaceous and Early Tertiary when the Pinaceae genera were diverging. It is not clear, however, whether the Adelgidae and Pinaceae co-diversified because the relationships among the Pinaceae genera are not fully resolved. We discuss implications for adelgid taxonomy, life cycle evolution, and evolution of the interaction between adelgids and their host plants.     

Systematics of the genera of Bodotriidae (Crustacea: Cumacea)

The cumacean family Bodotriidae includes 382 species in 31 genera grouped in three subfamilies: Bodotriinae, Mancocumatinae and Vaunthompsoniinae. Generic diagnoses are based on few characters that often have overlapping states among genera, complicating the understanding of the relationships within the group. The goals of this study are to illuminate the phylogenetic relationships among the genera of the Bodotriidae using morphological characters and to review the systematics of the family. For this purpose, all species within each genus were studied from the literature to code all the variability of genera for 109 variable morphological characters. Phylogenetic analyses show that there is independent reduction of the pleopods in two clades from a plesiomorphic state of five pairs, while the number of exopods of peraeopods has been reduced gradually in more derived groups of bodotriids. The subfamily Bodotriinae is the most derived and the Vaunthompsoniinae the most basal, and is paraphyletic with the Mancocumatinae embedded within it. No discriminatory characters were found between the subfamilies Mancocumatinae and Vaunthompsoniinae and they are not clearly separated in the phylogeny. Mancocumatinae is synonymized with Vaunthompsoniinae and all the genera of the former Mancocumatinae should be included within Vaunthompsoniinae. Analyses of character evolution justify a few other taxonomic changes. All genera were redescribed based on all the coded characters and a complete list of all valid species for each genus is included. Finally, dichotomous keys for identification to genus level are provided.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 1–58.     

Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes

Although Codfishes are probably one of the most studied groups of all teleost fishes worldwide owing to their great importance to fisheries, their phylogeny and classification are still far from being firmly established. In this study, we present phylogenetic relationships of 19 out of 22 genera traditionally included in the Gadidae based on the analysis of entire cytochrome b and partial cytochrome oxidase I genes (1530 bp). Maximum Parsimony, Maximum Likelihood, and Bayesian analyses all recovered five main clades that correspond to traditionally recognized groupings within Gadoids. The same clades were recovered with MP analysis based on 30 morphological characters (collected from the literature). Given these findings, we propose a revised provisional classification of Gadoids: one suborder Gadoidei containing two families, the Merlucciidae (1 genus) and the Gadidae (21 genera) distributed into four subfamilies: the Gadinae (12 genera), the Lotinae (3 genera), the Gaidropsarinae (3 genera), and the Phycinae (3 genera). Lastly, nuclear inserts of mitochondrial DNA (Numts) were identified in two species, i.e., Gadiculus argenteus and Melanogrammus aeglefinus.     

A new genus and species of bothriurid scorpion from the Brandberg Massif, Namibia, with a reanalysis of bothriurid phylogeny and a discussion of the phylogenetic position of Lisposoma Lawrence

Abstract. Brandbergia haringtoni , a new genus and species of bothriurid scorpion, is described from the Brandberg Massif, northwestern Namibia. A cladistic analysis, based on seventy-four morphological characters scored for thirty-one exemplar species representing all genera of Bothriuridae, and one genus from each of the six remaining families of Scorpionoidea, was conducted to test the phylogenetic placement of the new genus and whether it affects the internal relationships of Bothriuridae. The available data demonstrate, under a range of weighting regimes, that the new genus is the most basal bothriurid, and confirm the scheme of relationships among the remaining bothriurid genera that was recovered in a previous analysis: ( Brandbergia ( Lisposoma ( Thestylus ( Phoniocercus ( Tehuankea ( Cercophonius  +  Urophonius ) ( Bothriurus  +  Brachistosternus  + Orobothriurus  +  Centromachetes ( Timogenes  +  Vachonia ))))))). On the basis of this evidence, Lourenço's recent proposal of family Lisposomidae for Lisposoma is rejected and Lisposomidae is synonymized with Bothriuridae. The implications of the phylogeny for understanding the biogeography of Bothriuridae are discussed.     

Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher‐level taxa in studies of biodiversity,and correlates of species richness

We test a near‐complete genus level phylogeny of hoverflies (Diptera: Syrphidae) for consistency with a null model of clade growth having uniform probabilities of speciation and extinction among contemporaneous species. The phylogeny is too unbalanced for this null model. Importantly, the degree of imbalance in the phylogeny depends on whether the phylogeny is analysed at the genus level or species level, suggesting that genera ought not to be used uncritically as surrogates for species in large‐scale evolutionary analyses. Tests for a range of morphological, life‐history and ecological correlates of diversity give equivocal results, but suggest that high species‐richness may be associated with sexual selection and diet breadth. We find no correlation between species‐richness and either body size or reproductive rate.     

Resolving phylogeny at the family level by mitochondrial cytochrome oxidase sequences: phylogeny of carrion beetles (Coleoptera, Silphidae)

We investigated the phylogenetic relationships of carrion beetles (Coleoptera, Silphidae) using 2094 bp of their mitochondrial cytochrome oxidase subunit I and II and tRNA leucine gene sequences. Shorter fragments of this gene region previously have been used to establish generic relationships in insects. In this study, they provided more than sufficient resolution, although the third positions of the protein-coding sequences reached saturation for the deeper divergences. This first published phylogeny for the Silphidae comprises 23 species from 13 genera sampled across the geographic range of the family. In addition, we included species from three related families as outgroups. One of these families, the Agyrtidae, was, until recently, included in the Silphidae, but its resolution here justifies its current position as a separate family. The silphid subfamilies Nicrophorinae and Silphinae are monophyletic in all analyses. All genera for which several species were sampled are supported as monophyletic groups, with the exception of the genus Silpha. European and North American representatives of two Nicrophorus species described from both continents are supported as each others' closest relatives. The lineage that colonized Gondwanaland and that most likely originated in the Palearctic is the most basal within the Silphinae.     

A phylogeny of planorbid snails,with implications for the evolution of Schistosoma parasites

The Planorbidae represent one of the most important families of freshwater snails. They have a wide distribution and are significant both medically and economically as intermediate hosts for trematode worms. Digenetic trematodes of the genus Schistosoma cause schistosomiasis, a disease that infects 200 million people, and domestic animals throughout the tropics. Three of the four recognized species groups of Schistosoma rely on snails of the family Planorbidae to complete their life cycles. Each species group requires a specific planorbid genus-Bulinus, Biomphalaria, or Indoplanorbis. Our understanding of the relationships among the genera within the Planorbidae is rudimentary and based solely on internal anatomy and shell morphology. Two molecular markers, ribosomal 28S and actin exon 2, were sequenced and a phylogeny constructed for 38 taxa representing 16 planorbid genera. The phylogeny supports the division of the Planorbidae into two subfamilies, the Bulininae and Planorbinae. Interestingly, two representatives of the family Ancylidae fall within the Planorbidae highlighting the need for further analysis and possible reclassification of this group. A molecular based phylogeny of the genus Schistosoma was then mapped against the snail tree. The trees indicate that planorbid-transmitted Schistosoma appear not to be co-speciating with their current snail host lineages. Rather, host switching was prominent, including a switch involving two distantly related planorbid genera, Biomphalaria and Bulinus. Our study of the Planorbidae poses fundamental questions regarding how and when Schistosoma acquired new snail hosts, including how switches to relatively distant hosts are accomplished and why some available planorbids were not colonized.