Assessing the Phylogenetic Utility of DNA Barcoding Using the New Zealand Cicada Genus Kikihia

DNA Barcoding (Hebert et al. 2003) has the potential to revolutionize the process of identifying and cataloguing biodiversity; however, significant controversy surrounds some of the proposed applications. In the seven years since DNA barcoding was introduced, the Web of Science records more than 600 studies that have weighed the pros and cons of this procedure. Unfortunately, the scientific community has been unable to come to any consensus on what threshold to use to differentiate species or even whether the barcoding region provides enough information to serve as an accurate species identification tool. The purpose of my thesis is to analyze mitochondrial DNA (mtDNA) barcoding’s potential to identify known species and provide a well-resolved phylogeny for the New Zealand cicada genus Kikihia. In order to do this, I created a phylogenetic tree for species in the genus Kikihia based solely on the barcoding region and compared it to a phylogeny previously created by Marshall et al. (2008) that benefits from information from other mtDNA and nuclear genes as well as species-specific song data. I determined how well the barcoding region delimits species that have been recognized based on morphology and song. In addition, I looked at the effect of sampling on the success of barcoding studies. I analyzed subsets of a larger, more densely sampled dataset for the Kikihia Muta Group to determine which aspects of my sampling strategy led to the most accurate identifications. Since DNA barcoding would by definition have problems in diagnosing hybrid individuals, I studied two species (K. “murihikua” and K. angusta) that are known to hybridize. Individuals that were not obvious hybrids (determined by morphology) were selected for the case study. Phylogenetic analysis of the barcoding region revealed insights into the reasons these two species could not be successfully differentiated using barcoding alone.

Megabenthic communities in the waters around Svalbard during POLARSTERN cruise ARK-VIII/2 (EPOS II)

Composition and distribution of megabenthic communities around Svalbard were investigated in June/July 1991 with 20 Agassiz trawl and 5 bottom trawl hauls in depths between 100 and 2100 m. About 370 species, ranging from sponges to fish, were identified in the catches. Species numbers per station ranged from 21 to 86. Brittle stars, such as Ophiacantha bidentata, Ophiura sarsi and Ophiocten sericeum, were most important in terms of constancy and relative abundance in the catches. Other prominent faunal elements were eunephthyid alcyonarians, bivalves, shrimps, sea stars and fish (Gadidae, Zoarcidae, Cottidae). Multivariate analyses of the species and environmental data sets showed that the spatial distribution of the megabenthos was characterized by a pronounced depth zonation: abyssal, bathyal, off-shore shelf and fjordic communities were discriminated. However, a gradient in sediment properties, especially the organic carbon content, seemed to superimpose on the bathymetric pattern. Both main factors are interpreted as proxies of the average food availability, which is, hence, suggested to have the strongest influence in structuring megabenthic communities off Svalbard.

Radiolarian biostratigraphy in the central Indian Ocean

Identifiable radiolarians of stratigraphic importance were recovered at eight of the sites drilled on Leg 115. The assemblages range in age from Holocene to middle Eocene (Dictyoprora mongolfieri Zone, about 48 Ma). Faunal preservation is particularly good in two stratigraphic intervals: the Holocene through upper Miocene (0-9 Ma), and the lowermost Oligocene to middle Eocene (35-48 Ma). Fluctuating rates of silica accumulation at these drill sites during the Cenozoic reflect changing tectonic and paleoceanographic conditions. In particular, the gradual closure of the Indonesian and Tethyan seaways and the northward migration of the Indian subcontinent severely restricted zonal circulation and silica accumulation in tropical latitudes during the late Oligocene through middle Miocene. By the late Miocene the Indian subcontinent had moved sufficiently north of the equator to allow trans-Indian zonal circulation patterns to become reestablished, and biosiliceous sedimentation resumed. The composition of the radiolarian assemblages in the tropical Indian Ocean is closely comparable with that of the 'stratotype' sequences in the equatorial Pacific. However, there are some notable exceptions in Indian Ocean assemblages: (1) the scarcity of the genera Pterocanium and Spongaster in the Neogene; (2) the absence of the stratigraphically important Podocyrtis lineage, P. diamesa -> P. phyxis -> P. ampla, in the middle Eocene; and (3) the scarcity of taxa of the genus Dorcadospyris, with the exception of D. ateuchus. The succession of radiolarian events was tabulated for those stratigraphic intervals where the assemblages were well preserved. We identified 55 events in the middle Eocene to earliest Oligocene, and 31 events in the late Miocene to Holocene. The succession of events is closely comparable with that of the tropical Pacific. However, there are exceptions that appear to be real, rather than artifacts of sample preservation, mixing, and core disturbance.

