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1.
RADKA POLKOV MARTINA VYSKOILOV JEAN‐FRANOIS MARTIN HERMAN L. MAYS GEOFFREY E. HILL JOSEF BRYJA TOM&#x; ALBRECHT 《Molecular ecology resources》2007,7(6):1375-1378
Cardueline finches have become important models in studies of sexual selection and evolution of carotenoid‐based ornamentation. Here, we describe eight new polymorphic microsatellites isolated from the Scarlet rosefinch (Carpodacus erythrinus) and four from the House finch (Carpodacus mexicanus). Together with the cross‐species amplification of additional loci, originally published for two species of songbirds, we optimized a multiplex panel for C. erythrinus allowing genotyping of 22 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 34 individuals ranged from three to 38 and from 0.27 to 0.94, respectively. 相似文献
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B. Hausdorf 《Journal of Biogeography》2000,27(2):379-390
Aim Reconstruction of the historical biogeography of the Limacoidea sensu lato (including the Staffordiidae, Dyakiidae, Gastrodontoidea, Parmacelloidea, Zonitidae, Helicarionoidea and Limacoidea). Evaluation of the relative importance of dispersal and its consequences. Location World‐wide. Methods Weighted ancestral area analysis. Results The ancestral areas of the individual clades have been delimited using weighted ancestral area analysis and a sequence of possible vicariance and dispersal events has been suggested. The results of the ancestral area analysis have tentatively been correlated with Cretaceous and Tertiary palaeogeography. The widely overlapping distribution patterns of several families of the Limacoidea testify to extensive dispersal events. Dispersal capacity of land snails is correlated with body size. The significant negative correlation between body size and distribution area size corroborates the importance of passive dispersal for the evolution of the distribution patterns. Main conclusions The existence of extensive dispersal events of poor active dispersers like land snails diminishes the importance of recent distribution patterns for the reconstruction of palaeogeography. On the other hand, dispersal ensures that biogeographical data reflect the geographical configurations at a given time and renders the use of palaeobiogeographic data for the reconstruction of palaeogeographic configurations of the respective age possible. 相似文献
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BernhardHausdorf 《Zoological Journal of the Linnean Society》2002,134(3):347-358
The phylogeny of the Vitrinidae is reconstructed in a cladistic analysis based on characters of the genitalia, the copulation behaviour and the radula. The genera with an atrial stimulator turned out to be the earliest branches of the Vitrinidae, whereas the genera with a glandula amatoria form a monophyletic, taxonomically apomorphic group. The differences between the proposed phylogeny and previous hypotheses are discussed. The ancestral areas of the Vitrinidae and its sister group, the limacoid slugs Boettgerillidae–Limacidae–Agriolimacidae, are estimated using weighted ancestral area analysis. The Vitrinidae and the limacoid slugs might have originated by a vicariance event between Central Europe and the Near East. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 347–358. 相似文献
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Sergei V. Drovetski 《Journal of Biogeography》2003,30(8):1173-1181
Aim In this paper, I discuss the temporal and spatial aspects of historical biogeography and speciation in a widely distributed Holarctic subfamily of birds (Tetraoninae). Location Northern Holarctic. Results Using dated fossils, I calibrated the molecular clock for the mitochondrial control region at 7.23 ± 1.58% nucleotide divergence (maximum likelihood corrected) per million years. The data suggest that grouse (Tetraoninae) originated in the Middle Pliocene, 6.3 Ma. Grouse apparently originated in the northern part of western Nearctic, and Palearctic was colonized independently three times, first by the ancestor of all grouse in the Middle Pliocene, then by the ancestor of forest (Falcipennis, Tetrao and Lyrurus) and prairie (Centrocercus, Dendragapus and Tympanuchus) grouse in the Late Pliocene, and finally by the ancestral Lagopus in the Early Pleistocene. Only once Nearctic was colonized from Palearctic by a common ancestor of forest grouse. Sympatry and range symmetry were positively correlated with molecular divergence. These correlations suggest that peripatric isolation was the predominant mode of speciation throughout grouse history. Main conclusions Speciation events in grouse were driven by climatic oscillations of the Pliocene and Pleistocene. Isolation of small peripheral populations from widely distributed ancestors was the dominant mode of speciation in grouse. Isolations during interglacials both across Beringia, and in southern mountain areas when boreal habitats were restricted to high elevations, suggest an important role for vicariance in grouse speciation. 相似文献
