Plastomic data shed new light on the phylogeny,biogeography, and character evolution of the family Crassulaceae

Crassulaceae is a mid-sized family of angiosperms, most species of which are herbaceous succulents, usually with 5-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major “clades” in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia, and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago, shortly after the Cretaceous–Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

Phylogenetic relationships between isolated populations of the limestone‐dwelling microsnail Gyliotrachela hungerfordiana (Gastropoda: Vertiginidae)

The vertiginid species Gyliotrachela hungerfordiana, an obligate limestone‐dwelling microsnail, is relatively widespread and is found on a large number of isolated limestone hills in Peninsular Malaysia. To elucidate the pattern of colonization of these hills, we conducted a molecular phylogenetic analysis on G. hungerfordiana subpopulations from 15 separate limestone outcrops. As outgroups, we also included five related Peninsular Malaysian Vertiginidae (Gyliotrachela frequens, Gyliotrachela transitans, Gyliotrachela salpinx, Gyliotrachela depressispira and Paraboysidia tarutao), one population each. A combined analysis of nuclear (internal transcribed spacer 1) and mitochondrial (cytochrome c oxidase 1) sequences showed that (1) G. hungerfordiana is monophyletic; (2) there is a clear geographical pattern in the phylogenetic relationships between G. hungerfordiana populations, with genetic distances increasing with geographic distance; (3) this pattern is disturbed by a few long‐distance (north‐west to south‐east and north to south) colonizations.     

Historical biogeography of Rhododendron section Vireya and the Malesian Archipelago

Aim Vireya rhododendrons are distinctive and easily recognizable by their general form; however, they are virtually circumscribed geographically, predominantly distributed throughout the biogeographically intriguing Malesian Archipelago. Hypotheses of the evolutionary relationships of the group have been proposed but the biogeography of vireyas has not been analysed based on molecular phylogeny. Recently, the first detailed molecular phylogenetic investigation of section Vireya was completed based on cp‐ and nrDNA sequence data, therefore making this cladistic biogeographic study of vireya rhododendrons possible. Location Malesia, Australia, Solomon Islands, Taiwan, Himalayas, north Vietnam and south China. Methods Based on distribution maps, areas of endemism were determined for the biogeographic region of Malesia. Area relationships were analysed based on a recent molecular phylogeny of species in section Vireya. The method of paralogy‐free subtree analysis was applied. Results Individual distribution maps were produced for 74 species of Rhododendron section Vireya. Species clades with bootstrap support proved to be biogeographically informative. Major clades correspond to three regions: eastern Malesia, western/middle Malesia and Taiwan/north Vietnam/south China. Within eastern Malesia, Australia, New Guinea, the Bismarck Archipelago and Solomon Islands are related. In western Malesia, northern Philippines, Borneo, southern Moluccas and north and west Sulawesi are related. These areas are more distantly related to Sumatra, the Malay peninsula, Java, Bali, Palawan, Lesser Sunda islands and the southern Philippines. The position of the Himalayas is equivocal and part of a basal polytomy in the summary area cladogram. Main conclusions Two alternative hypotheses are proposed for the evolution of vireya rhododendrons based on the pattern of area relationships. The first hypothesis is that the vireyas are an old group, with ancestors present on Gondwana, rifting north in the Cretaceous. The second alternative hypothesis is that vireyas are a young group that has dispersed eastwards from India to Australia and the Solomon Islands since the current Malesian islands formed.     

Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

Background and Aims

Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented.

Methods

A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications.

Key Results

The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions.

Conclusions

This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.     

Phylogeny,biogeography, and morphological ancestral character reconstruction in the Mediterranean genus Fumana (Cistaceae)

Fumana is a diverse genus of the Cistaceae family, consisting of 21 currently accepted species. In this study, nuclear (ITS) and plastid (matK, trnT‐L) molecular markers were used to reconstruct the phylogeny and to estimate divergence times, including 19 species of Fumana. Phylogenetic analyses (Bayesian Inference, Maximum Parsimony and Maximum Likelihood) confirmed the monophyly of Fumana and did not support the infrageneric divisions previously established. The results support four main clades that group species that differ in vegetative and reproductive characters. Given the impossibility to define morphological characters common to all species within the clades, our proposal is to reject infrageneric divisions. Molecular dating and ancestral area analyses provide evidence for a Miocene diversification of the genus in the north‐western Mediterranean. Ancestral state reconstructions revealed ancestral character states for some traits related to xeric and arid habitats, suggesting a preadaptation to the Mediterranean climate.     

