Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.     

基于5个基因片段的野胡麻属系统位置研究

对单种属野胡麻属(原隶属于广义玄参科)及其可能近缘类群广泛取样,选择合适外类群,通过对4个叶绿体基因联合数据(trnL-F、rps16、rbcL、rps2)、核基因ITS片段、叶绿体基因与核基因ITS片段联合数据,进行最大简约法和贝叶斯法分析,探讨野胡麻属在科级系统位置及其与近缘类群系统发育关系。结果表明,所有系统树都支持野胡麻属先和肉果草属构成姐妹群关系,叶绿体基因联合系统树支持率分别为97%[Bootstrap(BS)]和100%[Posterior probability(PP)];ITS系统树支持率分别为99%(BS)和100%(PP);叶绿体基因和ITS联合系统树支持率均为100%(BS和PP)。野胡麻属、肉果草属与通泉草属一起构成一单系群,叶绿体基因联合系统树、ITS系统树、叶绿体基因和ITS联合系统树的支持率均为100%(BS和PP)。形态学证据也支持野胡麻属、肉果草属和通泉草属这3个属的近缘关系。本研究结果支持单种属野胡麻属隶属于透骨草科的通泉草亚科,与肉果草属亲缘关系最近,这两个属进而与通泉草属近缘,可能隶属于通泉草属内,与岩白翠亲缘关系较近,也可能与通泉草属互为姐妹群关系。     

In vitro study on the effect of cytokines and auxins addition to growth medium on the micropropagation and rooting of Paulownia species (Paulownia hybrid and Paulownia tomentosa)

This study represents an efficient preliminary protocol for in vitro mass production of two Paulownia species (Paulownia hybrid and Paulownia tomentosa) seedlings by using seed explant. Different concentrations of benzyladenine (BA) or Kinetin (Kin) (0.0, 2.0, 4.0, 6.0, 8.0 and 10.0 mg/L) were tested during multiplication stage. The number of shoots/explants was significantly increased with increasing either BA or Kin concentration; however, the shoot length significantly decreased. Data show that media fortified by BA (10 mg/L) combined with indole butyric acid (IBA) at 1.0 or 1.5 mg/L recorded the highest number of shoots/explant (9.13 and 9.25, respectively). After six weeks during the multiplication stage, data cleared that media fortified by benzyladenine (10 mg/L) combined with IBA at 0.5 mg/L recorded the highest shoot length (3.23 cm). The inclusion of indole butyric acid (IBA) or naphthalene acetic acid (NAA) at 1.0–1.5 mg/L to the medium significantly increased the number of roots/plantlets and the highest root length. The results indicated that IBA supplementation was more effective than NAA for in vitro rooting of both Paulownia species. The best treatment for multiplication was 10 mg/L and 8.0–10 mg/L BA for P. hybrid and P. tomentosa, respectively. Peat moss and sand (1:1, v/v) or peat moss and sand (1:2, v/v) were investigated as soil mixture during the adaptation stage. The results referred that Paulownia species plantlets were successfully survived (100 %) in soil mixture contained peat moss: sand (1:2, v/v). This mixture recorded the highest values of plantlet height and number of leaves/plantlets.     

Comparative analysis of microRNAs and putative target genes in hybrid clone <Emphasis Type="Italic">Paulownia</Emphasis> ‘yuza 1’ under drought stress

Drought stress in plants often leads to reduced productivity and limited geographic distribution, which can affect human life and ecosystems. The responses of diploid and tetraploid Paulownia tomentosa × Paulownia fortunei to drought have been reported, but the effects of drought stress on the levels of microRNA (miRNA) expression have not been published so far. Here, we constructed four small RNA (sRNA) libraries and four corresponding degradome libraries of well-watered and severe drought-treated diploid and tetraploid plants to identify the miRNAs and their putative target genes in Paulownia ‘yuza 1’, a P. tomentosa × P. fortunei hybrid clone, by sRNA and degradome sequencing. The putative target genes of miRNAs were annotated with gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. Three conserved and 21 novel miRNAs responsive to drought stress were found, in which 15 were identified as the main drought responsive miRNAs that conferred higher resistance in tetraploid than in diploid of Paulownia ‘yuza 1’. Our results will lay the foundation for investigating the roles of miRNAs in Paulownia and other trees in response to drought.     

