Preliminary phylogeny of Valerianaceae (Dipsacales) inferred from nuclear and chloroplast DNA sequence data

Valerianaceae is a relatively small (ca. 350 species), but morphologically diverse angiosperm clade. Sequence data from the entire ndhF gene, the trnL-F intergenic spacer region, the trnL intron, the matK region, the rbcL-atpB intergenic spacer region and internal transcribed spacer (ITS) region of nuclear ribosomal DNA were collected for 21 taxa within Dipsacaceae and Valerianaceae (1 and 20, respectively). These data were included in several phylogenetic analyses with previously published sequences from Dipsacales. Results from these analyses (maximum parsimony, maximum likelihood, and Bayesian analysis) are in strong agreement with many of the conclusions from previous studies, most importantly: (1) Valerianaceae is sister to Dipsacaceae; (2) Triplostegia is more closely related to species of Dipsacaceae than to Valerianaceae; and (3) Valeriana appears not to be monophyletic, with Valeriana celtica falling outside the remainder of the species of Valeriana sampled here (with very strong support). With the exception of V. celtica, these data support two major clades within Valeriana; one that is exclusively New World and another that is distributed in both the Old and New World. Although the species of Valerianaceae and its sister group Dipsacaceae plus Triplostegia, are widely distributed in the Northern Hemisphere, and the data imply that Valerianaceae diversified initially in Asia (the Himalayan Patrinia and Nardostachys falling at the base of the clade), the center of modern species diversity for the group is in the Andes of South America with as many as 175 species restricted to that region. Although the exclusively South American taxa form a clade in the chloroplast and combined ITS and chloroplast analyses, support values tend to be low. Future studies will need to include additional data, in the form of both characters and taxa, before any strong conclusions about the character evolution, diversification, and biogeography of the South American valerians can be made.     

Phylogeny of Thaumastodermatidae (Gastrotricha: Macrodasyida) inferred from nuclear and mitochondrial sequence data

Background

Phylogenetic relationships within Gastrotricha are poorly known. Attempts to shed light on this subject using morphological traits have led to hypotheses lacking satisfactory statistical support; it seemed therefore that a different approach was needed.

Methodology/Principal Findings

In this paper we attempt to elucidate the relationships within the taxonomically vast family Thaumastodermatidae (Macrodasyida) using molecular sequence data. The study includes representatives of all the extant genera of the family and for the first time uses a multi-gene approach to infer evolutionary liaisons within Gastrotricha. The final data set comprises sequences of three genes (18S, 28S rDNA and COI mtDNA) from 41 species, including 29 thaumastodermatids, 11 non-thaumastodermatid macrodasyidans and a single chaetonotidan. Molecular data was analyzed as a combined set of 3 genes and as individual genes, using Bayesian and maximum likelihood approaches. Two different outgroups were used: Xenotrichula intermedia (Chaetonotida) and members of the putative basal Dactylopodola (Macrodasyida). Thaumastodermatidae and all other sampled macrodasyidan families were found monophyletic except for Cephalodasyidae. Within Thaumastodermatidae Diplodasyinae and Thaumastodermatinae are monophyletic and so are most genera. Oregodasys turns out to be the most basal group within Thaumastodermatinae in analyses of the concatenated data set as well as in analyses of the nuclear genes. Thaumastoderma appears as the sister taxon to the remaining species. Surprisingly, Tetranchyroderma is non-monophyletic in our analyses as one group of species clusters with Ptychostomella while another appears as the sister group of Pseudostomella.

Conclusions/Significance

Results in general agree with the current classification; however, a revision of the more derived thaumastodermatid taxa seems necessary. We also found that the ostensible COI sequences from several species do not conform to the general invertebrate or any other published mitochondrial genetic code; they may be mitochondrially derived nuclear genes (numts), or one or more modifications of the mitochondrial genetic code within Gastrotricha.     

