A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes

Even though the marsupial order Diprotodontia is one of the most heavily studied groups of Australasian marsupials, phylogenetic relationships within this group remain contentious. The more than 125 living species of Diprotodontia can be divided into two main groups: Vombatiformes (wombats and koalas) and Phalangerida. Phalangerida is composed of the kangaroos (Macropodidae, Potoroidae, and Hypsiprymnodontidae) and possums (Phalangeridae, Burramyidae, Petauridae, Pseudocheiridae, Tarsipedidae, and Acrobatidae). Much of the debate has focused on relationships among the families of possums and whether possums are monophyletic or paraphyletic. A limitation of previous investigations is that no study to date has investigated diprotodontian relationships using all genera. Here, we examine diprotodontian interrelationships using a nuclear multigene molecular data set representing all recognized extant diprotodontian genera. Maximum parsimony, maximum likelihood, and Bayesian methods were used to analyze sequence data obtained from protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF. We also applied a Bayesian relaxed molecular clock method to estimate times of divergence. Diprotodontia was rooted between Vombatiformes and Phalangerida. Within Phalangerida, the model-based methods strongly support possum paraphyly with Phalangeroidea (Burramyidae + Phalangeridae) grouping with the kangaroos (Macropodiformes) to the exclusion of Petauroidea (Tarsipedidae, Acrobatidae, Pseudocheiridae, and Petauridae). Within Petauroidea, Tarsipedidae grouped with both Petauridae and Pseudocheiridae to the exclusion of Acrobatidae. Our analyses also suggest that the diprotodontian genera Pseudochirops and Strigocuscus are paraphyletic and diphyletic, respectively, as currently recognized. Dating analyses suggest Diprotodontia diverged from other australidelphians in the late Paleocene to early Eocene with all interfamilial divergences occurring prior to the early Miocene except for the split between the Potoroidae and Macropodidae, which occurred sometime in the mid-Miocene. Ancestral state reconstructions using a Bayesian method suggest that the patagium evolved independently in the Acrobatidae, Petauridae, and Pseudocheiridae. Ancestral state reconstructions of ecological venue suggest that the ancestor of Diprotodontia was arboreal. Within Diprotodontia, the common ancestor of Macropodidae was reconstructed as terrestrial, suggesting that tree kangaroos (Dendrolagus) are secondarily arboreal.     

The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes

Squamate reptiles number approximately 8000 living species and are a major component of the world's terrestrial vertebrate diversity. However, the established relationships of the higher-level groups have been questioned in recent molecular analyses. Here we expand the molecular data to include DNA sequences, totaling 6192 base pairs (bp), from nine nuclear protein-coding genes (C-mos, RAG1, RAG2, R35, HOXA13, JUN, alpha-enolase, amelogenin and MAFB) for 19 taxa representing all major lineages. Our phylogenetic analyses yield a largely resolved phylogeny that challenges previous morphological analyses and requires a new classification. The limbless dibamids are the most basal squamates. Of the remaining taxa (Bifurcata), the gekkonids form a basal lineage. The Unidentata, squamates that are neither dibamids nor gekkonids, are divided into the Scinciformata (scincids, xantusiids, and cordylids) and the Episquamata (remaining taxa). Episquamata includes Laterata (Teiformata, Lacertiformata, and Amphisbaenia, with the latter two joined in Lacertibaenia) and Toxicofera (iguanians, anguimorphs and snakes). Our results reject several previous hypotheses that identified either the varanids, or a burrowing lineage such as amphisbaenians or dibamids, as the closest relative of snakes. Our study also rejects the monophyly of both Scleroglossa and Autarchoglossa, because Iguania, a species-rich lineage (ca. 1440 sp.), is in a highly nested position rather than being basal among Squamata. Thus iguanians should not be viewed as representing a primitive state of squamate evolution but rather a specialized and successful clade combining lingual prehension, dependence on visual cues, and ambush foraging mode, and which feeds mainly on prey avoided by other squamates. Molecular time estimates show that the Triassic and Jurassic (from 250 to 150 Myr) were important times for squamate evolution and diversification.     