Phylogenetic relationships among gekkotan lizards inferred from C-mos nuclear DNA sequences and a new classification of the Gekkota

A phylogeny of gekkotan lizards was derived from C- mos nuclear DNA sequence data. Forty-one currently recognized genera, representing all major gekkotan lineages, were included in the study. A total of 378 bp of partial C- mos gene sequences was obtained and aligned. Maximum parsimony (MP) and maximum likelihood (ML) trees were generated based on unweighted analysis using P AUP *; similar tree topologies were recovered by both methods. The Eublepharidae were monophyletic and its relationship to other major clades was poorly resolved. The Pygopodidae of Kluge (1987) was monophyletic, but relationships within this group differed from those retrieved by previous analyses. The Diplodactylini + padded carphodactylines were the sister group of pygopods + padless carphodactylines. The Gekkonidae were monophyletic, but we found no evidence in support of the Teratoscincinae, as Teratoscincus was embedded well within the gekkonids. Both MP and ML analyses supported the basal position of Sphaerodactylus within the gekkonids, in contrast to morphologically based hypotheses. We propose a new higher order classification of the Gekkota that reflect these results. Five gekkotan families: Eublepharidae, Gekkonidae, Pygopodidae, Diplodactylidae, and Carphodactylidae are recognized. The higher order status of the sphaerodactyls will require more intensive sampling of this group. Our results support the hypothesis that the early cladogenesis of the Gekkota was associated with the split of Eastern Gondwanaland from Western Gondwanaland. Divergences among living genera in the Eublepharidae and the Eastern Gondwanan lineages (Diplodactylidae, Pygopodidae and Carphodactylidae) may be older than those in the Gekkonidae.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 353–368.     

Danaea (Marattiaceae) revisited: biodiversity,a new classification and ten new species of a neotropical fern genus

Revision of the Neotropical fern genus Danaea (Marattiaceae) has resulted in the recognition of ten new species, which are here for the first time presented to the scientific audience. Morphological and molecular data suggest that the genus consists of three monophyletic subgenera that are circumscribed here. A key is provided to aid species identification. The geographical ranges of the species are summarized and discussed with regard to speciation. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 360–385.     

Phylogenetics of the allodapine bee genus Braunsapis: historical biogeography and long-range dispersal over water

Aim A previous study of the allodapine bee genus Braunsapis suggested an African origin, with dispersal events into Madagascar and Asia, and from Asia into Australia. We re‐examine the phylogeny of this genus, using an expanded set of taxa from Madagascar and Malawi and additional sequence data, in order to determine the number of dispersals and the timeframe over which they occurred. Location Africa, Madagascar, Malawi, Asia and Australia. Methods One nuclear (EF‐1α F2) and two mitochondrial (CO1 and Cyt b) gene regions were sequenced for 36 allodapine bee species (including members of the genera Braunsapis, Nasutapis, Allodape, Allodapula, and Macrogalea) and one ceratinine species (Ceratina japonica). We used Bayesian analyses to examine phylogenetic structure and a penalized likelihood approach to estimate approximate ages for key divergences in our phylogeny. Results Our analyses indicate a tropical African origin for Braunsapis in the early Miocene followed by very early dispersal into Asia and then a subsequent dispersal, following Asian diversification, into Australia during the late Miocene. There have also been two dispersals of Braunsapis from Africa to Madagascar and this result, when combined with phylogenetic and biogeographical data for other allodapines, suggests that these bees have the ability to cross moderately large ocean expanses. These dispersals may have been aided by the West Wind Drift, but rafting across the Mozambique Channel is also possible, and could be aided by the existence of developmental stages that require minimal or no feeding and by tolerance to sea water and spume. Accumulating evidence suggests that many biogeographical patterns in the southern hemisphere may be better explained by dispersal than by Gondwanan vicariance hypotheses. Our results add to this growing body of data and raise the possibility that some puzzling trans‐Indian Ocean distributions may also be explained by historical dispersal events across oceanic barriers that now seem insuperable.     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

Phylogenetic relationships and biogeographical history of the genus Rhinoclemmys Fitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea)

