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Population Size, Genetic Diversity and molecular Evidence of a Recent Population Bottleneck in Hynobius chinensis, an Endangered Salamander Species

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Asian Herpetological Research 2018年第3期9卷 149-164页

作者： Eric Gilbert KAZITSA Shichao WEI Yunhai PU Xingyan WU Lin SONG Lei GAO Fuyuan QIU Yue GUO Zhaoquan ZHU Hua WU Institute of evolution and ecology School of Life Sciences Central China Normal University 152 Luoyulu Hongshan District Wuhan 430079 China Wildlife Conservation Station of Hubei Province 438 Xiongchu Avenue Hongshan District Wuhan 430079 China

Severe population declines can reduce species to small populations, offering permissive conditions for deleterious processes. For example, following such events, species can become prone to inbreeding and genetic drift which can lead to a loss of genetic diversity and evolutionary potentials. Hynobius chinensis is a poorly studied very rare and declining endangered amphibian species endemic to China in Changyang County. We investigated adult census population size by monitoring breeding populations from 2015 to 2018, developed microsatellite markers from the transcriptome and used them to investigate genetic diversity, and a population bottleneck in this species. We found H. chinensis in 4 different localities in a total area of 2.18 km^2 and estimated the overall adult census population size at 386–404 individuals. The adult census size（mean ± SE） per breeding pond ranged from 44 ± 6 to 141 ± 8 individuals and appeared smaller than that reported in closely related species in undisturbed habitats. We developed and characterized 13 microsatellite markers in total. Analysis of data at 7 loci（N = 118） in Hardy-Weinberg equilibrium gathered from the largest population showed that genetic diversity level was low. The average number of alleles per locus was 2.14. The observed and expected heterozygosities averaged 0.38 and 0.40, respectively. The inbreeding coefficient was –0.06. All tests performed to investigate a population bottleneck, i.e. The Garza-Williamson test, Heterozygosity excess test, Mode shift test of allele frequency, and effective population size estimates detected a population bottleneck. The contemporary and the historical effective population sizes were estimated at 36 and 234 individuals, respectively. We argue that as bottleneck effects, the studied population may have become prone to genetic drift and inbreeding, losing microsatellite alleles and heterozygosity. Our results suggest that populations of H. chinensismay have been extirpated in the stud

关键词： transcriptome microsatellites adult census population size effective population size genetic drift inbreeding

A phylogeographic break and bioacoustic intraspecific differentiation in the Buff-barred Warbler(Phylloscopus pulcher)(Aves:Passeriformes,Phylloscopidae)

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Chinese Birds 2014年第1期5卷 3-14页

作者： Martin Packert Yue-Hua Sun Balduin S Fischer Dieter Thomas Tietze Jochen Martens Senckenberg Natural History Collections Museum of ZoologyKonigsbrücker Landstraβe 159D-01109 DresdenGermany Key Laboratory of Animal ecology and Conservation Institute of ZoologyChinese Academy of Science Institute of ecology Evolution and DiversityGoethe UniversityMax-von-Laue-Straβe 1360439 Frankfurt am MainGermany Institute of Pharmacy and molecular Biotechnology University of HeidelbergIm Neuenheimer Feld 36469120 HeidelbergGermany Institut für Zoologie Johannes Gutenberg-Universitat55099 MainzGermany