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The arcto‐Tertiary relictual flora is comprised of many genera that occur non‐contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more‐continuous arcto‐Tertiary forest. The historical biogeographic events leading to the present‐day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes‐DIVA method handles both types of uncertainty. Thus, we used Bayes‐DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto‐Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present‐day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto‐Tertiary species endemic in the neotropics. 相似文献
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Jukun Song Qiuyan Xu Haodeng Zhang Xinhai Yin Chen Zhu Ke Zhao Jianguo Zhu 《Journal of cellular biochemistry》2018,119(6):4559-4569
Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, and the 5‐year survival rate was only 7.7%. To improve prognosis, a screening biomarker for early diagnosis of pancreatic cancer is in urgent need. Long non‐coding RNA (lncRNA) expression profiles as potential cancer prognostic biomarkers play critical roles in development of tumorigenesis and metastasis of cancer. However, lncRNA signatures in predicting the survival of a patient with PDAC remain unknown. In the current study, we try to identify potential lncRNA biomarkers and their prognostic values in PDAC. LncRNAs expression profiles and corresponding clinical information for 182 cases with PDAC were acquired from The Cancer Genome Atlas (TCGA). A total of 14 470 lncRNA were identified in the cohort, and 175 PDAC patients had clinical variables. We obtained 108 differential expressed lncRNA via R packages. Univariate and multivariate Cox proportional hazards regression, lasso regression was performed to screen the potential prognostic lncRNA. Five lncRNAs have been recognized to significantly correlate with OS. We established a linear prognostic model of five lncRNA (C9orf139, MIR600HG, RP5‐965G21.4, RP11‐436K8.1, and CTC‐327F10.4) and divided patients into high‐ and low‐risk group according to the prognostic index. The five lncRNAs played independent prognostic biomarkers of OS of PDAC patients and the AUC of the ROC curve for the five lncRNAs signatures prediction 5‐year survival was 0.742. In addition, targeted genes of MIR600HG, C9orf139, and CTC‐327F10.4 were explored and functional enrichment was also conducted. These results suggested that this five‐lncRNAs signature could act as potential prognostic biomarkers in the prediction of PDAC patient's survival. 相似文献
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Magalie S. Leduc Rachael S. Hageman Qingying Meng Ricardo A. Verdugo Shirng‐Wern Tsaih Gary A. Churchill Beverly Paigen Rong Yuan 《Aging cell》2010,9(5):823-836
The IGF‐1 signaling pathway plays an important role in regulating longevity. To identify the genetic loci and genes that regulate plasma IGF‐1 levels, we intercrossed MRL/MpJ and SM/J, inbred mouse strains that differ in IGF‐1 levels. Quantitative trait loci (QTL) analysis of IGF‐1 levels of these F2 mice detected four QTL on chromosomes (Chrs) 9 (48 Mb), 10 (86 Mb), 15 (18 Mb), and 17 (85 Mb). Haplotype association mapping of IGF‐1 levels in 28 domesticated inbred strains identified three suggestive loci in females on Chrs 2 (13 Mb), 10 (88 Mb), and 17 (28 Mb) and in four males on Chrs 1 (159 Mb), 3 (52 and 58 Mb), and 16 (74 Mb). Except for the QTL on Chr 9 and 16, all loci co‐localized with IGF‐1 QTL previously identified in other mouse crosses. The most significant locus was the QTL on Chr 10, which contains the Igf1 gene and which had a LOD score of 31.8. Haplotype analysis among 28 domesticated inbred strains revealed a major QTL on Chr 10 overlapping with the QTL identified in the F2 mice. This locus showed three major haplotypes; strains with haplotype 1 had significantly lower plasma IGF‐1 and extended longevity (P < 0.05) than strains with haplotype 2 or 3. Bioinformatic analysis, combined with sequencing and expression studies, showed that Igf1 is the most likely QTL gene, but that other genes may also play a role in this strong QTL. 相似文献
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In this study, a state‐of‐the‐art approach in modelling fish habitats, using high‐resolution topographical data, obtained from unmanned aerial vehicle, was applied. Habitat Suitability Indices are used to predict how changes in discharge affect instream fish habitats. Habitat Suitability Indices regarding depth and velocity for two size classes (small sized fish 5–15 cm total length and large sized >15 cm total length) of Salmo pelagonicus and Barbus balcanicus were used, in combination with a two‐dimensional hydraulic‐hydrodynamic model, for the estimation of the weighted usable area (WUA) in a mountainous stream. Computational mesh and/or digital terrain model (DTM) resolution selection may influence the accuracy of WUA results, especially