Thesis (M.S.)--Oregon State University, 2009. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Thesis (M.S.)--Wake Forest University. Dept. of Biology, 2003. / Vita. Includes bibliographical references (leaves 20-22).

Thesis (Ph. D.)--Brigham Young University. Dept. of Integrative Biology, 2006. / Includes bibliographical references (p. 122-130).

Το γένος Trachelipus περιλαμβάνει οργανισμούς σχετικά στενόοικους οι οποίοι ζουν είτε στην παρόχθια βλάστηση ρεμάτων και ποταμών είτε σε υγρά δάση. Στη χώρα μας έχουν καταγραφεί 8 από τα 50 είδη του γένους, 4 από τα οποία είναι ενδημικά της Ελλάδας. Το ένα από αυτά εξαπλώνεται από την Κρήτη μέχρι την Ήπειρο, ένα στα νησιά του κεντρικού Αιγαίου, ένα στην Κρήτη και ένα στο νότιο Ευβοϊκό. Η κατανομή κάθε είδους είναι ασυνεχής, είτε λόγω γεωγραφικών (νησιωτικοί πληθυσμοί κλπ) είτε λόγω ενδιαιτηματικών παραγόντων. Η διάκριση μεταξύ των ειδών έχει γίνει βάσει περιορισμένου αριθμού μορφολογικών χαρακτήρων και δεν είναι βέβαιο ότι αντανακλά τις πραγματικές φυλογενετικές σχέσεις τους. Από τα αποτελέσματα προηγούμενης μελέτης διαπιστώθηκε έντονη απόκλιση μεταξύ των προτύπων της γενετικής ποικιλότητας και εκείνης της τρέχουσας ταξινόμησης σε ορισμένες ομάδες πληθυσμών του γένους αυτού. Επιπλέον, φάνηκε σημαντικός βαθμός γενετικής απομόνωσης μεταξύ των πληθυσμών ενός είδους, ενισχύοντας την άποψη περί ισχυρής μεταπληθυσμιακής συγκρότησής τους. Στην παρούσα μελέτη, συλλέχθηκαν 47 πληθυσμοί στην ηπειρωτική Ελλάδα, οι οποίοι στη μεγάλη τους πλειοψηφία ανήκαν στο είδος Trachelipus kytherensis (σύμφωνα με την ισχύουσα ταξινόμηση). Σε αυτούς προστέθηκαν και τα δεδομένα των Parmakelis et al 2008 (16 πληθυσμοί) έτσι ώστε να είναι πιο ολοκληρωμένη η μελέτη και η εξαγωγή συμπερασμάτων για το γένος Trachelipus. Συνολικά μελετήθηκαν γενετικά 63 πληθυσμοί του γένους, χρησιμοποιώντας ως μοριακούς δείκτες τα μιτοχονδριακά γονίδια 16S rRNA και COI. Έπειτα από απομόνωση του DNA και τον πολλαπλασιασμό των συγκεκριμένων τμημάτων με PCR προσδιορίστηκε η αλληλουχία των βάσεων, και υπολογίστηκε η γενετική διαφοροποίηση εντός και μεταξύ των πληθυσμών. Για την ανάλυση των φυλογενετικών σχέσεων μεταξύ των πληθυσμών ή/και των ειδών χρησιμοποιήθηκαν οι μέθοδοι της Σύνδεσης Γειτόνων (Neighbor Joining-NJ), της Μέγιστης Φειδωλότητας (Maximum Parsimony-MP) και της Μπεϊεσιανής Συμπερασματολογίας (Bayesian Inference-BI). Το τελικό μήκος των αλληλουχιών μετά την επεξεργασία ήταν 386 θέσεις για το γενετικό τόπο 16S rRNA και 512 θέσεις για το γενετικό τόπο COI. Με τα δεδομένα αυτά δεδομένα πραγματοποιήθηκε τόσο ανεξάρτητη όσο και συνδυασμένη ανάλυση. Από τα αποτελέσματα φαίνονται πληθυσμοί οι οποίοι παρα το ότι είναι πολύ κοντινοί γεωγραφικά, και μέχρι σήμερα θεωρείται πως ανήκουν στο ίδιο είδος (Trachelipus kytherensis), εμφανίζουν μεγάλες γενετικές αποστάσεις μεταξύ τους και ομαδοποιούνται σε διαφορετικούς και αρκετά απομακρυσμένους κλάδους των δένδρων σε όλες τις αναλύσεις (NJ, MP, BI). Η τοπολογία των κλάδων, καθώς και η απουσία σαφούς γεωγραφικού προτύπου στην ομαδοποίηση των πληθυσμών του T. kytherensis, καταδεικνύει ότι πιθανότατα δεν έχουμε να κάνουμε με ένα μόνο είδος, αλλά με περισσότερα που είναι δύσκολο να διακριθούν μορφολογικά, τουλάχιστον με τους μέχρι σήμερα χρησιμοποιούμενους ταξινομικούς διαγνωστικούς χαρακτήρες. Αυτό ενισχύεται και από τις γενετικές αποστάσεις που καταγράφηκαν στην παρούσα μελέτη και εμφανίζονται ιδιαίτερα αυξημένες (μέγιστες παρατηρηθείσες γενετικές απόστασεις: 27,3% COI, 17,6% 16S rRNA) ακόμα και σε σχέση με αυτές που έχουν αναφερθεί σε άλλες έρευνες για τη διάκριση ειδών ισοπόδων. Επισημαίνεται η ιδιαίτερα μεγάλη γενετική διαφοροποίηση μεταξύ των αντιπροσώπων του γένους. Επιπλέον καταδεικνύεται πως η Πελοπόννησος φιλοξενεί τα είδη Trachelipus ‘kytherensis’ και T. aegaeus (τουλάχιστον στη χερσόνησο της Αργολίδας) αλλά και πιθανόν μια τρίτη μορφή στα βόρεια (νέο είδος;) η οποία εμφανίζεται ευρύτερα στην ηπειρωτική Ελλάδα. Θα είχε ιδιαίτερο ενδιαφέρον λοιπόν να μελετηθούν αυτές οι πιθανές «ζώνες επαφής» ως προς τη γονιδιακή τους ροή, ώστε να εκτιμηθεί το ποσοστό απομόνωσης των πληθυσμών και, κατ’ επέκταση, του κάθε είδους. / The phylogenetic relationships among terrestrial isopod species are still largely unknown because