Phylogenetic relationships of wild silkmoths (Lepidoptera: Saturniidae) inferred from four protein-coding nuclear genes

Abstract.  The Saturniidae, or wild silkmoths, number approximately 1861 species in 162 genera and nine subfamilies including Cercophaninae and Oxyteninae. They include some of the largest and most spectacular of all Lepidoptera, such as the moon or luna moths, atlas moths, emperor moths, and many others. Saturniids have been important as sources of wild silk and/or human food in a number of cultures, and as models for comparative studies of genetics, development, physiology, and ecology. Seeking to improve the phylogenetic framework for such studies, we estimated relationships across Saturniidae, sampling all nine subfamilies plus all five tribes of Saturniinae. Seventy-five exemplars (45 Saturniidae plus 30 bombycoid outgroups) were sequenced for four protein-coding nuclear gene regions (5625 bp total), namely CAD (the fusion protein carbamoylphosphate synthetase/aspartate transcarbamylase/dihydroorotase), DDC (dopa decarboxylase), period, and wingless. The data, analyzed by parsimony and likelihood, gave a strongly resolved phylogeny at all levels. Relationships among subfamilies largely mirrored the pre-cladistic hypothesis of Michener, albeit with significant exceptions, and there was definitive support for the morphology-based proposal that Ludiinae form a tribe (Micragonini) within Saturniinae. In the latter subfamily, the African tribe Urotini was shown to be paraphyletic with respect to Bunaeini and Micragonini, also in accord with recent morphological findings. Relationships within the New World subfamilies Arsenurinae, Ceratocampinae and Hemileucinae nearly always accord with previous morphology-based phylogenies when both are clearly resolved. Within Hemileucinae, Hemileucini are paraphyletic with respect to the monotypic Polythysanini. A preliminary biogeographical analysis supports ancestral restriction to the New World, followed by dispersal and/or vicariance splitting most of the family into a largely New World versus a largely Old World clade.     

A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes

Evolutionary relationships of the order Carnivora have been extensively studied. However, phylogenetic studies based on different types of data, species samples, and methods of analysis provide contradictory results. Consequently, phylogenetic relationships of Carnivora remain contentious. Here, the sequence of 12 mitochondrial genes (10,842 nucleotides) from a total of 38 carnivore species was used to investigate the phylogeny of the caniform (dog-like) carnivores. An analysis using maximum parsimony, maximum likelihood, and Bayesian approaches provided a unique and well-supported solution to most contentious relationships within Caniformia. The clade Arctoidea was shown to consist of three major monophyletic groups: Pinnipedia, Ursidae, and Musteloidea. Within Pinnipedia, the families Otariidae and Odobenidae formed a clade, sister to Phocidae. Within Musteloidea, there was a sister relationship between true mustelids (i.e., excluding the skunks) and procyonids, and between ailurids and mephitids (skunks). Despite a high level of confidence obtained at most nodes, uncertainty remained about the relative position of the three major arctoid clades.     

Phylogenetic utility of ribosomal genes for reconstructing the phylogeny of five Chinese satyrine tribes (Lepidoptera,Nymphalidae)

