Molecular phylogeny of Enchytraeidae (Oligochaeta) indicates separate invasions of the terrestrial environment

Enchytraeidae is a family of soil inhabiting small‐ to medium‐sized oligochaete worms using degradable plant material as a food source and primarily adapted to terrestrial or semi‐terrestrial environments. The molecular phylogeny based upon both mitochondrial and nuclear genes indicates early segregations of the two genera Enchytraeus and Lumbricillus leaving the remaining genera included in this study as a later segregated major monophyletic branch. Extant members of the two former genera dominate in decaying seaweed in the littoral zone along the sea although members of in particular the genus Enchytraeus have also invaded other habitats. Historically the littoral zone of the sea is undoubtedly the first terrestrial or semi‐terrestrial habitat where dead plant material accumulates to any greater extent and Enchytraeus and Lumbricillus may represent early successful attempts to exploit this resource. Inland soils probably had to await the emergence of land plants in order to provide a similar food resource and here the major branch of enchytraeid genera diversified into a high number of species in the numerous decomposer networks of this varied environment. A subdivision into the genera Enchytraeus and Lumbricillus on the one hand and a branch of mainly inland genera on the other is supported by differences in two somewhat neglected morphological features. Firstly, in Enchytraeus and Lumbricillus the testes are enclosed in a testis sac within which the male cells mature, by one possible exception a unique feature among Oligochaeta, The other enchytraeid genera studied and Oligochaeta in general lack this sac and the male cells mature directly in the cavity of the testicular segment. Secondly, species of Enchytraeus and Lumbricillus generally have a higher reproductive output than species of the inland terrestrial branch and this may represent an adaptation to the unpredictable littoral zone compared to the more stable nature of inland habitats. In the older literature the genus Mesenchytraeus is considered to have a basic position within the entire family but our molecular data do not support this expectation. In Enchytraeidae the nephridia are elaborate organs of a characteristic and constant shape covering species from different genera in a pattern following the molecular phylogeny. Other much used morphological features such as shape of setae, anteclitellar origin of the dorsal vessel and various modifications of the intestine have arisen more than once.     

Phylogenetics of some Enchytraeidae (Annelida: Oligochaeta): A preliminary investigation of relationships to the Haplotaxidae

In phylogenetic considerations of the Oligochaeta and the family Enchytraeidae, Propappus has been considered the ancestral or even the archetypal enchytraeid genus. Three nominal species are presently included in Propappus Michaelsen, 1905, P. volki Michaelsen, 1916, P. arhyncotus Sokolskaja, 1972, and the type species of the genus, P. glandulosus Michaelsen, 1905. Examination of type material of P. glandulosus and P. volki, as well as other material of the latter, showed that these species have a single pair of testes in segment XI and a single pair of ovaries in segment XIII. According to current classifications of the Oligochaeta, these species of Propappus cannot be retained in the Enchytraeidae. A phylogenetic analysis including two species of Propappus and 29 species of Haplotaxidae suggest a sister group relationship between Propappus and some Enchytraeidae and Haplotaxidae.     

Oligochaetes (Naididae, Tubificidae, Opistocystidae, Enchytraeidae, Sparganophilidae and Alluroididae) of Guyana

About 50 species in more than 20 genera of the microdrile oligochaete families Tubificidae, Naididae, Opistocystidae, and Enchytraeidae and the freshwater megadrile families Sparganophilidae and Alluroididae were identified in recent collections made in Guyana. Only seven species in these families were previously recorded from Guyana. The aquatic oligochaete fauna has similar components to those of the southeastern United States, other locations in South America, and across lower latitudes in the northern hemisphere. A high diversity of species is found in the naidids especially in the genera Pristina and Pristinella, especially considering the small number of locations that have been sampled. The collections include approximately 12 new species of rhyacodrilines (Tubificidae), Dero, Pristina, Pristinella (Naididae), Brinkhurstia (Alluroididae), Hemienchytraeus and Aspidodrilus (Enchytraeidae). This is the first record of Aspidodrilus from outside of Africa and the first new record since 1952.     

Oligochaetes (Naididae,Tubificidae, Enchytraeidae and Alluroididae) of Guyana,Peru and Ecuador

More than 41 species in 23 genera of the microdrile oligochaete families Tubificidae, Naididae, Opistocystidae, and Enchytraeidae and the freshwater megadrile family Alluroididae have been identified in recent collections made in Peru, Guyana and Ecuador. Just less than 70% of our species records are new for one or more of these countries and one is a new, albeit tentative, generic record for the South American continent. About 16 species new to science remain to be described. One of these is only the second reported species of Brinkhurstia (Alluroididae) and possesses unusual, single, very elongate penial setae. All of our species records are pertinent to tests of different hypotheses about historical and phylogenetic relationships among organisms of northern and southern South America and North America. The species, including new ones, with limited distributions are of particular significance to such hypotheses.     