In vitro study on the effect of cytokines and auxins addition to growth medium on the micropropagation and rooting of Paulownia species (Paulownia hybrid and Paulownia tomentosa)

This study represents an efficient preliminary protocol for in vitro mass production of two Paulownia species (Paulownia hybrid and Paulownia tomentosa) seedlings by using seed explant. Different concentrations of benzyladenine (BA) or Kinetin (Kin) (0.0, 2.0, 4.0, 6.0, 8.0 and 10.0 mg/L) were tested during multiplication stage. The number of shoots/explants was significantly increased with increasing either BA or Kin concentration; however, the shoot length significantly decreased. Data show that media fortified by BA (10 mg/L) combined with indole butyric acid (IBA) at 1.0 or 1.5 mg/L recorded the highest number of shoots/explant (9.13 and 9.25, respectively). After six weeks during the multiplication stage, data cleared that media fortified by benzyladenine (10 mg/L) combined with IBA at 0.5 mg/L recorded the highest shoot length (3.23 cm). The inclusion of indole butyric acid (IBA) or naphthalene acetic acid (NAA) at 1.0–1.5 mg/L to the medium significantly increased the number of roots/plantlets and the highest root length. The results indicated that IBA supplementation was more effective than NAA for in vitro rooting of both Paulownia species. The best treatment for multiplication was 10 mg/L and 8.0–10 mg/L BA for P. hybrid and P. tomentosa, respectively. Peat moss and sand (1:1, v/v) or peat moss and sand (1:2, v/v) were investigated as soil mixture during the adaptation stage. The results referred that Paulownia species plantlets were successfully survived (100 %) in soil mixture contained peat moss: sand (1:2, v/v). This mixture recorded the highest values of plantlet height and number of leaves/plantlets.     

Polyphyly of the grass tribe Hainardieae (Poaceae: Pooideae): identification of its different lineages based on molecular phylogenetics, including morphological and cytogenetic characteristics

The small pooid grass tribe Hainardieae comprises six genera with approximately ten species; however, this tribe was not accepted by all previous taxonomic treatments. To study the relationships among these genera and to infer the phylogeny and evolutionary patterns, we used sequence variation of the internal transcribed spacers (ITS) of nuclear ribosomal and chloroplast (cp) matK DNA and morphology. Many genera of the Aveneae/Poeae tribe complex additionally were included. Both molecular datasets showed Hainardieae to be highly polyphyletic, and its genera to branch with different groups of the Aveneae/Poeae. Parapholis and Hainardia are corroborated as being closely related, and belonging to a firmly supported Eurasian clade together with Catapodium incl. Scleropoa, Cutandia, Desmazeria, Sphenopus, Vulpiella (subtribe Parapholiinae) and with Cynosurus as sister to this assemblage. The other genera of traditionally recognised Hainardieae are positioned phylogenetically distant: Mediterranean Narduroides is verified as more or less related to Festuca and relatives (subtribe Loliinae), whereas the west Eurasian Pholiurus is close to the lineage of Poa and relatives (subtribe Poinae). North American Scribneria is sister to Deschampsia and both genera should be unified under a common subtribe (Aristaveninae or Holcinae). The phylogenetic position of the Algerian genus Agropyropsis (close to Narduroides and within the Loliinae) is suggested on morphology only, because no molecular data was obtained for it. Considering classification, we support the abandonment of tribe Hainardieae and argue to abandon Poeae subtribe Scribneriinae. Poeae subtribe Parapholiinae is redefined with a novel genus content, due to the exclusion of Agropyropsis and Pholiurus and the inclusion of Vulpiella.     

Concurrent evolution of ancient sister lakes and sister species: the freshwater gastropod genus <Emphasis Type="Italic">Radix</Emphasis> in lakes Ohrid and Prespa

Ancient sister lakes are considered to be ancient lakes lying in close geographic proximity, sharing a related origin and significant time of co-existence, usually having hydrological connection as well as a balanced degree of faunal overlap and distinctness. A paradigm for studying sister lake relationships are the ancient lakes Ohrid and Prespa in the Balkans, which are characterized by high degrees of endemicity. Three general patterns of endemic species can be distinguished for these lakes: (1) taxa that are endemic to either lake, with no close relatives in the respective sister lake, (2) closely related but distinct endemic taxa in both lakes (sister species) and (3) shared endemic taxa occurring in both lakes. In the present paper, two endemic freshwater pulmonate gastropod species, Radix relicta (Lake Ohrid) and R. pinteri (Lake Prespa), are used to study the evolution of presumed sister species based on biogeographical and comparative DNA data from world-wide Radix taxa. Phylogenetic, phylogeographical and parametric bootstrap analyses all suggest a sister group relationship of R. relicta and R. pinteri (pattern 2 of endemic diversity). Sister to these two taxa is the widespread R. ampla, which does not occur in the vicinity of lakes Ohrid and Prespa. The southern feeder spring complexes of Lake Ohrid are inhabited by another lineage (Radix sp. 1), which resembles Radix relicta in morphology/anatomy. For Lake Prespa, the widespread R. auricularia was reported in addition to the endemic R. pinteri. Comparative phylogenetic data favour a western Adriatic zoogeographical affinity of lakes Ohrid and Prespa over an Aegean-Anatolian faunal connection. The status of lakes Ohrid and Prespa as sister lakes is evaluated in the light of current knowledge on gastropod speciation and endemism in these hotspots of biodiversity.     

