The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data

The pantropical Zingiberaceae is the largest family in the order Zingiberales with 53 genera and over 1200 species. Classifications of the family first proposed in 1889 and refined by others since that time recognize four tribes (Globbeae, Hedychieae, Alpinieae, and Zingibereae) based on morphological features, such as number of locules and placentation in the ovary, development of staminodia, modifications of the fertile anther, and rhizome-shoot-leaf orientation. New phylogenetic analyses based on DNA sequences of the nuclear internal transcribed spacer (ITS) and plastid matK regions suggest that at least some of these morphological traits are homoplasious and three of the tribes are paraphyletic. The African genus Siphonochilus and Bornean genus Tamijia are basal clades. The former Alpinieae and Hedychieae for the most part are monophyletic taxa with the Globbeae and Zingibereae included within the latter. The results of these phylogenetic investigations are used to propose a new classification of the Zingiberaceae that recognizes four subfamilies and four tribes: Siphonochiloideae (Siphonochileae), Tamijioideae (Tamijieae), Alpinioideae (Alpinieae, Riedelieae), and Zingiberoideae (Zingibereae, Globbeae). Morphological features congruent with this classification and the taxonomic status of various monotypic genera are discussed.     

A molecular phylogeny of apple snails (Gastropoda, Caenogastropoda, Ampullariidae) with an emphasis on African species

Ampullariids are widespread in Africa, Asia, South- and Central America, and the Caribbean Islands. Basal phylogenetic relationships of the African genera Afropomus and Saulea have been inferred based on anatomical evidence. Until recently the Viviparidae was regarded as the sister-group of Ampullariidae, but recent molecular data infer a sister-group relationship with Campanilidae. We have used members of both families as outgroups in the present investigation on ampullariid phylogeny. We have used data from portions of five molecular loci, that is, the nuclear genes 18S rRNA, 28S rRNA and H3, and the mitochondrial genes 16S rRNA and COI. Our data most often infer a basal position of Afropomus . The West African species Saulea is inferred as the basal member of a clade including the South American Marisa and Pomacea . We hypothesize that evolutionary lineages leading to Saulea and the American genera were isolated from each other by vicariance events (Gondwanaland break-up 130–110 Mya). Our individual gene analyses inferred two major clades of the African Lanistes . However, in some analyses they were not inferred as sister-groups making Lanistes paraphyletic. The African and Asian genus Pila is most often inferred to be monophyletic (except for the generally unresolved 28S). Our analyses most often inferred a sister-group relationship between Lanistes and Pila . The very low genetic diversity of the endemic radiation of Lanistes in Lake Malawi suggests that the morphological divergence has happened much faster than the molecular divergence as is also evidenced from the cichlid radiations.     

Furanoterpenoids from Siphonochilus aethiopicus

Two new furanoterpenoid derivatives, namely 4a alpha H-3,5 alpha,8 alpha beta-trimethyl-4,4a,9-tetrahydro-naphtho[2,3-b]-furan-8-one and 2-hydroxy-4a alpha H-3,5 alpha, 8a beta-trimethyl-4,4a,9-tetrahydronaphtho[2,3-b]-furan-8-one, were isolated from Siphonochilus aethiopicus, a member of the family Zingiberaceae. Their structures were elucidated using high field NMR techniques.     

Genetc divergence and phylogeny of the Salmoninae based on allozyme data

The data on 31–37 allozyme loci in 21 species of nine salmonid genera are used for phylogenetic analysis by seven distance methods and several variants of cladistic analysis. Monophyletic origin for all genera and three sub-families of the Salmonidae is corroborated. The closest phylogenetic relationships are characteristic of Parasalmo and Oncorhynchus (bootstrap support is 88–99%), Brachymystax and Hucho (68–97%), and the clade ( Brachymystax + Hucho )+ Salmo (up to 85%). The patterns of phylogenetic relationships in the group Salmo-Parasalmo-Oncorhynchus are analogous to those in the group Parahucho-Hucho-Brachymystax. The position of Parahucho in phylogenetic trees of the Salmoninae is extremely unstable, although it is most likely associated with the clade ( Brachymystax + Hucho)+Salmo ) or Salvelinus. When using the out group analysis, Salvelinus appears as the earliest branch of the Salmoninae tree, whereas if the molecular clock is assumed, the basal position is occupied by Oncorhynchus. However, the latter genus is probably characterized by a substantially increased rate of molecular evolution.     