Satyrinae is one of twelve subfamilies of the butterfly family Nymphalidae, which currently includes nine tribes. However, phylogenetic relationships among them remain largely unresolved, though different researches have been conducted based on both morphological and molecular data. However, ribosomal genes have never been used in tribe level phylogenetic analyses of Satyrinae. In this study we investigate for the first time the phylogenetic relationships among the tribes Elymniini, Amathusiini, Zetherini and Melanitini which are indicated to be a monophyletic group, and the Satyrini, using two ribosomal genes (28s rDNA and 16s rDNA) and four protein-coding genes (EF-1α, COI, COII and Cytb). We mainly aim to assess the phylogenetic informativeness of the ribosomal genes as well as clarify the relationships among different tribes. Our results show the two ribosomal genes generally have the same high phylogenetic informativeness compared with EF-1α; and we infer the 28s rDNA would show better informativeness if the 28s rDNA sequence data for each sampling taxon are obtained in this study. The placement of the monotypic genus Callarge Leech in Zetherini is confirmed for the first time based on molecular evidence. In addition, our maximum likelihood (ML) and Bayesian inference (BI) trees consistently show that the involved Satyrinae including the Amathusiini is monophyletic with high support values. Although the relationships among the five tribes are identical among ML and BI analyses and are mostly strongly-supported in BI analysis, those in ML analysis are lowly- or moderately- supported. Therefore, the relationships among the related five tribes recovered herein need further verification based on more sampling taxa.     

A phylogenetic analysis of Myriapoda (Arthropoda) using two nuclear protein-encoding genes

Nucleotide and inferred amino acid sequences from two nuclear protein-encoding genes, elongation factor-aα and RNA polymerase II, were obtained from 34 myriapods and 14 other arthropods to determine phylogenetic relationships among and within the myriapod classes. Phylogenetic analyses using maximum parsimony and maximum likelihood methods recovered all three represented myriapod classes (Chilopoda, Diplopoda, Symphyla) and all multiply sampled chilopod and diplopod orders, often with high node support. In contrast, relationships between classes and between orders were recovered less consistently and node support was typically lower. The temporal structure of phylogenetic diversification in Myriapoda may explain this apparent pattern of the phylogenetic recovery.     

Systematics and evolution of the cutworm moths (Lepidoptera: Noctuidae): evidence from two protein-coding nuclear genes

Abstract. A broad molecular systematic survey of Noctuidae was undertaken to test recent hypotheses on the problematic definitions and relationships of the subfamilies, with special emphasis on the ‘trifines.’ An initial hypothesis of noctuid classification to the subtribal level was synthesized from recent reviews, and then sampled as broadly as possible. Concatenated sequences for the nuclear genes elongation factor‐1α (EF‐1α; 1200 bp) and dopa decarboxylase (DDC; 700–1100 bp) were analysed for a total of 146 exemplar species, twice that of a previous study. Trees were estimated using likelihood, distance, and both equally weighted and ‘six‐parameter’ parsimony. Of the 144 possible nodes, bootstrap support (BP) was ≥ 50% for ～80, and ≥ 80% for ～60. There was very strong support (BP ≥ 90%) for an ‘L.A.Q.’ clade encompassing nearly all quadrifine noctuids plus Arctiidae and Lymantriidae, decisively rendering Noctuidae paraphyletic. We present a new classification for Noctuoidea in which Noctuidae sensu stricto is restricted to trifines; most quadrifine subfamilies are raised to full families. Within the ‘L.A.Q.’ clade, Aganainae and Herminiinae were strongly grouped, but other relationships were weakly supported, probably due to limited taxon sampling. Nolidae and Euteliinae + Stictopterinae are generally grouped with the ‘L.A.Q.’ clade, but with weak support. All analyses favour the broadest definitions proposed for the trifine clade (our Noctuidae sensu stricto) although support is not strong, except that the exemplar of Eustrotiinae: Eublemmini is placed securely in the ‘L.A.Q.’ clade. Numerous recent proposals for dismantling and recombining the ‘Hampsonian’ traditional trifine subfamilies are strongly supported, most notably a broadly defined ‘true cutworm’ clade (Noctuinae s.l.), encompassing the greater part of the traditional subfamilies Amphipyrinae, Cuculliinae, Hadeninae and Noctuinae s.s. (BP ≥ 95%). Within this clade there is strong support for Apameini s.s.+ Xylenini s.l. and for Noctuinae s.s. and divisions thereof, but little support for monophyly or subdivision of Hadeninae. Noctuinae s.l. invariably are allied with Heliothinae, scattered remnants of the traditional Amphipyrinae, and several smaller groups in a broader ‘pest clade’, albeit with weak support. Relationships among the remaining ‘lower’ trifines are not strongly resolved. Mapping of a preliminary synopsis of species diversities, host use patterns and latitudinal distributions on the phylogeny suggests that the diversification of trifines may have been promoted, to a degree unique among Macrolepidoptera, by the Tertiary expansion of seasonal, open habitats and their associated herbaceous floras.     