Background: According to current taxonomy only three out of 27 Sinohimalayan leaf warbler species(Phylloscopidae) are considered genetically uniform across their entire breeding range along the Southeastern margin of the Qinghai-Tibetan Plateau, the Buff-barred Warbler(Phylloscopus pulcher) being one of them. Because marked differentiation among Himalayan and Chinese populations has been recently demonstrated for a number of Phylloscopus species(or sister species) we investigated the intraspecific variation of a mitochondrial gene, songs and morphology of P. pulcher in a phylogeographic ***: We sequenced a fragment of the mitochondrial cytochrome b, reconstructed haplotype networks and analyzed DNA polymorphism among Himalayan and Chinese populations. We measured time and frequency parameters of two distinct song types and analyzed among population-differentiation in a principal component analysis and a discriminant analysis. We also compared measurements of body size dimensions taken from museum ***: The mitochondrial haplotype network(cytb) was divided into two distinct clusters corresponding to geographic origin of samples. Pairwise genetic distances among Himalayan and Chinese mt DNA lineages account for 1.3% which coincides with Pleistocene lineage separation at roughly 650,000 years ago. Genetic diversity is slightly higher in the Chinese part of the species' range with respect to haplotype and nucleotide diversity while the less diversified Himalayan population lineage shows signs of recent range expansion. The vocal repertoire of P. pulcher comprises two distinct verse types that are combined with short interspersed click notes to long continuous song displays. Trill verse types showed significant differences among regions in almost all measured frequency and time parameters: Chinese males displayed more rapid and more broad-banded trills at a lower pitch. In contrast,warbling verse types showed a distinctively different structure

关键词： Phylloscopidae Phylogeography East–west divide Territorial songs Phylloscopus pulcher vegetus

molecular phylogeny and species separation of five morphologically similar Holosticha-complex ciliates(Protozoa, Ciliophora) using ARDRA riboprinting and multigene sequence data

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Chinese Journal of Oceanology and Limnology 2010年第3期28卷 542-548页

作者：高凤伊珍珍龚骏 Al-RASHEID Khaled A. S. 宋微波 Laboratory of Protozoology Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education College of Life Science South China Normal University Laboratory of Protozoology Institute of Evolution and Marine Biodiversity Ocean University of China Zoology Department King Saud University

To separate and redefine the ambiguous Holosticha-complex, a confusing group of hypotrichous ciliates, six strains belonging to five morphospecies of three genera, Holosticha heterofoissneri, Anteholosticha sp. popl, Anteholosticha sp. pop2, A. manca, A. gracilis and Nothoholostichafasciola, were analyzed using 12 restriction enzymes on the basis of amplified ribosomal DNA restriction analysis. Nine of the 12 enzymes could digest the DNA products, four （HinfⅠ, Hind Ⅲ, Msp Ⅰ, Taq Ⅰ） yielded species-specific restriction patterns, and Hind Ⅲ and Taq Ⅰ produced different pattems for two Anteholosticha sp. populations. Distinctly different restriction digestion haplotypes and similarity indices can be used to separate the species. The secondary structures of the five species were predicted based on the ITS2 transcripts and there were several minor differences among species, while two Anteholosticha sp. populations were identical. In addition, phylogenies based on the SSrRNA gene sequences were reconstructed using multiple algorithms, which grouped them generally into four clades, and exhibited that the genus Anteholosticha should be a convergent assemblage. The fact that Holosticha species clustered with the oligotrichs and choreotrichs, though with very low support values, indicated that the topology may be very divergent and unreliable when the number of sequence data used in the analyses is too low.

关键词： Ciliophora phylogeny ARDRA SSrRNA gene ITS2 secondary structure

New Gene evolution in Plants

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New Gene Evolution in Plants

Assigning hatchlings to eggs:Is relative mass assignment an accurate method?

第十届全国小麦基因组学及分子育种大会

作者： Manyuan Long Department of ecology and evolution The University of Chicago

New gene origination is an important evolution process that can be led to by a dozen of molecular mechanisms including duplication and de novo origination under positive *** and study of new gene origination require high-quality sequences of genomes for adequate comparative genomics *** concept of new genes and identificati on pipeline will be discussed with emphasis on plant *** the de novo genes are taken as example to interpret how to identify new genes from 13 recently divergedOryzaspecies and to understand de novo ***,we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of *** pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments,we detected at least 175 de novo open reading frames in the focal species *** subspecies japonica,which were all detected in RNA sequencing-based *** spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo *** recent divergence of Oryza,an average of 51.5 de novo genes per million years were *** observed evolutionary patterns in which excess indels and early transcription were favored in origination with a stepwise formation of gene *** data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection and a similar approach can be applied to investigate gene evolution in wheat and related wild species

