The influence of regional processes, such as dispersal, on ecological communities has been the focal point of considerable ecological research. Evidence has shown that dispersal can impact community composition through interactions with predation, the introduction of keystone species, and maintenance of species lost due to competitive exclusion. Ecological communities can be characterized by several metrics including species richness, diversity, evenness, abundance and species co-occurrence patterns. Negative species co-occurrence patterns have historically been attributed to competitive interactions between species causing pairs of species to never co-occur. However, little attention has been paid to the contribution of dispersal on species co-occurrence patterns. I have experimentally investigated the influence of dispersal on species co-occurrence patterns in addition to local species richness, total species abundance, evenness, and Simpson’s diversity. Local species richness significantly increased with dispersal, with variation in total local richness being mainly attributed to differences in the rotifer community. Local diversity, total abundance, and evenness were not significantly influenced by changes in the level of dispersal. Species co-occurrence patterns were greatly affected by changes in dispersal, with negative species co-occurrence patterns peaking at intermediate levels of dispersal. The potential for dispersal to increase the number of rare species within a community suggested that the presence of rare species could be behind the changes in the co-occurrence patterns between dispersal treatments. The effect size of the co-occurrence tests increased with the removal of rare species in the intermediate dispersal treatment and decreased in the remaining dispersal treatments. Likely, through mass effects, the presence of rare species, and the establishment of keystone predators changes in the level of dispersal strongly influenced species co-occurrence patterns. I conclude that external processes, like dispersal, can influence species co-occurrence patterns and that caution should be taken when interpreting the mechanisms driving species co-occurrence patterns across landscapes. / Thesis (Master, Biology) -- Queen's University, 2011-09-28 15:00:40.972

Photoidentification surveys of bottlenose dolphins (Tursiops truncatus) were conducted from December of 2002 through December of 2003 in Chocolate Bay, Texas, and the adjacent Gulf of Mexico area. The research represented the continuation of an ongoing study of the dolphins of this area. Behavioral sampling was carried out on a small resident community of dolphins that seasonally reside in Chocolate Bay, as well as on dolphins found along the gulf coastline. Resident dolphins had a daily behavioral pattern, with peaks of foraging activity in the morning, traveling at midday, and socializing in late afternoon. Gulf dolphins had small mean group sizes of 3.4 and were primarily observed foraging and traveling, with little socializing. When resident and gulf dolphins interacted, the mean group size increased to 12 and the proportion of social behavior increased. Association indices demonstrated no long-lasting associations among adult male dolphins, while strong associations existed between several females. Females revealed two patterns of association; they were either members of a female band with other mother-calf pairs, or were solitary with no strong affiliations with any dolphins other than their calf. Males seemed to disperse upon maturation, which maintained the community size of approximately 35 animals. Behavioral evidence indicates the resident community is matrilinealy related and composed largely of adult females and their offspring. A few adult males remain resident, while most young males disperse from the community and may rove among the gulf population. Although mating probably occurs between resident and gulf dolphins, sources of both maternity and paternity for residents need to be determined, and further behavioral work needs to be carried out to support this hypothesis.

Photoidentification surveys of bottlenose dolphins (Tursiops truncatus) were conducted from December of 2002 through December of 2003 in Chocolate Bay, Texas, and the adjacent Gulf of Mexico area. The research represented the continuation of an ongoing study of the dolphins of this area. Behavioral sampling was carried out on a small resident community of dolphins that seasonally reside in Chocolate Bay, as well as on dolphins found along the gulf coastline. Resident dolphins had a daily behavioral pattern, with peaks of foraging activity in the morning, traveling at midday, and socializing in late afternoon. Gulf dolphins had small mean group sizes of 3.4 and were primarily observed foraging and traveling, with little socializing. When resident and gulf dolphins interacted, the mean group size increased to 12 and the proportion of social behavior increased. Association indices demonstrated no long-lasting associations among adult male dolphins, while strong associations existed between several females. Females revealed two patterns of association; they were either members of a female band with other mother-calf pairs, or were solitary with no strong affiliations with any dolphins other than their calf. Males seemed to disperse upon maturation, which maintained the community size of approximately 35 animals. Behavioral evidence indicates the resident community is matrilinealy related and composed largely of adult females and their offspring. A few adult males remain resident, while most young males disperse from the community and may rove among the gulf population. Although mating probably occurs between resident and gulf dolphins, sources of both maternity and paternity for residents need to be determined, and further behavioral work needs to be carried out to support this hypothesis.

