Academic literature on the topic 'Skinks Phylogeny Molecular aspects'

AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.

The phylogenetic relationships amongst 29 species of Carlia and Lygisaurus were estimated using a 726-base-pair segment of the protein-coding mitochondrial ND4 gene. Results do not support the recent resurrection of the genus Lygisaurus. Although most Lygisaurus species formed a single clade, this clade is nested within Carlia and includes Carlia parrhasius. Due to this new molecular evidence, and the paucity of diagnostic morphological characters separating the genera, Lygisaurus de Vis 1884 is re-synonymised with Carlia Gray 1845. Our analysis is also inconsistent with a previous suggestion that Lygisaurus timlowi should be removed to Menetia, a genus that is distantly related relative to outgroups used here. Intraspecific variation in Carlia is, in several instances, greater than interspecific distance. The most strikingly divergent lineages are found within C. rubrigularis, which appears to be paraphyletic, with southern populations more closely related to C. rhomboidalis than to northern populations of C. rubrigularis. The two C. rubrigularis–C. rhomboidalis lineages form part of a major polytomy at an intermediate level of divergence. Lack of resolution at this level, however, does not appear to be due to saturation or loss of phylogenetic signal. Rather, the polytomy probably reflects a period of relatively rapid diversification that occurred sometime during the Miocene.

The Himalayas represent a renowned biodiversity hotspot and an important biogeographic realm that has influenced origin and diversification of multiple taxa. A recent herpetological investigation of the eastern Himalayas of the Indian state of Arunachal Pradesh led to the discovery of a unique lineage of ablepharine skink, which is herein described as a new genus along with a new species. The findings are based an integrated taxonomic approach incorporating data from external morphology, microCT scans of the skull and molecular data. The molecular phylogeny of ablepharine skinks is also presented that suggests taxonomic amendments. Discovery of this unique lineage of skinks further highlights the biogeographic importance of the eastern Himalayas as a source for origin of several relic biota.

Skinks from the genera Eulamprus, Gnypetoscincus and Nangura are a prominent component of the reptile fauna of the mesic forests of the east coast of Australia and have been the subject of numerous ecological studies. Highly conserved morphology and the retention of ancestral traits have limited our understanding of the relationships within and among these genera beyond an initial identification of species groups within Eulamprus. To address this deficit and to explore the relationships between Eulamprus and the monotypic genera Nangura and Gnypetoscincus, sections of two mitochondrial genes (ND4 and 16S rRNA) were sequenced and subjected to Bayesian phylogenetic analysis. This phylogenetic analysis supports recognition of the three species groups proposed for Eulamprus (murrayi, quoyii and tenuis) and indicates that this genus is paraphyletic, with Gnypetoscincus and Nangura being proximal to basal lineages of the tenuis group. To resolve these and broader problems of paraphyly, we suggest that each of the species groups from 'Eulamprus' should be recognised as a distinct genus. The phylogenetically and ecologically distinct water skinks of the quoyii group would be retained within Eulamprus and the diverse species of the tenuis group allocated to Concinnia. We suggest placing the monophyletic murrayi group, endemic to the rainforests of central eastern Australia, in a new genus (yet to be formally described). The sequencing data also revealed the existence of a genetically divergent but morphologically cryptic lineage within E. murrayi and substantial diversity within E. quoyii. There is evidence for two major habitat shifts from rainforest towards drier habitats, one leading to the quoyii group and the second defining a clade of three species within the tenuis complex. These ecological transitions may represent adaptations to general drying across eastern Australia during the late Miocene–Pliocene. Each of the major areas of east coast tropical or subtropical rainforest contains multiple phylogenetically diverse endemic species, reflecting the long-term persistence and high conservation value of wet forest habitats in each area.

