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Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area

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Marine Life Science & Technology 2024年第2期6卷 349-362页

作者： Zhixin Zhang Jinxin Zhou Jorge García Molinos Stefano Mammola Ákos Bede‑Fazekas Xiao Feng Daisuke Kitazawa Jorge Assis Tianlong Qiu Qiang Lin CAS Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Guangdong Provincial Key Laboratory of Applied Marine Biology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Marine Biodiversity and Ecological Evolution Research Center South China Sea Institute of OceanologyGuangzhou 510301China Global Ocean and Climate Research Center South China Sea Institute of OceanologyGuangzhou 510301China Institute of Industrial Science The University of Tokyo5-1-5 KashiwanohaKashiwaChiba 277-8574Japan Arctic Research Center Hokkaido UniversitySapporoHokkaido 001-0021Japan Finnish museum of natural history University of HelsinkiHelsinkiFinland Molecular Ecology Group(MEG) Water Research Institute(IRSA)National Research Council of Italy(CNR)28922 Verbania PallanzaItaly National Biodiversity Future Center(NBFC) PalermoItaly Institute of Ecology and Botany HUN-REN Centre for Ecological ResearchVácrátótHungary Department of Environmental and Landscape Geography ELTE Eötvös Loránd UniversityBudapestHungary Department of Biology University of North CarolinaChapel HillNC 27599USA Centre of Marine Sciences University of AlgarveCampus de GambelasFaroPortugal CAS Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of SciencesQingdao 266071China university of Chinese Academy of Sciences Beijing 100049China

Correlative species distribution models(SDMs)are important tools to estimate species’geographic distribution across space and time,but their reliability heavily relies on the availability and quality of occurrence *** can be biased when occurrences do not fully represent the environmental requirement of a *** tested to what extent species’physiological knowledge might influence SDM *** on the Japanese sea cucumber Apostichopus japonicus within the coastal ocean of East Asia,we compiled a comprehensive dataset of occurrence *** then explored the importance of incorporating physiological knowledge into SDMs by calibrating two types of correlative SDMs:a naïve model that solely depends on environmental correlates,and a physiologically informed model that further incorporates physiological information as *** further tested the models’sensitivity to calibration area choices by fitting them with different buffered areas around known *** with naïve models,the physiologically informed models successfully captured the negative influence of high temperature on *** and were less sensitive to the choice of calibration *** naïve models resulted in more optimistic prediction of the changes of potential distributions under climate change(i.e.,larger range expansion and less contraction)than the physiologically informed *** findings highlight benefits from incorporating physiological information into correlative SDMs,namely mitigating the uncertainties associated with the choice of calibration *** these promising features,we encourage future SDM studies to consider species physi-ological information where available.

关键词： Bayesian approach Climate change Habitat suitability Physiological knowledge Species distribution model

Are hyoliths Palaeozoic lophophorates?

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National Science Review 2020年第2期7卷 453-469页

作者： Fan Liu Christian B Skovsted Timothy P Topper Zhifei Zhang Degan Shu State Key Laboratory of Continental Dynamics Shaanxi Key Laboratory of Early Life and Environments Department of Geology Northwest University Department of Palaeobiology Swedish Museum of Natural History

The phylogenetic position of hyoliths has long been unsettled, with recent discoveries of a tentaculate feeding apparatus(‘lophophore’) and fleshy apical extensions from the shell(‘pedicle’) suggesting a lophophorate affinity. Here, we describe the first soft parts associated with the feeding apparatus of an orthothecid hyolith, Triplicatella opimus from the Chengjiang biota of South China. The tuft-like arrangement of the tentacles of T. opimus differs from that of hyolithids, suggesting they collected food directly from the substrate. A reassessment of the feeding organ in hyolithids indicates that it does not represent a lophophore and our analysis of the apical structures associated with some orthothecids show that these represent crushed portions of the shell and are not comparable to the brachiopod pedicle. The new information suggests that hyoliths are more likely to be basal members of the lophotrochozoans rather than lophophorates closely linked with the Phylum Brachiopoda.