A Mata Atlântica é uma floresta tropical úmida considerada um \"hotspot\" de biodiversidade e endemismo. É uma das florestas mais antigas do mundo e uma das maiores florestas da América, abrangendo aproximadamente 150 milhões de hectares em condições ambientais altamente heterogêneas. Estudos em diferentes ambientes da Mata Atlântica, nos núcleos de Picinguaba e Santa Virginia no Parque Estadual da Serra do Mar (PESM), têm sido realizados para determinar a diversidade de espécies e alterações da estrutura das comunidades de bactérias, tanto na filosfera, quanto na dermosfera e solo rizosférico. No entanto, pouco se sabe sobre as funções ecológicas dessas bactérias, e sobre as interações ecológicas entre as comunidades microbianas e os ambientes onde se desenvolvem. Assim o objetivo desse trabalho foi explorar as interações entre as comunidades microbianas da filosfera, dermosfera e solo coletado sobre a projeção da copa de duas espécies arbóreas da Mata Atlântica ao longo de um gradiente altitudinal, usando análises de co-ocorrência, a partir dos dados obtidos por pirosequenciamento da região V4 do gene rRNA 16S de bactérias, para determinar padrões de associações de bactérias em diferentes níveis taxonômicos em cada microambiente. Para esse estudo, foi proposta a hipótese de que mesmo que as condições ambientais sejam diferentes em cada tipo de floresta (gradiente altitudinal), pode existir grupos de bactérias específicos que co-ocorrem na filosfera, dermosfera ou solo das plantas, funcionando como taxons chaves na estruturação das comunidades bacterianas. Com base do sequenciamento dos genes rRNA 16S, as comunidades bacterianas associadas à filosfera e dermosfera de E. edulis e G. opposita nas diferentes florestas foram mais similares entre si do que as do solo. Actinobacteria, Firmicutes, Bacteroidetes e Proteobacteria foram mais abundantes em todos os microambientes estudados. Diferenças nas estruturas das comunidades bacterianas na filosfera, dermosfera e solo foram observadas ao longo do gradiente altitudinal, independente da espécie de planta. Na floresta de terras baixas, a comunidade bacteriana associada à filosfera foi mais similar entre E. edulis e G. opposita. No solo, a comunidade bacteriana foi mais similar dentro de cada tipo de floresta do que entre florestas, sugerindo um efeito da fisionomia da floresta nas comunidades de bactérias dos solos. Explorando as redes de co-ocorrência das comunidades bacterianas em cada microambiente observou-se que no nível de UTOs, cada microambiente têm diferentes táxons chaves que podem regular as interações ecológicas da comunidade. Embora táxons chaves não representam as UTOs mais abundantes em cada microambiente, eles pertencem, predominantemente às classes Alphaproteobacteria e Gammaproteobacteria, sugerindo que na filosfera, dermosfera e solo o core microbioma não pode ser definido ao nível de UTO, mas possivelmente a níveis taxonômicos mais elevados representando grandes grupos microbianos que apresentam funções redundantes. / The Atlantic Forest is a rainforest considered a hotspot of biodiversity and endemism. It is one of the oldest forests in the world and one of the largest forests of America, covering approximately 150 million hectares in highly heterogeneous environmental conditions. Studies in different environments of the Atlantic forest, in the Picinguaba and Santa Virginia areas in the Serra do Mar State Park (PESM) have been conducted to determine the species diversity and changes in the structure of the bacterial communities in the phyllosphere, dermosphere and rhizosphere. However, little is known on the ecological functions of these bacteria, and on the ecological interactions between microbial communities and the environment in which they develop. The aim of this study was to explore the interactions between the microbial communities of the phyllosphere, dermosphere and rhizosphere of two tree species of the Atlantic Forest along an altitudinal gradient. Co-occurrence analysis based on data obtained by pyrosequencing of the 16S rRNA gene V4 region of bacteria to determine patterns of bacterial associations in different taxonomic levels in each microenvironment. For this study, the hypothesis that even if the environmental conditions are different in each type of forest (altitudinal gradient), there may be specific groups of bacteria that co-occur in the phyllosphere, dermosphere or rhizosphere, functioning as keystone taxa in the bacterial communities. Based on the sequencing of 16S rRNA genes, bacterial communities associated with the E. edulis and G. opposita phyllosphere and dermosphere in different forests were more similar to each other than the rhizosphere. Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes were the more abundant taxa in all studied microenvironments. Differences in the bacterial community structures in the phyllosphere, dermosphere and rhizosphere were observed along the altitudinal gradient, regardless of the plant species. In the lowland forest, the bacterial community associated with the phyllosphere was more similar between E. edulis and G. opposita. The rhizosphere bacterial community was more similar within each forest type than between forests, suggesting an effect of the forest physiognomy on the bacterial communities of the rhizosphere. Exploring the co-occurrence networks in the bacterial communities of each microenvironment it was observed that at the OTU level each microenvironment has different keystoine taxa that may regulate the ecological interactions in the community. Although the keystone taxa do not represent the most abundant OTUs in each microenvironment, they belong predominantly to Alphaproteobacteria and Gammaproteobacteria classes, suggesting that in the phyllosphere, dermosphere and rhizosphere the core microbiome cannot be determined at the OTU level, but possibly at higher taxonomic levels representing microbial groups having redundant functions.

