No description available.

No description available.

The fossil record is the primary source of information on the history of life. As such, it is important to understand the limitations of this record. One critical area in which there is still much work to be done is in understanding how the fossil record, and our interpretation of it, may be biased. Herein, the fidelity between the life and death assemblage of an extant brachiopod with respect to morphological variability is studied using geometric morphometrics. The results from several analyses confirm a high degree of morphological variability with little change in mean shape between the living and sub-fossil assemblage. Additionally, there is no evidence of distinct morphogroups in either assemblage. These trends persist at all depths and size classes indicating that this species could be recognized as a single, rather than multiple, species if only fossil data were available. The second chapter involves the recognition and quantification of a worker bias in monographs of brachiopods and bivalves. Most specimens studied came from the 65th to 69th percentile of their species' bulk-collected size-frequency distribution. This indicates a significant bias toward monograph specimens that are larger than the mean size of the bulk sample. When compared at the species level, this bias was found to be highly consistent among the 86 species included in the study. Thus, size measurements of monographed specimens reliably and consistently record a similar size class for any given species, and this bias is easily corrected during meta-analyses. Chapter three focuses on bivalves and brachiopods from a modern tropical shelf and quantifies the magnitude of time averaging (temporal mixing) for these two different organisms. This is accomplished by dating a suite of shells from each site using amino acid racemization calibrated with several radiocarbon dates. By studying the age distributions for each species it is determined that, despite some site to site differences, both bivalve and brachiopod species exhibit a similar time averaging magnitude when collected from the same region or depositional system. This indicates that fossil assemblages of these species may have very similar resolution. / Ph. D.