Molecular phylogeny and phylogeography ofLupinus (Leguminosae) inferred from nucleotide sequences of therbcL gene and ITS 1 + 2 regions of rDNA

Total DNA was extracted from 55 species of theLeguminosae (including 29 species ofLupinus). The chloroplast generbcL and the ITS 1 + 2 regions of nuclear RNA genes were amplified by polymerase chain reaction (PCR) and sequenced directly. The sequences obtained were evaluated with character state (Maximum Parsimony) and distance methods (Neighbour Joining). Phylogenetic trees obtained with both data sets and methods are mostly congruent.Genisteae andCrotalarieae are sister groups and share ancestry with theThermopsideae/Podalyrieae. The genusLupinus, which forms a monophyletic clade within theGenisteae, shows a distinct Old-New World disjunction and appears to be divided into several more or less distinct groups: (1) The species from the eastern part of South America. (2) The homogeneous rough-seeded group (Scabrispermae) of the Old World species which is well distinguished from the smooth-seeded group (Malacospermae). (3) Within the rather heterogeneous smooth-seeded lupins a smaller subgroup withL. angustifolius, L. hispanicus andL. luteus is recognized. (4) Also separated are North American lupins and South American species with a western distribution. Genetic distances imply that the genusLupinus evolved during the last 12–14 million years, ruling out the hypothesis that the present Old-New World disjunction can be interpreted as a result of the continental drift. The genetic data suggest an origin in the Old World and an independant colonisation of the Eastern parts of South America as opposed to North America and the Western parts of South America.     

Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia

The Larreoideae subfamily is the major representative of the family Zygophyllaceae in South America, where several of its members are common to dominant in arid regions of the Southern Cone. However, there are currently no phylogenetic analyses of the subfamily that may help to understand its origin and diversification. Additionally, there are taxonomic discrepancies around Bulnesia Gay (1845), one of its more important genera. Accordingly, we performed a phylogenetic analysis combining chloroplast (rbcL and trnL-F) and nuclear (ITS) DNA sequences. Bayesian and Parsimony analyses were performed to highlight the intergeneric relationships within Larreoideae. All genera with the exception of Bulnesia are monophyletic and we propose to redefine Bulnesia, dividing it in two genera. Furthermore, other taxonomic issues of the remaining genera are solved. This study represents the first approximation to clarify the phylogenetic relationships amongst all Larreoideae genera, producing a phylogenetic framework that can be used in future macro-ecological studies.     

Phylogenetic Relationships and the Radiation of Sigmodontine Rodents in South America: Evidence from Cytochrome b

Phylogenetic relationships among South American sigmodontine rodents were examined based on the complete sequence for the mitochondrial cytochrome b gene [1140 base pairs (bp)] for 66 species and between 759 and 1140 bp for an additional 19 species. Thirty-eight South American genera were represented, coming from eight of nine tribes. Outgroups included the North American murid rodents Peromyscus, Reithrodontomys, Scotinomys, and Neotoma, the Old World murine rodents Mus and Rattus, and the geomyoid genera Thomomys, Geomys, Dipodomys, and Perognathus as the most distant outgroup. The South American sigmodontines were supported as a monophyletic lineage. Within this radiation several clear-cut suprageneric groupings were identified. Many of the currently recognized tribal groupings of genera were found fairly consistently, although not always with high levels of bootstrap support. The various tribes could not be linked hierarchically with any confidence. In addition, several genera stand out as unique entities, without any apparent close relatives. The overall pattern suggests a rapid radiation of the sigmodontines in South America, followed by differentiation at the tribal and generic levels.     