A Mata Atlântica é uma floresta tropical úmida considerada um \"hotspot\" de biodiversidade e endemismo. É uma das florestas mais antigas do mundo e uma das maiores florestas da América, abrangendo aproximadamente 150 milhões de hectares em condições ambientais altamente heterogêneas. Estudos em diferentes ambientes da Mata Atlântica, nos núcleos de Picinguaba e Santa Virginia no Parque Estadual da Serra do Mar (PESM), têm sido realizados para determinar a diversidade de espécies e alterações da estrutura das comunidades de bactérias, tanto na filosfera, quanto na dermosfera e solo rizosférico. No entanto, pouco se sabe sobre as funções ecológicas dessas bactérias, e sobre as interações ecológicas entre as comunidades microbianas e os ambientes onde se desenvolvem. Assim o objetivo desse trabalho foi explorar as interações entre as comunidades microbianas da filosfera, dermosfera e solo coletado sobre a projeção da copa de duas espécies arbóreas da Mata Atlântica ao longo de um gradiente altitudinal, usando análises de co-ocorrência, a partir dos dados obtidos por pirosequenciamento da região V4 do gene rRNA 16S de bactérias, para determinar padrões de associações de bactérias em diferentes níveis taxonômicos em cada microambiente. Para esse estudo, foi proposta a hipótese de que mesmo que as condições ambientais sejam diferentes em cada tipo de floresta (gradiente altitudinal), pode existir grupos de bactérias específicos que co-ocorrem na filosfera, dermosfera ou solo das plantas, funcionando como taxons chaves na estruturação das comunidades bacterianas. Com base do sequenciamento dos genes rRNA 16S, as comunidades bacterianas associadas à filosfera e dermosfera de E. edulis e G. opposita nas diferentes florestas foram mais similares entre si do que as do solo. Actinobacteria, Firmicutes, Bacteroidetes e Proteobacteria foram mais abundantes em todos os microambientes estudados. Diferenças nas estruturas das comunidades bacterianas na filosfera, dermosfera e solo foram observadas ao longo do gradiente altitudinal, independente da espécie de planta. Na floresta de terras baixas, a comunidade bacteriana associada à filosfera foi mais similar entre E. edulis e G. opposita. No solo, a comunidade bacteriana foi mais similar dentro de cada tipo de floresta do que entre florestas, sugerindo um efeito da fisionomia da floresta nas comunidades de bactérias dos solos. Explorando as redes de co-ocorrência das comunidades bacterianas em cada microambiente observou-se que no nível de UTOs, cada microambiente têm diferentes táxons chaves que podem regular as interações ecológicas da comunidade. Embora táxons chaves não representam as UTOs mais abundantes em cada microambiente, eles pertencem, predominantemente às classes Alphaproteobacteria e Gammaproteobacteria, sugerindo que na filosfera, dermosfera e solo o core microbioma não pode ser definido ao nível de UTO, mas possivelmente a níveis taxonômicos mais elevados representando grandes grupos microbianos que apresentam funções redundantes. / The Atlantic Forest is a rainforest considered a hotspot of biodiversity and endemism. It is one of the oldest forests in the world and one of the largest forests of America, covering approximately 150 million hectares in highly heterogeneous environmental conditions. Studies in different environments of the Atlantic forest, in the Picinguaba and Santa Virginia areas in the Serra do Mar State Park (PESM) have been conducted to determine the species diversity and changes in the structure of the bacterial communities in the phyllosphere, dermosphere and rhizosphere. However, little is known on the ecological functions of these bacteria, and on the ecological interactions between microbial communities and the environment in which they develop. The aim of this study was to explore the interactions between the microbial communities of the phyllosphere, dermosphere and rhizosphere of two tree species of the Atlantic Forest along an altitudinal gradient. Co-occurrence analysis based on data obtained by pyrosequencing of the 16S rRNA gene V4 region of bacteria to determine patterns of bacterial associations in different taxonomic levels in each microenvironment. For this study, the hypothesis that even if the environmental conditions are different in each type of forest (altitudinal gradient), there may be specific groups of bacteria that co-occur in the phyllosphere, dermosphere or rhizosphere, functioning as keystone taxa in the bacterial communities. Based on the sequencing of 16S rRNA genes, bacterial communities associated with the E. edulis and G. opposita phyllosphere and dermosphere in different forests were more similar to each other than the rhizosphere. Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes were the more abundant taxa in all studied microenvironments. Differences in the bacterial community structures in the phyllosphere, dermosphere and rhizosphere were observed along the altitudinal gradient, regardless of the plant species. In the lowland forest, the bacterial community associated with the phyllosphere was more similar between E. edulis and G. opposita. The rhizosphere bacterial community was more similar within each forest type than between forests, suggesting an effect of the forest physiognomy on the bacterial communities of the rhizosphere. Exploring the co-occurrence networks in the bacterial communities of each microenvironment it was observed that at the OTU level each microenvironment has different keystoine taxa that may regulate the ecological interactions in the community. Although the keystone taxa do not represent the most abundant OTUs in each microenvironment, they belong predominantly to Alphaproteobacteria and Gammaproteobacteria classes, suggesting that in the phyllosphere, dermosphere and rhizosphere the core microbiome cannot be determined at the OTU level, but possibly at higher taxonomic levels representing microbial groups having redundant functions.

Ακολουθώντας μακροικολογική προσέγγιση, στόχος της διατριβής είναι η μελέτη των προτύπων συγκρότησης των νησιωτικών βιοκοινοτήτων. Συγκεκριμένα, στόχος είναι η διερεύνηση των προτύπων συνεμφάνισης ειδών, των προτύπων ανομοιότητας στη σύνθεση ειδών και της επίδρασης περιβαλλοντικών παραγόντων σε αυτά, καθώς και των προτύπων εγκιβωτισμού σε νησιωτικές βιοκοινότητες. Για το σκοπό αυτό, συνέλεξα μεγάλο αριθμό δεδομένων από διάφορα νησιωτικά συστήματα του κόσμου, καταρτίζοντας πίνακες παρουσίας-απουσίας ειδών για κάθε νησιωτικό σύστημα. Στη συνέχεια προσπάθησα να αναδείξω γενικά προτύπα συγκρότησης των νησιωτικών βιοκοινοτήτων. Αρχικά, αξιολόγησα δύο δείκτες («φυσικός» δείκτης και δείκτης CS), οι οποίοι εξετάζουν τα πρότυπα συνεμφάνισης σε επίπεδο ζευγών ειδών, ως προς την καταλληλότητα τους για τη διερεύνηση των προτύπων συνεμφάνισης ειδών. Τα αποτελέσματα καταδεικνύουν ότι και οι δύο δείκτες είναι κατάλληλοι ως δείκτες διερεύνησης των προτύπων συνεμφάνισης των ειδών. Mε τη χρήση αυτών των δύο δεικτών ανιχνεύονται σημαντικά πρότυπα συνεμφάνισης ειδών σε πολύ λιγότερες περιπτώσεις σε σύγκριση με τον δείκτη C-score που εξετάζει τα πρότυπα συνεμφάνισης σε επίπεδο ολόκληρου πίνακα παρουσίας-απουσίας ειδών. Γενικά, τα περισσότερα πρότυπα συνεμφάνισης ανιχνεύονται στις νησιωτικές κοινότητες των σπονδυλωτών και των φυτών. Ακολούθως, διερεύνησα τα προτύπα ανομοιότητας στη σύνθεση ειδών διάφορων ομάδων οργανισμών σε ωκεάνια και ηπειρωτικά νησιωτικά συστήματα, σε μερικές περιπτώσεις υπό το πρίσμα των διαφορετικών ικανοτήτων διασποράς των τάξων. Τα αποτελέσματα έδειξαν ότι η ανομοιότητα στη σύνθεση ειδών μεταξύ νησιών επηρεάζεται από την ομάδα οργανισμών που μελετάται. Τάξα με μεγάλη ικανότητα διασποράς τείνουν να έχουν χαμηλότερο βαθμό ανομοιότητας μεταξύ νησιών σε σύγκριση με άλλα τάξα με μικρότερη ικανότητα διασποράς. Η ανομοιότητα στη σύνθεση ειδών μεταξύ νησιών επηρεάζεται επίσης από τον τύπο νησιωτικού συστήματος. Τα ωκεάνια νησιωτικά συστήματα τείνουν να έχουν υψηλότερο βαθμό ανομοιότητας στη σύνθεση ειδών μεταξύ νησιών από ότι τα ηπειρωτικά νησιωτικά συστήματα (αποδείχθηκε για τις κοινότητες σαυρών). Οι διαφορές στην έκταση και η απόσταση μεταξύ των νησιών επηρεάζουν σημαντικά την ανομοιότητα στη σύνθεση ειδών μεταξύ νησιών. Οι διαφορές