in boulder and cobble‐bed streams with complex habitat structures. The aim of the study is to examine the sensitivity of various hydraulic‐hydrodynamic modelling geometry configurations on WUA at ungauged or poorly gauged streams. Comparisons of three different geometry configurations: (1) identical computational mesh and DTM resolution (SensComb); (2) finest computational mesh resolution combined with different DTM resolutions (SensDTM); (3) finest DTM resolution combined with different computational mesh resolutions, as part of two‐dimensional hydrodynamic modelling, were applied to test the differences in WUA (SensMesh). WUA maps were generated for both fish species and class sizes for each modelling geometry configuration and compared with each other for assessing the sensitivity of the two‐input data (computational mesh and DTM). Results provided by both indices and their spatial distribution indicated the optimal DTM and computational mesh resolution as well as the sensitivity of a specific hydraulic‐habitat model on them. 相似文献
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Bitian Liu Yunhong Zhan Xiaonan Chen Xiaoru Hu Bin Wu Shen Pan 《Journal of cellular physiology》2021,236(2):1321-1331
The role of cancer‐associated fibroblasts (CAFs) has been thoroughly investigated in tumour microenvironments but not in bladder urothelial carcinoma (BLCA). The cell fraction of CAFs gradually increased with BLCA progression. Weighted gene co‐expression network analysis (WGCNA) revealed a specific gene expression module of CAFs that are relevant to cancer progression and survival status. Fifteen key genes of the module were consistent with a fibroblast signature in single‐cell RNA sequencing, functionally related to the extracellular matrix, and significant in survival analysis and tumour staging. A comparison of the luminal‐infiltrated versus luminal‐papillary subtypes and fibroblast versus urothelial carcinoma cell lines and immunohistochemical data analysis demonstrated that the key genes were specifically expressed in CAFs. Moreover, these genes are highly correlated with previously reported CAF markers. In summary, CAFs play a major role in the progression of BLCA, and the 15 key genes act as BLCA‐specific CAF markers and can predict CAF changes. WGCNA can, therefore, be used to sort CAF‐specific gene set in cancer tissues. 相似文献
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Ning Xu Shao‐Hao Chen Ting‐Ting Lin Hai Cai Zhi‐Bin Ke Ru‐Nan Dong Peng Huang Xiao‐Dong Li Ye‐Hui Chen Qing‐Shui Zheng 《Journal of cellular and molecular medicine》2020,24(8):4402-4414
Lymph node metastasis is one of the most important independent risk factors that can negatively affect the prognosis of prostate cancer (PCa); however, the exact mechanisms have not been well studied. This study aims to better understand the underlying mechanism of lymph node metastasis in PCa by bioinformatics analysis. We analysed a total of 367 PCa cases from the cancer genome atlas database and performed weighted gene co‐expression network analysis to explore some modules related to lymph node metastasis. Gene Ontology analysis and pathway enrichment analysis were conducted for functional annotation, and a protein‐protein interaction network was built. Samples from the International Cancer Genomics Consortium database were used as a validation set. The turquoise module showed the most relevance with lymph node metastasis. Functional annotation showed that biological processes and pathways were mainly related to activation of the processes of cell cycle and mitosis. Four hub genes were selected: CKAP2L, CDCA8, ERCC6L and ARPC1A. Further validation showed that the four hub genes well‐distinguished tumour and normal tissues, and they were good biomarkers for lymph node metastasis of PCa. In conclusion, the identified hub genes facilitate our knowledge of the underlying molecular mechanism for lymph node metastasis of PCa. 相似文献
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Yan Yao Tingting Zhang Lingyu Qi Chao Zhou Junyu Wei Fubin Feng Ruijuan Liu Changgang Sun 《Journal of cellular and molecular medicine》2019,23(12):8410-8419
Long non‐coding RNAs (lncRNAs), which competitively bind miRNAs to regulate target mRNA expression in the competing endogenous RNAs (ceRNAs) network, have attracted increasing attention in breast cancer research. We aim to find more effective therapeutic targets and prognostic markers for breast cancer. LncRNA, mRNA and miRNA expression profiles of breast cancer were downloaded from TCGA database. We screened the top 5000 lncRNAs, top 5000 mRNAs and all miRNAs to perform weighted gene co‐expression network analysis. The correlation between modules and clinical information of breast cancer was identified by Pearson's correlation coefficient. Based on the most relevant modules, we constructed a ceRNA network of breast cancer. Additionally, the standard Kaplan‐Meier univariate curve analysis was adopted to identify the prognosis of lncRNAs. Ultimately, a total of 23 and 5 modules were generated in the lncRNAs/mRNAs and miRNAs co‐expression network, respectively. According to the Green module of lncRNAs/mRNAs and Blue module of miRNAs, our constructed ceRNA network consisted of 52 lncRNAs, 17miRNAs and 79 mRNAs. Through survival analysis, 5 lncRNAs (AL117190.1, COL4A2‐AS1, LINC00184, MEG3 and MIR22HG) were identified as crucial prognostic factors for patients with breast cancer. Taken together, we have identified five novel lncRNAs related to prognosis of breast cancer. Our study has contributed to the deeper understanding of the molecular mechanism of breast cancer and provided novel insights into the use of breast cancer drugs and prognosis. 相似文献
