Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data

A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria . Aragoa is sister to genus Plantago . Plantago subgenus Littorella is sister to the other subgenera of Plantago . The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans . Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni , endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 323–338.     

Phylogeny of the Afro-Madagascan Aristea (Iridaceae) revisited in the light of new data on pollen morphology

Scanning and electron microscopic studies of the pollen grains of several species of the sub-Saharan African and Madagascan genus Aristea of c . 50 species, supplement data from an earlier study and enable us to include these species in a phylogenetic analysis. TEM examination of a range of pollen grains of representative pollen types in Aristea makes it possible to reinterpret past SEM results so that apertures covered with exine masses and previously called sulculate, are now seen to be either zonasulculate or dizonasulculate. Revised and expanded data are combined in a matrix together with new data for seed morphology in the genus, which like the capsules is remarkably diverse, including angular seeds with reticulate sculpturing, lamellate or triangular-columnar seeds with smooth or reticulate surfaces and with smooth or papillate or areolate margins. This new phylogenetic analysis suggests that Aristea should remain treated as comprising three subgenera. In subgenus Eucapsulares we add a new section Latifolieae for A. latifolia , which seems an isolated relic restricted to the mountains of the Cape Region of South Africa, an area of winter rainfall. Species with similar unspecialized capsule and seed morphology occur only in eastern south and tropical Africa and Madagascar, but they have derived pollen morphology whereas the pollen of A. latifolia is plesiomorphic. This species appears to be the closest living ancestor of the genus. In subgenus Aristea we continue to recognize three sections, sect. Racemosae , sect. Singulares and sect. Aristea. Nesting of subgenus Pseudaristea within section Racemosae of subgenus Aristea is probably an artefact of the analysis and does not receive bootstrap support, and hence we continue to recognize this group of species at subgeneric rank.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 41–68.     

Pollen morphology and phylogenetic relationships in neotropical Phyllanthus (Euphorbiaceae)

In order to provide new insights into phylogenetic relationships among the neotropical taxa of Phyllanthus , 28 illustrations are provided of the pollen grains of 22 selected species studied from 11 sections of the subgenera represented in the neotropics. Special attention has been given to subgenus Conami because of its variability in pollen morphology: of eight species illustrated, the apertures are diploporate colpi in three species and pores in five species; exine ornamentation is vermiculate in two species and pilate in the other six species. The six species in the neotropical sections Pityrocladus and Microglochidion (subgenus Emblica ) are characterized by prolate grains with an increased number of colpi (4–8). Of particular interest are species in which the pollen exine is clypeate (with exine shields); clypeate pollen grains are illustrated in two species of subgenus Xylophylla and in one species of section Cyclanthera that has unique exine shields with single central pila. The pollen of the one Brazilian phylloclade-bearing species illustrated (in section Choretropsis ) has 3-colporate grains with reticulate exine, typical for subgenus Phyllanthus , and very different from the clypeate grains of the West Indian phylloclade-bearing species in section Xylophylla . This pollen evidence clearly demonstrates homoplasy in the origin of phylloclades in Phyllanthus . Pollen morphological data suggest that the neotropical taxa of Phyllanthus have arisen following colonization from Africa (subgenus Kirganelia ) and Asia (subgenus Emblica ). © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 325–338.     

Patterns of morphological evolution in Marmota (Rodentia, Sciuridae): geometric morphometrics of the cranium in the context of marmot phylogeny, ecology and conservation

