Investigation of heterotrophs reveals new insights in dinoflagellate evolution

Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.

The macroevolutionary dynamics of activity pattern in mammals: Primates in context

Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.

Molecular characterization and phylogenetic analysis of Paratrichodina africana Kazubski and El-Tantawy, 1986 based on 18S rRNA gene data with the evolutionary hypothesis of trichodinids

In this study, we provided the morphological data and the first 18S rRNA gene data of Paratrichodina africana Kazubski and El-Tantawy, 1986, isolated from hybrids of Oreochromis niloticus × Oreochromis mossambicus in Chongqing, China. Morphologically, P. africana is mainly characterized by the triangular blade and prominent anterior projection. The present population is consistent with the original populations in the overall appearance of the adhesive disc, and falls within the morphometry range of the original descriptions. Phylogenetically, P. africana was clustered into one large clade with Trichodinella and Tripartiella species, which was nested within Trichodina ones with strong support. By combining morphological and molecular data, our results revealed that the validity of the genus Paratrichodina was doubtful, and suggested that the three genera Trichodinella, Tripartiella, and Paratrichodina should be incorporated into one independent genus. In addition, we provided morphological and molecular data of additional eight trichodinids, and further performed the phylogenetic analysis and traced the evolution history of trichodinids' five morphological and bionomical characters for the first time by taking advantage of the current GenBank data. According to the present results, one evolutionary hypothesis of trichodinids was proposed as follows. The most recent common ancestor of trichodinids inhabiting the freshwater environment as a symbiont of vertebrates should evolve from the ancestor with a long-spiral adoral ciliary turn. The first differentiated Trichodina species should be parasitic on one vertebrate distributed in the freshwater environment. During their evolution, some trichodinids expanded to the marine environment, and some switched to invertebrates in the freshwater environment. The denticle of some freshwater Trichodina species became narrower, and the adoral ciliary spiral turn got shorter, forming the ancestor-oid organism with a short-spiral adoral ciliary turn. Then, those Trichodinella, Tripartiella, and Paratrichodina species might evolve from those ancestor-oid organisms with short-spiral adoral ciliary turn.

Origin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics

Megascolecid earthworms of the pheretimoid group are dominant detritivores of soil ecosystems in the Japanese Archipelago and East Asia. However, their diversity and phylogenetic relationships are poorly understood. We assembled whole mitogenome sequences for 197 megascolecid earthworms collected throughout Japan to study the phylogenetic relationships, phylogeography, divergence times, and diversification of important morphological characteristics among pheretimoid earthworms. Using 197 mitogenome sequences and 24 published mitogenome sequences from the East Asian mainland (221 sequences in total), we constructed a maximum likelihood tree and found that the pheretimoid earthworms currently assigned to Amynthas, Metaphire, Duplodicodrilus, and Manus are involved in the most senior genus Amynthas; thus, Amynthas can be treated as the sole genus encompassing all of the above genera. Within the Amynthas group, we identified three major lineages that led to four groups of endemic species in Japan. These lineages originated from different lineages on the East Asian mainland and Taiwan Island, indicating multiple colonization events from the East Asian mainland by different ancestral lineages, possibly after the Miocene. We also assembled nuclear ribosomal DNA sequences encompassing the 18S to 28S rRNA genes. The nuclear gene tree showed major groups consistent with the mitogenome tree except for different (and not well-resolved) relationships among major clades. Our molecular data covered 115-158 native and 7 non-native Amynthas group species in Japan in terms of DNA-based species delimitation. Our findings provide a basis for understanding the evolutionary relationships among diversified megascolecid earthworms in the Amynthas group in Japan and adjacent regions.

Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia's adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).

Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales)

BACKGROUND

Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae.

RESULTS

All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (P_i > 0.02) and five noncoding regions (P_i > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution.

CONCLUSIONS

Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.

Morphology and evolution of the mesopleuron in Bethylidae (Hymenoptera: Chrysidoidea) mapped on a molecular phylogeny

The mesopleuron of Bethylidae has morphostructural characters that remain poorly understood, explored, and defined. The wide range of variability of this sclerite has generated confusion both in taxonomic and cladistic studies. Aiming to solve this issue, we describe the general mesopleural anatomy of Bethylidae. Our goal is to propose primary homologies by matching external and internal structures (muscles and apodemes). We reconstruct the ancestral state of the main mesopleural structures by applying the maximum-likelihood method on ten selected character states. The phylogeny of Bethylidae is built by analyzing a dataset of COI and 28S sequences, using maximum-likelihood and Bayesian inference methods. The Bethylidae and all subfamilies are recovered as monophyletic in both resulting phylogenies, with high clade support values. Although the two analyses yielded similar results, we used the tree resulting from the Bayesian inference to map the evolution of the morphological characters, as it is better supported. The study of mesopleural anatomy allows exploration and discussion of the evolution of characters and their present states in Bethylidae and Hymenoptera in general. Reconstruction of the ancestral states shows that many characters arose independently in Bethylidae subfamilies.