This thesis concerns the molecular phylogenetics of three tribes of the family Bovidae, the Antilopini, Neotragini, and Tragelaphini. None of these tribes have been studied extensively with molecular techniques. The tribe Antilopini is one of the most speciose tribes (it includes 6 genera with 20 species) and the classification of several species of the genus Gazella is not clear. The tribe Neotragini is thought to be paraphyletic. Mitochondrial sequences of the cytochrome c oxidase ill and cytochrome b genes totalling 1083 base pairs have been determined for 52 taxa and used to determine phylogenetic relationships using cladistic and distance methods. Karyological analysis identified polymorphisms in several species (especially in Gazella saudiya and G. subgutturosa). Karyotypes of G. dorcas pelzelni and an XXY karyotype of a G. dorcas individual are shown for the first time. The main conclusions are that the Antilopini and the Tragelaphini are monophyletic and that the tribe Neotragini is paraphyletic. There is a lack of phylogenetic resolution between tribes which is probably due to the rapid radiation of the different tribes about 20 million years ago. The genus Taurotragus in the tribe Tragelaphini is shown to be paraphyletic and it would be appropriate to incorporate these taxa in the genus Tragelaphus. The genus Gazella could be paraphyletic, due to the position of Antilope cervicapra, in which case the genus needs to be split into two genera or renamed as Antilope. It is also argued that the use of the subgenus Trachelocele should be discontinued and that its only species, G. subgutturosa should be included in the subgenus Gazella. G. rufifrons and G. thomsonii may be more appropriately considered as conspecific. Cytogenetic and sequence data reveal that the herd of G. saudiya in Al Areen Wildlife Park is hybridised with G. bennettii and it is argued that it is important to identify unhybridised G. saudiya in other collections, since this species is on the brink of extinction. This case study demonstrates the need to genetically screen individuals which are part of a captive breeding program, especially if they are intended for reintroduction into the wild.

Thesis (MSc)--Stellenbosch University, 2003.
ENGLISH ABSTRACT: The evolutionary history of the African tribe Tragelaphini (spiral-horn antelope) is controversial. Past phylogenetic relationships among species were based on morphology or limited fossil evidence and are in conflict with mitochondrial DNA sequencing studies that have been conducted more recently. Although the group is distinguished from other African ungulates by the presence of spirally-twisted horns, the nine recognized extant species differ considerably in morphology, feeding habits and their habitat preference. The present study aims to resolve the phylogenetic uncertainties of the Tragelaphini using nuclear DNA sequence data derived from four independent DNA loci (MGF, PRKCl, SPTBN and THY). These data were combined with all previously published DNA sequences to produce a molecular supermatrix comprising approximately 6000 characters. Both parsimony and model based phylogenetic analyses of the nuclear DNA support the associations resulting from the analysis of mitochondrial genes. These findings suggest that the morphological characters previously used to delimit species within the group are subject to convergent evolution. The molecular phylogeny presented herein suggests that early members of Tragelaphini diverged from the other bovids during the mid-Miocene approximately 15.7 million years before present (MYBP). The common nyala (Tragelaphus enqest; and lesser kudu (Tragelaphus imberbis) representing the most basal species, separated from the other tragelaphids approximately 7.1 MYBP. This was subsequently followed by the radiation of those species adapted to a more tropical environment and they include the mountain nyala (Tragelaphus buxtom), bongo (Tragelaphus euryceros), sitatunga (Tragelaphus spekel) and bushbuck (Tragelaphus scriptus), and the arid adapted clade comprising the giant eland (Taurotragus derbianus), common eland (Taurotragus oryx) and greater kudu (Tragelaphus strepsiceros). It is thought that this split occurred at the Miocene-Pliocene boundary approximately 5.4 MYBP. The timing of evolutionary events within the tribe suggests climatic oscillations and subsequent biotic shifts as the major driving forces underpinning speciation in the tribe Tragalaphini.