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Avian Research 2017年第3期8卷 176-179页

作者： J.Dylan Maddox Pritzker Laboratory for molecular Systematics and evolution Field Museum of Natural HistoryChicagoIL 60605USA Environmental Sciences American Public University SystemCharles TownWV 25414USA

Background: Accurately assigning hatchlings to the eggs from which they hatched is a prerequisite to understanding how the composition and environment of eggs affect the growth and survival of nestlings. Correctly assigning hatchlings to their eggs can be a challenging endeavor, however, because multiple eggs within the same clutch can hatch at essentially the same time. Egg and hatchling mass are highly correlated in most bird species, and thus assigning eggs to hatchlings using their relative mass(e.g., matching the heaviest hatchling to the heaviest candidate egg) could prove extremely ***: To assess its potential utility, I applied relative mass assignment(RMA) retrospectively to a dataset of 133 Common Grackle(Quiscalus quiscula) nests in which all egg-hatchling dyads were determined ***: I found that RMA correctly assigned approximately 90% of hatchlings to their eggs when 2-4 hatchlings were present between checks. The number of nests in which hatchlings could not be assigned to their egg, however, increased monotonically from 13 to 46 to 78% for nests containing 2, 3, and 4 hatchlings, respectively, due to the greater likelihood that the mass of hatchlings or their candidate eggs was ***: Although RMA correctly identified the vast majority of egg-hatchling dyads, researchers should use this method with caution, because it will always inflate positive egg-size effects and thus could potentially result in erroneously reporting significant effects.

关键词： Egg mass Hatchling mass Maternal effects Hatching synchrony

Evaluation of bias on the assessment of diet breadth of herbivorous insects using molecular methods

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Insect Science 2017年第2期24卷 194-209页

作者： Gissela De la Cadena Anna Papadopoulou Jean-Michel Maes Jesus Gomez-Zurita Animal Biodiversity and evolution Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra) Barcelona Spain Department of Integrative ecology Estacion Biologica de Donana (EBD-CSIC) Seville Spain Museo entomologico de Leon Leon Nicaragua

The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is funda- mental to ecology and conservation. Recent research on DNA-based inference of trophic associations suggests that the host range of phytophagous insects in the tropics may be wider than previously thought based on traditional observation. However, the reliability of molecular inference of ecological associations, still strongly dependent on PCR and thus exposed to the risk of contamination with environmental DNA, is under debate. Here, we explored alternative procedures to reduce the chance of amplification of external, nondiet DNA, including surface decontamination and analysis of mid/hind guts, comparing the results with those obtained using the standard protocol. We studied 261 specimens in eight species of Neotropical Chrysomelidae that yielded 316 psbA-trnH intergenic spacer sequences （cpDNA marker of putative diets） from unique and multiple-band PCR results. The taxonomic identity of these sequences was inferred using the automated pipeline BAGpipe, yielding results consistent with 31 plant families. Regardless of the proto- col used, a wide taxonomic spectrum of food was inferred for all chrysomelid species. Canonical Correspondence Analysis using these data revealed significant differences at- tributed mainly to species （expectedly, since they represent different ecologies）, but also to treatment （untreated vs. cleaned/gut samples） and PCR results （single vs. multiple bands）. molecular identification of diets is not straightforward and, regardless of the species＇ niche breadth, combining approaches that reduce external contamination and studying multiple individuals per species may help increasing confidence in results.