Phylogenetics and evolution of the Macaronesian members of the genus Aichryson (Crassulaceae) inferred from nuclear and chloroplast sequence data

Aichryson is a genus of annual or perennial herbs, comprising approximately 13 species. The genus is nearly endemic to Macaronesia, with the center of diversity on the Canary Islands. Previous studies indicate that Aichryson is monophyletic and sister to a clade comprising two other genera, Monanthes and Aeonium. However, phylogenetic relationships within the genus have yet to be investigated. Phylogenetic relationships were estimated for Aichryson using DNA sequence data from both the nuclear and chloroplast genome. Parsimony analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set. These combined analyses provide a well-resolved topology that is used to investigate patterns of evolution within the genus. For example, although typically herbaceous in habit, two members display a woody growth form. Our analyses indicate that woodiness is a derived feature in Aichryson that has arisen once. Furthermore, the data presented suggest that the Aichryson pachycaulon group, a group of five subspecies, are in fact not monophyletic and that a reexamination of classification is necessary. The present study indicates that the biogeographical patterns exhibited by Aichryson appear to be rare, occurring in only one other known genus.The authors would like to thank Susana Fontinha of the Madeiran Botanical Garden for plant material of Madeiran Aichryson; Drs. D. Crawford and J. Archibald, as well as two anonymous reviewers for helpful comments; Eastern Illinois Undergraduate Honors Research Fund, and University of Kansas Plant Biology Research Award. Additional financial support for this work was provided by the Department of Ecology and Evolutionary Biology and the Museum of Natural History and Biodiversity Research Center, University of Kansas and a Kansas NSF EPSCoR First Award (NSF 32171) to MEM.     

Phylogenetics and diversification of Cotyledon (Crassulaceae) inferred from nuclear and chloroplast DNA sequence data

Crassulaceae includes approximately 35 genera and 1500 species of leaf and stem succulent flowering plants. The family is nearly cosmopolitan in distribution, but is particularly diverse in southern Africa, where five genera comprising approximately 325 species are found. One of these genera, Cotyledon, includes 10 species that are largely confined to South Africa, where they are commonly found on rocky hillsides, coastal flats, and cliff faces. Species of Cotyledon are characterized by five-parted, pendulous, sympetalous flowers, but the genus is highly diverse in growth form, flower color and size, and leaf morphology. One particularly variable species, C. orbiculata, has been divided into five varieties based on leaf morphology and biogeography; however, the monophyly of this species as well as the relationships among the varieties have not previously been investigated. Parsimony analyses of a combined data set of DNA sequences from chloroplast and nuclear genome provided the first estimate of phylogeny for Cotyledon, and resulted in two minimum-length trees and a fully resolved phylogeny for the genus. Results indicate that C. orbiculata is not monophyletic and suggest the need for additional studies and a revised classification within the genus.     

Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data

Chloroplast gene matK sequence data were used to estimate the phylogeny of 112 species of Crassulaceae sampled from 33 genera and all six recognized subfamilies. Our analyses suggest that five of six subfamilies recognized in the most recent comprehensive classification of the family are not monophyletic. Instead, we recovered a basal split in Crassulaceae between the southern African CRASSULA: clade (Crassuloideae) and the rest of the family (Sedoideae). These results are compatible with recent studies of cpDNA restriction site analyses. Within Sedoideae, four subclades were also recovered: KALANCHOE:, Leucosedum, Acre, and AEONIUM:; evidence also exists for a TELEPHIUM: clade and SEMPERVIVUM: clade. The genus SEDUM: is highly polyphyletic with representatives spread throughout the large Sedoideae clade. Sympetaly and polymerous flowers have arisen multiple times in Crassulaceae and thus are not appropriate characters upon which to base subfamilial limits, as has been done in the past. One floral character, haplostemy, appears to be confined to the well-supported CRASSULA: clade. Our analyses suggest a southern African origin of the family, with subsequent dispersal northward into the Mediterranean region. From there, the family spread to Asia/eastern Europe and northern Europe; two separate lineages of European Crassulaceae subsequently dispersed to North America and underwent substantial diversification. Our analyses also suggest that the original base chromosome number in Crassulaceae is x = 8 and that polyploidy has played an important role in seven clades. Three of these clades are exclusively polyploid (SEMPERVIVUM: clade and two subclades within the KALANCHOE: and AEONIUM: clades), whereas four (Crassula, Telephium, Leucosedum, and ACRE: clades) comprise both diploid and polyploid taxa. Polyploidy is particularly rampant and cytological evolution especially complex in the ACRE: clade.     

