Phylogenetics and evolution of phyllotaxy in the Solomon's seal genus Polygonatum (Asparagaceae: Polygonateae)

Polygonatum is the largest and most complex genus in tribe Polygonateae, comprising approximately 57 species widely distributed in the warm temperate, subtropical and boreal zones of the Northern Hemisphere. However, phylogenetic relationships in the genus remain poorly understood. The objectives of this study were to reconstruct the phylogenetic relationships of the genus using four plastid markers, and to examine the evolution of leaf arrangement in Polygonatum in the phylogenetic context of its closely related taxa. Thirty Polygonatum species were sampled to infer phylogenetic relationships using maximum‐likelihood and Bayesian analyses. The evolution of leaf arrangements was reconstructed using Bayesian, parsimony and likelihood methods. The phylogenetic analyses supported the current generic delimitation of Polygonatum, with Heteropolygonatum recognized as a distinct genus. Three major lineages in Polygonatum were well supported, largely correlated with geographical distribution and the most recent classification at the sectional level. However, our results did not support the currently recognized series, especially the two large series Verticillata and Alternifolia. Bayesian analyses support the alternate‐leaf arrangement as the ancestral state for Polygonatum, but parsimony and maximum‐likelihood analyses suggest an equivocal state for crown Polygonatum. Leaf arrangement was found to be evolutionarily labile. A new nomenclatural combination was made: P olygonatum section S ibirica (L.I.Abramova) Y.Meng, comb. nov. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 435–451.     

Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.     

Taxonomy and biogeography of Diapensia (Diapensiaceae) based on chloroplast genome data

Diapensia L. is the second largest genus of Diapensiaceae. The taxonomic treatment within Diapensia and relationships within Diapensiaceae have been disputed. Chloroplast genome sequence data have proved to be useful for plant phylogenetic analyses and species delimitation. In this study, we de novo sequenced and assembled 22 chloroplast genomes of 15 species of Diapensiaceae, including all recognized species of Diapensia with multiple samples. A super‐matrix containing a total of 107 genes and 18 taxa was constructed for phylogenetic analyses to resolve phylogenetic relationships among genera of the family and within Diapensia. The resulting phylogenetic tree showed the following strongly supported relationships: (Galax, (Pyxidanthera, (Berneuxia, ((Schizocodon, Diapensia), and Shortia s.s.)))). The dated phylogeny and reconstructed lineage‐through‐time plot for the family indicated rapid diversification in the Neogene and an acceleration of diversification rate after c. 8 Ma. Biogeographic analysis suggested that Diapensia originated in the Northeast Asian mountains approximately 6.06 Ma, followed by northward dispersal to the Arctic and southwestward dispersal to the Himalaya–Hengduan Mountains. Phylogenetic relationships within Diapensia were well resolved. Based on the phylogenetic results, we proposed to reinstate the species status of Diapensia bulleyana Forrest ex Diels, and raised D. purpurea f. albida to the species rank (D. albida [W. E. Evans] J. F. Ye comb. & stat. nov.). The distribution ranges of all species delineated based on the phylogenetic results were revised accordingly based on specimen occurrences. Our study adds new examples for the power of plastid genome data for resolving phylogenetic relationships and clarifying taxonomic disputes among closely related species.     

Reclustering the cluster flies (Diptera: Oestroidea,Polleniidae)

A phylogenetic analysis of selected oestroid taxa based on 66 morphological traits and sequences from three nuclear protein‐coding genes (CAD, MAC, MCS) resolved the composition and phylogenetic position of the former subfamily Polleniinae of the Calliphoridae – here resurrected at family rank as Polleniidae Brauer & Bergenstamm, 1889 stat. rev. Six species are transferred from the family Rhinophoridae to the Polleniidae: the Palaearctic genus Alvamaja Rognes, along with its single species Alvamaja chlorometallica Rognes, and five Afrotropical species comprising the carinata‐group formerly in the genus Phyto Robineau‐Desvoidy but here assigned to genus Morinia Robineau‐Desvoidy, i.e. M. carinata (Pape, 1987) comb.n. , M. lactineala (Pape, 1997) comb.n. , M. longirostris (Crosskey, 1977) comb.n. , M. royi (Pape, 1997) comb.n. and M. stuckenbergi (Crosskey, 1977) comb.n. The Polleniidae are monophyletic and, in agreement with most recent phylogenetic reconstructions, sister to the Tachinidae. The female of A. chlorometallica and a new species of Morinia of the carinata‐group (Morinia tsitsikamma sp.n. from South Africa) are described. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:25B0C220‐DEE4‐4B0C‐88EA‐35FDE298EBC5 .     