robust analyses have started to appear only relatively recently. Species-level taxonomy has been based mainly on a few secondary sexual characters of males, although recent analyses based on molecular markers have indicated that species definitions based on morphology may underestimate the true levels of divergence among populations. Furthermore, within several genera or species groups, morphological characters do not provide clear-cut taxonomic resolution, so that many changes in the interpretation of nominal species have appeared in the literature. The genus Trachelipus comprises of relatively stenoecious animals living in habitats generally threatened by human activities, such as humid forest sites and riparian habitats. It includes some 50 species distributed around the Palaearctic, with 8 species recorded from Greece, 4 endemic to the country. The distribution of species is discontinuous due to the increasing fragmentation of its habitats and the expansion of agricultural land and dry woodland. Projected climatic change will restrict further gene flow between Trachelipus populations, as dry habitats are expected to expand in Greece. Species–level taxonomy has been based on a few morphological characters, mainly the secondary sexual characters of males, exhibiting significant variation, and is controversial. Very high intraspecific genetic divergence among several populations has been documented. In this study we attempt a phylogeographic analysis among the Greek endemic species of the genus. We sampled 47 populations from several sites in mainland Greece. In our analyses we incorporated data from previous work (16 populations) in order to better estimate possible geographic structure in the patterns of divergence among populations, and to throw new light in the systematics of the species. Overall, 63 populations were considered. After total DNA extraction, we sequenced the two PCR amplified mtDNA gene fragments, namely 16S rRNA and cytochrome oxidase subunit I (COI), and calculated the genetic divergence within and among the populations studied, as well as their phylogenetic relationships. The methods for phylogenetic reconstruction used were Neighbor Joining (NJ), Maximum Parsimony (MP) and Bayesian Inference (BI) for each mtDNA sequence data and the concatenated dataset. The phylogenetic trees obtained from the molecular data – from all three phylogenetic methods (NJ, MP, BI) - produced trees with quite congruent topologies. Some populations that are considered conspecific exhibit large genetic distances and cluster in different clades. The highly-structured phylogenetic tree and the lack of an overall geographic pattern in the clustering of Trachelipus populations indicates that very probably we are not dealing with a single species, but rather with a number of cryptic species, hardly distinguished by means of currently used morphological characters. This is further corroborated by the genetic distances separating the clades hosting nominal T. kytherensis populations (max_dCOI=27.3% and max_d16S rRNA=17.6%). In general, it can be argued that the genetic distances recorded in the present study are quite large compared with those reported for different species and even genera in other studies of terrestrial isopods. Furthermore, it is evident than there are two species present in the Peloponnese, i.e. Trachelipus ‘kytherensis’ and T. aegaeus (in Argolis peninsula). In northern Peloponnese, a third form is also present (new species?) that occurs throughout the central and northern part of mainland Greece. These ‘contact zones’ should be further investigated in terms of genetic flow and isolation of the populations and/or species. Both the phylogeny presented here and the genetic distances separating populations appear to justify the necessity of further investigation into the phylogeny of the Greek Trachelipus species using a population by population approach. It is likely that morphology inadequately describes real variation inside and among species; hence, diagnoses based on the morphological characters used so far for the delineation of Trachelipus species should be reconsidered under the light of more extensive molecular phylogenetic analyses.