The molecular phylogeny of Alpinia (Zingiberaceae): a complex and polyphyletic genus of gingers

Alpinia is the largest, most widespread, and most taxonomically complex genus in the Zingiberaceae with 230 species occurring throughout tropical and subtropical Asia. Species of Alpinia often predominate in the understory of forests, while others are important ornamentals and medicinals. Investigations of the evolutionary relationships of a subset of species of Alpinia using DNA sequence-based methods specifically test the monophyly of the genus and the validity of the previous classifications. Seventy-two species of Alpinia, 27 non-Alpinia species in the subfamily Alpinioideae, eight species in the subfamily Zingiberoideae, one species in the subfamily Tamijioideae, and three species in the outgroup genus Siphonochilus (Siphonochiloideae) were sequenced for the plastid matK region and the nuclear internal transcribed spacer (ITS) loci. Parsimony analyses of both individual and combined data sets identified six polyphyletic clades containing species of Alpinia distributed across the tribe Alpinieae. These results were supported by a Bayesian analysis of the combined data set. Except in a few specific cases, these monophyletic groupings of species do not correspond with either Schumann's (1904) or Smith's (1990) classification of the genus. Here we build on previous molecular analyses of the Alpinioideae and propose the next steps necessary to recognize new generic boundaries in the Alpinieae.     

On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza?

Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza , with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza , incline us to retain both lineages as distinct genera.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 261–269.     

Sperm competition in frogs: testis size and a 'sterile male' experiment on Chiromantis xerampelina (Rhacophoridae)

The allometric relationship between body mass and testis mass was calculated using data from 16 genera (37 species) of African and Japanese frogs. Having controlled for body mass, the relative testis mass of Chiromantis xerampelina, Rhacophorus arboreus and R. schlegelli was considerably heavier than predicted (3.8–14.6 times more). All three species have multi-male breeding. Although the result is consistent with sperm competition having selected for increased sperm production in anurans, the phylogenetic distribution of well documented multi-male spawning is confined to the Rhacophoridae. Thus, multi-male mating may have arisen only once effectively reducing the analysis to two data points. However, in the four foam-nesting Rhacophorids whose breeding behaviour has been studied there is also a correlation between relative testis mass and the intensity of sperm competition. This suggests that even within the Rhacophoridae, sperm competition leads to larger testes. Direct evidence for sperm competition in C. xerampelina is provided by a 'sterile male' experiment, which shows that peripheral males are capable of fertilizing eggs.     

Progress in understanding the phylogeny of the Plasmodium vivax lineage

There has been some controversy about the evolutionary origin of Plasmodium vivax, particularly whether it is of Asian or African origin. Recently, a new malaria species which closely related to ape P. vivax was found in chimpanzees, in addition, the host switches of P. vivax from ape to human was confirmed. These findings support the African origin of P. vivax. Previous phylogenetic analyses have shown the position of P. vivax within the Asian primate malaria parasite clade. This suggested an Asian origin of P. vivax. Recent analyses using massive gene data, however, positioned P. vivax after the branching of the African Old World monkey parasite P. gonderi, and before the branching of the common ancestor of Asian primate malaria parasites. This position is consistent with an African origin of P. vivax. We here review the history of phylogenetic analyses on P. vivax, validate previous analyses, and finally present a definitive analysis using currently available data that indicate a tree in which P. vivax is positioned at the base of the Asian primate malaria parasite clade, and thus that is consistent with an African origin of P. vivax.     

Floral structure and ontogeny in Globba (Zingiberaceae)

We present new comparative morphological and ontogenetic data on flowers and bulbils of Globba (Zingiberaceae) to clarify their homologies. Globba flowers are characteristically Zingiberaceous, possessing a single stamen and epigynous (``supragynopleural') nectaries, but are unusual as the anther bears triangular lateral outgrowths and the style is held tightly in position across the curvature of the filament like a bowstring. Floral ontogeny in Globba is similar to other Zingiberaceae. Characteristic features, such as anther wings, occur late in development, shortly before anthesis. Unusually Globba has zygomorphic style anatomy with only two abaxial vascular bundles, in contrast to most other Zingiberaceae, which possess three stylar traces. The ovary is unilocular and lacks septa. Bulbils have enclosing bracts and replace flowers in the lower part of the inflorescence; they consist of a shoot with an enlarged corky storage root forming the bulk of the propagule.     