AFRIKAANSE OPSOMMING; Die evolusionêre geskiedenis van die ras Tragelaphini (spiraalhoringwildsbokke) is kontroversieël. Vorige filogenetiese verwantskappe tussen die spesies is gebaseer op morfologie of beperkte fossiel bewyse. Meer onlangse studies, gebaseer op mitochondriale ONS nukleotieddata, is in teenstryding met baie van die evolusionêre hypotese afkomstig van morfologiese studies. Alhoewel die groep van die ander hoefdiere uitgeken kan word deur die aanwesigheid van spiraalvormige horings, verskil die nege hedendaagse spesies grootliks ten opsigte van morfologie, voedingswyse en habitat. Die hoof doelwit van hierdie studie was om die filogenetise verwantskappe tussen die Tragelaphini spesies te ontleed deur gebruik te maak van nukluêre ONS nukleotieddata afkomstig van vier onafhanklike ONS merkers (MGF, PRKCl, SPTBN en THY). Die data verkry is saamgevoeg by vorige gepubliseerde ONS nukleotidedata om 'n "supermatris" van sowat 6000 karakters te produseer. Parsimonie en modelgebaseerde filogenetise analise van die nukluêre ONS nukleotieddata het ooreengestem met die resultate van vorige mitochondriale studies. Hierdie bevindings dui daarop dat die morfologiese karakters wat voorheen gebruik is om die evolusionêre verwantskappe tussen die Tragelaphini spesies te ontleed onderhewig is aan konvergente evolusie. Die molekulêre filogenie wat hierin beskryf word stel voor dat die ras Tragelaphini gedurende die mid- Miocene, omtrent 15.7 miljoen jaar (MJ) gelede van die ander lede van die subfamilie Bovinae geskei het. Tragelaphus angasi en Tragelaphus imberbis, die mees basale spesies in die filogenie, het omtrent 7.1 MJ gelede van die ander lede van die Tragelaphini geskei. Hierdie skeiding is gevolg deur 'n split tussen die spesies aangepas vir 'n meer tropiese habitat (Tragelaphus buxtoni, Tragelaphus euryceros, Tragelaphus spekei en Tragelaphus scriptus) en die spesies aangepas vir 'n droë habitat (Taurotragus derbianus, Taurotragus oryx en Tragelaphus strepsiceros) Hierdie finale skeiding het gedurende die Miocene-Pliocene oorgang plaasgevind. Die tydsberekening van die evolusionêre gebeurtenisse wat binne die Tragelaphini ras plaasgevind het, gekoppel aan paleoklimaatdata, dui aan dat veranderinge in klimaat en die geassosieerde habitatveranderinge verantwoordelik was vir die spesiasie patroon wat ons vandag in die Tragelaphini ras waarneem.

Thesis (MSc)--University of Stellenbosch, 2006.
ENGLISH ABSTRACT: The present study aims to determine the phylogenetic relationships among the sand lizards, Pedioplanis. In addition, a single mitochondrial gene is used to investigate the geographic genetic structure of the widey distributed P. burchelli. With 11 species, Pedioplanis is the most speciose genus among the southern African genera of the family Lacertidae. All the species are restricted to the subcontinent with the exception of three (P. namaquensis, P. undata and P. benguellensis), which extend their range northwards into Angola. A total of 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) are used to determine the phylogenetic relationships among ten of the eleven Pedioplanis species. The first well resolved gene tree for the genus, drawn from 100 individuals, is presented and this is largely congruent with a phylogeny derived from morphology. Contrary to some previous suggestions, Pedioplanis forms a monophyletic assemblage with Heliobolus and Nucras. The genus Pedioplanis is monophyletic with P. burchelli/P. laticeps forming a sister clade to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The “P. undata” species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical groupings that probably diverged during the mid-Miocene. The development of the Benguella Current could have initiated isolation mechanisms associated with changes in habitat that could have generated barriers and played a role in the evolution of this group. At the lower taxonomic level, the mtDNA phylogeographic structure of the wide spread P. burchelli in South Africa reveal at least six distinct clades that are geographically partitioned. The first one is restricted to the eastern mountains along the Great Escarpment (GE). The next three are found along the Cape Fold Mountains (CFM): the north-west CFM, central CFM and eastern CFM. The fifth one shares samples from central CFM and GE. The last clade is restricted to the eastern central mountains of the GE. These six geographic groupings are genetically divergent from each other and they started separating in the early Pliocene period. Phylogeographic studies on other taxa in the region have found different levels of genetic structuring among or within taxa. The fact that P. burchelli is restricted to high altitude areas could have resulted in limited dispersal and consequently contributed to its geographic structure. However, the exact cause of the pattern obtained is not readily apparent. Habitat fragmentation in the past is probably one of the most influential factors shaping the genetic distribution of the species across South Africa. The inclusion of nuclear markers will shed more light on the evolutionary history of P. burchelli in South Africa.