Host specificity of avian haemosporidian parasites is unrelated among sister lineages but shows phylogenetic signal across larger clades

Parasites can vary in the number of host species they infect, a trait known as “host specificity”. Here we quantify phylogenetic signal—the tendency for closely related species to resemble each other more than distantly related species—in host specificity of avian haemosporidian parasites (genera Plasmodium, Haemoproteus and Leucocytozoon) using data from MalAvi, the global avian haemosporidian database. We used the genetic data (479 base pairs of cytochrome b) that define parasite lineages to produce genus level phylogenies. Combining host specificity data with those phylogenies revealed significant levels of phylogenetic signal while controlling for sampling effects; phylogenetic signal was higher when the phylogenetic diversity of hosts was taken into account. We then tested for correlations in the host specificity of pairs of sister lineages. Correlations were generally close to zero for all three parasite genera. These results suggest that while the host specificity of parasite sister lineages differ, larger clades may be relatively specialised or generalised.     

The phylogenetic relationships and generic limits of finches (Fringillidae)

Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.     

Phylogeny of Heterokonta: Incisomonas marina,a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes

Environmental rDNA sequencing has revealed many novel heterokont clades of unknown morphology. We describe a new marine heterotrophic heterokont flagellate, Incisomonas marina, which most unusually lacks an anterior cilium. It glides and swims with its cilium trailing behind, but is predominantly sedentary on the substratum, with or without a cilium. 18S rDNA sequence phylogeny groups Incisomonas strongly within clade MAST-3; with others it forms a robust sister clade to Solenicola, here grouped with it as new order Uniciliatida, placed within new class Nanomonadea encompassing MAST-3. Our comprehensive maximum likelihood heterokont phylogeny shows Nanomonadea as sister to MAST-12 plus Opalinata within Opalozoa, and that Actinophryida are not Opalozoa (previously suggested by distance trees), but highly modified raphidomonads, arguably related to Heliorapha (formerly Ciliophrys) azurina gen., comb. n. We discuss evolution of Actinophryida from photosynthetic raphidophytes. Clades MAST-4,6-11 form one early-branching bigyran clade. Olisthodiscus weakly groups with Hypogyristea not Raphidomonadea. Phylogenetic analysis shows that MAST-13 is all Bicosoeca. Some gliding uniciliates similar to Incisomonas marina seem to have been misclassified: therefore we establish Incisomonas devorata comb. n. for Rigidomastix devoratum, revise the genus Rigidomastix, transfer Clautriavia parva to Kiitoksia. We make 17 new familes (13 heterokont (three algal), two cercozoan, two amoebozoan).     

Redefining Phrymaceae: the placement of Mimulus, tribe Mimuleae, and Phryma

Chloroplast trnL/F and nuclear ribosomal ITS and ETS sequence data were used to analyze phylogenetic relationships among members of tribe Mimuleae (Scrophulariaceae) and other closely related families in Lamiales. The results of these analyses led to the following conclusions. (1) The Australian genera Glossostigma and Peplidium and the taxonomically isolated Phryma join four genera of tribe Mimuleae to form a well-supported clade that is distinct from other families in the Lamiales. We refer to that clade as the subfamily Phrymoideae. (2) The genera Mazus and Lancea (tribe Mimuleae) together form a well-supported clade that we recognize as the subfamily Mazoideae. Mazoideae is weakly supported as sister to Phrymoideae. We assign Mazoideae and Phrymoideae to a redefined family Phrymaceae. (3) Mimulus is not monophyletic, because members of at least six other genera have been derived from within it. In light of the molecular evidence, it is clear that species of Phrymaceae (about 190 species) have undergone two geographically distinct radiations; one in western North America (about 130 species) and another in Australia (about 30 species). Phylogenetic interpretations of morphological evolution and biogeographical patterns are discussed.     

