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

Effects of climate change and anthropogenic activity on ranges of vertebrate species endemic to the Qinghai - Tibet Plateau over 40 years

Over the past 40 years, the climate has been changing and human disturbance has increased in the vast Qinghai¿Tibet Plateau (QTP). These 2 factors are expected to affect the distribution of a large number of endemic vertebrate species. However, quantitative relationships between range shifts and climate change and human disturbance of these species in the QTP have rarely been evaluated. We used occurrence records of 19 terrestrial vertebrate species (birds, mammals, amphibians, and reptiles) occurring in the QTP from 1980 to 2020 to quantify the effects of climate change and anthropogenic impacts on the distribution of these 4 taxonomic groups and estimated species range changes in each species. The trend in distribution changes differed among the taxonomic groups, although, generally, ranges shifted to central QTP. Climate change contributed more to range variation than human disturbance (the sum of the 4 climatic variables contributed more than the sum of the 4 human disturbance variables for all 4 taxonomic groups). Suitable geographic range increased for most mammals, amphibians, and reptiles (+27.6%, +18.4%, and +27.8% on average, respectively), whereas for birds range decreased on average by 0.9%. Quantitative evidence for climate change and human disturbance associations with range changes for endemic vertebrate species in the QTP can provide useful insights into biodiversity conservation under changing environments.This project was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (2019QZKK0501); the Strategic Priority Research Program of Chinese Academy of Sciences (CAS) (XDB31000000); the National Natural Science Foundation of China (32070410; 32100396); the Youth Innovation Promotion Association of CAS (2021370); and the Sichuan Science and Technology Program (2023NSFSC0197)INTRODUCTION METHODS Species distribution data Statistical analyses RESULTS DISCUSSION ACKNOWLEDGMENT

Bioinformatic analysis of gene regulation in Geobacter sulfurreducens

Background Geobacteraceae are a family of microorganisms from the delta subdivision of Proteobacteria. They have potential for environmental bioremediation and electricity generation. In this presentation, we describe our recent bioinformatic analyses of gene regulation in Geobacter sulfurreducens, a model representative of this family. Results and conclusion We have developed an online database, GSEL (Geobacter Sequence Elements), which compiles regulatory information for G. sulfurreducens. We have recently completed the development of a new, significantly expanded and updated, relational version 2 of the GSEL database and its accompanying online query system, which compiles manually curated information on operon organization and transcription regulatory elements in the genome of G. sulfurreducens. GSEL v. 2 incorporates a graphical browser and provides significantly expanded search capabilities. It also includes new information on predicted and/or experimentally validated genome regulatory sites and provides links to information from microarray experiments stored in public gene expression databases, and to original publications describing how particular regulatory interactions were identified. Using sequence and gene expression analyses, we investigated target genes and promoters regulated by RpoN, an alternative RNA polymerase sigma factor, which regulates a variety of important cellular processes in G. sulfurreducens. Our current studies are focusing on an investigation of several transcription regulatory systems involved in RpoN-dependent regulatory pathways. We have investigated target regulatory sites for an enhancer binding protein, PilR, which participates in RpoN-dependent transcriptional regulation of the pilA gene encoding structural pilin. We predicted multiple PilR-regulated sites upstream of operons related to biosynthesis, assembly, and function of pili and flagella, type II secretory pathways, and cell wall biogenesis. We also investigated sequence changes and molecular classification of the TetR family of transcriptional regulators. In G. sulfurreducens, we identified RpoN-regulated promoters upstream of several operons containing tetR family genes. The genome of G. sulfurreducens contains nine tetR family genes. Some of them are located upstream of operons encoding functionally important c-type cytochromes. In order to better understand the roles of TetR family members in the ability of Geobacteraceae to participate in electron transfer, we investigated phylogenetic relationships among TetR proteins in Geobacteraceae and in other microbial species. We identified their conserved and variable domains, which may be important for the diversity of their functional roles, and classified them into subgroups based on sequence similarities

Analysis of virulence genes and antimicrobial resistance of Vibrio parahaemolyticus isolated from shellfish in 2018

Objective To analyze the virulence genes and antimicrobial resistance of 140 Vibrio parahaemolyticus strains from shellfish collected from farms and markets. Methods Virulence genes and antimicrobial resistance genes were detected by PCR amplification method, and antimicrobial resistance was determined by disk diffusion test. Results None of the 140 strains carried tdh gene, and trh gene was detected in one strain. All strains were resistant to ampicillin, some strains were resistant to cefazolin, cefuroxime sodium, streptomycin, amikacin, sulphamethoxazole/trimethoprim, tetracycline and florfenicol. All strains were sensitive to cefepime, gentamicin, imipenem, meropenem, ofloxacin and doxycycline. Six strains showed multi-antimicrobial resistance to two or more categories of antimicrobials. The resistance genes strA and strB were detected in streptomycin resistant strains, tetA was detected in tetracycline resistant strains, sul2 was detected in sulphamethoxazole/trimethoprim resistant strains, and floR was detected in florfenicol resistant strain. Conclusion Most of Vibrio parahaemolyticus strains didn't carry virulence genes and showed antimicrobial resistance to a certain extent. Some strains had more than one antimicrobial resistance gene, which exhibited multi-antimicrobial resistance. These results indicated that enhancing the monitoring of pathogenicity and antimicrobial resistance of Vibrio parahaemolyticus in aquatic products should be continued