Thesis (PhD) - Stellenbosch University, 2011. / ENGLISH ABSTRACT: The Albertine Rift is characterized by a heterogeneous landscape which may, at least in part, drive the exceptional biodiversity found across all taxonomic levels. Notwithstanding the biodiversity and beauty of the region, large areas are poorly understood because of political instability with the inaccessibility of most of the region as a contributing factor. The majority of studies in the Albertine Rift have focussed on charismatic mega fauna, with other taxa receiving less attention. One of the taxonomically and numerically more abundant small mammal genera is the genus Praomys, an African endemic with a wide distribution range spanning most of west, central and east Africa. Four species are typically recognized from the Albertine Rift namely P. degraaffi, P. jacksoni, P. misonnei and P. verschureni. In this study I used a combination of DNA sequence data (mitochondrial control region, mitochondrial cytochrome b and 7th intron of the nuclear ß-fibrinogen gene) as well as morphometric data (traditional and geometric) to investigate the systematics of the Praomys taxa occurring in the Albertine Rift. To allow meaningful DNA assessments and in an attempt to identify potential drivers of diversifications, other Praomys species were also included from public sequence data bases for comparisons. The main focus was on P. jacksoni (the numerically most abundant taxon; also, up to 2005, all Praomys in the Albertine Rift were mostly collected as “jacksoni”) and P. degraaffi (an Albertine Rift endemic). A surprising finding was the presence of P. mutoni; this represents a range extension for this species into the Albertine Rift. Distinct evolutionary lineages were found in both P. jacksoni (confirmed by sequence data as well as morphometrics) as well as P. degraaffi (based only on sequence data; insufficient samples precluded a full morphometric investigation). These lineages (in both P. jacksoni as well as P. degraaffi) appear to be separated along a north – south gradient; however, further investigations should confirm this. To further investigate the genetic patterns at local scales across the Albertine Rift, as well as introgression between species as revealed by sequence data, a species-specific microsatellite library was developed for P. jacksoni. Twelve polymorphic markers were identified of which nine also amplified in P. degraaffi. Introgression was confirmed between the two focal species with almost 20% of the individuals analysed being jacksoni-degraaffi hybrids. This is perhaps not so surprising given that there is considerable overlap in their ranges (between ~ 1500 m a.s.l. to 2450 m a.s.l.) as well as the relative ages of the species (the divergence time between these two species were estimated at 3.8 Mya). The presence of distinct lineages within each of these species was confirmed by microsatellite analyses (these lineages diverged approcimately at same time at ca. 3.4 Mya). As suggested by sequence and morphometric data, these lineages had a largely north – south distribution but with considerable overlap in the central Albertine Rift in the vicinity of Lake Kivu. The phylogeographic patterns obtained for both focal species were not consistent with the physical barriers such as the rivers, lakes or mountains, nor were they exclusively associated with Pleistocene phenomena such as the change of the course of the rivers or uplift; rather, the lineages predate the Pleistocene and fall firmly in the Pliocene (>3 Mya). Biogeographically, the north - south location of lineages with a centrally - located contact zone could be a result of parapatric speciation due to habitat fragmentation or past climate change, followed by secondary contact. Barcoding using genetic information provides a useful tool to identify unknown taxa, cryptic diversity or where different life stages are difficult to identify. From an invasion biology perspective, it allows for the rapid identification of problem taxa against a known data base. By adopting such a barcoding approach (senso lato), the presence of three invasive rodents was confirmed in the Democratic Republic of the Congo (DRC); these are Rattus rattus (black rat), R. norvegicus (Norway rat) and Mus musculus domesticus (house mouse). A comparison with global data available for these species revealed two possible introduction pathways namely via the shipping port at Kinshasa/Matadi (with strong links to Europe) and via the slave trade routes in the east (strong links to the Arab world and the east). Of these three taxa, only R. rattus is currently documented from the DRC although the others have received mention in the gray literature. These findings draw attention to the lack of any official policy regarding biosecurity in the DRC, and argue for the development of strict control measures to prevent further introductions. / AFRIKAANSE OPSOMMING: Die Albertine Rift word gekenmerk deur 'n heterogene landskap wat kan, ten minste gedeeltelik, die uitsonderlike biodiversiteit wat oor al die taksonomiese vlakke gevind word teweeg bring. Nieteenstaande die biodiversiteit en die skoonheid van die streek, is groot gebiede onbekend as gevolg van politieke onstabiliteit met die ontoeganklikheid van meeste van die streek as 'n bydraende faktor. Die meerderheid van studies in die Albertine Rift het gefokus op die charismatiese mega fauna, met ander taxa wat minder aandag ontvang. Een van die taksonomies en numeries meer volop klein soogdier genera is die genus Praomys, 'n Afrika endemiese groep met 'n wye verspreiding wat strek oor die grootste deel van van wes-, sentraal en oos-Afrika. Vier spesies word tipies erken van die Albertine Rift naamlik P. degraaffi, P. jacksoni, P. misonnei en P. verschureni. In hierdie studie het ek 'n kombinasie van DNA volgorde data (mitochondriale beheer streek, mitochondriale sitochroom b en 7de intron van die kern ß-fibrinogeen geen) sowel as morfometriese data (tradisioneel en meetkundig) gebruik om die sistematiek van die Praomys taxa te ondersoek. Om betekenisvolle DNA aanslae toe te laat en in 'n poging om potensiële aandrywers van diversiteit te identifiseer, is ander Praomys spesies van openbare volgorde data basisse vir vergelykings ingesluit. Die hooffokus is op P. jacksoni (die numeries volopste takson, ook, tot en met 2005 is alle Praomys in die Albertine Rift meestal as "jacksoni" versamel) en P. degraaffi ('n Albertine Rift endemiese spesie). 'n Verrassende bevinding was die teenwoordigheid van P. mutoni, dit verteenwoordig' n verspreidingsuitbreiding vir hierdie spesie in die Albertine Rift. Bepaalde evolusionêre ontwikkelingslyne was in beide P. jacksoni (bevestig deur die volgorde data sowel as morfometrie) sowel as P. degraaffi (wat slegs gebaseer is op die volgorde data, onvoldoende monsters verhinder 'n volledige morfometriese ondersoek). Hierdie lyne (in beide P. jacksoni sowel as P. degraaffi) word geskei langs 'n noord - suid gradiënt, maar verdere ondersoeke moet dit bevestig. Om die genetiese patrone op plaaslike skaal oor die Albertina Rift verder te ondersoek, sowel as introgressie tussen spesies soos geopenbaar deur die volgorde data, is 'n spesie-spesifieke mikrosatelliet biblioteek ontwikkel vir P. jacksoni. Twaalf polimorfiese merkers is geïdentifiseer waarvan nege ook amplifiseer in P. degraaffi. Introgressie is bevestig tussen die twee brandpunt spesies met byna 20% van die individue wat ontleed is as jacksoni-degraaffi basters. Dit is miskien nie so verbasend gegee dat daar aansienlike oorvleueling is in hul gebiede (tussen ~ 1500 m bo seespieel tot 2450 m bo seespieel), sowel as die relatiewe ouderdomme van die spesies (die divergensie tussen hierdie twee spesies is geskat op 3,8 Mya). Die teenwoordigheid van verskillende lyne in elk van hierdie spesies is bevestig deur mikrosatelliet ontleding (hierdie lyne het gedivergeer ongeveer 3,4 Mya). Soos voorgestel deur die DNA volgorde en morfometriese data, het hierdie lyne 'n grootliks noorde – suid verspreiding, maar met 'n aansienlike oorvleueling in die sentrale Albertine Rift in die omgewing van die Kivumeer. Die filogeografiese patrone wat vir beide die brandpunt spesies gevind is nie in ooreenstemming met die fisiese struikelblokke soos die riviere, mere of berge nie, en hou ook nie uitsluitlik verband met die Pleistoseen verskynsels soos die verandering van die loop van die riviere nie; die afstammelinge is eerder veel ouer as die Pleistoseen en val binne die Plioseen (> 3 Mya). Biogeografies, die noorde – suid plasing van die lyne met 'n sentraal geleë kontak sone kan die gevolg wees van parapatriese spesiasie te danke aan habitatfragmentasie as gevolg van verandering in die klimaat, gevolg deur 'n sekondêre kontak. Strepieskodering met behulp van genetiese inligting verskaf 'n nuttige instrument om onbekend taxa, kriptiese diversiteit of waar verskillende lewensfases moeilik is om te identifiseer, te identifiseer. Vanuit 'n indringerbiologie perspektief, maak hierdie benadering dit moontlik om vinnige identifikasies van die probleem taksa teen' n bekende data basis te bekom. Deur gebruik te maak van so 'n strepieskoderingsbenadering (senso lato), is die teenwoordigheid van drie indringende knaagdiere bevestig in die Demokratiese Republiek van die Kongo (DRK), naamlik Rattus rattus (swart rot), R. norvegicus (Noorweë rot) en Mus musculus domesticus (huis muis). 'n Vergelyking met die globale data wat beskikbaar is vir hierdie spesies het aan die lig gebring dat twee moontlike betree-roetes bestaan, naamlik via die skeepshawe by Kinshasa / Matadi (met sterk skakels na Europa), en via die slawehandel roetes in die ooste (sterk skakels na die Arabiese wêreld en die ooste) . Van hierdie drie taxa, is tans slegs R. rattus van die Demokratiese Republiek van die Kongo gedokumenteer, hoewel die ander melding ontvang in die grys literatuur. Hierdie bevindinge vestig die aandag op die gebrek aan enige amptelike beleid ten opsigte van biosekuriteit in die Demokratiese Republiek van die Kongo, en argumenteer vir die ontwikkeling van streng beheermaatreëls om verdere indringerspesies te voorkom.

