One statistical approach with a long history in the social sciences is a multivariate method called Structural Equation Modeling (SEM). The development of SEM followed the evolution of factor and path analyses, multiple regression analysis and MACOVA. One of the key innovations of factor analysis and SEM is that they group a set of multivariate statistical approaches that condense variability among a set of variables in fewer latent (unobserved) factors. Most biological systems are multivariate, which are not easily dissected into their component parts. However, most biologists use only univariate statistical methods, which have definitive limitations in accounting for more than a few variables simultaneously. Therefore, the implementation of methodologies like SEM into biological research is necessary. However, SEM cannot be applied directly to most biological datasets or generalized across species because of the hierarchical pattern of evolutionary history (i.e., phylogenetic non-independence or signal). This report includes the theoretical grounds for the development of Phylogenetic SEM in preparation of the development of utilitarian algorithms. I have divided this report in six parts: (1) a brief introduction to factor analysis and SEM from historical perspective and a brief description of its utility; (2) a summary of the implications of using biological data and the underlying hierarchical structure due to shared common ancestry or phylogeny; (3) a summary of the two most common comparative methods to incorporate the phylogeny in univariate analyses (i.e., phylogenetic independent contrasts and phylogenetic generalized least squares); (4) I describe how some intermediate output from both comparative methods can be used to estimate the variance–covariance matrix that has been corrected for phylogenetic signal; (5) I describe how to perform a exploratory factor analysis, specifically principal component analysis, with the corrected variance–covariance matrix; and (6) I describe the development of the phylogenetic confirmatory factor analysis and phylogenetic SEM. I hope that this report encourages other researchers to develop adequate multivariate analysis that incorporate the evolutionary principles in its analyses. / text

We are coming to understand that the ecological importance of diatoms is not limited to primary productivity, as many diatoms produce extracellular polymeric substances (EPS), which are vital components in algal and bacterial “biofilms.” While great effort has been made to chemically identify the types of molecules and polymers used to create and modify diatom EPS there is still much about the process we do not know. Rather than studying this process chemically, we have elected to search for the genes involved in EPS production and secretion. We assembled transcriptomes from three EPS-producing diatoms (Cyclophora tenuis, Lucanicum concatenatum, Thalassionema frauenfeldii) and two diatoms which do not (Astrosyne radiata, Thalassionema sp. ‘BlueH20’). In an attempt to limit the differences to EPS-related transcripts, the taxa were selected in a phylogenetic framework (which is also discussed in this dissertation), where EPS-producing taxa were closely-related to taxa which did not produce EPS (A. radiata, C. tenuis, L. concatenatum as one set, T. frauenfeldii and T. sp. ‘BlueH20’ as the other). The resulting pool of transcripts sorted for contigs which appeared in the EPS-producing taxa but not their closely-related non EPS-producing counterparts, and those contigs were then compared to two annotated diatom genomes and sorted by function, looking specifically for genes related to secretion, polysaccharide assembly or modification and carbohydrate metabolism. In the Thalassionema clade, 41 contigs with the aforementioned annotations were found, while 22 such contigs were found in the Cyclophora/Lucanicum/Astrosyne clade. These putative EPS-related markers are identified in this dissertation for further study on their function and evolution across diatoms. / text

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No description available.

No description available.

The bull shark, Carcharhinus leucas, is an important euryhaline predator that is exploited throughout its range for meat and fins. This species is taxonomically paired with the pigeye shark, C. amboinensis. Validity of this group has not been directly tested using molecular markers. Genetic variation and phylogeny was examined with concatenated datasets of mitochondrial genes (cytb, cox1 and 12stRNA16s) for nineteen species, from three families within the order Carcharhiniformes. Whilst there were indications of species pairings within the genus, there was no evidence to suggest that the bull and pigeye sharks should be considered a species group. Phylogenetic analysis failed to resolve Carcharhinus, but confirmed Negaprion as a sister taxon and placed Prionace glauca within Carcharhinus. It remains unclear if the family Sphyrnidae, arose from a Rhizoprionodon or Scoliodon ancestor and future revision of this complex group of sharks is required. Like other large carcharhinid species, C. leucas exhibits a low reproductive rate and long generation times. It is susceptible to localised depletions and such declines have been documented. The global stock structure was assessed by analysing the mitochondrial control region in 245 individuals sampled from eight populations in three ocean basins. The bull shark exhibits relatively high haplotype diversity (0.896 ± 0.010) when compared to other globally-distributed sharks and the nucleotide diversity was similar to others from the genus (0.00465 ± 0.00014). There was significant stock structure found among populations (ΦST=0.736, p<0.00001) and among ocean basins (ΦCT=0.527, p=0.00653). Geneflow between the US Atlantic coastline and Gulf of Mexico was sufficient to consider the area to be a single panmictic population. Coalescent analyses suggest an Indian Ocean origin with population divergences associated with warm interglacials and increased habitat with drop in sea level during the recent Wisconsin glaciation. Seven discrete stock management units for bull sharks are proposed.

Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply divergent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be present in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discovered 23 novel foamy-like elements in teleost hosts. These viruses form a robust, reciprocally monophyletic sister clade with sarcopterygian host FV, with class III mammal endogenous retroviruses being the sister group to both clades. Some of these foamy-like retroviruses have larger genomes than any known retrovirus, exogenous or endogenous, due to unusually long gag-like genes and numerous accessory genes. The presence of genetic features conserved between mammalian FV and these novel retroviruses attests to a foamy-like replication biology conserved for hundreds of millions of years. We estimate that some of these viruses integrated recently into host genomes; exogenous forms of these viruses may still circulate.

Societies where workers sacrifice their own reproduction and cooperatively nurture the offspring of a reproductive queen caste have originated repeatedly across the Tree of Life. The attainment of such reproductive division of labor enabled the evolution of remarkable diversity in development, behavior, and social organization in the Hymenoptera (ants, bees, and wasps). Wasps of the family Vespidae exhibit a gamut of social levels, ranging from solitary to highly social behavior. The highly social yellowjackets and hornets (Vespinae) have well developed differences in form and function between queens and workers, large colony sizes, and intricate nest architecture. Moreover, certain socially parasitic species in the Vespinae have secondarily lost the worker caste and rely entirely on the workers of a host species to ensure the survival of parasitic offspring. Understanding the evolution of behavioral traits in the Vespinae over long periods of time would be greatly enhanced by a robust hypothesis of historical relationships. In this study, I analyze targeted genes and transcriptomes to address three goals. First, infer phylogenetic relationships within yellowjackets (Vespula and Dolichovespula) and hornets (Vespa and Provespa). Second, test the hypothesis that social parasites are more closely related to their hosts than to any other species (Emery's rule). Third, test the protein evolution hypothesis, which states that accelerated evolution of protein coding genes and positive selection operated in the transition to highly eusocial behavior. The findings of this study challenge the predominant understanding of evolutionary relationships in the Vespinae. I show that yellowjacket genera are not sister lineages, instead recovering Dolichovespula as more closely related to the hornets, and placing Vespula as sister to all other vespine genera. This implies that traits such as large colony size and high paternity are mostly restricted to a particular evolutionary trajectory (Vespula) from an early split in the Vespinae. I demonstrate that obligate and facultative social parasites do not share immediate common ancestry with their hosts, indicating that socially parasitic behavior likely evolved independently of host species. Moreover, obligate social parasites share a unique evolutionary history, suggesting that their parasitic behavior might have a genetic component. Lastly, I analyze transcriptomic data to infer a phylogeny of vespid wasps and use this phylogeny to discover lineage-specific signatures of positive selection. I identify more than two hundred genes showing signatures of positive selection on the branch leading to the highly eusocial yellowjackets and hornets. These positively selected genes involve functions related mainly to carbohydrate metabolism and mitochondrial activity, in agreement with insights from studies of bees and ants. Parallels of functional categories for genes under positive selection suggests that at the molecular level the evolution of highly eusocial behavior across the Hymenoptera might have followed similar and narrow paths.

Retortamonads (Retortamonadida; genera Chilomastix and Retortamonas) are a small group of protists comprising intestinal commensals of both vertebrates and invertebrates and one free-living species of the genus Chilomastix. Molecular phylogenetic studies showed that retortamonads are closely related to diplomonads, Carpediemonas, Dysnectes, Hicanonectes, Kipferlia and two undescribed lineages of free-living Carpediemonas-like organisms, together forming the monophyletic excavate group Fornicata. For a long time Retortamonadida have been assumed to be a monophyletic group. However, first molecular phylogenetic study including sequence data from both Retortamonas and Chilomastix suggested that Retortamonadida are paraphyletic and that diplomonads branch within Retortamonadida. Retortamonads still remain poorly studied protist group and their phylogeny is unclear. We sequenced and analysed SSU rDNA of ten Retortamonas and four Chilomastix SSU rDNA sequences. In addition, we sequenced SSU rDNA of an undescribed enteromonad lineage. The phylogenetic tree of Fornicata was largely unresolved and the phylogenetic position of the genus Chilomastix remained unclear. On the other hand, the genus Retortamonas and diplomonads formed a robust clade. Retortamonas sequences split into three host-specific lineages. The...

Genus Frustulia was chosen for this work due to the continuity of the previous research of our phycological group. Using molecular techniques, it was found that a number of morphologically defined species of diatoms is cryptic species complex, which may have limited dispersal. The aim of this study was to: 1) evaluate the diversity of the genus Frustulia in northern Europe by molecular methods and classify found species in the phylogenetic context of related species; 2) find out if it possible to identify the isolated species in natural samples by using morphological characters. There have been analyzed 234 strains by molecular methods. Isolated ones were in four clades. 86 % of the strains belonged to a generic complex F. crassinervia-saxonica. Two strains were identified as species F. gaertnerae and F. septentrionalis. The last line was not described yet so it was labeled as F. sp. This line is closely related to the species F. maoriana, which is considered to be endemic in New Zealand. Phylogeny of the genus was created based on a dataset of four molecular markers. Published morphometric data were then compared with 264 cells photos taken by scanning electron microscope. There was done surveillance comparison of the results of the analysis of quantitative and qualitative characters with...