A phylogenetic analysis of tribe Areceae (Arecaceae) using two low-copy nuclear genes

 A phylogenetic study of the largest tribe of palms, the Areceae, was conducted using sequences of two low-copy nuclear genes. Previous morphological and plastid DNA studies have not supported the monophyly of the tribe, but have placed its members in a large clade that includes the monophyletic tribes Geonomeae, Cocoeae, Podococceae, and Hyophorbeae. We analyzed this large clade to test the monophyly of tribe Areceae with nuclear data, to explore relationships among its subtribes, and to identify other monophyletic groups. For 54 palm species, including members of all 17 subtribes of tribe Areceae, we sequenced regions of the malate synthase (MS) and phosphoribulokinase (PRK) genes. Simultaneous analysis of these regions revealed 52 shortest trees, all of which resolved tribe Areceae as polyphyletic. Subtribes Iguanurinae, Dypsidinae, Oncospermatinae, and Arecinae were also resolved as polyphyletic. A clade of Indo-Pacific taxa was resolved with strong support, and would be a suitable target for more focused study. Received February 7, 2001; accepted April 9, 2002 Published online: December 3, 2002     

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

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

Sperm morphology of five species of Colostethus (Anura, Dendrobatidae) from Brazil, with phylogenetic comments

We describe the sperm ultrastructure of five species of Colostethus from Brazil. The general structures of the spermatozoa (acrosomal complex and flagellar apparatus) were similar to species within the Bufonoidea. Colostethus brunneus, Colostethus sp. (aff. trilineatus), Colostethus nidicola and Colostethus sp. had biflagellated spermatozoa, whereas the spermatozoa of Colostethus stepheni had a single flagellum, a characteristic previously unknown for this genus. In addition, the spermatozoa of this species showed some mitochondria within the thick, undulating membrane. These characteristics are apparently common to dendrobatid species that have a single flagellum. Based on these findings, we tentatively consider biflagellarity to be an apomorphic condition in the Dendrobatidae. In addition, the results described here do not support the proposed regrouping of the ‘brunneus’ and ‘alagoanus’ groups in a monophyletic ‘trilineatus’ group.     

A timescale and phylogeny for "bandicoots" (Peramelemorphia: Marsupialia) based on sequences for five nuclear genes

Relationships among the living and recently extinct genera of bandicoots (Marsupialia: Peramelemorphia) have proven difficult to discern. Previous phylogenetic studies have used only morphology or mitochondrial DNA and have reported conflicting results in regards to their relationships. Most phylogenetic reconstructions recognize a basal split between the bilby Macrotis (Thylacomyidae) and the Peramelidae. The Peramelidae is composed of the Peramelinae (Isoodon and Perameles), Echymiperinae (Echymipera and Microperoryctes), and Peroryctinae (Peroryctes). Within Peramelidae, Echymipera and Microperoryctes usually group together to the exclusion of Peroryctes. This clade is sister to the Peramelinae. Placement of the recently extinct pig-footed bandicoot (Chaeropus: Chaeropodidae) has been ambiguous. We address the interrelationships and estimate times of divergence for the living bandicoot genera using a 6 kilobase concatenation consisting of protein-coding regions of five nuclear genes (ApoB, BRCA1, IRBP, Rag1, and vWF). We analyzed this concatenation using maximum parsimony, maximum likelihood, and Bayesian methods and estimated times of divergence using two Bayesian relaxed molecular clock methods. In all concatenated analyses, all nodes associated with the Peramelemorphia were robustly supported (bootstrap support percentages=100; posterior probabilities=1.00). Macrotis was recovered as basal to the remaining living bandicoots. Within the Peramelidae, Echymipera and Microperoryctes grouped to the exclusion of Peroryctes and this clade was sister to the Peramelinae. Only Rag1 amplified for Chaeropus; analyses based on this gene provide moderate support for an association of Chaeropus plus Peramelidae to the exclusion of Macrotis. Both relaxed clock Bayesian methods suggest that the living bandicoots are a relatively recent radiation originating sometime in the late Oligocene or early Miocene with subsequent radiations in the late Miocene to early Pliocene.     