Evolutionary changes in gene expression profiles associated with the coevolution of male and female genital parts among closely related ground beetle species

Background

The coevolutionary dynamics of corresponding male and female sexual traits, including genitalia, may be driven by complex genetic mechanisms. Carabus (Ohomopterus) ground beetles show correlated evolution in the size of their functionally corresponding male and female genital parts. To reveal the genetic mechanisms involved in the evolution of size, we investigated interspecific differences in gene expression profiles in four closely related species (two species each with long and short genital parts) using transcriptome data from genital tissues in the early and late pupal stages.

Results

We detected 1536 and 1306 differentially expressed genes (DEGs) among the species in males and 546 and 1959 DEGs in females in the two pupal stages, respectively. The DEGs were clustered by species-specific expression profiles for each stage and sex to identify candidate gene clusters for genital size based on the expression patterns among the species and gene ontology. We identified one and two gene clusters in females and males, respectively, all from the late pupal stage; one cluster of each sex showed similar expression profiles in species with similar genital size, which implies a common gene expression change associated with similar genital size in each sex. However, the remaining male cluster showed different expression profiles between species with long genital parts, which implies species-specific gene expression changes. These clusters did not show sex-concordant expression profiles for genital size differences.

Conclusion

Our study demonstrates that sex-independent and partly species-specific gene expression underlies the correlated evolution of male and female genital size. These results may reflect the complex evolutionary history of male and female genitalia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08865-2.

Nutlet micromorphology and character evolution of Lappula species (Boraginaceae) and its systematic implications

BACKGROUND

The macro/micro-morphology of nutlets in 11 species (and 22 accessions) of the Boraginaceae family was investigated using stereomicroscope and scanning electron microscopy to evaluate the taxonomic relevance of the traits. To evaluate the phylogenetic significance of the character evolution, phylogenetic analysis was carried out by comparing available DNA sequence data from GenBank with selected original nutlet data.

RESULTS

The Rochelieae nutlets' shape varied from ovoid (ovoid, ovoid-triangular, and ovoid-rectangular) to pyramid. Six major patterns were recognized based on the nutlet ultrastructure characters. Rocheliae is characterized by a transition from "without appendage" to "with tubercles and prickles" on the nutlet disk, and also via a shift from "lack of prickles" to "glossy prickles".

CONCLUSIONS

The results show that the nutlet ultrastructure pattern of Rochelieae is systematically informative at the genus level, but not at the species level. Findings demonstrated that glochid is not an ancestral trait but is a synapomorphy and the transition to this trait occurred in the genus Lappula. The close boundary of nutlet microstructures between L. barbata and L. microcarpa has been discussed.

Phylogenetic estimation and morphological evolution of Alsineae (Caryophyllaceae) shed new insight into the taxonomic status of the genus Pseudocerastium

Pseudocerastium is a monotypic genus in Caryophyllaceae endemic to China. The genus has been widely accepted since it was described in 1998, however its phylogenetic position within Caryophyllaceae has never been studied. In the present study, the whole plastid genome and nuclear ribosomal internal transcribed spacer (ITS) sequences of Pseudocerastium stellarioides was obtained through genome skimming, and the phylogenetic position of the species was studied for the first time. Plastid phylogenomic analysis of Caryophyllaceae revealed that Pseudocerastium is clustered within the tribe Alsineae with strong support. Phylogenetic analyses based on an enlarged taxon sampling of Alsineae using five DNA regions (matK, rbcL, rps16 intron, trnL-F and ITS) revealed that P. stellarioides was nested deeply within Cerastium with strong support. Analyses of morphological character evolution suggest that the ancestral states in Alsineae include three styles and a six-lobed capsule at the apex, while both Cerastium and Pseudocerastium have five styles and ten lobes at the apex of the capsule, further supporting their close relationship. The species Pseudocerastium stellarioides is similar to Cerastium wilsonii in morphology, but differs in having villous indumentum on the lower part of the filaments and compressed globose seeds. Therefore, based on the present molecular and morphological evidence, the generic name Pseudocerastium is reduced here as a new synonym of Cerastium and the species P. stellarioides is transferred to Cerastium as C. jiuhuashanense.