Higher‐level molecular phylogeny of jumping plant lice (Hemiptera: Sternorrhyncha: Psylloidea)

Jumping plant lice (Hemiptera: Psylloidea) are known for a few deleterious pest species worldwide, yet the phylogeny of the group has been poorly understood until very recently. Here, we reconstruct the higher‐level phylogeny for the superfamily Psylloidea based on multilocus DNA sequences, three mitochondrial (COI‐tRNA^leu‐COII, 12S, 16S) and five nuclear (18S, 28S D2, 28S D3, 28S D6–7a, 28S D9–10) gene fragments, using maximum likelihood and Bayesian inference phylogenetic frameworks. Our results are largely congruent with the recent phylogenomic study and partly support prior classification of Psylloidea based mainly on morphology, with the following major exceptions: the family Calophyidae is revealed as polyphyletic, Aphalaridae as paraphyletic with respect to most other taxa of Psylloidea, and Liviidae as paraphyletic with respect to Calophyinae, Psyllidae and Triozidae. Our phylogenetic hypothesis identifies Phacopteronidae and the genus Cecidopsylla Kieffer as the very basal taxa within extant Psylloidea. Sister‐group relationships of Rhinocolinae with Togepsyllinae and of Pachypsyllinae with Homotomidae are also suggested. We present specific discussions for each group of interest recovered in our phylogenetic analysis. One nomenclatorial change is proposed: Spanioneura longicauda (Konovalova) comb.n. , from Psylla Geoffroy.     

The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Taxonomic revision of the dolphin genus Lagenorhynchus

Evolutionary relationships among cetaceans within the family Delphinidae have been difficult to resolve due to the high number of species and their relatively rapid radiation. This is the case for the dolphin species currently placed in the genus Lagenorhynchus, and their relations to Cephalorhynchus and Lissodelphis species. Phylogenetic relationships among these species have been investigated using multiple lines of evidence, and that evidence consistently suggests that the six species currently assigned to Lagenorhynchus do not form a monophyletic group. Here, we summarize findings from studies of morphology, genetics, historical biogeography, and acoustics that offer insight into the phylogenetics of these taxa. We present the taxonomic basis for revision of Lagenorhynchus, propose retention of Lagenorhynchus albirostris and reassignment of the remaining five species into other existing generic names, namely Leucopleurus acutus, Sagmatias australis, Sagmatias cruciger, Sagmatias obliquidens, and Sagmatias obscurus. Making these revisions now so that the taxonomy better reflects evolutionary relationships among these species will ensure that future studies include the most appropriate taxa for investigating the complex phylogenetic and systematic relationships among cetaceans. However, comprehensive analyses using multiple lines of evidence are still needed to clarify the phylogenetic relationships within and among the Lissodelphininae genera Cephalorhynchus, Lissodelphis, and Sagmatias.     

Phylogeny and taxonomy of the genus Phylloporia (Hymenochaetales)

Based on 28 taxa, including six species of Phylloporia, and respectively one representative of 17 genera of the Hymenochaetales, a phylogenetic analysis of a region of the large subunit of the nuclear encoded ribosomal DNA was performed. Molecular sequence data as well as morphological and anatomical features show the genus to be monophyletic. Next related to Phylloporia is Fulvifomes. The phylogenetic relationships of Phylloporia are discussed. In addition the genus Phylloporia is monographed; 12 species are accepted and described with a key.     

Past and present diversity and distribution in the parasitic wasp family Megalyridae (Hymenoptera)

The phylogenetic relationships of extant and extinct Megalyridae are analysed at the genus level. The dataset comprises seven outgroup taxa, all eight extant genera and a number of extinct taxa that have been associated with Megalyridae, including two genera from Maimetshidae, whose affinity with Megalyridae is uncertain. Analytical results are unstable because some of the fossil taxa have many missing entries. The most stable results are produced when the maimetshid taxa and Cretodinapsis are excluded. When included, these taxa fall outside crown‐group Megalyridae, the maimetshid taxa being the sister of Orthogonalys (Trigonalidae). Based on the results of our analyses, we synonymize the fossil genera Rubes Perrichot n.syn . and Ukrainosa Perrichot & Perkovsky n.syn . with Prodinapsis, creating the new combinations Prodinapsis bruesi n.comb . and Prodinapsis prolata n.comb . When comparing past and present distributions of Megalyridae with the results of the phylogenetic analyses, it is evident that the genera radiated in the Mesozoic, and that the family as a whole was much more widespread then. The present‐day distribution is essentially relictual, with range contraction since the early Tertiary probably being the result of climate deterioration, which caused the disappearance of tropical forests throughout the Palaearctic.     