应用ITS序列分析探讨偏花报春的系统位置

对于偏花报春Primula secundiflora Franch. 的系统位置,主要有两种意见,一种认为偏花报春具有典型的钟状花冠,应置于钟花报春组Sect．Sikkimensis;而另一种意见则依据其他特征将其置于灯台报春组sect．Proliferae。通过对偏花报春、灯台报春组4种植物和钟花报春组3种植物核糖体DNA中的内转录间隔区(ITS)的序列测定及分析,并结合形态学及染色体特征的比较论证,认为偏花报春应置于灯台报春组。     

Phylogeny of Cyttaria inferred from nuclear and mitochondrial sequence and morphological data

Cyttaria species (Leotiomycetes, Cyttariales) are obligate, biotrophic associates of Nothofagus (Hamamelididae, Nothofagaceae), the southern beech. As such Cyttaria species are restricted to the southern hemisphere, inhabiting southern South America (Argentina and Chile) and southeastern Australasia (southeastern Australia including Tasmania, and New Zealand). The relationship of Cyttaria to other Leotiomycetes and the relationships among species of Cyttaria were investigated with newly generated sequences of partial nucSSU, nucLSU and mitSSU rRNA, as well as TEF1 sequence data and morphological data. Results found Cyttaria to be defined as a strongly supported clade. There is evidence for a close relationship between Cyttaria and these members of the Helotiales: Cordierites, certain Encoelia spp., Ionomidotis and to a lesser extent Chlorociboria. Order Cyttariales is supported by molecular data, as well as by the unique endostromatic apothecia, lack of chitin and highly specific habit of Cyttaria species. Twelve Cyttaria species are hypothesized, including all 11 currently accepted species plus an undescribed species that accommodates specimens known in New Zealand by the misapplied name C. gunnii, as revealed by molecular data. Thus the name C. gunnii sensu stricto is reserved for specimens occurring on N. cunninghamii in Australia, including Tasmania. Morphological data now support the continued recognition of C. septentrionalis as a species separate from C. gunnii. Three major clades are identified within Cyttaria: one in South America hosted by subgenus Nothofagus, another in South America hosted by subgenera Nothofagus and Lophozonia, and a third in South America and Australasia hosted by subgenus Lophozonia, thus producing a non-monophyletic grade of South American species and a monophyletic clade of Australasian species, including monophyletic Australian and New Zealand clades. Cyttaria species do not sort into clades according to their associations with subgenera Lophozonia and Nothofagus.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Phylogenetic relationships within the leaf-mining flies (Diptera: Agromyzidae) inferred from sequence data from multiple genes

The leaf-mining flies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, flowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian analyses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. Specifically, both analyses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our findings and discuss host-use evolution in light of current agromyzid taxonomy and two recent hypotheses of relationships based on morphological data.     

The evolution of sex ratios and sex-determining systems

Sex determination is a fundamental process governed by diverse mechanisms. Sex ratio selection is commonly implicated in the evolution of sex-determining systems, although formal models are rare. Here, we argue that, although sex ratio selection can induce shifts in sex determination, genomic conflicts between parents and offspring can explain why single-factor systems (e.g. XY/XX or ZW/ZZ) are common even in species that experience selection for biased sex ratios. Importantly, evolutionary shifts in sex determination do not always result in the biased production of sons and daughters sensu sex ratio theory. Thus, equal sex ratios might be an emergent character of sex-determining systems even when biased sex ratios are favored by selection.     

Molecular phylogeny and evolution of Sorex shrews (Soricidae: insectivora) inferred from mitochondrial DNA sequence data

Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.     