Phylogenetic estimation and morphological evolution of Alsineae (Caryophyllaceae) shed new insight into the taxonomic status of the genus Pseudocerastium

Pseudocerastium is a monotypic genus in Caryophyllaceae endemic to China. The genus has been widely accepted since it was described in 1998, however its phylogenetic position within Caryophyllaceae has never been studied. In the present study, the whole plastid genome and nuclear ribosomal internal transcribed spacer (ITS) sequences of Pseudocerastium stellarioides was obtained through genome skimming, and the phylogenetic position of the species was studied for the first time. Plastid phylogenomic analysis of Caryophyllaceae revealed that Pseudocerastium is clustered within the tribe Alsineae with strong support. Phylogenetic analyses based on an enlarged taxon sampling of Alsineae using five DNA regions (matK, rbcL, rps16 intron, trnL-F and ITS) revealed that P. stellarioides was nested deeply within Cerastium with strong support. Analyses of morphological character evolution suggest that the ancestral states in Alsineae include three styles and a six-lobed capsule at the apex, while both Cerastium and Pseudocerastium have five styles and ten lobes at the apex of the capsule, further supporting their close relationship. The species Pseudocerastium stellarioides is similar to Cerastium wilsonii in morphology, but differs in having villous indumentum on the lower part of the filaments and compressed globose seeds. Therefore, based on the present molecular and morphological evidence, the generic name Pseudocerastium is reduced here as a new synonym of Cerastium and the species P. stellarioides is transferred to Cerastium as C. jiuhuashanense.

Proctodeal extrusion as a defensive behavioral response in blister beetles (Coleoptera: Meloidae)

Defensive mechanisms in blister beetles (Coleoptera: Meloidae) include a wide variety of behavioral responses, chemical defense, and conspicuous external colorations. Although some of these mechanisms have been previously described, proctodeal extrusion, a defensive behavior involving the extrusion of inner abdominal membranes from the proctodeal region which appear intensely red or orange colored when the hemolymph is seen through them, has not been reported to date. Here, we tested the ability to display proctodeal extrusion in response to threat stimuli in wild populations of three blister beetle species inhabiting Central Spain: Berberomeloe majalis (Linnaeus, 1758), Berberomeloe comunero Sánchez-Vialas, García-París, Ruiz & Recuero, 2020, and Physomeloe corallifer (Germar, 1818). In addition, we observed and recorded various other defensive behaviors such as immobility, antennal threat display, autohemorrhage (reflex bleeding), defecation, and thanatosis (death feigning). The frequency at which proctodeal extrusion was observed differed among species, as did the stress intensity needed for extrusion and the probability of proctodeal extrusion in response to a particular threatening stimulus. Our findings indicate that, although proctodeal extrusion might be a widespread potential defensive mechanism in Meloidae, the ability to elicit it is not generalized across lineages. Physomeloe and Berberomeloe are endemic to the semi-arid Mediterranean region, and species adapted to such a climate would have developed strategies that limit hydric stress such as proctodeal extrusion, which mirrors the effect of autohemorrhage but without the fluid loss.

Phylogenomic relationships and character evolution of the grape family (Vitaceae)

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

A fossil-calibrated phylogeny reveals the biogeographic history of the Cladrastis clade, an amphi-Pacific early-branching group in papilionoid legumes

The early-branching Cladrastis clade of papilionoid legumes (Leguminosae, Papilionoideae) has an intriguing amphi-Pacific disjunct distribution in eastern Asia and temperate-tropical Americas. Here we used nuclear and three plastid regions to reconstruct the phylogenetic relationships and divergence times in the Cladrastis clade, as well as the evolution of morphological characters that might have been key in its biogeographic history. The ancestral character state estimation revealed that the most recent common ancestor of the Cladrastis clade was deciduous trees possessing compressed, winged fruits. The Cladrastis clade was inferred to have originated in the mid-latitude thermophilic forests of North America in the early Eocene, followed by the split between ancestors of wing-fruited Platyosprion and the non-wing-fruited group, and later the divergence of Cladrastis s.s. from the non-wing-fruited group in middle Eocene. Platyosprion and Cladrastis s.s. display an "out-of-North-America" biogeographic pattern and might have migrated to Asia via the Bering land bridge (BLB) or the North Atlantic land bridges (NALB) during middle to late Eocene. Our results, coupled with the relatively well documented fossil record for the clade, suggest that Platyosprion experienced an extinction event in North America caused by climatic cooling around the Eocene-Oligocene transition, which drove a major vegetation shift in western North America, in turn serving as a barrier for the vicariance of Pickeringia and Styphnolobium. The evolution of shrubby habit and sclerophyllous leaves in the former might be adaption to the chaparral vegetation in southwestern North America; the latter gained the trait of moniliform, succulent fruit. Styphnolobium further dispersed southward to tropical North America in the Oligocene, and eastward to Asia through BLB during middle Miocene. Subsequent sundering of BLB facilitated the vicariance of St. affine and St. japonicum.