AFRIKAANSE OPSOMMING: Die huidige studie stel ten doel om ‘n filogenie daar te stel vir die Sand akkedisse, Pedioplanis. ‘n Enkele mitochondriale geen is ook gebruik om die geografiese genetiese struktuur van die wydverspreide P. burchelli vas te stel. Met 11 spesies is Pedioplanis die mees spesieryke genus onder die suidelike Afrika genera wat aan die Lacertidae familie behoort. Al die spesies is beperk tot die subkontinent met die uitsondering van drie (P. namaquensis, P. undata en P. benguellensis), wat ‘n uitgebreide verspreiding het noordwaarts tot in Angola. ‘n Totaal van 2200 nukleotied posisies wat afkomstig is van twee mitochondriale merkers (ND2 en 16S rRNA) en een nukluêre geen (RAG-1) is gebruik om die filogenetiese verwantskappe tussen 10 van die 11 Pedioplanis spesies vas te stel. Die eerste goed geondersteunde geen boom vir die genus, gebasseer op 100 individue, is verkry en dit is meestal ooreenstemmend met ‘n filogenie gebasseer op morfologie. In teenstelling met sekere voorstelle van die verlede vorm Pedioplanis ‘n monofiletiese groep tesame met Heliobolus en Nucras. Die genus Pedioplanis is monofileties met P. burchelli/P. laticeps wat ‘n suster groep vorm van al die oorblywende lede van die genus. Twee herkenbare geografiese lyne kan geidentifiseer word in die wydverspreide P. namaquensis; een kom in Namibia voor, terwyl die ander een in Suid Afrika voorkom. Die “P. undata” spesies kompleks is monofileties, maar een van die spesies wat deel uitmaak van die groep, P. inornata, is parafileties. Verwantskappe tussen die subspesies van P. lineoocellata is meer kompleks as wat aanvanklik aanvaar is. ‘n Geisoleerde bevolkimg wat voorheen toegesê is aan P. l. pulchella is parafileties en verteenwoordig ‘n suster groep van die benaamde subspesies. Die filogenie identifiseer twee biogeografiese groeperings wat moontlik gedivergeer het gedurende die middel-Miocene. Die ontwikkeling van die Benguella stroom het dalk versperrings geinisiëer as gevolg van die gesamentlike veranderinge in habitat wat dalk ook ‘n rol gespeel het in die evolusie van die groep. Op die laer taksonomiese vlak het die mtDNA filogeografiese struktuur van die wydverspreide P. burchelli in Suid Afrika ten minste ses groepe aangetoon wat geografies van mekaar geskei is. Die eerste een is beperk tot die oostelike berge wat aan die Groot Eskarpement (GE) behoort. Die volgende drie word gevind in die Kaapse Vouberge (KVB): die noord-westelike KVB, sentrale KVB en oostelike KVB. Die vyfde een deel eksemplare van beide die GE en die KVB. Die laaste groep is beperk tot die oostelike en sentrale berge van die GE. Hierdie ses geografiese groepe is geneties geskei van mekaar en hulle het begin om apart te ontwikkel gedurende die vroë Pliocene periode. Ander filogeografiese studies in die area het verskillende vlakke van genetiese struktuur vertoon tussen en binne taksa. Die feit dat P. burchelli beperk is tot hoogliggende dele kon moontlik bygedrae het tot die geografiese struktuur. Die presiese oorsaak van die patroon wat verkry is, is nie ooglopend nie. Habitat fragmentasie in die verlede is moontlik een van die mees invloedrykste faktore wat die genetiese verspreiding van die spesie in Suid Afrika beinvloed het. Die insluiting van nukluêre merkers sal meer lig warp op die evolusionêre geskiedenis van P. burchelli in Suid Afrika.

Thesis (DPhil)--University of Stellenbosch, 2008.