Made available in DSpace on 2015-04-17T14:55:35Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 2235639 bytes, checksum: 291aab03aba8f48238a6dd3742ae925c (MD5) Previous issue date: 2010-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The genus Hylaeamys is considered one of the most complex and diverse of the Sigmodontinae sub-family. They inhabit in evergreen and semi-evergreen forest of cis- Andean tropical and subtropical lowlands and foot-hills from Venezuela and Guianas southward through the Amazonian and the Atlantic rain forest to Paraguay and northern Argentina. Actually seven species can be grouped within that genera but their number and distribuition remains uncertain, especially the number of species in the Atlantic Forest. Analysis of the geographic variation from this species is necessary and justify the relevance of this work. Qualitativy, quantitativy and phylogeographic analyses turn able to observe morphological and geographic variation patterns from different populations through the Atlantic forest. Morphological data corroborate the hypothesis that are two different species in this forest: H. oniscus at the São Francisco Northern bank and H. laticeps at the São Francisco southern bank from southern Bahia to Rio de Janeiro. This work shows that these species are phylogenetically closer to species from western Amazonian rain forest (H .acritus and H. perenensis) than the species that lives in the eastern Amazonian (H. yunganus), and the one living in the dry forests of Cerrado (H. megacephalus). For a better comprehension of the phylogenetically relations between Atlantic Forest species further investigation must be taken including a large number of specimens and collected localities. / O gênero Hylaeamys é considerado um dos mais complexos e diversos da subfamília Sigmodontinae e se distribui nas florestas tropicais e semitropicais desde a Venezuela e as Guianas, passando pela Amazônia e pela Floresta Atlântica, até o Paraguai e norte da Argentina. Sete espécies se encontram inseridas nesse gênero, no entanto, as suas delimitações e respectivas distribuições permanecem incertas, principalmente no que diz respeito ao número de espécies que ocorrem na Floresta Atlântica. Uma análise da variação geográfica das diferentes populações do gênero, ao longo desse bioma, faz-se, então, necessária e justifica a relevância deste trabalho. Análises qualitativas e quantitativas das variações geográficas, bem como uma análise filogeográfica permitiram avaliar os padrões de variações morfológicas e biogeográficas das populações do gênero ao longo da Floresta Atl6antica. Através das análises morfológicas, foi possível corroborar a hipótese de que existem, efetivamente, duas espécies do gênero na Mata Atlântica: a H. oniscus, que ocorre ao norte da foz do rio São Francsico, e a H. laticeps, ao sul do rio São Francisco, desde o sul do estado da Bahia até o estado do Rio de Janeiro. O estudo permitiu verificar que essas espécies apresentaram-se filogeneticamente mais próximas das espécies da Floresta Amazônica ocidental (H. acritus e H. perenensis) e distintas das espécies que ocorrem na Floresta Amazônica oriental (H. yunganus) e nas Florestas Secas do Cerrado (H. megacephalus). No entanto, para uma melhor compreensão das relações filogeográficas entre as espécies inseridas no bioma Mata Atlântica, é preciso incluir um maior número de amostras oriundas de diversas localidades, entre elas, a região ao norte do rio São Francisco.

Sarus cranes (Grus antigone) are the tallest members of the crane family, Gruidae. They are found in four geographically distinct regions: northwest India (Indian Sarus- Grus antigone antigone), southeast Asia (Burmese Sarus- Grus antigone sharpei) and northern Australia (Australian Sarus- Grus antigone gillae). Although the three subspecies are morphologically distinct, their genetic distinctness is unclear. In this study, I focused on control region sequences of mitochondrial DNA (mtDNA) to assess the genetic and phylogeographic distinctness of Sarus subspecies. I used samples from four fragmented populations, seven from India, 16 from southeast Asia, five from Myanmar and eight from Australia. Phylogenetic trees were estimated using two Brolga crane sequences (G. rubicunda) as outgroups. All phylogenetic trees had low resolution, but AMOVA showed that all four Sarus populations are differentiated from each other. Nested clade phylogenetic analysis showed that most of the southeast Asian haplotypes are found at the center, suggesting that the Thai population includes the maximum number of ancestral haplotypes. Sarus cranes probably originated in southeast Asia and migrated both north towards India and south towards Australia during the last glacial maximum.