关键词： orthothecid the Chengjiang Lagerst¨atte Cambrian soft parts lophophore

A chromosome-level genome assembly reveals that a bipartite gene cluster formed via an inverted duplication controls monoterpenoid biosynthesis in Schizonepeta tenuifolia

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Molecular Plant 2023年第3期16卷 533-548页

作者： Chanchan Liu Samuel J.Smit Jingjie Dang Peina Zhou Grant T.Godden Zheng Jiang Wukun Liu Licheng Liui Wei Lin Jinao Duan Qinan Wu Benjamin R.Lichman School of Pharmacy Nanjing University of Chinese MedicineNanjingChina Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization Nanjing University of Chinese MedicineNanjingChina Centre for Novel Agricultural Products Department of BiologyUniversity of YorkYork YO105DDUK florida museum of natural history University of FloridaGainesileFLUSA Department of Pathogen Biology School of Medicine and Holistic Integrative MedicineNanjing University of Chinese MedicineNanjngChina

Biosynthetic gene clusters(BGCs)are regions of a genome where genes involved in a biosynthetic pathway are in *** origin and evolution of plant BGCs as well as their role in specialized metabolism remain largely *** this study,we have assembled a chromosome-scale genome of Japanese catnip(Schizonepeta tenuifolia)and discovered a BGC that contains multiple copies of genes involved in four adjacent steps in the biosynthesis of p-menthane *** BGC has an unprecedented bipartite structure,with mirrored biosynthetic regions separated by 260 *** bipartite BGC includes identical copies of a gene encoding an old yellow enzyme,a type of flavin-dependent *** vitro assays and virus-induced gene silencing revealed that this gene encodes the missing isopiperitenone *** enzyme evolved from a completely different enzyme family to isopiperitenone reductase from closely related Mentha spp.,indicating convergent evolution of this pathway *** analysis revealed that this bipartite BGC has emerged uniquely in the *** lineage and through insertion of pathway genes into a region rich in monoterpene *** cluster gained its bipartite structure via an inverted *** discovered bipartite BGC for p-menthane biosynthesis in *** has similarities to the recently described duplicated p-menthane biosynthesis gene pairs in the Mentha longifolia genome,providing an example of the convergent evolution of gene *** work expands our understanding of plant BGCs with respect to both form and evolution,and highlights the power of BGCs for gene discovery in plant biosynthetic pathways.

关键词： specialized metabolism monoterpenoids biosynthetic gene cluster Lamiaceae biosynthesis chromosomal inversion

Experimental evidence for ovarian hypofunction in sparrow hybrids

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Chinese Birds 2016年第1期7卷 79-83页

作者： Fabrice Eroukhmanoff Melissah Rowe Emily R.A.Cramer Fredrik Haas Jo S.Hermansen Anna Runemark Arild Johnsen Glenn-Peter Saetre Department of Biosciences Center for Ecological and Evolutionary SynthesisUniversity of Oslo natural history museum University of Oslo Department of Biology Ecology BuildingLund University

Background: Postzygotic isolation in the form of reduced viability and/or fertility of hybrids may help maintain species boundaries in the face of interspecific gene flow. Past hybridization events between house sparrows(Passer domesticus) and Spanish sparrows(P. hispaniolensis) have given rise to a homoploid hybrid species, the Italian sparrow(P. italiae). Although genetic incompatibilities are known to isolate these three species, the biological consequences of these incompatibilities are still unknown in early generation ***: We investigated whether F1 hybrids between house and Spanish sparrows experience reduced viability or fertility. More specifically, we generated hybrids through controlled crosses in aviaries, and compared ovaries of female hybrids with female of pure?species ***: We found that overall, hybrid ovaries were underdeveloped and that half of all female hybrids exhibited symptoms of ovarian hypofunction(ovarian atrophy and complete absence of developed follicles).Conclusions: Fertility in hybrids is a common consequence or post?zygotic barriers between species. We discuss these results in light of previous findings on genetic incompatibilities between the parent species and the potential role of incompatibilities in hybrid speciation, a rare evolutionary process in birds.