ENGLISH ABSTRACT: Sub-Antarctic islands represent the only mid to high latitude terrestrial biomes in the Southern Hemisphere. These islands have various geological origins and histories, well-preserved terrestrial ecosystems and high levels of species endemism. In an attempt to understand the evolution and biogeography of terrestrial taxa in the South Polar Region, the first broad-scale molecular phylogeny was constructed for the unique terrestrial group, the ameronothroid mites (genus Halozetes (Oribatida)), collected from sub-Antarctic and Maritime Antarctic localities. Phylogenetic analyses based on a combined mitochondrial (cytochrome oxidase subunit I (COI)) and nuclear (histone-3 (H3)) sequence dataset indicated that the evolution of these mites were habitat specific (i.e. intertidal, supralittoral and terrestrial). Notwithstanding criticisms levelled against a molecular clock, the mites were evolutionary young (<10myo), contrary to their status as an ancient group predating Gondwana fragmentation. Biogeographic analyses indicated a complex pattern mainly sculpted by multiple independent dispersal events across the Antarctic Polar Frontal Zone similar to previous findings for other marine and terrestrial taxa. Also, the molecular phylogeny displayed considerable discourse with contemporary taxonomy suggesting the need for taxonomic revisions and reassessment of morphological characters. Sub-Antarctic Marion Island, the larger of the two islands comprising the Prince Edward Island archipelago (PEI), has experienced extensive glaciation and volcanism. To assess the impact of historical events (volcanism (including recent eruptions) and glaciation) and contemporary mechanisms (gene flow) on the genetic spatial distribution of species from Marion Island, two mite species namely Eupodes minutus (Prostigmata) and Halozetes fulvus (Oribatida) as well as a single plant species, Azorella selago (Apiaceae), were selected as model organisms. For independent phylogeographic analyses, mitochondrial sequence data (COI) were obtained for both mite species, while chloroplast sequence (trnH-psbA) and amplified fragment length polymorphism (AFLP) data were generated for the cushion plant, A. selago. Since A. selago is typified by two growth forms namely discrete cushions and continuous mats, it was essential to examine the growth dynamics prior to phylogeographic analyses. The sequence and fragment data indicated that both mite and plant species were significantly substructured across Marion Island. Manual comparisons indicated unique populations on the western (Kaalkoppie for H. fulvus, La Grange Kop for E. minutus and Mixed Pickle for A. selago), eastern (Bullard Beach for H. fulvus and Kildalkey Bay for E. minutus), northern (Middelman and Long Ridge for H. fulvus) and southern side (Grey Headed for H. fulvus and Watertunnel for A. selago) of the island. Importantly, the western side had unique localities for all species. Interestingly, based on the H. fulvus data, the western populations were relatively young, characterized by high migration rates, small effective (female) population sizes with no isolation-by-distance. The opposite scenario was found for the eastern populations. This spatial genetic structure described for species on Marion Island can be ascribed to both historical events and environmental conditions. These areas with their unique genetic composition are of special conservational concern; consequently this research will contribute to an active management plan for PEI, South Africa’s only Special Nature Reserve.
AFRIKAANSE OPSOMMING: Sub-Antarktiese eilande verteenwoordig die enigste terrestriële bioom in die middel tot hoër breedtegrades van die Suidelike Halfrond. Hierdie eilande besit ‘n verskeidenheid van geologiese oorspronge en geskiedenisse, goed-bewaarde terrestriële ekosisteme en hoë vlakke van endemisme. In ‘n poging om die evolusie en biogeografie van terrestriële taksa in die Suid Pool Area te verstaan, is die eerste grootskaalse molekulêre filogenie saamgestel vir ‘n unieke terrestriële groep, die ameronothoïed miete (genus Halozetes (Oribatida: Ameronothroidea)), vanaf menigte sub-Antarktiese en Maritime Antarktiese lokaliteite. Filogenetiese analises gebaseer op die saamgestelde mitochondriale (sitokroom oksidase subeenheid I (COI)) en nukluêre (histoon-3 (H3)) basispaarvolgordes het aangedui dat die evolusie van hierdie miete habitat spesifiek is (m.a.w inter-gety, supralitoraal en terrestrieël). Ongeag die kritiek teenoor ‘n molekulêre klok, is hierdie miete evolusionêr jonk (<10mjo), wat teenstrydig is met hulle status as ‘n antieke groep wat terugdateer voor Gondwana fragmentasie. Biogeografiese analises het ‘n komplekse patroon aangedui wat grotendeels gekarakteriseer word deur menigte onafhanklike verspreidingsgebeurtenisse bo-oor die Antarktiese Polêre Frontale Zone, wat ooreenstemmend is met vorige bevindinge vir ander mariene en terrestriële taksa. Die molekulêre filogenie het ook aansienlik verskil van die tradisionele taksonomie, dus is taksonomiese aanpassings en herklassifisering van morfologiese karakters noodsaaklik. Sub-Antarktiese Marion Eiland, die groter eiland van die Prins Edward eilandgroep (PEI), het uitermate glasiasie en vulkanisme ondervind. Om die impak van historiese gebeurtenisse (vulkanisme (insluitend onlangse uitbarstings) en glasiasie) en kontemporêre meganismes (geenvloei) op die genetiesgespasieërde verspreiding van spesies vanaf Marion Eiland te bepaal, was twee mietspesies naamlik Eupodes minutus (Prostigmata) en Halozetes fulvus (Oribatida) asook ‘n enkele plantspesie, Azorella selago (Apiaceae), gekies as model organismes. Vir onafhanklike filogeografiese analises, was die mitochondriale basispaarvolgorde (COI) vir beide mietspesies bepaal, terwyl chloroplast basispaarvolgorde (trnH-psbA) asook geamplifiseerde fragmentlengte polimorfisme (AFLP) data gegenereer was vir die kussingplant, A. selago. Aangesien A. selago gekenmerk word deur twee groeivorme, naamlik diskrete kussings en aaneenlopende matte, was dit noodsaaklik om eers die groeidinamika van die plant te ondersoek alvorens ‘n filogeografiese studie kon geskied. Die basispaarvolgordebepalings en fragmentdata het aangedui dat beide mietspesies sowel as die plantspesie betekenisvolle substruktuur vertoon regoor Marion Eiland. Informele vergelykings het unieke populasies aangedui op die westelike (Kaalkoppie vir H. fulvus, La Grange Kop vir E. minutus en Mixed Pickle vir A. selago), oostelike (Bullardstrand vir H. fulvus en Kildalkeybaai vir E. minutus), noordelike (Middelman en Long Ridge vir H. fulvus) en suidelike kant (Grey Headed vir H. fulvus en Watertunnel vir A. selago) van die eiland. Die westelike kant besit dus unieke lokaliteite vir al die spesies. Interressantheidhalwe het die H. fulvus data getoon dat die westelike populasies relatief jonk is en gekarakteriseer word deur hoë migrasiesyfers en klein effektiewe (vroulike) populasiegroottes met geen isolasie-oor-afstand nie. Die resultate vir die populasies aan die oostelike kant van die Marion Eiland was presies teenoorgesteld. Dié beskryfde substruktuur vir die spesies op Marion Eiland is afkomstig van beide historiese gebeurtenisse asook omgewingstoestande. Hierdie areas met hul unieke genetiese samestelling, is belangrik vir natuurbewaring. Hierdie navorsing sal bydra tot die bestuursriglyne van PEI, Suid Afrika se enigste Spesiale Natuurreservaat.

Orientador: Renato Goldenberg
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Miconia é um é um dos maiores gêneros de angiospermas. Tradicionalmente, tem sido considerado complexo e mal circumscrito, assim como outros gêneros aparentados. Estudos filogenéticos recentes, baseados em marcadores moleculares, têm atestado a natureza polifilética de Miconia e suas onze seções. Neste trabalho, é apresentado um estudo filogenético-molecular aprofundado de um dos grupos naturais encontrados em estudos anteriores, o "subclado Miconia discolor", do "clado Miconia IV". Para tanto, foram utilizados sequências de quatro marcadores plastidias (psaI-accD; psnK-L; atpF-H; trnS-G) e dois nucleares (ITS e ETS). Os resultados obtidos permitiram esclarecer o relacionamento interno e externo do grupo. Por meio da otimização de caracteres morfológicos e biogeográficos, são sugeridas hipóteses evolutivas, como a evolução de inflorescências glomeruladas e pseudantos a partir de inflorescências com ramos escorpióides amplos, e a irradiação da diversidade na Floresta Atlântica a partir de poucas colonizações. Os resultados também permitiram a primeira proposição moderna de classificação ingra-genérica para Miconia, através da formalização e circunscrição de novos