North American Glyptodontines (Xenarthra, Mammalia) in the Upper Pleistocene of northern South America

The Glyptodontidae is one of the most conspicuous groups in the Pleistocene megafauna of the Americas. The Glyptodontinae were involved in the Great American Biotic Interchange (GABI) and their earliest records in North America are about 3.9 Ma, suggesting an earlier formation of the Panamanian landbridge. Taxonomically it is possible to recognize two Pleistocene genera of Glyptodontinae:Glyptodon (ca. 1.8 – 0.008 Ma), restricted to South America, andGlyptotherium (ca. 2.6 – 0.009 Ma), including records in both North and Central America. Here we present the first report of the genusGlyptotherium in South America, from the Late Pleistocene of several fossil localities in Falcón State, northwestern Venezuela. A comparative analysis of the material, represented by cranial and postcranial parts, including the dorsal carapace and caudal rings, suggests a close affinity withGlyptotherium cylindricum (Late Pleistocene of Central Mexico). This occurrence in the latest Pleistocene of the northernmost region of South America Supports the bidirectional faunal migration during the GABI and the repeated re-immigration from North America of South American clades, as has been reported in other members of the Cingulata (e.g., Pampatheriidae).      

A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia

The Anisophylleaceae comprise 29-34 species of shrubs and trees occurring in lowland forests and swamps in tropical Africa, Asia, and South America. These species are placed in four genera with disjunct geographic distributions; Anisophyllea has 25-30 species in South America, Africa, and Malesia; Combretocarpus has one species in Sumatra and Borneo; Poga one species in equatorial Africa; and Polygonanthus two in the Amazon Basin. Here we use a phylogeny based on six nuclear and plastid loci sequenced for 15 species representing the four genera to infer their relationships and the relative and absolute ages of the range disjunctions. Combretocarpus is sister to the other three genera, and Polygonanthus then sister to Poga and Anisophyllea. Ansiophyllea, represented by 12 species from all three continents, is monophyletic. A relaxed Bayesian clock calibrated with the oldest fossils from a relevant outgroup, Tetramelaceae, suggests that the disjunctions between Combretocarpus, Poga, and Polygonanthus date back to the Cretaceous, Mid-, and Upper Eocene, whereas the intercontinental disjunctions within Anisophyllea appear to date back only some 22-23 million years and thus probably result from long-distance dispersal.     

A new species of Acanthosyris (Santalaceae) from Bolivia and a key to the woody South American Santalaceae

Acanthosyris asipapote, a new species from the vicinity of Santa Cruz, Bolivia, is described and illustrated. It is most similar to A. paulo-alvinii Barroso, known only from the state of Bahia, Brazil, but differs by leaf characters, pilose filaments, and smaller seeds. A key to the five woody genera and nine species of Santalaceae in South America is provided. Cervantesia, Jodina, and Myoschilos are probably monotypic; Santalum (in South America) has a single species, and Acanthosyris has five species.     

Revised classification and evolution of leucotrichiine microcaddisflies (Trichoptera: Hydroptilidae) based on morphological and molecular data

Hydroptilidae constitute the most diverse caddisfly family, with over 2000 species known from every habitable continent. Leucotrichiinae are exclusively New World microcaddisflies, currently including over 200 species and 17 genera. Phylogenetic analyses of Leucotrichiinae relationships based on 114 morphological characters and 2451 molecular characters from DNA sequences were conducted. DNA sequences analysed were from one mitochondrial gene, cytochrome oxidase I (653 bp), and four nuclear genes, carbamoylphosphate synthase (802 bp), elongation factor 1α (352 bp), histone 3 (308 bp) and 28S rDNA (336 bp). The morphological matrix included 94 taxa (with representatives of all included genera) and the molecular matrix included 62 taxa. Individual and combined datasets were analysed under parsimony and Bayesian inference. In addition, a relaxed molecular clock divergence time estimate was conducted to determine the age of the subfamily and major lineages. All Bayesian inference analyses strongly suggest a monophyletic Leucotrichiinae, which initially diverged at approximately 124 Ma into two monophyletic groups of genera. These groups are herein elevated to tribal status, Alisotrichiini trib.n. and Leucotrichiini Flint sensu n. Several genera of Leucotrichiini were not recovered as monophyletic clades and some nomenclatural changes are proposed to reflect their phylogenetic history. These include the synonymy of Abtrichia with Peltopsyche; transfer of Betrichia hamulifera to Costatrichia; transfer of Betrichia alibrachia and Costatrichia falsa to Leucotrichia; and transfer of Costatrichia fluminensis to Acostatrichia. Additionally, Tupiniquintrichia gen.n. is described to include Peltopsyche maclachlani and Leucotrichia procera. According to our results, crown diversifications of both Alisotrichiini trib.n. (～80 Ma) and Leucotrichiini sensu n. (～103 Ma) occurred after complete separation of South America from Africa. Current distributions of most leucotrichiine genera are probably a result of migration from South America towards the north using the proto‐Caribbean archipelago (100 to 49 Ma). This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:FB6A3385-323D-41AF-B4BE-E19A393A493C .     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