Living benthic foraminifera of the western and southern Arabian Sea

Sediments from the western and southern part of the Arabian Sea were collected periodically in the spring intermonsoon between March and May 1997 and additionally at the end of the Northeast Monsoon in February 1998. Assemblages of Rose Bengal stained, living deep-sea benthic foraminifera, their densities, vertical distribution pattern, and diversity were analysed after the Northeast Monsoon and short-time changes were recorded. In the western Arabian Sea, foraminiferal numbers increased steadily between March and the beginning of May, especially in the smaller size classes (30-63 µm, 63-125 µm). At the same time, the deepening of the foraminiferal living horizon, variable diversity and rapid variations between dominant foraminiferal communities were observed. We interpret these observations as the time-dependent response of benthic foraminifera to enhanced organic carbon fluxes during and after the Northeast Monsoon. In the southern Arabian Sea, constant low foraminiferal abundances during time, no distinctive change in the vertical distribution, reduced diversity, and more stable foraminiferal communities were noticed, which indicates no or little influence of the Northeast Monsoon to benthic foraminifera in this region.

Abundance and biomass of mesozooplankton in the Levantine Basin during the Bilim 2 cruise in April 2008

The Sesame dataset contains mesozooplankton data collected during April 2008 in the Levantine Basin (between 33.20 and 36.50 N latitude and between 30.99 and 31.008 E longitude). Mesozooplankton samples were collected by using a WP-2 closing net with 200 µm mesh size during day hours (07:00-18:00). Samples were taken from 0-50, 50-100, 100-200 m layers at 5 stations in Levantine Basin The dataset includes samples analyzed for mesozooplankton species composition, abundance and total mesozooplankton biomass. Sampling volume was estimated by multiplying the mouth area with the wire length. Sampling biomass was measured by weighing filters and then determined by sampling volume. The samples were sieved sequentially through meshes of 500 and 200 micron to separate the mesozooplankton into size fractions. The entire sample (1/2) or an aliquot of the taxon-specific mesozooplankton abundance and the total abundance of the mesozooplankton were was analyzed under the binocular microscope. Minimum 500 individuals of mesozooplankton were identified and numerated at higher taxonomic level. Taxonomic identification was done at the METU- Institute of Marine Sciences by Alexandra Gubanova,Tuba Terbiyik using the relevant taxonomic literatures. Mesozooplankton abundance and biomass were estimated by Zahit Uysal and Yesim Ak.

Cretaceous calcareous nannofossils of DSDP Leg 77 holes

Five of the six sites drilled during Leg 77 of the Deep Sea Drilling Project yielded Cretaceous sediments. Two of these sites, 535 and 540, form a composite section that spans the upper Berriasian through most of the Cenomanian. Olive black marly limestones in this interval yield relatively rich, well-preserved nannofossil assemblages that allow biostratigraphic subdivision of the sequence. This composite section provides important information on the Early Cretaceous history of the Gulf of Mexico, as well as additional information on tropical Lower Cretaceous nannofossil assemblages. The post-Cenomanian nannofossil (and sedimentary) record is limited to a thin, condensed section of Santonian through lower Maestrichtian pelagic sediments at one site (538) and is absent or represented by redeposited material at the other sites. Two new genera, Perchnielsenella and Darwinilithus, are described. Two new taxa, Darwinilithus pentarhethum and Lithraphidites acutum ssp. eccentricum, are described; and two new combinations, Rhagodiscus reightonensis and Perchnielsenella stradneri, are propose.