táxons: Miconia sect. Discolor, e subseções Albicans, Chrysophylla, Discolor e Multispicata, subordinadas à nova seção. Adicionalmente, uma revisão taxonômica é apresentada para a recém proposta subseção Discolor, incluindo descrições, ilustrações, imagens de Microscopia Eletrônica de Varredura, comentários, e uma chave dicotômica de identificação para as espécies. A subseção é composta 32 espécies, das quais três são novas. Trinta e dois nomes heterotípicos foram sinonimizados, e 39 lectotipificações foram propostas. A subseção pode ser reconhecida por apresentar as folhas densamente cobertas por tricomas ramificados na face abaxial (nunca formando um indumento aracnóide), inflorescências geralmente glomeruladas, raramente curtamente scorpióides, lobos do cálice caducos no fruto, e uma distribuição restrita ao sudeste da América do Sul, ocorrendo na Floresta Atlântica e no Cerrado
Abstract: Miconia is one of the biggest genera in angiosperms. It has been traditionally considered very complex and badly circumscribed, and other close genera as well. Phylogenetic studies based on molecular markers have been confirming the polyphily of Miconia and its eleven sections. Here I present a deeper molecular and phylogenetic study of a natural group found out in older studies, the "Miconia discolor subclade", from the "Miconia IV clade". I used sequences of four plastid (psaI-accD; psnK-L; atpF-H; trnS-G) and two nuclear markers (ITS and ETS). The results clarified the inner and outer relationship of that group. Evolutionary hypotheses are suggested by the optimization of morphological and biogeographical charcaters. For example, the evolution of glomerulate inflorescences and pseudanthia from inflorescences of wide, scorpioid branches, and the diversification of the genus in the Atlantic Forest from few colonizations. Additionally, the results allowed the first modern infra-generic rearrangement by the proposition and circumscription of new taxa: Miconia sect. Discolor, with the subsections Albicans, Chrysophylla, Discolor and Multispicata. A revision of the new Miconia subsect. Discolor is presented, with descriptions, illustrations, Scanning Electron Microscopy images, comments, and a taxonomic key for species. The subsection has 32 species and three of them are new. I synonymized 32 heterotypic names proposed 39 lectotipifications. The subsection can be recognized by the abaxial leaf surface usually densely covered by branched trichomes (never forming a cobweb indument), inflorescences usually glomerulate, rarely shortly scorpioid, calyx lobes caducous in fruit, and a distribution restricted to the southeast of South America, in the Atlantic Forest and Cerrado
Doutorado
Biologia Vegetal
Doutora em Biologia Vegetal

Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and population genetic methodologies. Chapter two characterizes positive destabilizing selection on the luxA gene of bioluminescent bacteria. Our data suggests that bacterial ecology and environmental osmolarity are likely driving the evolution of the luxA gene in bioluminescent bacteria. Chapter 3 examines relationships among bacteria within the genus Photorhabdus. Our analyses produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus. Additionally, we show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Chapter 4 characterizes the morphology of the head and feeding apparatus of fungal feeding and insect infective female morphs of the nematode Deladenus siricidicola using scanning electron microscopy. Results showed dramatic differences in head, face, and stylet morphology between the two D. siricidicola female morphs that were not detected in previous studies using only light microscopy. Chapter five utilizes comparative transciptomics to identify putative plant and insect parasitism genes in the nematode Deladenus siricidicola. Results from this study provide the first transcriptomic characterization for the nematode Deladenus siricidicola and for an insect parasitic member of the nematode infraorder Tylenchomorpha. Additionally, numerous plant parasitism gene homologues were discovered in both D. siricidicola libraries suggesting that this nematode has co-opted these plant parasitism genes for other functions. Chapter six utilizes a phylogenomic approach to estimate the phylogeny of the nematode infraorder Tylenchomorpha.