στο υψόμετρο επηρεάζουν σε μικρότερο βαθμό την ανομοιότητα στη σύνθεση ειδών και κυρίως φαίνεται να επιδρούν στα ωκεάνια νησιά και στις κοινότητες των τάξων με μεγάλη ικανότητα διασποράς, όπως είναι τα πτηνά και οι νυκτερίδες. Τέλος, διερεύνησα τον βαθμό εγκιβωτισμού των νησιωτικών βιοκοινοτήτων χρησιμοποιώντας τον δείκτη εγκιβωτισμού NODF. Σε συνδυασμό με ένα μηδενικό μοντέλο που διατηρεί σταθερό το άθροισμα των στηλών και των σειρών του πίνακα παρουσίας-απουσίας ειδών, ανιχνεύονται αρκετές «αντι-εγκιβωτισμένες» νησιωτικές βιοκοινότητες. Οι περισσότερες από αυτές επιδεικνύουν σημαντικό πρότυπο συνεμφάνισης ειδών. Αρκετές «αντι-εγκιβωτισμένες» βιοκοινότητες έχουν πολύ υψηλό βαθμό αντι-εγκιβωτισμού δηλαδή έχουν αρκετά νησιά τα οποία δεν έχουν κανένα κοινό είδος. Αυτό μπορεί να οφείλεται είτε στην ύπαρξη διαφορετικών δεξαμενών ειδών για τα νησιά του ίδιου νησιωτικού συστήματος είτε στη μειωμένη ικανότητα διασποράς των ειδών και κατά συνέπεια στη διαμόρφωση ξεχωριστών βιοκοινοτήτων στα νησιά. / Following a macroecological approach the aim of this thesis is the study of the assembly patterns of insular communities. In particular, the aim is to investigate species co-occurrence patterns, compositional dissimilarity patterns as well as the effect of environmental factors on those patterns and also to investigate nestedness patterns of insular communities. I collected a large number of data from various insular systems of the world, compiling species presence-absence matrices for each insular system and Ι attempted to describe general assembly patterns of insular communities. First, I evaluated the statistical properties of two metrics ("natural" and CS), that are used to examine co-occurrence patterns at the species-pair level, to determine if they can be used in the investigation of species co-occurrence patterns. The results show that both metrics can be used in the investigation of these patterns. Using the "natural" and the CS metrics, significant species co-occurrence patterns are identified in very few cases. On the contrary, using the CS metric, significant species co-occurrence patterns are identified in many cases. The majority of the significant species co-occurrence patterns are identified in the communities of vertebrates and plants. Also, I investigated compositional dissimilarity patterns of various taxa in oceanic and continental shelf insular systems, in some cases taking into account the differences in the dispersal ability among taxa. The results showed that compositional dissimilarity patterns are dependent on the taxon. Taxa with good dispersal abilities tend to have level lower levels of between-island compositional dissimilarity than taxa with poor dispersal abilities. Compositional dissimilarity patterns are also dependent on island type. Oceanic insular systems tend to have a higher level of compositional dissimilarity than continental shelf insular systems (clearly demonstrated for lizards). Inter-island distance, as well as area differences between islands, have an important effect on compositional dissimilarity between islands. Elevation differences between islands have a weaker effect on compositional dissimilarity. Significant effects of elevation differences between islands are only observed in oceanic insular systems and in the communities of taxa with good dispersal abilities such as birds and bats. Finally, I investigated the nestedness degree of insular communities. Using the NODF metric in combination with a null model that preserves the column and row sums of the species presence-absence matrix, we can detect several "anti-nested" insular communities. The majority of these communities also exhibit a significant species co-occurrence pattern. Several "anti-nested" communities have high values of the anti-nestedness index, indicating that they have many island pairs that have no species in common. A possible explanation for this is that for a given insular system there may be more than one species source pool. Poor dispersal abilities of various species can also lead to the assembly of distinct communities on different islands.