Benthic foraminifera in surface sediments of the Arabian Sea

Assemblages of living deep-sea benthic foraminifera, their densities, vertical distribution pattern, and diversity, were investigated in the intermonsoon period after the northeast monsoon in the Arabian Sea in spring 1997. Foraminiferal numbers show a distinct gradient from north to south, with a maximum of 623 foraminifera in 50 cm**3 at the northern site. High percentages of small foraminifera were found in the western and northern part of the Arabian Sea. Most stations show a typical vertical distribution with a maximum in the first centimeter and decreasing numbers with increasing sediment depths. But at the central station, high densities can be found even in deeper sediment layers. Diversity is very high at the northern and western sites, but reduced at the central and southern stations. Data and faunal assemblages were compared with studies carried out in 1995. A principal component analysis of intermonsoon assemblages shows that the living benthic foraminifera can be characterized by five principal component communities. Dominant communities influencing each site differ strongly between the two years. In spring 1997, stations in the north, west and central Arabian Sea were dominated by opportunistic species, indicating the influence of fresh sedimentation pulses or enhanced organic carbon fluxes after the northeast monsoon.

Profiles of diatoms, pollen, XRD, XRF and organic composition of two sediment cores (PG2022 and PG2023) from Lake Kyutyunda in Yakutia, NE Siberia, Russia

Although the climate development over the Holocene in the Northern Hemisphere is well known, palaeolimnological climate reconstructions reveal spatiotemporal variability in northern Eurasia. Here we present a multi-proxy study from north-eastern Siberia combining sediment geochemistry, and diatom and pollen data from lake-sediment cores covering the last 38,000 cal. years. Our results show major changes in pyrite content and fragilarioid diatom species distributions, indicating prolonged seasonal lake-ice cover between ~13,500 and ~8,900 cal. years BP and possibly during the 8,200 cal. years BP cold event. A pollen-based climate reconstruction generated a mean July temperature of 17.8°C during the Holocene Thermal Maximum (HTM) between ~8,900 and ~4,500 cal. years BP. Naviculoid diatoms appear in the late Holocene indicating a shortening of the seasonal ice cover that continues today. Our results reveal a strong correlation between the applied terrestrial and aquatic indicators and natural seasonal climate dynamics in the Holocene. Planktonic diatoms show a strong response to changes in the lake ecosystem due to recent climate warming in the Anthropocene. We assess other palaeolimnological studies to infer the spatiotemporal pattern of the HTM and affirm that the timing of its onset, a difference of up to 3,000 years from north to south, can be well explained by climatic teleconnections. The westerlies brought cold air to this part of Siberia until the Laurentide ice-sheet vanished 7,000 years ago. The apparent delayed ending of the HTM in the central Siberian record can be ascribed to the exceedance of ecological thresholds trailing behind increases in winter temperatures and decreases in contrast in insolation between seasons during the mid to late Holocene as well as lacking differentiation between summer and winter trends in paleolimnological reconstructions.

Cenozoic radiolarians from the Bahamas

Radiolarians from two sites north of Little Bahama Bank (Sites 627 and 628) are correlated with assemblages from sites on the southeastern U.S. coastal plain and continental shelf and from DSDP Sites 391 and 534 in the Blake-Bahama Basin. Results show that deposition of biogenic silica-rich sediments occurred in this region from the late Oligocene through middle Miocene, although the record is interrupted by unconformities. Radiolarians help constrain the age of a mass-transported deposit at Site 627 that appears to be coeval with the Great Abaco Member of the Blake Ridge Formation.