Phylogeny of Schisandraceae based on morphological data: evidence from modern plants and the fossil record

Schisandraceae are traditionally subdivided in two genera, Schisandra and Kadsura, based on differences in the organisation of the floral receptacle, the carpels, and the presence or absence of a ``pseudostigma'. Recently, phylogenetic analyses utilizing ITS sequence data and morphological data resulted in incongruent tree topologies, with the morphological trees suggesting monophyly of the two genera, whereas ITS trees did not resolve Schisandra and Kadsura as monophyletic clades. In the present paper we study seed morphology and leaf epidermal features of 22 species of Schisandraceae in order to provide additional data for a morphological data matrix. Seed morphological characters are highly homoplastic and do not yield further evidence for monophyly of the two genera. Instead, a number of characters appear to support sister group relationships between taxa within the genera, such as, for instance, for K. coccinea and K. scandens, both of which have large seeds along with a multi-layered mesotesta. Considering leaf epidermal characteristics, species of Kadsura were found to be consistently amphistomatic, whereas species of Schisandra are always hypostomatic. Phylogenetic analysis using the extended data matrix resulted in weakly supported Kadsura and Schisandra clades with five and four synapomorphies indicating monophyly of Kadsura and Schisandra, respectively. Fossils ascribed to Schisandraceae date back to the Late Cretaceous. These are tri-and hexacolpate pollen types displaying a combination of features found in modern Schisandraceae and partly also in Illiciaceae. Leaf remains from this period are poorly preserved and difficult to ascribe to Schisandraceae because of the lack of synapomorphies for the family. In the Early Cainozoic, leaf and seed remains from North America and Europe unambiguously belong to the family. Seeds from the Eocene of North America show some similarities to the modern Schisandra glabra from North America, while fossils from Europe show more similarities to modern Asian species.     

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.     

Phylogenetics of Darwiniothamnus (Asteraceae: Astereae) – molecular evidence for multiple origins in the endemic flora of the Galápagos Islands

Aim The aims of this study were (1) to investigate whether the two growth forms of Darwiniothamnus Harling (Asteraceae) originated from the colonization of a single ancestor, (2) to identify the closest relative(s) of Darwiniothamnus, and (3) to review molecular phylogenies from other plant groups to infer the origin of Galápagos endemics. Location Darwiniothamnus is endemic to the Galápagos Islands. Methods All putative relatives of Darwiniothamnus plus 38 additional species were included. Nucleotide sequences of the internal transcribed spacers of the nuclear ribosomal DNA were used for Bayesian and parsimony analyses. Results Darwiniothamnus is polyphyletic. Two species (D. lancifolius (Hook. f.) Harling and D. tenuifolius (Hook. f.) Harling) are woody shrubs that usually grow to 1–2 m in height; they belong to a clade composed of species otherwise restricted to the Caribbean. These two species are sister to Erigeron bellidiastroides Griseb., a herbaceous species endemic to Cuba. The third species (D. alternifolius Lawesson & Adsersen) is a perennial herbaceous plant, woody at the base and reaching only up to 50 cm in height. It is sister to two Chilean (Coquimbo–Valparaiso region) species that also have a perennial herbaceous habit: E. fasciculatus Colla and E. luxurians (Skottsb.) Solbrig. They are placed in an assemblage restricted to South America. The review of previous molecular phylogenetic studies revealed that two of the endemic genera and endemic species of three non‐endemic genera have their closest relatives in South America. Endemic species belonging to three non‐endemic genera have sister species in North America or the West Indies. One endemic genus and endemic species in three non‐endemic genera have sister taxa with a widespread continental distribution, or their molecular phylogenies yielded equivocal results. Main conclusions The flora of Galápagos has affinities with both North America (including the Antilles) and South America. Darwiniothamnus exhibits both patterns: two species of this genus are sister to a taxon endemic to Cuba, supporting a connection between the Cocos plate and the West Indies; the third species, D. alternifolius, provides a link with the Coquimbo–Valparaiso region, suggesting a biogeographical connection between the Nazca plate and southern South America.     