Section-level relationships of North American <Emphasis Type="Italic">Agalinis</Emphasis> (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions

Background  

The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (= Gerardia), and between Agalinis and closely related genera within Orobanchaceae.     

Brief communication: Ectocranial suture closure in Pongo: Pattern and phylogeny

Ectocranial suture fusion patterns have been shown to contain biological and phylogenetic information. Previously the patterns of Homo, Pan, and Gorilla have been described. These data reflect the phylogenetic relationships among these species. In this study, we applied similar methodology to Pongo to determine the suture synostosis progression of this genus, and to allow comparison to previously reported data on other large‐bodied hominoids. We hypothesized these data would strengthen the argument that suture synostosis patterns reflect the phylogeny of primate taxa. Results indicate that the synostosis of vault sutures in Pongo is similar to that reported for Gorilla (excluding Pan and Homo). However, the lateral‐anterior pattern of fusion, in which there is a strong superior to inferior pattern, for Pongo is unique among these species, reflecting its phylogenetic distinctness among great ape taxa. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

A genome-wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics

The genus Liriomyza Mik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships among Liriomyza species have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genus Liriomyza using various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target-capture-based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well-supported in our best estimates of the molecular phylogeny. Liriomyza violivora (Spencer) is a sister group to all remaining sampled Liriomyza species, and the well-known polyphagous vegetable pests [L. huidobrensis (Blanchard), L. langei Frick, L. bryoniae. (Kaltenbach), L. trifolii (Burgess), L. sativae Blanchard, and L. brassicae (Riley)]. belong to multiple clades that are not particularly closely related on the trees. Often, closely related Liriomyza species feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes between Liriomyza species and their host plants drive diversification in this genus. Instead, Liriomyza exhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate for Liriomyza species provides considerable new information on the evolution of host-use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies.     

Molecular systematics of small-eared shrews (Soricomorpha,Mammalia) within Cryptotis mexicanus species group from Mesoamérica

Cryptotis mexicanus species group is the most diverse group of Cryptotis shrews in the Mesoamerican highlands (ca.13 species). In México, eight endemic species occurs and several taxa are endangered. The species’ limits and phylogenetic relationships of these taxa have been recently examined using morphology; nevertheless, little is known about phylogenetic relationships among Cryptotis species at the molecular level. Therefore, our research included a mitochondrial DNA marker as a source of additional information to corroborate taxonomic identification and produce a phylogenetic hypothesis of the C. mexicanus species group. We were particularly interested in the status of Cryptotis magnus, a species considered as relict on the basis of primitive characters. Based on the analyses of genetic sequences of a high number of Cryptotis species, outgroups, and phylogenetic analyses of parsimony and Bayesian inference, we confirmed that Cryptotis genus consists of different lineages that represent species groups. A detailed analysis suggests that C. magnus is a species that shares an evolutionary history with the C. mexicanus species group because it is imbedded within this group. In particular, our data strongly support that C. magnus and Cryptotis phillipsii are sister groups, a pair of species that inhabit allopatrically Southern México.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Finding arboreal snakes in an evolutionary tree: phylogenetic placement and systematic revision of the Neotropical birdsnakes

The genus Pseustes Fitzinger, 1843 is composed of three recognized species, Pseustes poecilonotus, P. shropshirei and P. sulphureus, which may be the largest sized colubrid snake in the New World. The group has a complex systematic history that has yet to be untangled using modern molecular phylogenetic approaches. The systematic position, within‐group diversity and distribution are therefore uncertain. We obtained samples of four species from multiple specimens across their distribution and analysed one nuclear and two mitochondrial genes to determine the phylogenetic placement of the genus and infer relationships among Pseustes lineages. We find strong support for the paraphyly of Pseustes with respect to the monotypic genus Spilotes, both of which are nested within a clade of at least 23 other New World Colubrinae genera. Based on our results, we formally revise the taxonomy of P. poecilonotus and P. sulphureus, resurrecting the taxon P. polylepis for populations of P. poecilonotus from South America and allocating P. sulphureus to the genus Spilotes which renders both genera monophyletic. Additionally, we identify two lineages that are putatively new and currently unrecognized species. Finally, the placement of P. sulphureus, the type species of Pseustes, in the genus Spilotes, requires the allocation of the senior synonym Phrynonax be considered for the remaining Pseustes taxa.     

Strong correlation between cross-amplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci

The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species.     

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well‐supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time‐frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.