Select freshwater mussels in the genera Fusconaia, Pleurobema, and Pleuronaia were collected primarily in the upper Tennessee River basin from 2012 to 2014 for phylogenetic and morphological assessments. Freshwater mussels in these genera are similar in appearance, hence the need for phylogenetic verification and morphological assessment. Phylogenetic analyses of the mitochondrial gene ND1 and the nuclear gene ITS1 revealed three unrecognized, phylogenetically distinct species. These species were separated from their closest congener by 2.85%, 3.17%, and 6.32% based on pairwise genetic distances of ND1. Gaps created from aligning ITS1 sequences were coded as fifth characters, which phylogenetically separated most closely related species. Analyses of ND1 agreed with previous literature on the phylogenetic distinctiveness of Pleuronaia species, with the exception of the DNA sequences of P. gibberum, which grouped outside this genus based on the analyses conducted in this study. Morphological variation was recorded for eight of the species to include quantitative and qualitative characters as well as geometric morphometric analyses. Three decision trees were created from quantitative and qualitative characters using classification and regression tree analyses. The best-performing tree used quantitative and qualitative characters describing shell-only scenarios and obtained 80.6% correct classification on terminal nodes. Canonical variates analysis on geometric morphometric shell data revealed large morphological overlap between species. Goodall's F-tests between pairs of species revealed significant differences (a=0.05) between all but one species pairs; however, examination of landmarks on shells concluded large overlap of landmarks between species pairs. Lack of morphologically distinct characters to readily identify these phylogenetically distinct species indicates large morphological overlap among these species. Biologists need to be cognizant that morphologically cryptic species may exist in systems often explored. Three dichotomous keys were created from classification trees to identify select individuals in the genera Fusconaia, Pleurobema, and Pleuronaia; two of these keys, one for shells and one for live mussels were tested by participants with varying mussel identification skills to represent novices and experts. Both keys used continuous (quantitative) and categorical variables to guide participants to identifications. Novices, who had no prior mussel identification experience, correctly identified mussels with a 50% accuracy using the shell key and with a 51% accuracy using the live key. Experts, who had at least three years of experience identifying mussels, correctly identified mussels with a 58% accuracy using the shell key and with a 68% accuracy using the live key; however one expert noted that they did not use the live key to correctly identify one mussel. Morphological overlap of variables between mussels likely resulted in failure to consistently identify mussels correctly. Important management decisions and project implementations require accurate assessment of species' localities and populations. Incorrect species identification could hinder species' recovery efforts or prevent projects that otherwise could have continued if species are misidentified. If a mussel collection is thought to be a new record or could affect a project, I recommend that molecular genetic identifications be used to verify the species identity. / Master of Science