关键词： Hybrid fitness Hybridization Ovary Sparrows Speciation

Phylogenetic definitions for 25 higher-level clade names of birds

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Avian Research 2022年第2期13卷 109-126页

作者： George Sangster Edward L.Braun Ulf S.Johansson Rebecca T.Kimball Gerald Mayr Alexander Suh naturalis Biodiversity Center Darwinweg 2PO Box 95172300RALeidenthe Netherlands Department of Biology University of FloridaGainesvilleFL32607USA Department of Zoology Swedish Museum of Natural HistoryP.O.Box 50007SE–10405StockholmSweden Senckenberg Research Institute and natural history museum Frankfurt Ornithological SectionSenckenberganlage 2560325Frankfurt am MainGermany School of Biological Sciences University of East AngliaNorwichNR47TUUK

Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic ***,the nomenclature of higher-level taxa has not become more stable,due to the lack of regulation of taxon names above the level of superfamily by the ICZN,and the usage of rank-based nomenclature,which is not tied to clades in a *** of regulation and the instability of rank-based nomenclature impede effective communication among *** review support for higher-level avian clades using a set of 10 phylogenomic data sets,and identify clades that are supported by congruency of at least four of *** provide formal definitions of the names of these clades based on the rules of the recently published *** names of 25 clades are here defined using minimum-crown-clade(n=23),minimum-clade(n=1)and maximum-crown-clade(n=1)*** new names are introduced here:Dinocrypturi,Pteroclimesites,Musophagotides,Phaethoquornithes and *** also review diagnostic apomorphies of the relevant clades,and identify known synonyms and *** establishing a formal link between higher-level taxon names and well-supported phylogenetic hypotheses,our phylogenetic definitions will provide a solid basis for the stabilization of avian higher-level nomenclature.

关键词： Aves Congruence PhyloCode Phylogenetic nomenclature Phylogenomics Rankless taxonomy

A Century of Spinosaurs-A Review and Revision of the Spinosauridae with Comments on Their Ecology

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Acta Geologica Sinica(English Edition) 2017年第3期91卷 1120-1132页

作者： David William Elliott HONE Thomas Richard HOLTZ School of Biological and Chemical Sciences Queen Mary University of London Department of Geology University of MarylandCollege Park Department of Paleobiology National Museum of Natural History

The spinosaurids represent an enigmatic and highly unusual form of large tetanuran theropods that were first identified in 1915. A recent flurry of discoveries and taxonomic revisions of this important and interesting clade has added greatly to our knowledge. Spinosaur body fossils are however generally rare and most species are known from only limited skeletal remains. Their unusual anatomical adaptations to the skull, limbs and axial column all differ from other large theropods and point to an unusual ecological niche and a lifestyle intimately linked to water.

关键词： Theropoda Megalosauroidea Baryonychinae Spinosaurinae palaeoecology

Morphological observation and rbcL gene sequences studies of two new species,Grateloupia dalianensis *** et ***,*** *** *** et ***,***.(Halymeniaceae,Rhodophyta) from China

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Acta Oceanologica Sinica 2012年第2期31卷 109-120页

作者： ZHAO Dan WANG Hongwei SHENG Yingwen LV Jianzhou LUAN Rixiao College of Life Sciences Liaoning Normal University Dalian 116029 China Dalian natural history museum Dalian 116023 China

A few species in the genus Grateloupia （Halymeniaceae, Rhodophyta） have been investigated in detail with respect to morphological observations and molecular analyses. In this study, the au- thors document the vegetative and reproductive structures of two new species of Grateloupia, G. dalianensis *** et ***, ***, and G. yinggehaiensis *** et ***, ***. They both have the morphological character that carpogonial ampullae and auxiliary cell ampullae are the simple Grateloupia-type. The two species can be distinguished from other species of the genus by their distinctive morphological features respectively. Bused on ribulose-l,5-bisphosphate carboxylase/oxygenase （rbcL） gene sequences, the phylogenetic tree obtained in the study indicated that they are both embedded within the Grateloupia clade. G. dalianensis clusters a subclade with G. asiatica, and G. yinggehaiensis forms a single monophyletic subclade with G. hawaiiana.