Housekeeping genes for phylogenetic analysis of eutherian relationships

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.     

The genus Hedychium (Zingiberaceae) in Thailand

Sirirugsa, P. & Larsen K. 1995. The genus Hedychium (Zingiberaceae) in Thailand. -Nord. J. Bot. 15: 301–304. Copenhagen. ISSN 0107–05513.
Three new species of Hedychium from Thailand are described and illustrated, H. samuiense, H. tomentosum , and H. biflorum . A key to the species occurring in Thailand is provided.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

First molecular evidence for reassessing phylogenetic affinities between genets (Genetta) and the enigmatic genet-like taxa Osbornictis, Poiana and Prionodon (Carnivora, Viverridae)

Gaubert, P., Tranier, M., Delmas, A.-S., Colyn, M. & Veron, G. (2004). First molecular evidence for reassessing phylogenetic affinities between genets ( Genetta ) and the enigmatic genet-like taxa Osbornictis , Poiana and Prionodon (Carnivora, Viverridae). — Zoologica Scripta, 33 , 117–129.
The subfamily Viverrinae is a composite group of carnivores comprising the large and plantigrade terrestrial civets ( Civettictis , Viverricula and Viverra ) and the slender and generally more arboreal genets and genet-like taxa ( Genetta , Prionodon , Poiana , Osbornictis ), both having Asiatic and African representatives. The problematic phylogenetic relationships between genets and genet-like taxa are addressed for the first time from a molecular perspective through complete cytochrome b gene sequences. We used a large taxonomic sample set including some very rare and crucial species such as Osbornictis piscivora , Poiana richardsonii (museum specimen material) and Genetta johnstoni . The results from parsimony, distance and maximum likelihood analyses do not support the monophyly of the Viverrinae and contradict previous morphological hypotheses. The Asiatic linsangs ( Prionodon spp.) are excluded from the Viverrinae and represent either a basal Feliformia or Viverridae. The other genet-like taxa constitute a strongly supported monophyletic African group, in which the African linsang (represented by Poiana richardsonii ) is a sister group to the genets. The aquatic genet Osbornictis piscivora is included within the latter clade, and the genus Osbornictis should be considered a junior synonym of Genetta . African and Asiatic terrestrial civets are monophyletic, but their phylogenetic affinities with the genet-like clade are inconclusive using our data set. On the basis of our molecular results, morphological convergences and adaptations to peculiar habitats and ways of life within genets and genet-like taxa are discussed.     

Use of mitochondrial DNA sequences to test the Ceratomorpha (Perissodactyla:Mammalia) hypothesis

Wood (J. Mamm. 18, 106–118; 1937) united the superfamilies Tapiroidea sensu stricto and Rhinocerotoidea in the suborder Ceratomorpha and aligned the Ceratomorpha with the suborder Hippomorpha within the order Perissodactyla. Although the monophyly of the Ceratomorpha appears now well-supported in paleontological and morphological analyses, the molecular relationship among the three extant superfamilies Tapiroidea, Rhinocerotoidea, and Equoidea has not yet been examined due to the limited amount of molecular information on tapirs. In the present study, we examined the phylogenetic position of Tapiroidea, represented by the complete mitochondrial cytochrome b gene (1140 bp) of a lowland tapir ( Tapirus terrestris ), and a Indian tapir ( Tapirus indicus ), relative to modern horses, zebras, donkeys, and rhinoceroses. The phylogenetic analyses using standard parsimony, neighbour-joining and maximum likelihood algorithms revealed monophyly of the Perissodactyla and three clearly distinct lineages: the modern horses, tapirs, and rhinoceroses. However, the sister-taxon relationship of the tapirs to either the rhinoceroses or the horses was not resolved conclusively in the bootstrap analysis. Spectral analysis, in which phylogenetic information is displayed independently of any selected tree, revealed that the DNA sequences available do not contain enough phylogenetic signal for any of the alternative hypotheses on the basal diversification of perissodactyls. The short branch lengths among the three perissodactyl lineages suggest that they diverged within a relatively short period, a finding consistent with molecular divergence datings and the fossil evidence that indicates a major radiation of the early perissodactyls approximately 54–50 million years ago.     

Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes

Ursing, B. M., Slack, K. E. & Arnason, U. (2000) Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes. — Zoologica Scripta , 29 , 83–88.
Extant artiodactyls (even-toed hoofed mammals) are traditionally divided into three main lineages: Suiformes (pigs, peccaries and hippopotamuses), Tylopoda (camels and llamas) and Ruminantia (bovids, deer, tragulids and giraffes). Recent molecular studies have not supported a close relationship between pigs and hippopotamuses, however, instead grouping hippopotamuses with Cetacea (whales, dolphins and porpoises). In this study we have sequenced the complete mitochondrial genome of a tylopod — the alpaca (Lama pacos), the only artiodactyl suborder not previously represented by a complete mitochondrial sequence. This sequence was included in phylogenetic analyses together with the complete mitochondrial protein-coding sequences of other artiodactyls plus two cetaceans. Despite the length of the data set, the relationship between Suina (Suiformes sine Hippopotamidae), Tylopoda and Ruminantia/Hippopotamidae/Cetacea could not be fully resolved, however, a basal position of the alpaca (Tylopoda) relative to the other artiodactyls/cetaceans was unsupported.     

Tanacetum joharchii sp. nov. (Asteraceae–Anthemideae) from Iran, and its taxonomic position based on molecular data

Tanacetum joharchii Sonboli & Kazempour Osaloo sp. nov. (Asteraceae–Anthemideae) is described and illustrated from the Khorasan province, northeast Iran. Tanacetum joharchii is a suffruticulose species from rocky limestone mountains in Hezarmasjed and Binalud (Khorasan province) at altitudes of 1900–2500 m a.s.l. The diagnostic morphological characteristics that distinguish it from the allied species T. kotschyi are presented. In addition, a distribution map of T. joharchii and the related species is given. In order to provide some hypothesis on its phylogenetic position, a molecular phylogenetic analysis based on nrDNA ITS sequence data of 14 representatives of the genus Tanacetum was performed.     

Combining Biogeographic and Phylogenetic Data to Examine Primate Speciation: An Example Using Cercopithecin Monkeys

We combined phylogenetic and biogeographic data to examine the mode of speciation in a group of African monkeys, the Cercopithecini. If allopatric speciation is the major force producing species, then there should be a positive relationship between the relative divergence time of taxa and their degree of geographic range overlap. Alternatively, an opposite relationship between divergence time and geographic range overlap is consistent with sympatric speciation as the main mechanism underlying the cercopithecin radiation. We collected biogeographic and phylogenetic data for 19 guenon species from the literature. We digitized geographic range maps and utilized three different phylogenetic hypotheses based on Y chromosome, X chromosome, and mitochondrial (mtDNA) data. We used regressions with Monte Carlo simulation to examine the relationship between the relative time since divergence of taxa and their degree of geographic range overlap. We found that there was a positive relationship between relative divergence time and the proportion of geographic range overlap between taxa using all three molecular data sets. Our findings provide evidence for allopatric speciation being the common mode of diversification in the cercopithecin clade. Because most of these primates are forest adapted mammals, the cyclical contraction and expansion of African forests from the late Miocene to the present has likely been an important factor driving allopatric speciation. In addition, geographic barriers such as the Congo and Sanaga rivers have probably played a complementary role in producing new species within the clade.     

Deep divergence among mitochondrial lineages in African jackals

Recently, molecular analyses revealed that African and Eurasian golden jackals are distinct species. This finding suggests re‐investigation of the phylogenetic relationships and taxonomy of other African members of the Canidae. Here, we provide a study on the phylogenetic relationship between populations of African jackals Lupulella mesomelas and L. adusta inferred from 962 bp of the mitochondrial cytochrome b (cytb) gene. As expected from its disjunct distribution, with one population in eastern Africa and the other one in southern Africa, we found two mitochondrial lineages within L. mesomelas, which diverged about 2.5 million years ago (Ma). In contrast, in L. adusta with its more continuous distribution in sub‐Saharan Africa, we found only a shallower genetic diversification, with the exception of the West African population, which diverged around 1.4 Ma from the Central and East African populations. Both divergence ages are older than, for example the 1.1–0.9 million years between the grey wolf Canis lupus and the African golden wolf C. lupaster. One taxonomic implication of our findings might be that the two L. mesomelas populations warrant species status. However, genome‐wide data with adequate geographical sampling are needed to substantiate our results.     

The chromosomes of afrotheria and their bearing on Mammalian genome evolution

Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.