For nearly a century, amphibian metamorphosis has served as an important model of how thyroid hormones regulate vertebrate development. Consequently metamorphosis has been studied in a number of ways including: morphologically, developmentally, ecologically, and from an endocrine perspective. Over the last two decades, much has been learned about the molecular basis of anuran (frog) metamorphosis. However, very little is known about the molecular underpinnings of urodele (salamander) metamorphosis. Using the axolotl and axolotl hybrids as models, I present some of the first studies on the gene expression changes that occur during urodele metamorphosis. In Chapter 1, the motivation for the research described in the subsequent chapters is presented and the literature is briefly reviewed. In Chapter 2, the first microarray analysis of urodele metamorphosis is presented. This analysis shows that hundreds of genes are differentially expressed during thyroid hormone-induced metamorphic skin remodeling. Chapter 3 extends the analysis presented in Chapter 2 by showing that the transcriptional patterns associated with metamorphic skin remodeling are robust even when the concentration of thyroid hormone used to induce metamorphosis is varied by an order of magnitude. Chapter 4 makes use of the differentially expressed genes identified in Chapters 2 and 3 to articulate the first model of urodele metamorphosis to integrate changes in morphology, gene expression, and histology. In addition, Chapter 4 outlines a novel application for piecewise linear regression. In turn, Chapter 5 makes use of the model presented in Chapter 4 to demonstrate that full siblings segregating profound variation in metamorphic timing begin to diverge in phenotype early during larval development. In Chapter 6 the conclusions drawn from the research are summarized and future directions are suggested.

There is variation in Neandertal permanent dentition in both the size and shape of first molars. Ecogeography as well as chronology would be expected to account for at least some of the variation observed. Occlusal outlines of maxillary and mandibular first molar casts from European Neandertals, (Spy 1, Scladina 4A-4, Engis 2, l’Hortus 2, 4, 5, and 8, La Quina H5, Malarnaud 1) were generated through photostereomicroscopy and non-landmark smooth tracing methods, and occlusal areas, buccolingual breadths and mesiolingual lengths were measured by calibrated Motic 3.0MP microscope cameras. Principal component (PC) scores of elliptical Fourier harmonic descriptors were calculated using SHAPE v1.3, yielding a total of 76 and 67 PC scores for mandibular and maxillary data respectively. Of the maxillary outlines analyzed, a strong correlation exists between PC1 (58.4% of variance) and occlusal area, explaining size influence. On PC1, the smallest (Engis 2), is followed by Scladina 4A-A, Hortus 8, La Quina 5 and Spy 1. On PC2 (23% of variance), Scladina 4A-A is an outlier. On PC3 (12.6%), Hortus 8 is separated from the others whereas Scladina 4A-A is difficult to classify. PC4 accounts for 5.8% of the variance and separates Spy 1 from La Quina 5. Spy 1 appears as distinct on PC1, PC3, and PC4 while Scladina 4A-A is relatively distinct on all axes. In a cluster analysis of PC scores Spy 1 and La Quina 5 are linked by the shortest distance and joined secondarily to Hortus 8, whereas Scladina 4A-A and Engis 2 are relatively distinct from the others. Mandibular results indicate that Malarnaud is distinct on PC1 (40% of variance) and again on PC2 (27%), while La Quina 5 appears as slightly distinct on PC3 (14%), though grouped with Engis 2, while Hortus 2 and 4 group together this axis as well as PC1. PC4 (12%) again separates Malarnaud, and presents Hortus 5 as an outlier. Overall, chronology correlates better than geography to the variance observed in occlusal first molar shape in these European Neandertals, with some inconsistencies most likely due to individual biological variability. This study demonstrates a new method to compute the elliptical Fourier descriptors of molar occlusal outlines, and applies these to explain variation in these Neandertals with respect to ecogeographic and chronological situation.

