Parasite Species Associated With Wild Plateau Pika (Ochotona Curzoniae) In Southeastern Qinghai Province, China

A survey was conducted to determine the prevalence and seasonal abundance of egg, larval, and adult stages of helminths; oocyts of protozoans; and ectoparasites of plateau pikas (Ochotona curzoniae) in seven areas of southeastern Qinghai Province, China, during August 2006 and May 2007. Fecal samples collected from 430 plateau pikas were examined by the modified McMaster technique, which revealed that 83% of the samples contained eggs from two or more helminth species. Mean fecal egg counts were generally moderate and showed the same trend irrespective of the age or sex of the pikas. The prevalence and counts of cestode eggs showed strong seasonal relationships that corresponded with the rainfall pattern in the study area during the study period. Of the 430 plateau pika examined at necropsy, 89% contained adult nematode or cestode species, but none of these contained adult trematode species or protozoans. Overall, six genera of adult nematodes including Oesophagostomum sp., Cephaluris coloradensis, Eugenuris schumakowiescsi, Haemonchus sp., Trichuris sp., and Chbertiinae sp.; three genera of adult cestodes including Schizorchis sp., Ochotonae sp., and Hymenolepis nana; three ectoparasite species including Hypoderma curzonial, Pulex sp., and Ixodes ovatus; and one proscolex stage of a cestode, Echinococcus multilocularis or Echinococcus shiquicus, were encountered during the study. Other genera examined occurred in low numbers, which did not allow any meaningful comparisons. Overall, results suggest that four parasite species, Hypoderma curzonial, Pulex sp., Ixodes ovatus Neumann, and Cephaluris coloradensis, may be regulating factors in controlling future numbers of plateau pika in this study area. These data provide evidence of a natural biologic control mechanism of plateau pika on grassland habitats, and may be of use for identifying the mechanism of transmission of parasites between plateau pika, livestock, and humans

Profound Climatic Effects on Two East Asian Black-Throated Tits (Ave: Aegithalidae), Revealed by Ecological Niche Models and Phylogeographic Analysis

Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

Aim: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the "time-for-speciation effect"). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of a large radiation of passerine birds. Location: Global Time period: Early Miocene to present Major taxa studied: Babblers (Aves: Passeriformes) Methods: Using a comprehensive phylogeny of extant species (~90% sampled) and distributions of the world's babblers, we reconstructed their biogeographic history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographic distribution regions. Results: We found thatbabblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of Zosteropsduring the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands. Main conclusions: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific region, which provides new insights into the generation of global biodiversity hotspots.A near-complete phylogeny of babblers has been reconstructed in BEAST 1.8.4 based on 12 gene loci

Past hybridization between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus)

Introduction: Incomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species.Results: The mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present.Conclusions: We suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion

Evolutionary genomics of the pandemic 2009 H1N1 influenza viruses (pH1N 1v)

There are ongoing health risks posed by the pandemic 2009 H1N1 influenza viruses. This research provides a detailed phylogenetic analysis in 394 sequences of H1N1 viruses, taken from swine, human and avian sources from 1918 to 2009, to estimate a temporal reconstruction of reassortment history of 2009 H1N1 viruses. H1N1 influenza viruses were first isolated from swine in 1930; in Europe, avian H1N1 viruses were first detected in pigs in 1979. Pigs have been considered a possible “mixing vessel” in which genetic material can be exchanged. There is a potential for novel progeny viruses to arise, to which humans would be susceptible

An Unstructured Phylogeographic Pattern with Extensive Gene Flow in an Endemic Bird of South China: Collared Finchbill (Spizixos semitorques)

Recent phylogeographical studies indicated that glacial oscillations played a key role on the phylogeographic pattern of extant species. As most studies have previously been carried out on heavily ice-covered regions, such as in European and North American regions, potential effects of climatic oscillations on species that are distributed on ice-free regions are less known. To address this, we investigated the phylogeographic pattern of an avian species endemic to South China, which was not glaciated during the Pleistocene glaciations. By using 2142 bp mitochondrial DNA, we identified 89 haplotypes defined by 39 polymorphic sites. A combination of high haplotype diversity (0.786–1.00) and low nucleotide diversity (0.00132–0.00252) was detected among geographic populations. Explicit genetic divergence was observed between S. s. semitorques and S. s. cinereicapillus but not detected among geographic populations of S. s. semitorques. Divergence time of the two subspecies was dated back to 87 Kyr which is congruent with the interglacial MIS 5. A weak phylogeographic structure due to strong gene flow among geographic populations was identified in this species, suggesting complex topography of South China has not formed barriers for this species

Present and past ecological niche models for the Great Tit (Parus major)

This presentation was given as part of the GIS Day@KU symposium on November 14, 2018. For more information about GIS Day@KU activities, please see http://gis.ku.edu/gisday/2018/PLATINUM SPONSORS: KU Department of Geography and Atmospheric Science KU Institute for Policy & Social Research GOLD SPONSORS: KU Libraries State of Kansas Data Access & Support Center (DASC) SILVER SPONSORS: Bartlett & West Kansas Applied Remote Sensing Program KU Center for Global and International Studies BRONZE SPONSORS: Boundles

Encoding Enhanced Complex CNN for Accurate and Highly Accelerated MRI

Magnetic resonance imaging (MRI) using hyperpolarized noble gases provides a way to visualize the structure and function of human lung, but the long imaging time limits its broad research and clinical applications. Deep learning has demonstrated great potential for accelerating MRI by reconstructing images from undersampled data. However, most existing deep conventional neural networks (CNN) directly apply square convolution to k-space data without considering the inherent properties of k-space sampling, limiting k-space learning efficiency and image reconstruction quality. In this work, we propose an encoding enhanced (EN2) complex CNN for highly undersampled pulmonary MRI reconstruction. EN2 employs convolution along either the frequency or phase-encoding direction, resembling the mechanisms of k-space sampling, to maximize the utilization of the encoding correlation and integrity within a row or column of k-space. We also employ complex convolution to learn rich representations from the complex k-space data. In addition, we develop a feature-strengthened modularized unit to further boost the reconstruction performance. Experiments demonstrate that our approach can accurately reconstruct hyperpolarized 129Xe and 1H lung MRI from 6-fold undersampled k-space data and provide lung function measurements with minimal biases compared with fully-sampled image. These results demonstrate the effectiveness of the proposed algorithmic components and indicate that the proposed approach could be used for accelerated pulmonary MRI in research and clinical lung disease patient care