Green lacewing phylogeny, based on three nuclear genes (Chrysopidae, Neuroptera)

Abstract.  Systematic relationships among higher taxa within Chrysopidae, a large and agriculturally significant neuropteran family, are poorly understood. A molecular phylogenetic survey of Chrysopidae was performed with three nuclear genes, namely wingless (546 bp), phosphoenolpyruvate carboxykinase (483 bp), and sodium/potassium ATPase alpha subunit (410 bp). We examined 83 species in 24 genera, mainly from Japan, Eurasia and Africa. Parsimony and Bayesian analyses of combined datasets of a total of 1439 bp demonstrated that (1) monophyly of the subfamily Chrysopinae was supported but the relationship between Nothochrysinae and Apochrysinae was unclear, although the two subfamilies together may constitute the sister taxon of Chrysopinae; (2) of the three tribes examined within Chrysopinae (Ankylopterygini, Belonopterygini and Chrysopini), monophyly of Ankylopterygini and Belonopterygini was supported, but the relationships among the three remain unclear; (3) seven sub-clades in Chrysopini were indicated, namely (i) Brinckochrysa , (ii) Chrysemosa  +  Suarius , (iii) Chrysotropia  +  Nineta , (iv) Mallada  +  Chrysoperla  +  Peyerimhoffina , (v) Cunctochrysa  +  Meleoma  +  Nipponochrysa  +  Apertochrysa albolineatoides , (vi) Chrysopa  +  Plesiochrysa , and (vii) Dichochrysa  +  Apertochrysa eurydera ; and (4) most genera were monophyletic, except for Apertochrysa and Cunctochrysa , each of which was shown to have two distinct origins. Our molecular analysis allowed the assignment of several species of uncertain affinities to known genera. There was some disagreement between the molecular and previously published morphological phylogenies, but in general our results confirmed existing morphological hypotheses of evolution within the family.     

Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera

We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A + T composition (79.3%–80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA^Gln and ND2 (64–87 bp), conserved ATACTAA motif between tRNA^{Ser (UCN)} and ND1, and characteristic features of the A + T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA^Asn/tRNA^{Ser (AGN)}, instead of the rearrangement tRNA^{Ser (AGN)}/tRNA^Asn, found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea + Noctuoidea + Geometroidea) + Pyraloidea) + Papilionoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae + (Hesperiidae + (Pieridae + ((Lycaenidae + Riodinidae) + Nymphalidae)))) were strongly supported in all analyses (0.98–1 by BI and 96–100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.     

A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes

Jørgensen, A., Madsen, H., Nalugwa, A., Nyakaana, S., Rollinson, D., Stothard, J. R. & Kristensen, T. K. A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes. —Zoologica Scripta, 40, 126–136. Mutational saturation of inspected DNA loci and topological incongruence in the phylogenetic inferences have previously confounded attempts to resolve the evolutionary relationships within the freshwater snail genus Bulinus. Traditionally, the 37 species of Bulinus are placed within the four species groups and the evolutionary divergence between groups is substantial. With an intention to shed new light on species group relationships, the present study was designed to investigate the basal divergences in the phylogeny of Bulinus using highly conserved nuclear genes. The resolved phylogeny inferred that the four species groups of Bulinus were monophyletic and Shimodaira‐Hasegawa topology tests found them to be significantly supported. The Bulinus truncatus/tropicus species complex and Bulinus wrighti (Bulinus reticulatus group) formed a well‐supported sister‐group relationship. The Bulinus africanus species group was the sister‐group to the clade (Bulinus truncatus/tropicus + B. wrighti) with the Bulinus forskalii species group as the sister‐group to these taxa. The sister‐group relationship between Indoplanorbis and Bulinus was non‐significant and the basal clade support of Bulinus improved upon exclusion of Indoplanorbis. The finding of basal long branches of Bulinus species originating from Madagascar strongly suggests the presence of additional cryptic species and an evolutionary scenario influenced by this island’s geological vicariance from the African mainland. Speciation by polyploidy was inferred to have evolved within a clade in the Bulinus truncatus/tropicus species complex. Although the monophyletic status of each species group was firmly supported, it was difficult to establish species group concepts equally across the variations and place this precisely in a specific temporal framework.     