The species of two genera in Insecta: Hemiptera: Adelgidae were investigated through the lenses of genetics, morphology, life cycle and host species. The systematics are unclear due to complex life cycles, including multigenerational polymorphism, host switching and cyclical parthenogenesis. I studied the hemlock adelgids, including the nonnative invasive hemlock woolly adelgid on the east coast of the United States, that are currently viewed as a single species. I used multivariate morphometric analyses to identify morphological differences among hemlock adelgid lineages. With principal component analyses and MANOVA, the six lineages that were used in this study were found to be significantly different from each other. The findings of this project provide evidence for taxonomic designation of different hemlock adelgid lineages, which will hopefully inform regulation of these distinct lineages, as these distinctions between the lineages of hemlock adelgids could equate to other biological differences, ex. cold tolerance, host specialization, fecundity and dispersal ability. I also investigated the relationship between species Pineus similis, Pineus abietinus through phylogeny, genetic distances, life cycle and host species. This was done through using three mitochondrial (COI, COII, cytB) and one nuclear (EF1a) gene, in Maximum Parsimony, Maximum Likelihood and Bayesian analyses, along with genetic distance measurements. The P. similis and P. abietinus on Pinus could not be separated within the Bayesian analyses, and P. similis and P. abietinus on Abies had low calculated distance measurements (2.98%) compared to the average distance between species within the genus (28.07%). These two studies emphasize the current confusion within the Adelgidae family, and the results presented in this thesis stress the importance of using components of multiple species concepts to better understand the systematics of these lineages.

The phylogeny of the turtle genus Pseudemys is poorly understood. In Virginia, many turtles have been found with indicator traits of both eastern river cooters (Pseudemys concinna concinna) and northern red bellied cooters (Pseudemys rubriventris). This study explores morphological evidence for hybridization between the two species across three riverine sites in east central Virginia. Museum voucher groups for each species were analyzed for relative shell height and plastron length. The shape of the plastral scutes and upper jaw were analyzed using landmark-based morphometric software. These metrics were compared with measurements taken from 188 field-caught Pseudemys specimens. Across phenotypic metrics, field specimens resembled northern red bellied cooters. Geometric morphometric analysis showed extreme variation. Thirteen field specimens exhibited indicator traits of both species. Because species boundaries do not appear to be well-resolved using accepted phenotypes and morphometrics, we suggest that additional research utilizing molecular methods and genetic analysis be conducted.

<p>In terms of forensic entomology, one area that is scrutinized most is the estimation of a minimum post mortem interval (mPMI) based on insects that are present at a crime scene. The identification of the insects found at the scene if the first step to calculate a mPMI. However, currently there are no methods that can present the courts with accurate statistical error rates in identification, because the current methods are reliant on an expert’s use of a morphological key to identify the specimen, and this identification method does not produce a confidence value. This project aimed to test a method of identification using geometric morphometrics that can produce confidence intervals to provide to the courtrooms. </p><p> Before any identification could start, a standard preservation protocol was developed to ensure that all diagnostic features are preserved, and specimens can be identified in the same way. A clearing method was designed to clear specimens within 24hrs using potassium hydroxide, so they can be dissected and mounted the next day. The dissection of the specimens was a simple six-step procedure to split the mouth hooks, the cuticle and the posterior spiracle. This procedure ensures that all diagnostic features are preserved on a microscope slide.</p><p> With all of the features preserved, the microscope slide is photographed for storage and an investigator can perform geometric morphometrics to identify the insect. This study tested the application of geometric morphometrics to distinguish between three genera of Calliphoridae (<i>Calliphora</i>,<i>Lucilia</i>, <i>Phormia</i>), from three locations in the US (Delaware, Indiana, California). Results showed significant (p-value: <0.05) variation in shape among all genera. When genera were tested for shape differences based on location, these variations were also significant (p-value: <0.05). The implication of these results is that enough shape difference exists to distinguish between these genera and to distinguish between populations.</p>