Southern African biogeographic boundaries delimit the phylogeographic distribution of some coastal and estuarine invertebrates. This study investigated the impact of these boundaries on the phylogeographic distribution of two intertidal red seaweeds, Gelidium pristoides and Hypnea spicifera using the mitochondrial Cox2-3 spacer and the nuclear ITS1 regions. G. pristoides spores have short distance-dispersal, while long distance-dispersal is more likely in H. spicifera via spores and drifting fertile thallus fragments. Both markers revealed a south-western and south-eastern lineage within G. pristoides but the breaks between lineages do not coincide with any recognised biogeographic limits. The Cox2-3 spacer revealed a boundary between the two lineages at the Alexandria Coastal Dunefield (ACD) and ITS1 at the Gamtoos-Van Stadens Dunefields (GVD) which is approximately 80km west of the ACD. The minor difference between the two markers regarding location of the phylogeographic boundary is probably due to the dating differences between the two dunefields. The ACD as developed currently is superimposed on the ancient dunefields which formed during the Pleistocene, coinciding with the Cox2-3 spacer sequences divergence which dates back 500,000 - 580,000 years. The GVD formed during the Holocene (6,500 - 4,000 years ago), coinciding with the ITS1 sequences divergence which dates 4,224 - 4,928 years ago. Thus, these phylogeographic boundaries probably appeared without the influence of biogeographic boundaries, but rather due to the lack of suitable habitat in the dunefields, coupled with short dispersal-distances of the spores. Analysis of the ITS1 and Cox2-3 spacer regions in H. spicifera revealed that the species is characterized by uniform genetic structure along the coastline. This reflects the species`s potential for long range expansion as it inhabits both the intertidal and subtidal zones; and this presumably leads to high gene flow among populations. The ITS1 sequences showed minimal genetic variation of one substitution between the gametophyte and tetrasporophyte generations within H. spicifera. This suggests the predominance of asexual reproduction, which reduces gene flow and fixes alleles between generations. ANOSIM and Bray-Curtis cluster analyses showed scale-dependant variation in the abundances of epifauna (mainly amphipod, isopod, mollusc and polychaete species) on G. pristoides. At small local (within site) and large (among sites) scales, there were weak and no structure in epifaunal abundances respectively. However, at larger, biogeographic scales, samples from the same biogeographic region tended to be clustered together. Thus, there was a group containing predominantly south coast samples and a group containing east coast samples mixed with the remaining south coast samples. Such scale-dependant variation in epifaunal abundances is probably due to the effects of factors driving species richness at small local (within site) scales (e.g. wave exposure, seaweed biomass) and at larger, biogeographic scales (e.g. surface sea temperature). Moreover, at very small (individual samples) scales; there was no correlation between epifauna composition and genotype of the seaweed. Seaweed samples characterized by distinct ITS1 or Cox2-3 spacer sequences did not show any significant differences in epifaunal composition. Although the distributional pattern of the epifaunal community observed at large biogeographic scale is not clear, it seems to be associated with the biogeographic regions. However, phylogeographic distribution of Gelidium pristoides is not connected to biogeographic regions. Thus, at larger, biogeographic scales, there is no correlation between phylogeographic distribution of G. pristoides and distribution of the associated fauna

With current biota under constant threat of extinction, it is important to ascertain where and how biological diversity is generated and partitioned. Phylogeographic studies can assist in the identification of places and processes that indicate the origin and maintenance of biodiversity. Forest fragmentation has a big effect on local extinction and loss of genetic diversity of forest-restricted taxa, along with divergence and speciation of forest biota. This study aims to understand the effects of these processes on a number of forest-dwelling butterflies using a comparative phylogeographic approach. Mitochondrial DNA of five different Papilio species with different degrees of forest specificity was analysed using phylogenetic methods. In addition, the subspecific taxonomy of P. ophidicephalus was investigated using morphometrics of discal spots on the wings and nuclear DNA analysis along with mitochondrial DNA analysis. The results show that the forest-restricted species (P. ophidicephalus and P. echerioides) have more genetic structure and less genetic diversity than the more generalist species (P. dardanus, P. demodocus and P. nireus). This could be due to inbreeding depression and bottlenecks caused by forest fragmentation. As forest patches become smaller, the population size is affected and that causes a loss in genetic diversity, and increasing habitat fragmentation disrupts gene flow. The intraspecific taxonomy of P. ophidicephalus is far from revealed. However, this study shows there is evidence for the different subspecies when comparing morphological results and genetic results. From the evidence provided here it is suggested that P. ophidicephalus should be divided into two separate species rather than five subspecies.