Diet-driven ecological radiation and allopatric speciation result in high species diversity in a temperate-cold water marine genus Dendronotus (Gastropoda: Nudibranchia)

While the majority nudibranch clades are more species rich in the tropics, the genus Dendronotus is mainly represented in Arctic and boreal regions. This distribution pattern remains poorly understood. An integrative approach and novel data provided valuable insights into processes driving Dendronotus radiation and speciation. We propose an evolutionary scenario based on molecular phylogenetics and morphological, ecological, ontogenetic data, combined with data on complex geology and paleoclimatology of this region. Estimated phylogenetic relationships based on four molecular markers (COI, 16S, H3 and 28S) shows strong correlation with radular morphology, diet and biogeographical pattern. Ancestral area reconstruction (AAR) provides evidence for a tropical Pacific origin of the genus. Based on AAR and divergence time estimates we conclude that the evolution of Dendronotus has been shaped by different processes: initial migration out of the tropics, diet-driven adaptive radiation in the North Pacific influenced by Miocene climate change, and subsequent allopatric speciation resulting from successive closings of the Bering strait and cooling of the Arctic Ocean during the Pliocene-Pleistocene. At the same time, contemporary amphiboreal species appear to have dispersed into the Atlantic fairly recently.

Phylogeny of Myxobolidae (Myxozoa) and the evolution of myxospore appendages in the Myxobolus clade

Genera Myxobolus Bütschli, 1882 and Henneguya Thélohan, 1892 (Myxobolidae) are specious myxozoan genera. They comprise nearly half of overall known myxozoan species diversity. A typical spore feature of Henneguya is the presence of two caudal appendages of the spore valves, which distinguishes them from species of the genus Myxobolus. Several Myxobolus spp., however, were reported to show aberrant spores with Henneguya-like caudal appendages. We found such aberrant spores in Myxobolus tsangwuensis and Myxobolus wulii. We studied the ultrastructure of M. wulii and Myxobolus oralis spores with caudal appendages by transmission electron microscopy (TEM). TEM of these aberrant spores revealed that their caudal appendages have the same ultrastructure as the appendages of Henneguya spp. Small caudal appendages of M. wulii spores observed only on TEM suggested that this character may be often overlooked and more Myxobolus species potentially have the ability to express the caudal appendages on the myxospore. In order to trace the evolution of this character, we performed broad phylogenetic analysis of all species of the family Myxobolidae which are available in GenBank including nearly 300 taxa. We found at least eight independent evolutionary origins of spores with two appendages, three origins of a single appendage and 12 apparent secondary losses of the spore projections. Therefore, genus Henneguya with typical two-tailed myxospores is polyphyletic, however a majority of its species has a common ancestor and groups in the second largest subclade of the Myxobolus clade. We also mapped the biological characteristics (host, site of infection and environment) of Myxobolidae species on the phylogenetic tree. We revealed an evident host-associated evolutionary pattern in all parts of the Myxobolus clade with a distinct and species-rich subclade containing almost exclusively species infecting species of the Order Cypriniformes.

A brainstorm on the systematics of Turnera (Turneraceae, Malpighiales) caused by insights from molecular phylogenetics and morphological evolution

With 145 species, Turnera is the largest genus of Turneraceae (Malpighiales). Despite several morphotaxonomic and cytogenetic studies, our knowledge about the phylogenetic relationships in Turnera remains mainly based on morphological data. Here, we reconstruct the most comprehensive phylogeny of Turnera with molecular data to understand the morphological evolution within this group and to assess its circumscription and infrageneric classification. We analyzed two nuclear and six plastid markers and 112 taxa, including species and infraspecific taxa, 97 from Turnera, covering the 11 series of the genus. Bayesian inference, maximum parsimony and maximum likelihood analyses show that Turnera, as traditionally circumscribed, is not monophyletic. The genus is divided into two well-supported independent clades; one of them is sister to the genus Piriqueta and is here segregated as the new genus Oxossia. According to our reconstructions, Turnera probably evolved from an ancestor without extrafloral nectaries and with solitary, homostylous flowers with yellow petals. The emergences of extrafloral nectaries and distyly, both common in extant taxa, played an important role in the diversification of the genus. An updated infrageneric classification reflecting the relationships within Turnera is now possible based on morphological synapomorphies and is here designed for further studies.

Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota)

The lichen genus Cetrelia represents a taxonomically interesting case where morphologically almost uniform populations differ considerably from each other chemically. Similar variation is not uncommon among lichenized fungi, but it is disputable whether such populations should be considered entities at the species level. Species boundaries in Cetrelia are traditionally delimited either as solely based on morphology or as combinations of morpho- and chemotypes. A dataset of four nuclear markers (ITS, IGS, Mcm7, RPB1) from 62 specimens, representing ten Cetrelia species, was analysed within Bayesian and maximum likelihood frameworks. Analyses recovered a well-resolved phylogeny where the traditional species generally were monophyletic, with the exception of Cetrelia chicitae and Cetrelia pseudolivetorum. Species delimitation analyses supported the distinction of 15 groups within the studied Cetrelia taxa, dividing three traditionally identified species into some species candidates. Chemotypes, distinguished according to the major medullary substance, clearly correlated with clades recovered within Cetrelia, while samples with the same reproductive mode were dispersed throughout the phylogenetic tree. Consequently, delimiting Cetrelia species based only on reproductive morphology is not supported phylogenetically. Character analyses suggest that chemical characters have been more consistent compared to reproductive mode and indicate that metabolite evolution in Cetrelia towards more complex substances is probable.

Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions

Background

Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall. We simulate clades with declining but positive diversification rates, as well those in which speciation rates decline below extinction rates so that they are losing richness for part of their history. We run these analyses both with simulated symmetric and asymmetric speciation rates to test whether BiSSE can be used to detect them correctly.

Results

For simulations with a neutral character, the fit for a BiSSE model with a neutral character is better than alternative models so long as net diversification rates remain positive. Once net diversification rates become negative, the BiSSE model with the greatest likelihood often has a non-neutral character, even though there is no such character in the simulation. BiSSE’s usefulness in detecting real asymmetry in speciation rates improves with clade age, even well after net diversification rates have become negative.

Conclusions

BiSSE is most useful in analyzing clades of intermediate age, before they have reached peak diversity and gone into decline. After this point, users of BiSSE risk incorrectly inferring differential evolutionary rates when none exist. Fortunately, most studies using BiSSE and similar models focus on rapid, recent diversifications, and are less likely to encounter the biases BiSSE models are subject to for older clades. For extant groups that were once more diverse than now, however, caution should be taken in inferring past diversification patterns without fossil data.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1174-5) contains supplementary material, which is available to authorized users.

Molecular phylogeny of Galium L. of the tribe Rubieae (Rubiaceae) - Emphasis on Chinese species and recognition of a new genus Pseudogalium

Galium L. is the largest genus in the tribe Rubieae, with about 667 species distributed worldwide. Previous researches mainly focused on species from the Americas and Europe. In the present paper, we greatly increased the number of samples examined from eastern Asia (especially China), representing the most comprehensive sampling of Galium to date. A total of 194 species and variations (subspecies) of Galium were sampled to determine phylogenetic relationships, using two nuclear and five chloroplast markers. Our data are largely consistent with all previous phylogenetic results and confirmed that Galium is non-monophyletic, as are most of its sections. Most members of Galium, including the Chinese taxa, fall into three large clades mixed with other genera from the Galium s.l. group; the exception being the distinct Galium paradoxum Maxim., the first diverged lineage in the Galium s.l. group, which was treated as a new genus (Pseudogalium L.-E. Yang, Z.-L. Nie & H. Sun, gen. nov.). The Galium s.s is a well-supported clade comprised entirely of Galium species, usually with six or more leaves per whorl, mostly from the Old World. Samples from G. maximowiczii (Kom.) Pobed, G. sect. Depauperata and sect. Aparinoides, together with a few from Asperula sect. Glabella and Microphysa (Schrenk ex Fisch. & C.A. Mey.) Pobed., form the second clade. The third clade comprises taxa purely from Galium that usually have four leaves per whorl, from both the New and Old World. Our results also indicated that the monotypic genus Microphysa should be retained and clarified phylogenetic relationships of some specific confused taxa from China. Unlike prior inferences, the combination of opposite leaves associated with two stipules is proposed as the ancestral characteristic of the Galium s.l. group and even the tribe. In addition, the shapes of different corolla and inflorescence types are important for distinguishing some taxa within Rubieae.

Osteology of Batrachuperus londongensis (Urodela, Hynobiidae): study of bony anatomy of a facultatively neotenic salamander from Mount Emei, Sichuan Province, China