Marmots are of great interest for both sociobiologists studying the evolution of mammal societies and conservationists trying to protect them from extinction. In contrast, their phylogeny and morphological evolution are poorly understood and studied. Recently, a phylogenetic analysis using cytochrome b provided the first reconstruction of marmot evolutionary history and suggested that a high level of sociality evolved at least twice independently in the two proposed marmot subgenera. A morphological analysis of the marmot mandible supported this subgeneric classification and showed interesting, and unexpected, patterns in the evolution of marmot skeletal characters. In the present study we investigated a more complex, and potentially informative structure, the ventral cranium. Geometric morphometric techniques were applied in the first analysis of cranial morphology including all marmot species. Three main phenetic groups were found, which reflect phylogeny (subgenus Petromarmota , and Palaearctic subgenus Marmota ) or geographical distribution (Palaearctic vs. Nearctic subgenus Marmota ). Convergence in skeletal characters due to size similarities, a common finding in the sciurid skeleton according to traditional morphological analyses, did not occur in the marmot ventral cranium. Despite a genetic distance between Marmota vancouverensis and Marmota caligata similar to that among different populations of the latter species, the Vancouver Island marmot had the most atypical ventral cranium in the subgenus Petromarmota . This finding confirmed results obtained with the mandible, and emphasized the uniqueness of M. vancouverensis and the usefulness of complementing molecular analyses with morphological studies for a thorough characterization of population divergence, and a careful planning of conservation strategies.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 385–407     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

Two new species from Gabon show the need to reduce Commitheca to the synonymy of Pauridiantha (Rubiaceae, Pauridiantheae)

Two new Pauridiantha species (Pauridiantheae, Rubiaceae) from Gabon are described and illustrated. Pauridiantha pleiantha is characterized by a combination of entirely glabrous stems, stipules with a narrow base, and large inflorescences. Pauridiantha smetsiana is characterized by entirely glabrous stems, narrow, early deciduous stipules, leaves red-tinged when dry, and small inflorescences. The two new species, especially P. smetsiana , close the morphological gap between Commitheca and Pauridiantha in combining typical Commitheca characters, such as glabrous stems and a narrow stipular base, with Pauridiantha characters, such as eucamptodromous venation. A detailed morphological comparison (including ovary structure, seed morphology, exotesta anatomy, and pollen morphology) between the two genera is given; in conclusion, Commitheca is relegated to the synonymy of Pauridiantha . The necessary new specific combinations are provided.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 105–117.     

Lobule shape evolution in Radula (Jungermanniopsida): one rate fits all?

The quantification of lobule shape for Radula spp. shows that there is overlap in lobule shape space occupied by subgenera, such that lobule shape does not always reflect relationships. Morphological convergence caused by lineages repeatedly traversing shared regions of morphospace appears commonplace in Radula, and means that many pairs of relatively unrelated species have similar lobule shapes. When observed over time, as in comparisons between fossil and extant species, this may give the impression of stasis if fossil species resemble modern species by chance, independent of their relatedness. This poses a challenge to relating fossils of known age to extant lineages, particularly when fossils are sterile. Significant rate variation between lineages was identified by Adams' Q‐mode analysis, with the fastest subgenus evolving 23 times more quickly than the slowest. Species of subgenus Volutoradula and subgenus Metaradula are apparently over‐dispersed throughout lobule morphospace according to Sidlauskas' method; morphometric branch lengths and hypervolumes in other subgenera can be explained by a stochastic process. In contrast, Bayesian analysis of macroevolutionary mixtures (BAMM) identified a single evolutionary rate as having the highest posterior probability. Consideration of the three independent accessions into auriculate lobule morphospace by Cladoradula and Radula, wherein convergent lobule shapes result from convergent lobule ontogenies and are correlated with bipinnately branched shoot systems and robust primary stems, leads to an ontogenetic hypothesis driven by structural requirements for light interception, under which auriculate lobules are a spandrel. It is speculated that lobules themselves, however, may be a key innovation facilitating radiation into microsites devoid of or depauperate in fungal endophytes. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 222–242.     