Rhinoclemmys is an interesting genus of turtles biogeographically and ecologically, being the only genus of the family Geoemydidae that occurs in the New World and inhabiting a wide range of habitats from aquatic to highly terrestrial. Here we present a molecular phylogeny of Rhinoclemmys using both mitochondrial and nuclear genes. Our results strongly support the monophyletic and subfamilial status of Rhinoclemmys within the monophyletic family Geoemydidae. Within Rhinoclemmys , two clades are strongly supported, i.e. R. annulata  +  R. pulcherrima and R. areolata  +  R. punctularia  +  R. diademata  +  R. funerea  +  R. melanosterna , but the positions of R. nasuta and R. rubida are still weakly supported. In terms of the biogeographical history, the results of this study, coupled with palaeontological evidence, corroborate the hypothesis that this group migrated from Asia to the Americas across the Bering Strait during the early Eocene. The radiation of Rhinoclemmys in Central and South America corresponds well with vicariance events, including the emergence of the Sierra Madres of Mexico and the Nuclear Highland, and dispersals across the Panama land bridge. Interestingly, our resulting phylogeny suggests this group invaded South America at least four times and that dispersal of R. nasuta to South America probably took place in the early Miocene before the emergence of the Isthmus of Panama. We finally discuss our phylogenetic results with regard to the monophyly of the family Geoemydidae and in the context of previous morphological analyses. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 751–767.     

The tribe Bryocorini (Insecta: Heteroptera: Miridae: Bryocorinae): phylogeny,description of a new genus,and adaptive radiation on ferns

A cladistic analysis of the tribe Bryocorini based on 68 morphological characters is conducted. Bryocorini are supported as a monophyletic group with Eccritotarsini as their sister taxon. Based on the phylogenetic analysis, we redefine the tribe Bryocorini to contain the following seven genera: Bryocorella Carvalho, 1956, Bryocoris Fallén, 1829, Bryophilocapsus Yasunaga, 2000, Cobalorrhynchus Reuter, 1906 gen. dist., D iplazicoris gen. nov. , Hekista Kirkaldy, 1902, and Monalocoris Dahlbom, 1851. The genus Bryocorella is transferred to Bryocorini from the tribe Eccritotarsini. The subgenus Cobalorrhynchus is treated as a separate genus. Diplazicoris is described as monotypic to accommodate D iplazicoris lombokianus sp. nov. An updated diagnosis of the tribe, a key to genera, and a diagnosis of each recognized genus are presented. Selected photomicrographs, scanning micrographs, and illustrations of the pretarsus, metepisternal scent efferent system, metafemoral trichobothria, and morphology of head, pronotum, and male and female genitalia are provided. Mapping of the host data on the revealed tree shows that Bryocorini represent one of the very few currently known examples of the adaptive radiation of a fairly large insect group on ferns. © 2015 The Linnean Society of London     

Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae)

Phylogenetic studies using DNA sequences of two chloroplast regions, rbcL and trnL-F, demonstrate that the proposed genus Ceterach is a small clade within the large genus Asplenium, and sister to the Phyllitis clade. The Ceterach clade is characterised by irregular anastomosing veins and often densely scaled leaf blades. Its taxonomic status as a group nested within Asplenium is confirmed, and it is accepted here as a subgenus with seven species. The Ceterach clade comprises four lineages that correspond to disjunct polyploid complexes: the A. aureum clade forming a polyploid complex (4×, 6×, 8×) in Macaronesia, the A. ceterach clade forming a polyploid complex (2×, 4×, 6×) in the Mediterranean Basin, the A. paucivenosum clade (4×, 6×) in central Asia, and the A. dalhousiae clade (2×) with a disjunct distribution in the Himalaya, Yemen and Eritrea, and southwestern North America. Asplenium paucivenosum is sister to all other members of the Ceterach clade, whereas A. dalhousiae is sister to the A. aureum clade that includes tetraploid A. aureum, hexaploid A. lolegnamense, and octoploid A. parvifolium. Asplenium ceterach and its variations – including the hexaploid A. ceterach subsp. mediterraneum subsp. nov. first described below – form a monophyletic unit, sister to a clade consisting of A. aureum and A. dalhousiae. Asplenium cordatum from Africa and A. haugthonii from the isolated atlantic island of St. Helena are not members of the Ceterach clade, which suggests that leaf blades with dense indumenta have evolved at least twice within asplenioid ferns. The allotetraploid species A. hybridum has the chloroplast DNA from A. ceterach, and therefore the latter species is the maternal ancestor of the former. The other parent of this hybrid species is A. sagittatum that is nested within the sister clade of Ceterach, the Phyllitis clade comprising A. sagittatum and A. scolopendrium. The findings suggest that the current distribution of Ceterach is either the result of long-distance dispersal or represents fragmented relicts of a previously more widely distributed species.     

Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae)

The Hawaiian Archipelago is the most isolated island system on the planet and has been the subject of evolutionary research for over a century. The largest radiation of species in Hawaii is the Hawaiian Drosophilidae, a group of approximately 1000 species. Dispersal to isolated island systems like Hawaii is rare and the resultant flora and fauna shows high disharmony with mainland communities. The possibility that some lineages may have originated in Hawaii and subsequently 'escaped' to diversify on continental landmasses is expected to be rarer still. We present phylogenetic analysis of 134 partially sequenced mitochondrial genomes of Drosophilidae (approx. 1.3 Mb of sequence total) to address major aspects of adaptive radiation and dispersal in Hawaii. We show that the genus Scaptomyza, a group that accounts for approximately one-third of the species-level diversity of Drosophilidae in the Hawaiian Islands, originated in Hawaii, diversified there, and subsequently colonized a number of island and continental landmasses elsewhere on the globe. We propose that a combination of small body size, rapid generation time and unique ecological and physiological adaptations have allowed this genus to effectively disperse and diversify.     

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.     

Molecular phylogeny of the tribe Erotini with description of a new genus from China (Coleoptera: Lycidae)

Erotini is a small tribe of net‐winged beetles known from the northern temperate zone. We investigated relationships and limits of tribes and genera using a molecular phylogeny inferred from rrnL, cox1 and nad5 mtDNA fragments. Lopheros Leconte, 1881 and Pseudaplatopterus Kleine, 1940 were inferred in current molecular analyses as terminal lineages within Erotini. Therefore, we consider Lopherotini Kazantsev, 2012 and Pseudaplatopterina Kazantsev, 2012 as junior synonyms of Erotini Leconte, 1881. The Platycis genus group comprises 19 species representing several genus‐group taxa previously placed in Platycis s. l. Konoplatycis Nakane, 1969 was recovered as a deeply rooted lineage of Erotini and we inferred another independent lineage for which we propose a new genus Sinoplatycis gen. nov. Additionally, we studied the diversity of Platycis s. l. in Asia, found their highest diversity in the temperate forest habitats of Eastern Asia and inferred the paraphyletic character of the subgenus Erotides s. str. Five new species are described from China: Sinoplatycis cardinalis sp. nov. , S. zhani sp. nov. (type species of Sinoplatycis gen. nov. ), Erotides brunnescens sp. nov. , E. pusillus sp. nov. and E. slipinskii sp. nov. The molecular phylogeny shows deep splits of Japanese species with respect to the continental Eurasian fauna and the role of shallow seas and mountain systems in the diversification of the Platycis genus group.     

Towards the natural classification of tectarioid ferns: Confirming the phylogenetic relationships of Pleocnemia and Pteridrys (eupolypods I)

The phylogenetic relationships of the two derived fern genera Pleocnemia and Pteridrys were considered ambiguous even with molecular evidence from previous studies. In the present study we determined the phylogenetic position based on five plastid DNA regions, namely atpA, atpB, rbcL, the rps4 + rps4–trnS intergenic spacer, and the trnL-F region, and an expanded taxonomic coverage including several accessions of each of the two genera. Our results showed that the monophyletic genus Pleocnemia belonged to the Dryopteridaceae and was not related to the Tectariaceae, as it had been in the past. Pleocnemia was found to be closely related to the bolbitidoid and lastreopsioid ferns. The monophyletic genus Pteridrys was found to be sister to a clade comprising Triplophyllum and Tectarias.l. Thus, the placement of this genus into Tectariaceae was confirmed. The sinus teeth, the unique similarity shared by Pleocnemia and Pteridrys, evolved independently in the two genera. Both genera appeared to have diverged from their closest extant relatives at least since the Eocene, whereas the crown group ages indicated radiation events in the Late Miocene for both genera.