The Longdong Stream Salamander Batrachuperus londongensis, living in a mountain stream environment at Mt. Emei in Sichuan Province, China, represents a rare species that is facultatively neotenic in the family Hynobiidae. Although the species has been known to science for some 40 years since its initial discovery in the late 1970s, anatomical details of its osteology remain poorly understood and developmental information is still lacking for the species. This study (1) provides a detailed osteological account of B. londongensis based on micro-CT scanning and clearing and staining of multiple specimens from the type locality; (2) provides a discussion of intraspecific variation related to life-history differences; and (3) presents a discussion on limb features related to morphological evolution of limb patterns correlative with ecological adaptation to mountain stream environments. Osteological comparisons with congeneric species has led to recognition of several diagnostic features that are unique to B. londongensis, including: vomers widely separated from one another, lacking a midline contact; presence of uncommon perichondral ossification of the ascending process of the palatoquadrate as part of the suspensorium; and presence of a prominent posterodorsal process of the scapular blade, which serves as a ligamentous insertion of the levator muscle of the scapula. In addition, some but not all neotenic individuals retain the palatine as a discrete element, indicative of its delayed absorption after sexual maturity. Postmetamorphic and neotenic individuals are strikingly different in the complexity of hyobranchial structures. Neotenes display a high degree of ossification of hyobranchial elements, tend to increase ossification of both hypobranchial I and ceratobranchial I during aging, and retain fully ossified ceratobranchial III and IV; in contrast, these elements remain entirely cartilaginous or are totally lost by resorption in postmetamorphic individuals. In addition, all postmetamorphic forms display an inverted "T"-shaped basibranchial II, whereas neotenes show transformation from a "fork"-shaped to the "T"-shaped configuration after sexual maturity. B. londongensis displays a mosaic of apomorphic and plesiomorphic states in its limb ossifications: presence of a single centrale element in both the manus and pes is a derived condition in Hynobiidae and other families as well, whereas retention of a postminimus in the pes is obviously plesiomorphic within Urodela. Reduction in number of digits from five to four in the pes and possession of a cornified sheath covering the terminal phalanges are also derived features shared with some but not all mountain stream salamanders that are adapted to a similar type of environment.

Atlantic forests to the all Americas: Biogeographical history and divergence times of Neotropical Ficus (Moraceae)

Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene. Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal.

Diversity and evolution of leaf anatomical characters in Taxaceae s.l.-fluorescence microscopy reveals new delimitating characters

Taxaceae s.l. comprise six genera (including Cephalotaxus) and about 35 species; The present study aims to give new insights into the evolution of this family, especially into the phylogenetic position of Cephalotaxus. Moreover, only little is known about comparative leaf anatomy of this family and this study aims to expose and interpret the diversity and evolution of leaf anatomical characters and to assess their applicability to identify taxa at the generic and species level. A detailed phylogeny was reconstructed, using both maximum likelihood and Bayesian inference, with a combined dataset of four molecular markers from the plastid and nuclear genomes. Leaf sections from 132 specimens, representing 32 species and four varieties (fresh and herbarium material) were inspected, using fluorescence microscopy. Ancestral characters were reconstructed using Mesquite. The phylogenetic analyses provided full support for Cephalotaxus as sister group to Taxaceae s.str. Within the latter, two monophyletic tribes Taxeae (comprising Austrotaxus, Pseudotaxus, and Taxus) and Torreyeae (comprising Amentotaxus and Torreya) were fully supported. Fluorescence microscopy was shown to be very useful for identifying leaf tissues and their constitution. We were able to show that particularly sclerified tissues have highest potential for the discrimination of both freshly collected samples and rehydrated herbarium specimens at the generic and species level. A correlation between the presence of different sclereid types could be shown and sclereids were hypothesized to pose a primitive trait in the evolution of Taxaceae s.l. New identification keys were generated on the basis of leaf anatomical characters. The microscopic method presented here is applicable for further studies within gymnosperms and probably in angiosperms, as well.

HISTORICAL EXAMINATION OF DELAYED PLUMAGE MATURATION IN THE SHOREBIRDS (AVES: CHARADRIIFORMES)

Delayed plumage maturation refers to the presence of nonadultlike immature plumages (juvenal plumage excluded). It is usually considered the result of selection for distinctive first-winter or first-summer appearance. In the present study, evolution of delayed plumage maturation is examined in the shorebirds: the sandpipers, plovers, gulls, and their allies. Nine plumage-maturation characters were identified, and their states were superimposed onto topologies generated during two recent investigations of shorebird relationships (Sibley and Ahlquist; revised Strauch). The characters were then optimized so as to assign character states to interior nodes of the trees in the most parsimonious way. Reconstructions of character evolution on six of the shortest revised Strauch trees were ambiguous with respect to delayed plumage maturation in the hypothetical ancestral shorebird. If plumage maturation was not delayed in the shorebird ancestor, optimization indicated that delay appeared when nonadultlike juvenal feathers were acquired. In contrast, on the single Sibley and Ahlquist tree, absence of delayed plumage maturation in the shorebird ancestor was indicated unambiguously, with three evolutionary novelties (nonadultlike juvenal feathers, seasonal plumage change, and a reduced first-spring molt) implicated in its acquisition. Optimization indicated that delayed plumage maturation in shorebirds can be explained plausibly without invoking selection for distinctive first-winter or first-summer appearance. Two of the novel conditions generating delayed plumage maturation (modified juvenal feathers and seasonal plumage change) did so only because they were acquired in a taxon possessing restricted first-year molts, which are primitive. Given these observations, it seems simplest to explain the delay in plumage maturation as an incidental consequence of the phylogenetic inertia of shorebird molts. The third novelty that generates delayed plumage maturation, a reduced first-spring molt, may have been acquired to reduce molt-associated energetic demands in young birds.