Microsporogenesis, microgametogenesis and pollen morphology of Passiflora spp. (Passifloraceae)

Microsporogenesis, microgametogenesis and pollen morphology of six species of genus Passiflora L. belonging to three subgenera ( Passiflora , Dysosmia , Decaloba ) were studied with light and scanning microscopy; P. caerulea was also examined with transmission microscopy. The tapetum is secretory, microspore tetrads are tetrahedral and pollen grains are two-celled when shed. Small Ubisch bodies are attached to a peritapetal membrane; they are a product of tapetal activity and the rough endoplasmic reticulum (ERr) appears to be involved in their origin. The pollen grains of all the species are subspheroidal, zonocolpate, geminicolpate. Each pair of colpi anastomoses at the poles. The exine is semitectate, reticulate, heterobrochate. The muri are simplibaculate, wavy. The lumina have clavate bacula of varying height. The colpus structure is similar to that of the lumina but generally with fewer and smaller bacula. Lumina size and amount of bacula inside the lumina vary between subgenera. The grains from subgenera Passiflora and Dysosmia differ from those of Decaloba in their size and number of colpi. The pollen and microsporangium morphology of the species of subgenera Passiflora and Dysosmia are more similar than those of subgenus Decaloba . The results are discussed in relation to the current taxonomic classification.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society of London , 2002, 139 , 383–394.     

Chromosome counts in Asian Artemisia L. (Asteraceae) species: from diploids to the first report of the highest polyploid in the genus

This work comprises 24 reports of chromosome numbers in 24 Artemisia L. species from Asia. Ten are included in the subgenus Dracunculus Besser and the rest belong to other subgenera. Seven counts are new reports, 14 are consistent with scarce previous ones, and three contribute new ploidy levels. That carried out in A. medioxima reports the highest ploidy level ever counted for the genus (16 x ). There is only one species with x  = 8 as the basic chromosome number. In the remaining x  = 9-based species, ploidy levels range from 2 x to 16 x , illustrating the great role played by polyploidy in the evolution of the genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 301–310.     

Morphological phylogenetics of Puya subgenus Puya (Bromeliaceae)

Puya , a large genus mostly from South America, has been taxonomically divided into two subgenera: Puyopsis and Puya. The latter includes only eight species distributed mainly in Chile, extending to Argentina, Bolivia, and Peru. The species of subgenus Puya are recognized by the presence of a sterile apex of the inflorescence branches, whereas those of subgenus Puyopsis have fertile flowers all along the branches. The objectives of this article were to determine whether this diagnostic character was synapomorphic for subgenus Puya , and to explore the relationships between its species. Parsimony analyses were performed for 43 taxa and 93 morphological characters, 87 of which were discrete and six continuous. In the analysis that included all characters, a single most parsimonious tree was found that supported subgenus Puya by two synapomorphic character states, including the diagnostic character of a sterile inflorescence branch apex and a blooming pattern in which flowers open gradually from base to apex. The trees were better supported when the continuous characters were included. Further studies are suggested to resolve the infrageneric classification of Puya and the relationships of the species belonging to subgenus Puya .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 93–110.     

A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887

The systematic biology of the subgenus Daphnia s . s . remains confused. Prior attempts at resolution used chiefly postabdominal claw morphology, chromosome numbers and rRNA gene sequences as characters for higher-level relations. Still, several taxa, such as Daphnia curvirostris Eylmann, 1878, have unclear affiliations. We addressed the position of D. curvirostris in this genus by estimating phylogenetic trees from a rapidly evolving protein coding gene (ND2), conducting broad geographical comparisons and carrying out detailed morphological comparisons. The Japanese ' curvirostris' was found to be a new divergent lineage in the subgenus Daphnia , and to possess distinctive morphological characteristics from D. curvirostris . We described this new species as Daphnia tanakai sp. nov. , and redescribed D. curvirostris . The polymorphic postabdominal claw morphology and the distinctive chromosome number of D. tanakai sp. nov. provided evidence for rapid evolution of these traits. Our new morphological, chromosomal and genetic assessment of Daphnia weakened the argument for division of the subgenus Daphnia ( Daphnia ) O. F. Müller, 1785 sensu Johnson, 1952, into two further subgenera.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 385–405.     