A RECORD OF PAULOWNIA IN THE TERTIARY OF NORTH AMERICA

Smiley , Charles J. (Macalester Coll., St. Paul, Minn.) A record of Paulownia in the Tertiary of North America. Amer. Jour. Bot. 48(2): 175–179. Illus. 1961.—Paulownia, an eastern Asiatic genus in the family Scrophulariaceae, has been identified from fossil leaves in the Ellensburg flora of Washington. Age of these fossils is late Miocene (Barstovian) to early Pliocene (Clarendonian). They are nearly identical to leaves of the living P. tomentosa (Thunberg) Steudel, a deciduous tree now growing in temperate parts of China and one that has escaped from cultivation in eastern United States. Identification is based on comparative leaf morphology. Modern and fossil Paulownia leaves may be distinguished from those of such other genera as Buettneria, Catalpa, and Cercis by secondary and tertiary venation. Central Washington environment during this time was well suited to the growth and reproduction of Paulownia, judging from such fossil associates as Liquidambar, Nyssa, Passiflora, Persea, Rhododendron, Ulmus, and Zelkova. Deciduous habit, present temperate environment, possible early Tertiary record in Alaska, later Tertiary records in middle latitudes of North America and Europe, and present occurrence in China indicate that Paulownia was once widely distributed over the northern hemisphere. Secular climatic trends toward cooler conditions since the Eocene appear to have resulted in the southward migration of Paulownia as a member of the Arcto-Tertiary Geoflora. Subsequent extinctions in Europe and North America may have resulted from Pleistocene glacial climates, and from barriers to further migrations to more southern latitudes.     

Anthocyanins of the bignoniaceae

The pattern of floral anthocyanins exhibits little variation in the family Bignoniaceae. Floral pigments of the genus Paulownia are consistent with an assignment to the Bignoniaceae. No evidence of a pigment syndrome associated with bat pollination could be detected. The 3-desoxyanthocyanidin, carajurin, appears to be unique to the genus Arrabidaea.     

Osteology Supports a Stem-Galliform Affinity for the Giant Extinct Flightless Bird Sylviornis neocaledoniae (Sylviornithidae,Galloanseres)

The giant flightless bird Sylviornis neocaledoniae (Aves: Sylviornithidae) existed on La Grande Terre and Ile des Pins, New Caledonia, until the late Holocene when it went extinct shortly after human arrival on these islands. The species was generally considered to be a megapode (Megapodiidae) until the family Sylviornithidae was erected for it in 2005 to reflect multiple cranial autapomorphies. However, despite thousands of bones having been reported for this unique and enigmatic taxon, the postcranial anatomy has remained largely unknown. We rectify this deficiency and describe the postcranial skeleton of S. neocaledoniae based on ~600 fossils and use data from this and its cranial anatomy to make a comprehensive assessment of its phylogenetic affinities. Sylviornis neocaledoniae is found to be a stem galliform, distant from megapodiids, and the sister taxon to the extinct flightless Megavitiornis altirostris from Fiji, which we transfer to the family Sylviornithidae. These two species form the sister group to extant crown-group galliforms. Several other fossil galloanseres also included in the phylogenetic analysis reveal novel hypotheses of their relationships as follows: Dromornis planei (Dromornithidae) is recovered as a stem galliform rather than a stem anseriform; Presbyornis pervetus (Presbyornithidae) is the sister group to Anseranatidae, not to Anatidae; Vegavis iaai is a crown anseriform but remains unresolved relative to Presbyornis pervetus, Anseranatidae and Anatidae. Sylviornis neocaledoniae was reconstructed herein to be 0.8 m tall in a resting stance and weigh 27–34 kg. The postcranial anatomy of S. neocaledoniae shows no indication of the specialised adaptation to digging seen in megapodiids, with for example, its ungual morphology differing little from that of chicken Gallus gallus. These observations and its phylogenetic placement as stem galliforms makes it improbable that this species employed ectothermic incubation or was a mound-builder. Sylviornis neocaledoniae can therefore be excluded as the constructor of tumuli in New Caledonia.     

Contribution to the study of the genus <Emphasis Type="Italic">Lemniscomys</Emphasis> (Rodentia: Muridae). Morphometric and molecular approaches

A total of 204 specimens belonging to eight species of the genus Lemniscomys were examined with standard morphometric measurements. Our results show that the seven Sub-Saharan species seem to follow a latitudinal gradient from the Center to the South of the African continent. The only North African species L. barbarus looks close to L. griselda and L. rosalia. We also applied a molecular analysis through PCR (Polymerase Chain Reaction) method for the amplification of the 16S rRNA gene. For the purpose of constructing a phylogenetic tree with Maximum Likelihood method, we extracted eight sequences from the GenBank library; seven belonging to the genus Lemniscomys and one to the genus Arvicanthis used as outgroup. We managed to identify a region comprised of 458 nucleotides of which 388 were common for all species and 70 were variable. The phylogenetic tree shows us that the sister group L. bellieri and L. macculus, is the most basal, while L. striatus and L. rosalia appears to be close to the sister group L. barbarus and L. zebra. We also noticed a difference between morphometric and molecular results; the latter are more in agreement with pelage patterns subdivision between Lemniscomys species. These differences can be explained by a high rate of phenotypic evolution that can surpass the molecular counterpart as in the case of the genus Gerbillus.