关键词： food-webs gut content insect plant interaction molecular ecology molec-ular taxonomy psbA-trnH intergenic spacer

New progress in understanding the origins of modern humans in China

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维普期刊数据库

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Science China Earth Sciences 2017年第12期60卷 2160-2170页

作者： GAO Xing PENG Fei FU QiaoMei LI Feng Key Laboratory of Vertebrate evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044 University of the Chinese Academy of Sciences Beijing 100049China Department of Early Prehistory and Quaternary ecology University of TubingenTubingen 72070Germany

Hypotheses concerning the origins of modern humans have been intensively debated, and two competing models, the recent "Out-of-Africa" and "Multiregional evolution" paradigms, have dominated research and discussions for decades. Evidence from China has played a fundamental role in this debate: regional continuity and replacement by populations in-migrated from Africa have both been suggested and supported mainly by paleoanthropologists and geneticists, respectively. As more evidence has accumulated, new results obtained, and more scholars from various disciplines become involved, supporters of the recent "Out-of-Africa" model agree more or less with the "Multiregional evolution" model regarding the complex history of modern humans and their interbreeding with other archaic populations(e.g., Neandertals). Recent discoveries of new human fossils, Paleolithic archaeological materials, and ancient DNA evidence in China have yielded a large body of information regarding the formation and development of modern humans in this region. However, controversies continue, including that most molecular biologists insist on the replacement of archaic populations by modern humans dispersed from Africa, while most paleoanthropologists and archaeologists propose an enhanced "Continuity with Hybridization" model. In this paper, we compile new results and progress in China and present the current debates and issues on the origins of modern humans. Finally, we offer several suggestions for future studies.

关键词： China Origins of modern humans Modern behavior Recent out-of-Africa Continuity with hybridization Interdisciplinary research

While neither universally applicable nor practical operationally, the biological species concept continues to offer a compelling framework for studying species and speciation

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National Science Review 2020年第8期7卷 1398-1400页

作者： Lexuan Gao Loren H.Rieseberg CAS Center for Excellence in molecular Plant Sciences Institute of Plant Physiology and Ecology Chinese Academy of Sciences Department of Botany and Biodiversity Research Centre University of British Columbia

Few topics in evolutionary biology have received as much scrutiny and debate as the nature of species and species concepts. This is partly because species are central to many fields of biology(but especially evolution, ecology, systematics, and conservation biology), and there does not appear to be a single concept that can satisfy the needs of these different disciplines [1].

关键词： REPRODUCTIVE ISOLATION GENE FLOW INTROGRESSION BARRIER

Spatio-temporal patterns of zooplankton in a main-stem dam affected tributary: a case study in the Xiangxi River of the Three Gorges Reservoir, China

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Science China(Life Sciences) 2019年第8期62卷 1058-1069页

作者： Xinghao Li Jie Huang Sabine Filker Thorsten Stoeck Yonghong Bi Yuhe Yu Weibo Song Laboratory of Protozoology Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdao266003China Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences and State Key Laboratory of Freshwater Ecologyand BiotechnologyInstitute of HydrobiologyChinese Academy of SciencesWuhan430072China Department of molecular ecology University of Technology KaiserslauternKaiserslautern67663Germany Department of ecology University of Technology KaiserslauternKaiserslautern67663Germany Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266003China

As the ecologically important recipient channels for riverine ecosystems, tributaries provide unique microhabitats for microorganisms, among which zooplankton constitutes the most important heterotrophic organisms. In particular, the reduced water velocity caused by dams is more favorable for zooplankton development;therefore, dammed rivers are expected to support extremely diverse and abundant zooplankton communities and notably different spatiotemporal distribution patterns. So far,however, only very few molecular studies support these assumptions. Using high-throughput sequencing, a high number of 350 operational taxonomic units(OTUs;97% cutoff) were retrieved from 30 samples collected in the Xiangxi River, the nearest large tributary upstream of the Three Gorges Dam. Zooplankton did not show significant spatial distribution in the channel. Instead,the community structures varied significantly over sampling dates, corroborating the seasonal patterns found in lakes and ponds in the subtropical zone. As expected, the community compositions were deterministically governed by environmental filtering processes(phylogenetic clustering), in which water velocity appeared to be much less important than other investigated environmental factors. Moreover, most of the detected phylotypes(OTUs) had a relatively high(>90%) sequence similarity to previously deposited sequences, suggesting a mediocre degree of genetic novelty within the zooplankton communities in the Xiangxi River.

关键词： zooplankton high-throughput sequencing spatiotemporal distribution genetic novelty tributary main-stem dam