Phylogeography, phylogeny and population structure were studied in two similarly distributed butterflies, the Bog Fritillary (Boloria eunomia) and the Small Pearl-bordered Fritillary (Boloria selene). Sequences of mitochondrial gen for COI and nuclear Wingless and Arginine Kinase were used for analyses, for reconstruction of evolutionary relationships within both species and for comparison of phylogeography patterns.

Os chamados ‘complexos de espécies’ são definidos como grupos de organismos que compartilham características morfológicas muito semelhantes. Os complexos de espécies representam um problema para os sistemas de classificação baseados apenas em caracteres morfológicos, uma vez que os critérios para delimitação de espécies são subjetivos e, por isso, variam de acordo com cada taxonomista. O complexo integrifolia, que reúne diversos taxa com características florais muito semelhantes à espécie Petunia integrifolia (Hook.) Schinz & Thell, é um exemplo dessa problemática taxonômica. A determinação de espécies dentro desse complexo, baseada apenas em caracteres morfométricos, é até hoje ainda muito controversa. Nesse trabalho, os espaçadores internos transcritos do DNA nuclear ribossomal (ITS1 e ITS2) e dois espaçadores intergênicos (trnS-trnG e psbA-trnH) do DNA plastidial (cpDNA) foram seqüenciados em 69 indivíduos pertencentes a cinco entidades taxonômicas do complexo integrifolia na tentativa de entender sua história evolutiva e melhor contribuir para a correta delimitação das espécies. Análises populacionais e filogeográficas dos três marcadores do cpDNA mostraram que apenas a entidade taxonômica descrita como Petunia interior pode ser considerada uma espécie distinta de Petunia integrifolia. As outras quatro entidades taxonômicas estão divididas em duas linhagens genéticas independentes e alopátricas, que surgiram mais ou menos na mesma época após um evento de diminuição populacional seguido de rápida expansão. Uma dessas linhagens está localizada na planície costeira do Rio Grande do Sul e Santa Catarina, enquanto a outra linhagem se distribui na porção continental do RS ao oeste da Lagoa dos Patos. Análises morfométricas mais detalhadas mostram que essas duas linhagens genéticas podem ser distinguidas taxonomicamente e, portanto, são definidas como duas subespécies de Petunia integrifolia. Há indícios de que um processo de especiação por adaptação a dois ambientes distintos (alta salinidade na planície costeira e baixa salinidade na porção continental) esteja envolvido na divergência dessas duas linhagens. No entanto, para confirmar essa hipótese, são necessários estudos adicionais. / “Species complex” are usually defined as group of species that are morphologically very similar and consequently are very difficult to distinguish. Species complexes, therefore, represent a serious problem to the classification systems based only in morphological characters, the criteria used to delimit species being subjective. The integrifolia complex, that congregates taxa with floral characteristics very similar to Petunia integrifolia (Hook.) Schinz & Thell, it is an example of this taxonomic challenge. The determination of the species inside of this complex, based only in morphometric characters, it is still very controversial. In this work, the internal transcribed spacers of the ribosomal nuclear DNA (ITS1 and ITS2) and two intergenic spacers (trnS-trnG and psbAtrnH) of the plastidial DNA (cpDNA) had been sequenced in 69 individuals pertaining to five taxonomic entities of the integrifolia complex, in the attempt to understand its evolutionary history and contribute to the better delimitation of the species. Populational and phylogeographic analyses of the three markers and of cpDNA had shown that only the taxonomic entity described as Petunia interior can be considered a distinct species of Petunia integrifolia. The four other taxonomic entities are divided in two independent and allopatric lineages, that diversified almost simultaneously after an event of population bottleneck followed by a fast expansion. One of these lineages is located in the coastal plain of the Rio Grande do Sul and Santa Catarina states, while to other lineage it’s distributed in the continental region of the Rio Grande do Sul to the west of the Lagoa dos Patos. Detailed morphometric analyses shown that these two lineages can be taxonomically distinguished and therefore, they may be considered as two subspecies of Petunia integrifolia. Some findings suggest that a process of adaptation to these two distinct environments (high salinity in the coastal plain and low salinity in the continental region) may be involved in the divergence of the two lineages. Additional studies are required to test this hypothesis.