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Nawal Shrestha Zhiheng Wang Xiangyan Su Xiaoting Xu Lisha Lyu Yunpeng Liu Dimitar Dimitrov Jonathan D. Kennedy Qinggang Wang Zhiyao Tang Xiaojuan Feng 《Global Ecology and Biogeography》2018,27(8):913-924
Aim
Understanding the evolution of the latitudinal diversity gradient (i.e. increase in species diversity towards the tropics) is a prominent issue in ecology and biogeography. Disentangling the relative contributions of environment and evolutionary history in shaping this gradient remains a major challenge because their relative importance has been found to vary across regions and taxa. Here, using the global distributions and a molecular phylogeny of Rhododendron, one of the largest genera of flowering plants, we aim to compare the relative contributions of contemporary environment, evolutionary time and diversification rates in generating extant species diversity patterns.Location
Global.Time period
Undefined.Major taxa studied
Rhododendron.Methods
We compiled the global distributions of all Rhododendron species, and constructed a dated molecular phylogeny using nine chloroplast genes and seven nuclear regions. By integrating these two datasets, we estimated the temporal trends of Rhododendron diversification, and explored the global patterns of its species diversity, net diversification rates, and species ages. Next, we reconstructed the geographical ancestral area of the clade. Finally, we compared the relative contribution of contemporary environment, time‐for‐speciation, and diversification rates on the species diversity pattern of Rhododendron.Results
In contrast to the predictions of the time‐for‐speciation hypothesis, we found that although Rhododendron originated at a temperate latitude, its contemporary species diversity is highest in the tropics/subtropics, suggesting an into‐the‐tropics colonization for this genus. We found that the elevated diversification induced by heterogeneous environmental conditions in the tropics/subtropics shapes the global pattern of Rhododendron diversity.Main conclusions
Our findings support tropical and subtropical mountains as not only biodiversity and endemism hotspots, but also as cradles for the diversification of Rhododendron. Our study emphasizes the need of unifying ecological and evolutionary approaches in order to gain comprehensive understanding of the mechanisms underlying the global patterns of plant diversity. 相似文献17.
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Santiago Martín‐Bravo Pedro Jimnez‐Mejías Tamara Villaverde Marcial Escudero Marlene Hahn Daniel Spalink Eric H. Roalson Andrew L. Hipp Carmen Benítez‐Benítez Leo P. Bruederle Elisabeth Fitzek Bruce A. Ford Kerry A. Ford Mira Garner Sebastian Gebauer Matthias H. Hoffmann Xiao‐Feng Jin Isabel Larridon tienne Lveill‐Bourret Yi‐Fei Lu Modesto Luceo Enrique Maguilla Jose Ignacio Mrquez‐Corro Mnica Míguez Robert Naczi Anton A. Reznicek Julian R. Starr 《植物分类学报：英文版》2019,57(6):695-718
The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space. 相似文献
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Andrey Pshenichnov Oleg Balanovsky Olga Utevska Ene Metspalu Valery Zaporozhchenko Anastasia Agdzhoyan Mikhail Churnosov Lyubov Atramentova Elena Balanovska 《American journal of physical anthropology》2013,152(4):543-550
The area of what is now the Ukraine has been the arena of large‐scale demographic processes that may have left their traces in the contemporary gene pool of Ukrainians. In this study, we present new mitochondrial DNA data for 607 Ukrainians (hypervariable segment I sequences and coding region polymorphisms). To study the maternal affinities of Ukrainians at the level of separate mitochondrial haplotypes, we apply an original technique, the haplotype co‐occurrence analysis. About 20% of the Ukrainian maternal gene pool is represented by lineages highly specific to Ukrainians, but is scarcely found in other populations. About 9% of Ukrainian mtDNA lineages are typical for peoples of the Volga region. We also identified minor gene pool strata (1.6–3.3%), each of which is common in Lithuanians, Estonians, Saami, Nenets, Cornish, and the populations of the North Caucasus. Am J Phys Anthropol 152:543–550, 2013. © 2013 Wiley Periodicals, Inc. 相似文献