关键词： Halymeniaceae Grateloupia Grateloupia dalianensis Grateloupia yinggehaiensis morphology rbcL gene

Using geophysical logs to identify Milankovitch cycles and to calculate net primary productivity(NPP) of the Late Permian coals,western Guizhou,China

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Journal of Palaeogeography 2019年第1期8卷 31-42页

作者： Zhi-Ming Yan Long-Yi Shao David Large Hao Wang Baruch Spiro College of Geoscience and Surveying Engineering China University of Mining and Technology (Beijing) Faculty of Engineering University of Nottingham Department of Earth Sciences Natural History MuseumLondon

Milankovitch periodicities of 123 kyr(eccentricity), 35.6 kyr(obliquity), and 21.2 kyr(precession) were identified in geophysical logs of three Late Permian coals: 17#, 18#, and 17 + 18#, from the Songhe mining area in western Guizhou Province. Based on the astronomic temporal framework, the periods of deposition of the 17#(5.6 m), 18#(6.4 m), and 17 + 18#(5.4 m) coals were constrained to 140.8–119.8 kyr, 160–136.2 kyr, and 135–114.9 kyr,respectively. The overall depositional period of the 18# coal of 160–136.2 kyr was further subdivided using the wavelet analysis method, into short and precise periods corresponding to the Milankovitch periodicities. It includes one eccentricity periodicity(123 kyr), three obliquity periodicities(35.6 kyr), and five precession periodicities(21.2 kyr). Different thicknesses of the subdivided coal sections, equivalent to the same time span of deposition, indicate different rates of coal deposition, i.e., thicker sections imply higher rates while the thinner sections represent lower rates. The combination of the measured average carbon concentration with the density of the coals gave rise to long-term average values of carbon accumulation rates for the Late Permian coals, in the range of 42.4–50.6 g?C?m^(-2)?a^(-1). This range corresponds to the long-term average carbon accumulation rates for the initial peat in the range of 60.6–72.3 g?C?m^(-2)?a^(-1). Based on the known quantitative relation between net primary productivity(NPP)values and long-term average carbon accumulation rates for the Holocene tropical peatlands, the range of NPP values for the Late Permian tropical peatlands was estimated as 242.4–433.8 g?C?m^(-2)?a^(-1).A comparison of existing information about peatland NPP levels of various ages and latitudes indicated that when conditions of high rain and high humidity prevail in the palaeo-peatland at given latitude, the NPP rates will vary with changes in atmospheric concentration of CO_2 and O_2. This relationship may le

关键词： Milankovitch cycle Coal deposition Peatland Long-term average carbon accumulation rate Net primary productivity Late Permian Guizhou Province

Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

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Current Zoology 2020年第5期66卷 505-514页

作者： Laurel R.Yohe Matteo Fabbri Michael Hanson Bhart-Anjan S.Bhullar Department of Earth&Planetary Science Peabody Museum of Natural HistoryYale UniversityNew HavenCT06511USA

Chemosensation is the most ubiquitous sense in animals,enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these *** there is a general conception that olfactory receptor(OR)genes evolve rapidly,the universality of this phenomenon across vertebrates,and its magnitude,are *** supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely *** combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or *** published genomes,we identified ORs in 21 tetrapods,including amphibia ns,reptiles,birds,and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding *** found that,for all clades investigated,most OR genes evolve nearly an order of magnitude faster than other protein-coding genes,with many OR genes showing signatures of diversifying selection across nearly all taxa in this *** rapid rate of evolution suggests that chemoreceptor genes are in "evolutionary overdrive,"perhaps evolving in response to the ever-changing chemical space of the *** obtain complementary morphological data,we stained whole fixed specimens with iodine,μCT-scanned the specimens,and digitally segmented chemosensory and nonchemosensory brain *** then estimated phenotypic variation within traits and among *** we found considerable variation in chemosensory structures,they were no more diverse than nonchemosensory *** suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space,whereas chemosensory phe no types and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.

关键词： chemosensation diversifying selection olfaction olfactory bulb olfactory receptor tetrapod