The phylogeny of the Noctuidae (Lepidoptera)

A new phylogenetic system of the Noctuidae is proposed. The system should, however, be regarded as provisional because it is primarily based on only two character complexes: the male genitalia and the tympanal region. The presence of preabdominal brush-organs and the length of tibial spurs in the adult male, the presence of a ventral cervical gland and the lack of the SV 2 setae on the first abdominal segment of the larvae are considered. The results confirm the monophyly of the Noctuidae. The Herminiinae are considered to represent the sister-group of all other Noctuidae. Remaining noctuid subfamilies are grouped in a series of clades for which the corresponding autapomorphies are given. Some formerly accepted subfamilies, such as the Acontiinae, prove to be polyphyletic. Accordingly, these subfamilies are subdivided into separate lineages. A sister-group relationship between the Noctuidae and the Aganaidae is supported. These two families may be united with the Arctiidae to form a still broader clade.     

Phylogeny of penaeoid shrimps (Decapoda: Penaeoidea) inferred from nuclear protein-coding genes

Penaeoidea is a diverse group of economically important marine shrimps. Attention to the evolutionary history of the penaeoids has been raised since studies using mitochondrial DNA markers and sperm ultrastructure contradict classification of the penaeoid families based on morphology and hence challenge the long standing taxonomy of this superfamily. In this study, DNA sequences of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α-subunit, were determined from 37 penaeoid genera to reconstruct the evolutionary relationships and to estimate divergence ages of the penaeoid shrimps. Phylogenetic analyses using maximum likelihood and Bayesian approaches strongly support the monophyly of Solenoceridae, Aristeidae and Benthesicymidae, but find Sicyoniidae nested within Penaeidae, making this family paraphyletic. Penaeoidea comprises two lineages: the former three families in one while the latter two in another. The diversification of these lineages may be related to bathymetry. The penaeid-like lineage diversified in the Triassic, earlier than the aristeid-like lineage with an origin in the Jurassic. Taxonomic revisions within Penaeoidea are also proposed for further investigation. Due to the paraphyly of Penaeidae and the high genetic divergence among the three penaeid tribes of Burkenroad [Burkenroad, M.D., 1983. Natural classification of Dendrobranchiata, with a key to recent genera. In: Schram, F.R. (Ed.), Crustacean Issues I. Crustacean Phylogeny. A.A. Balkema, Rotterdam, pp. 279–290], these tribes should be treated as having the same taxonomic rank as Sicyoniidae, while the family ranking of Benthesicymidae has to be re-considered owing to the low genetic divergence between the benthesicymids and the aristeids.     

Remarks on the family-level phylogeny of butterflies (Insecta, Lepidoptera, Rhopalocera)

1. Available evidence on butterfly family-level relationships is re-examined according to the principles of phylogenetic (cladistic) systematics. 2. The assumption of a sister-group relationship between the Hesperioidea and Papilionoidea seems a reasonably substantiated working hypothesis. 3. The Papilionoid families Papilionidae, Pieridae and Lycaenidae sensu Ehrlich (1958) are definable as monophyletic entities; of Ehrlich 's two remaining families, Nymphalidae and Libytheidae, the former is paraphyletic in terms of the latter. 4. The interrelationships between the Papilionoid families may be presented as Papilionidae + (Pieridae + [Lycanidae + Nymphalidae]). 5. In a phylogenetic system any given arrangement of taxa is either correct or not: Contrary to the pheneticists' view (Ehrlich and Ehrlich 1967) phylogenetic systematists cannot accept the existence of a multitude of valid classifications.     