Orientador: Shirlei Maira Recco Pimentel
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Dendropsophus minutus está amplamente distribuído ao Leste dos Andes, na América do Sul e possui uma grande diversidade acústica e morfológica, o que sugere que possa haver mais de uma espécie sob esse nome. Sua coloração dorsal pode ser classificada em dois padrões principais, hourglass e bivittata. No presente estudo, 14 parâmetros morfométricos e seqüências de DNA com 357 pares de bases do gene citocromo b mitocondrial foram analisados objetivando um melhor entendimento acerca da variação de D. minutus no Brasil. Tanto os resultados moleculares quanto os fenotípicos revelaram a presença de uma alta estruturação da diversidade dessa espécie, mostrando que a divergência entre populações é, geralmente, proporcional à distância geográfica, exceto no estado de São Paulo, sudeste do Brasil. Nessa região, a Serra do Mar está aparentemente agindo como uma barreira geográfica para o fluxo gênico, isolando duas linhagens. A primeira, formada pelas populações da Mata Atlântica, tem padrão hourglass de coloração dorsal. A segunda, do interior de São Paulo, assim como a população do Rio Grande do Sul, possui padrão bivittata de coloração dorsal. Esses resultados corroboram a hipótese de que o táxon D. minutus contém duas linhagens crípticas. Apesar disso, uma amostragem maior se faz necessária, bem como um melhor estudo de caracteres para defini-las como espécies ou não.
Abstract: In despite of its complex reproductive behavior, Dendropsophus minutus has a large distribution at East of Andes, South America and show high acoustic and morphologic diversity, suggesting that possibly more than one species may exist under this name. Its dorsum coloration has basically two main patterns, hourglass or bivittata. Here, 14 morphometric parameters and partial mitochondrial cytochrome b gene sequences (357 base pairs) were analyzed aiming to understand more about Brazilian D. minutus variation. Both molecular and morphologic results agree with a high structuration of this species diversity, showing population divergence generally proportional to their geographic distance, except in São Paulo State, southeastern Brazil. At this region, Serra do Mar high mountains are apparently acting as a barrier for dispersion, isolating two lineages. The first of them, formed by populations from Atlantic Rainforest domain, has an hourglass dorsum pattern, whereas the second, comprising inner São Paulo State populations gathered with D. minutus from Rio Grande do Sul (South Brazil), shows bivittata dorsum coloration pattern. These results corroborate the hypothesis that D. minutus could comprise more than one species, revealing two cryptic lineages. However, these lineages should not be defined as different species before sampling enlargement to the present study.
Mestrado
Biologia Celular
Mestre em Biologia Celular e Estrutural

Abstract According to palaeontological evidence, Chaetognatha (arrow worms), a group of small marine predators that are major components of the zooplankton throughout our world oceans, were already present in the Early Cambrian Chengjang, in the Middle Cambrian Burgess Shale. These animals are considered to be the earliest active predator metazoans and displayed a planktonic lifestyle with possible ecological preferences for hyperbenthic niches close to the sea bottom. Today, the taxon Chaetognatha comprises more than 150 described species from all geographical and vertical ranges of the ocean, and they are among the most abundant pelagic organisms. Chaetognatha are characterized by the presence of horizontally projecting fins and, at the anterior end, two groups of moveable, cuticularized grasping spines used in capturing prey. In spite of an increasing number of molecular studies and an emerging consensus for protostome affinities, the phylogenetic position of the Chaetognatha is still one of the most enigmatic issues in metazoan phylogeny. The chaetognath genome is likely the product of a unique evolutionary history and shows the long isolation of this group. Furthermore, morphological characteristics provide evidence for a long evolutionary distance that separates the Chaetognatha from its closest (unknown) metazoan relative and suggest that this taxon in many aspects seems to have explored its own evolutionary pathways in generating tissue and organ diversity. Both the genome and morphological characters include many autapomorphies of this group, in addition to a bizarre character mix of protostome and deuterostome features. Here, the current knowledge of the nervous system is reviewed in these remarkable creatures.

Molecular phylogeny of entomopathogenic fungi Metarhizium, Beauveria (199 Isolates) from different biocenoses of two climatic zones of the Novosibirsk Region (Western Siberia) was conducted using translation elongation factor gene (EF1a) sequence. Three species of Metarhizium and two species of Beauveria were identified: M. robertsii (54 isolates) M. brunneum (35 isolates) and M. pemphigum (2 isolates) B. bassiana (19 isolates) and B. pseudobassiana (9 isolates). Analisys of spatial distribution showed that M. robertsii preferred more xerophile habitats compared to M. brunneum. Moreover, genetic groups with different habitat association were revealed within M. robertsii. There are no differences in habitat association were registered for Beauveria species.