An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)

Background

Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task.

Results

Here, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types.

Conclusions

Our study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-017-0191-3) contains supplementary material, which is available to authorized users.

Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains

Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is postulated.

Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae) species

The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella) were found to be monophyletic; only E. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section.

From commensalism to parasitism in Carapidae (Ophidiiformes): heterochronic modes of development?

Phenotypic variations allow a lineage to move into new regions of the adaptive landscape. The purpose of this study is to analyse the life history of the pearlfishes (Carapinae) in a phylogenetic framework and particularly to highlight the evolution of parasite and commensal ways of life. Furthermore, we investigate the skull anatomy of parasites and commensals and discuss the developmental process that would explain the passage from one form to the other. The genus Carapus forms a paraphyletic grouping in contrast to the genus Encheliophis, which forms a monophyletic cluster. The combination of phylogenetic, morphologic and ontogenetic data clearly indicates that parasitic species derive from commensal species and do not constitute an iterative evolution from free-living forms. Although the head morphology of Carapus species differs completely from Encheliophis, C. homei is the sister group of the parasites. Interestingly, morphological characteristics allowing the establishment of the relation between Carapus homei and Encheliophis spp. concern the sound-producing mechanism, which can explain the diversification of the taxon but not the acquisition of the parasite morphotype. Carapus homei already has the sound-producing mechanism typically found in the parasite form but still has a commensal way of life and the corresponding head structure. Moreover, comparisons between the larval and adult Carapini highlight that the adult morphotype "Encheliophis" is obtained by going beyond the adult stage reached by Carapus. The entrance into the new adaptive landscape could have been realised by at least two processes: paedomorphosis and allometric repatterning.

The evolution of a key character, or how to evolve a slipper lobster

A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is presented here, while the former species 'Cancrinos' libanensis is re-described as Paracancrinos libanensis comb. nov. P. libanensis is shown to be closer related to the contemporary slipper lobsters than to Cancrinos claviger (lithographic limestones, Jurassic, southern Germany). A finely-graded evolutionary scenario for the slipper-lobster morphotype is reconstructed based on these fossil species and extant forms. The evolutionary changes that gave rise to the current plate-like antennae of Scyllaridae, a key apomorphy of this group, are traced back through time. The antenna of what is considered the oldest slipper lobster became petaloid and consisted of about 20 fully articulated elements. For this group the name Scyllarida sensu lato tax. nov. is introduced. In a next evolutionary step, the proximal articles became conjoined and a lateral extension appeared on peduncle element 3. The entire distal petaloid region is conjoined already at the node of Verscyllarida tax. nov. In modern slipper lobsters, Neoscyllarida tax nov., the distal region is no longer petaloid in shape but asymmetrical. The study also emphasizes that exceptionally preserved fossils need to be documented with optimal documentation techniques to obtain all available information.

Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae)

Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai-Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.

Colorful patterns indicate common ancestry in diverged tiger beetle taxa: Molecular phylogeny, biogeography, and evolution of elytral coloration of the genus Cicindela subgenus Sophiodela and its allies

We investigated the phylogenetic relationships among tiger beetles of the subtribe Cicindelina (=Cicindela s. lat.; Coleoptera: Cicindelidae) mainly from the Oriental and Sino-Japanese zoogeographic regions using one mitochondrial and three nuclear gene sequences to examine the position of the subgenus Sophiodela, currently classified in the genus Cicindela s. str., their biogeography, and the evolution of their brilliant coloration. The subgenus Sophiodela was not related to the other subgenera of Cicindela s. str. but was closely related to the genus Cosmodela. In addition, the Oriental genus Calochroa was polyphyletic with three lineages, one of which was closely related to Sophiodela and Cosmodela. The clade comprising Sophiodela, Cosmodela and two Calochroa species, referred to here as the Sophiodela group, was strongly supported, and most species in this clade had similar brilliant coloration. The Sophiodela group was related to the genera Calomera, Cicindela (excluding Sophiodela) and Cicindelidia, and these were related to Lophyra, Hipparidium and Calochroa, except species in the Sophiodela group. Divergence time estimation suggested that these worldwide Cicindelina groups diverged in the early Oligocene, and the Sophiodela group, which is found in the Oriental and Sino-Japanese zoogeographic regions, in the mid Miocene. Some components of the elytral pattern related to maculation and coloration in the Cicindelina taxa studied contained weak, but significant, phylogenetic signals and were partly associated with habitat types. Therefore, the brilliant coloration of the Sophiodela was related to both phylogeny and habitat adaptation, although the function of coloration needs to be studied.