Molecular systematics of the caracaras and allies (Falconidae: Polyborinae) inferred from mitochondrial and nuclear sequence data

The Polyborinae is the most diverse subfamily of the Falconidae in terms of both morphology and behaviour, and includes falconet‐shaped birds (Spiziapteryx), arboreal omnivores (Daptrius, Ibycter), as well as terrestrial generalists and scavengers (Caracara, Milvago and Phalcoboenus). The Polyborinae are endemic to the New World, with all but one species (Caracara cheriway) being restricted to Central and South America. Using over 7300 bp of mitochondrial and nuclear sequence data, we aim to clarify the taxonomy and biogeography of the Polyborinae. The genus Milvago was unexpectedly found to be polyphyletic, with Chimango Caracara Milvago chimango being related to the genus Phalcoboenus and Yellow‐headed Caracara Milvago chimachima being sister to Daptrius. Furthermore, very low genetic divergence was found among the four species of the genus Phalcoboenus, with the lowest divergence being between White‐throated Caracara Phalcoboenus albogularis and Mountain Caracara Phalcoboenus megalopterus. Our divergence time analyses revealed that the Polyborinae started to diversify in the Miocene, at about 14 Ma, and that the generalist/scavenger behaviour in the Falconidae appeared between 14 and 6.6 Ma. All speciation events within the caracaras occurred during the Pleistocene. This situation differs from the general pattern described for forest birds, in which most diversification events are older, occurring primarily in the Pliocene and Miocene.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.     

Phylogeny and evolution of Dyckia (Bromeliaceae) inferred from chloroplast and nuclear sequences

The genus Dyckia (Bromeliaceae) comprises more than 150 terrestrial or epilithic species with a strongly xeromorphic habit. Most of its members belong to the azonal rock vegetation of Neotropical savannas and forests of Brazil and adjacent countries. Dyckia is relatively species-rich compared with its closest relatives Encholirium (27 species) and Deuterocohnia (17 species). Here, we present the first molecular phylogenetic analysis of Dyckia using DNA sequence data from six plastid loci (matK gene, rps16 intron, petD intron, rpl32-trnL, rps16-trnK and trnD-trnT) and a portion of the nuclear gene phyC. A total of 124 accessions were included, corresponding to 79 taxa from six genera. Phylogenetic trees were generated using parsimony, likelihood and Bayesian methods. DNA sequence variation among Dyckia species turned out to be extremely low, and phylogenies were poorly resolved. The monophyly of Dyckia is supported, whereas evidence is provided that Encholirium is paraphyletic. Based on a dated plastid DNA tree, Dyckia experienced a recent radiation starting around 2.9 million years ago. Four major clades could be identified that roughly correspond to the geographic origin of the samples. A parsimony network based on plastid DNA haplotypes shows a star-like pattern, indicating recent range expansions. Our data are compatible with a scenario where Dyckia and Encholirium diverged in northeastern Brazil, whereas one lineage of Dyckia dispersed to southern Brazil from where a rapid colonization of suitable habitats was initiated. We discuss our results in relation to species delimitation in Dyckia.     

Evidence for three major clades within the snapping shrimp genus Alpheus inferred from nuclear and mitochondrial gene sequence data

The snapping shrimp genus Alpheus is among the most diverse of caridean shrimps, and analyses of taxa separated by the Isthmus of Panama have been used to estimate rates of molecular evolution. Although seven morphological groups have been informally suggested, no formal phylogenetic analysis of the genus has been previously attempted. Here we infer the phylogenetic relationships within Alpheus using sequence data from two nuclear genes, glucose-6-phosphate isomerase and elongation factor-1alpha, and from the mitochondrial gene cytochrome oxidase I. Three major clades corresponding to previously noted morphological features were identified. Discrepancies between earlier informal morphological groupings and molecular analyses largely consisted of species whose morphologies were not entirely typical of the group to which they had been assigned. The traditional placements of shrimp with highly sessile lifestyles and consequently simplified morphologies were also not supported by molecular analyses. Phylogenies for Alpheus suggest that specialized ecological requirements (e.g., symbiotic associations and estuarine habitats) and modified claw morphologies have evolved independently several times. These new analyses also support the sister species status of transisthmian pairs analyzed previously, although very similar pairs were not always resolved with the more slowly evolving nuclear loci. In addition, six new cryptic species were identified in the course of these studies plus a seventh whose status remains to be determined.     

Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology

Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30 m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily’s distribution is revealed. X = 9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.     

The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers

Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.