New Discoveries in the Canellaceae in the Antilles: How Phylogeny can Support Taxonomy

Six genera have been described in the family Canellaceae, four of them from the Neotropics and the other two from Africa and Madagascar. The Caribbean genera are Canella, Pleodendron and Cinnamodendron. Canella is a monotypic genus widespread in the region, and Pleodendron is present in the Greater Antilles and Costa Rica. Cinnamodendron occurs in the Greater Antilles (Cuba, Hispaniola, and Jamaica) as well as in South America. A recent phylogenetic analysis of the family shows that Cinnamodendron is not monophyletic because the South American species and the Antillean species are recovered in two different clades. The Antillean species formed a clade sister to Pleodendron. The synapomorphies of the Antillean species of Cinnamodendron are tetramerous flowers with eight petals, eight stamens, four carpels, and four placentae. Based on the results from the phylogenetic analysis major taxonomy changes are expected for the family.

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Resumen  Seis géneros han sido descritos en la familia Canellaceae, cuatro de estos para el neotrópico y los otros dos para Africa y Madagascar. En las Antillas se encuentran los géneros Canella, Pleodendron y Cinamodendron. Canella es un género monotípico de amplia distribución en la región del caribe y pleodendron se encuentra presente sólo en las antillas mayores y Costa Rica. Cinnamodendron ha sido dado tanto para las Antillas mayores como para America del Sur. Un análisis filogenético previo de la familia indica que el género Cinnamodendron no es monofilético. Existe una separación de las especies Sudamericanas y Antillanas en clados diferentes. Las especies de las Antillas forman un clado que es hermano de Pleodendron. Los carácteres sinapomórficos de las especies antillanas de Cinnamodendron son: flores tetrámeras con ocho petalos, ocho estambres, cuatro carpelos y cuatro placentas. Basados en los resultados de la filogenia del grupo, se anticipan cambios taxonómicos para la familia.

     

Phylogeny and biogeography of Chinese and Australasian Polystichum ferns as inferred from chloroplast trnL-F and rps4-trnS sequence data

Polystichum, one of the largest genera of ferns, occurs worldwide with the greatest diversity in southwest China and adjacent regions. Although there have been studies of Chinese Polystichum on its traditional classification, geographic distributions, and even a few on its molecular systematics, its relationships to other species outside China remain little known. Here, we investigated the phylogeny and biogeography of the Polystichum species from China and Australasia. The evolutionary relationships among 42 Polystichum species found in China (29 taxa) and Australasia (13 taxa) were inferred from phylogenetic analyses of two chloroplast DNA sequence data sets: rps4-trnS and trnL-F intergenic spacers. The divergence time between Chinese and Australasian Polystichum was estimated. The results indicated that the Australasian species comprise a monophyletic group that is nested within the Chinese diversity, and that the New Zealand species are likewise a monophyletic group nested within the Australasian species. The divergence time estimates suggested that Chinese Polystichum migrated into Australasia from around 40 Ma ago, and from there to New Zealand from about 14 Ma. The diversification of the New Zealand Polystichum species began about 10 Ma. These results indicated that Polystichum probably originated in eastern Asia and migrated into Australasia: first into Australia and then into New Zealand.     

Multi-locus phylogeny clarifies the systematics of the Australo-Papuan robins (Family Petroicidae, Passeriformes)

The Australo-Papuan family Petroicidae (Aves: Passeriformes) has been the focus of much systematic debate about its relationships with other passerine families, as well as relationships within the family. Mostly conservative morphology within the group limits the effectiveness of traditional taxonomic analyses and has contributed to ongoing systematic debate. To assess relationships within the family, we sampled 47 individuals from 26 species, representing the majority of genera and species, for four loci: 528 base pairs (bp) of C-myc, 501 bp of BA20454 and 336 bp of BA23989 from nuclear DNA and 1005 bp of the mitochondrial ND2 gene. There was consensus between individual loci and overall support for major lineages was strong. Partitioned Bayesian analyses of all four loci produced a fully resolved and very well-supported phylogeny that addresses many of the previous systematic debates in this group. The Eopsaltriinae as construed is monophyletic with the exception of Eopsaltria flaviventris, which is nested within Microeca as an unremarkable member of that genus. This relationship is corroborated by morphology and egg color and pattern. Petroicinae as currently construed was not monophyletic and comprised two lineages that are paraphyletic with respect to each other. The third subfamily, Drymodinae, remains incertae sedis. The mangrove robin, Peneonanthe pulverulenta, of tropical Australia and New Guinea is nested within a clade that also contained the sampled species of Peneothello and Melanodryas, a novel relationship. Preliminary biogeographic and divergence time estimates from these results are discussed and a new subfamily arrangement proposed.