Zygomorphy evolved from disymmetry in Fumarioideae (Papaveraceae, Ranunculales): new evidence from an expanded molecular phylogenetic framework

BACKGROUND AND AIMS

Fumarioideae (20 genera, 593 species) is a clade of Papaveraceae (Ranunculales) characterized by flowers that are either disymmetric (i.e. two perpendicular planes of bilateral symmetry) or zygomorphic (i.e. one plane of bilateral symmetry). In contrast, the other subfamily of Papaveraceae, Papaveroideae (23 genera, 230 species), has actinomorphic flowers (i.e. more than two planes of symmetry). Understanding of the evolution of floral symmetry in this clade has so far been limited by the lack of a reliable phylogenetic framework. Pteridophyllum (one species) shares similarities with Fumarioideae but has actinomorphic flowers, and the relationships among Pteridophyllum, Papaveroideae and Fumarioideae have remained unclear. This study reassesses the evolution of floral symmetry in Papaveraceae based on new molecular phylogenetic analyses of the family.

METHODS

Maximum likelihood, Bayesian and maximum parsimony phylogenetic analyses of Papaveraceae were conducted using six plastid markers and one nuclear marker, sampling Pteridophyllum, 18 (90 %) genera and 73 species of Fumarioideae, 11 (48 %) genera and 11 species of Papaveroideae, and a wide selection of outgroup taxa. Floral characters recorded from the literature were then optimized onto phylogenetic trees to reconstruct ancestral states using parsimony, maximum likelihood and reversible-jump Bayesian approaches.

KEY RESULTS

Pteridophyllum is not nested in Fumarioideae. Fumarioideae are monophyletic and Hypecoum (18 species) is the sister group of the remaining genera. Relationships within the core Fumarioideae are well resolved and supported. Dactylicapnos and all zygomorphic genera form a well-supported clade nested among disymmetric taxa.

CONCLUSIONS

Disymmetry of the corolla is a synapomorphy of Fumarioideae and is strongly correlated with changes in the androecium and differentiation of middle and inner tepal shape (basal spurs on middle tepals). Zygomorphy subsequently evolved from disymmetry either once (with a reversal in Dactylicapnos) or twice (Capnoides, other zygomorphic Fumarioideae) and appears to be correlated with the loss of one nectar spur.

Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae)

We assessed phylogenetic and systematic relationships among 17 out of 23 species of Theloderma and all three species of Nyctixalus from 2412bp sequences of the mitochondrial DNA genes of 12S rRNA, tRNA(val), and 16S rRNA using maximum likelihood and Bayesian inference methods. With the exception of T. moloch, Theloderma and Nyctixalus are confirmed to form a clade, in which each genus also forms a clade. Theloderma moloch is phylogenetically outside these clades and closer to samples from Chiromantis, Feihyla, Gracixalus, Kurixalus, Philautus, Polypedates, Raorchestes, and Rhacophorus. Within Theloderma, T. horridum and T. stellatum form the sister taxon to a clade comprising the remaining species. The basal split within the latter clade groups T. asperum, T. licin, T. petilum, and T. ryabovi as the sister to a clade comprising T. bicolor, T. chuyangsinense, T. corticale, T. gordoni, T. laeve, T. lateriticum, T. nebulosum, T. rhododiscus, and T. truongsonense. Our phylogenetic results indicate homoplastic evolution of four morphological characters: small vs. large body size, presence of vomerine teeth, presence of a vocal opening in males, and interdigital webbing on hands. The common ancestor of Theloderma and Nyctixalus is inferred to have arisen in the area including the current Sunda region.

Molecular phylogeny of Koenigia L. (Polygonaceae: Persicarieae): implications for classification, character evolution and biogeography

To examine the phylogenetic relationships of Koenigia sensu lato (Polygonaceae), 43 samples representing all species of Koenigia and closely related taxa (e.g., Aconogonon, Bistorta, and Persicaria) were sequenced for nuclear ITS and four plastid regions (trnL-F, atpB-rbcL, rbcL, and rpl32-trnL((UAG))). Phylogenetic analyses indicate that Koenigia recognized by Hedberg is paraphyletic and that the basal species K. delicatula should be reassigned to a separate new genus. Based on these findings, we further propose that the genus Koenigia sensu lato be circumscribed to include five species. Ancestral state reconstruction showed that the pollen apertures likely evolved in parallel in the Aconogonon-Koenigia-Bistorta clade and Persicaria clade and that tricolpate pollen is most likely to be the ancestral state. Quincuncial aestivation likely evolved during the early evolution of Koenigia and its close relatives. Our findings suggest that the uplift of the Himalayas has played an important role in promoting species diversification of Koenigia. Koenigia islandica expanded its range during Pleistocene glacial cycles by tracking changes in newly available habitats.