Molecular phylogeny of the subgenus Holothuria (Selenkothuria) Deichmann, 1958 (Holothuroidea: Aspidochirotida)

The subgenus Selenkothuria comprises 12 species of tropical shallow water sea cucumbers that share morphological features, such as rods in the body wall and tube feet, modified tentacles for suspension feeding, and cryptic colours. The taxonomic status of this taxon has been controversial, but currently it is accepted as a subgenus of the genus Holothuria. Phylogenetic analyses of mitochondrial genes [cytochrome c oxidase subunit 1 (COI), 16S RNA] of ten species of Selenkothuria and related subgenera showed the polyphyly of this subgenus; monophyly was rejected by a likelihood ratio test. A geographical split divides the species of this subgenus into three different groups: one Indo‐West‐Pacific (IWP) group and two American groups. The IWP group is more closely related to Holothuria (Semperothuria) cinerascens and to other subgenera such as Roweothuria, Holothuria, and Vaneyothuria, whereas the two American groups are more closely related to each other and to some species of the subgenus Halodeima. These results suggest multiple parallel originations and diversification of ossicle morphology within the subgenus Selenkothuria. The current scheme of subgenera for the genus Holothuria is not supported, suggesting the need for a new classification. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 109–120.     

Is genome downsizing associated with diversification in polyploid lineages of Veronica?

The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL‐trnL‐trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C‐values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C‐value, whereas ploidy and chromosome number are strongly correlated with both 1C‐ and 1Cx‐values. The estimated ancestral Veronica 1Cx‐value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 243–266.     

Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae)

The genome size of 51 populations of 20 species of the North American endemic sagebrushes (subgenus Tridentatae ), related species, and some hybrid taxa were assessed by flow cytometry, and were analysed in a phylogenetic framework. Results were similar for most Tridentatae species, with the exception of three taxonomically conflictive species:  Artemisia bigelovii Gray,  Artemisia pygmaea Gray, and  Artemisia rigida Gray. Genome size homogeneity (together with the high morphological, chemical, and karyological affinities, as well as low DNA sequence divergence) could support a recent diversification process in this geographically restricted group, thought to be built upon a reticulate evolutionary framework. The Tridentatae and the other North American endemic Artemisia show a significantly higher genome size compared with the other subgenera. Our comparative analyses including genome size results, together with different kinds of ecological and morphological traits, suggest an evolutionary change in lifestyle strategy linked to genome expansion, in which junk or selfish DNA accumulation might be involved. Conversely, weed or invasive behaviour in Artemisia is coupled with lower genome sizes. Data for both homoploid and polyploid hybrids were also assessed. Genome sizes are close to the expected mean of parental species for homoploid hybrids, but are lower than expected in the allopolyploids, a phenomenon previously documented to be related with polyploidy.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 631–649.     

Karyomorphology of Incarvillea (Bignoniaceae) and its implications in distribution and taxonomy

The karyomorphology of 11 species of the genus Incarvillea Juss. is reported. The chromosome numbers of all species studied are 2 n  = 22. The interphase nuclei and prophase chromosomes were found to be of the simple chromocentre type and the interstitial type, respectively. The asymmetry of the karyotype of I. arguta (two populations) in subgenus Amphicome is type 2A. The karyotypes of Incarvillea s inensis var. sinensis , I.  s inensis var. przewalskii, and I. olgae in subgenus Incarvillea are of asymmetry type 3A. The remaining nine species and one variety in subgenus Pteroscleris are also of asymmetry 3A. Data on three species and one variety studied are first reports. This study indicates that karyotype variation at the diploid level appears to be the predominant feature of chromosome evolution in the genus Incarvillea . According to this study of karyomorphology, morphological characteristics and geographical distribution, it seems that the three subgenera should be regarded as three independent genera. The geography of the genus is discussed.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 113–121.