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.     

Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia

The phylogeny of Decapoda is contentious and many hypotheses have been proposed based on morphological cladistic analyses. Recent molecular studies, however, yielded contrasting results despite their use of similar data (nuclear and mitochondrial rDNA). Here we present the first application of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, to reconstruct the phylogeny of major infraorders within Decapoda. A total of 64 species representing all infraorders of Pleocyemata were analyzed with five species from Dendrobranchiata as outgroups. Maximum likelihood and Bayesian inference reveal that the Reptantia and all but one infraorder are monophyletic. Thalassinidea, however, is polyphyletic. The nodal support for most of the infraordinal and inter-familial relationships is high. Stenopodidea and Caridea form a clade sister to Reptantia, which comprises two major clades. The first clade, consisting of Astacidea, Achelata, Polychelida and three thalassinidean families (Axiidae, Calocarididae and Eiconaxiidae), corresponds essentially to the old taxon suborder Macrura Reptantia. Polychelida nests within Macrura Reptantia instead of being the most basal reptant as suggested in previous studies. The high level of morphological and genetic divergence of Polychelida from Achelata and Astacidea justifies its infraorder status. The second major reptant clade consists of Anomura, Brachyura and two thalassindean families (Thalassinidae and Upogebiidae). Anomura and Brachyura form Meiura, with moderate support. Notably thalassinidean families are sister to both major reptant clades, suggesting that the stem lineage reptants were thalassinidean-like. Moreover, some families (e.g. Nephropidae, Diogenidae, Paguridae) are paraphyletic, warranting further studies to evaluate their status. The present study ably demonstrates the utility of nuclear protein-coding genes in phylogenetic inference in decapods. The topologies obtained are robust and the two molecular markers are informative across a wide range of taxonomic levels. We propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics.     

A molecular phylogeny of the hawkmoth genus Hyles (Lepidoptera: Sphingidae, Macroglossinae)

The hawkmoth genus Hyles is one of 15 genera in the subtribe Choerocampina of the subfamily Macroglossinae. Due to a remarkable uniformity, morphological characters usually used to identify and classify Lepidoptera at the species level cannot be used in this genus. Instead, we used DNA sequences comprising about 2300 bp derived from the mitochondrial genes COX I, COX II, and tRNA-leucine to elucidate the phylogeny of Hyles. The results corroborate the monophyly of Hyles but conflict with previous internal classifications of the genus based on morphology. Hyles seems to have evolved in the Neotropics during the Oligocene/Eocene epochs and the molecular data (which evolved clock-like) confirm the hypothesis that it is a very young genus that radiated on a global scale rather quickly. We hypothesize its sister group to be one of the genera Deilephila, Theretra or Xylophanes. The Nearctic may have been colonized rapidly by Hyles once the land bridge formed during the Pliocene, since within this same Epoch, the invasion of the Palaearctic appears to have proceeded from the East, via the Bering route. The colonization of Australia appears to have occurred rather early in Hyles radiation, although the route is not clear. We propose that the radiation of the Hyles euphorbiae-complex s. str. (HEC) occurred as recently as the Pliocene/Pleistocene boundary and that its roots can still be reconstructed in Asia. Hyles dahlii is closely related to the HEC, but a sister group relationship to the HEC s. str. cannot be corroborated unequivocally. HEC population ranges appear to have tracked climate oscillations during the Pleistocene Ice Ages, resulting in hybridization around the Mediterranean Sea as they repeatedly intermingled. Comparison of the phylogeny with food plant affiliations leads us to hypothesize that Euphorbia monophagy evolved at least two times independently within Hyles.