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A matter of time： Temporal variation in the introduction history and population genetic structuring of an invasive lizard

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Current Zoology 2015年第3期61卷 456-464页

作者： HalmahMOULE Kirilee CHAPLIN Rebecca D. BRAY Kimberly A. MILLER Michael B. THOMSON David G. CHAPPLE school of biological sciences Monash University Clayton Victoria 3800 Australia Department of sciences Museum Victoria Victoria 3001 Australia school of biological sciences University of Sydney Sydney NSW 2006 Australia allan wilson centre for molecular ecology and Evolution School of Biological Sciences Victoria University of Wellington Wellington 6140 New Zealand

Invasive species are considered one of the greatest threats to native ecosystems, second only to habitat loss and frag- mentation. Despite this, the temporal dynamics of invasions are poorly understood, with most studies focusing on a single time point, providing us with only a snapshot of the biology and genetics of the invader. We investigated the invasion of Lord Howe Island by the delicate skink Lampropholis delicata and assessed the introduction history and genetic structure of this species over a 5-year period. Using genetic data taken from 2007, and again in 2011/12, we examined changes in the population genetic struc- ture （whether new haplotypes had been introduced to the island, and shifts in haplotype frequencies） of the species on the island between these two time points. No new haplotypes were introduced to the island between 2007 and 2011/12; however, significant shifts in haplotype frequencies across the island were detected. We conclude that the delicate skink is expanding its range into the southern regions of the island and that the haplotype frequencies on Lord Howe Island are still in a state of highly dynamic flux. Our study highlights the importance of considering invasions as dynamic and studying them in such a way that enable us to better manage their impacts

关键词： biological invasion Genetic admixture Lampropholis delicata Lord Howe Island Population genetics,Unintentional introduction

Adélie penguins and temperature changes in Antarctica: a long-term view

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Integrative Zoology 2012年第2期7卷 113-120页

作者： Craig D.MILLAR Sankar SUBRAMANIAN Tim H.HEUPINK Siva SWAMINATHAN Carlo BARONI David M.LAMBERT allan wilson centre for molecular ecology and Evolution University of Auckland Griffith school of Environment and school of Biomolecular and Physical sciences Griffith UniversityAustralia Environment Protection Training and Research Institute HyderabadIndia Department of Earth sciences University of PisaPisaItaly

During the summer months,Adélie penguins represent the dominant biomass of terrestrial *** millions of individuals nest in ice-free areas around the coast of the ***,these modern populations of Adélie penguins have often been championed as an ideal biological indicator of ecological and environmental changes that we currently *** addition,Adélie penguins show an extraordinary record of sub-fossil remains,dating back to the late *** this time,temperatures were much lower than ***,this species offers unique long-term information,at both the genomic and ecological levels,about how a species has responded to climate change over more than 40000 years.

关键词： Adélie penguins climate change global warming penguin evolution

Diet analysis of small mammal pests: A comparison of molecular and microhistological methods

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Integrative Zoology 2016年第2期11卷 98-110页

作者： Surrya KHANAM Robyn HOWITT Muhammad MUSHTAQ James C.RUSSELL Department of Zoology PMAS Arid Agriculture University RawalpindiPakistan EcoGene® Landcare ResearchAucklandNew Zealand school of biological sciences University of AucklandAucklandNew Zealand Department of Statistics University of AucklandAucklandNew Zealand allan wilson centre University of AucklandAucklandNew Zealand

Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies *** this study,we investigated the food habits of 2 rodents,Rattus rattus(ship rat)and Mus musculus castaneus(house mouse)as well as an insectivore,Suncus murinus(shrew),present in human *** a microhistological approach and a DNA barcoding approach were used in the present *** DNA extraction,amplification was performed using group-specific primers targeting birds,plants and *** polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut *** findings from the application of both techniques were in agreement,but the detection of prey type with each technique was *** DNA barcoding approach gave greater species-level identification when compared to the microhistological method,especially for the invertebrate and avian ***,with both techniques,23 prey taxa were identified in the gut contents of the 3 species,including 15 plants,7 insects and a single bird *** conclude that with a selection of suitable“barcode genes”and optimization of polymerase chain reaction protocols,DNA barcoding can provide more accurate and faster *** detection from either technique alone can bias the dietary informa***,combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet,especially if the pest is an omnivore or insectivore species.

关键词： DNA barcoding group-specific primers microhistological diet analysis pest management small mammal pests

Navigating the currents of seascape genomics： how spatial analyses can augment population genomic studies

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Current Zoology 2016年第6期62卷 581-601页

作者： Cynthia RIGINOS Eric D. CRANDALL Libby LIGGINS Pim BONGAERTS Eric A, TREML school of biological sciences The University of Queensland St Lucia QLD 4072 Australia Division of Science and Environmental Policy California State University Seaside CA 93955 USA Institute of Natural and Mathematical sciences Massey University Auckland 0745 New Zealand Global Change Institute The University of Queensland QLD 4072 St Lucia Australia school of Biosciences The University of Melbourne VIC 3010 Australia

Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated sele

关键词： adaptation genetic-environment association landscape oceanography population genomics remote sensing seascape genetics.

Unraveling a genetic roadmap for improved taste in the domesticated apple

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molecular Plant 2021年第9期14卷 1454-1471页

作者： Liao Liao Weihan Zhang Bo Zhang Ting Fang Xiao-Fei Wang Yarning Cai Collins Ogutu Lei Gao Gang Chen Xiaoqing Nie Jinsheng Xu Quanyan Zhang Yiran Ren Jianqiang Yu Chukun Wang Cecilia H.Deng Baiquan Ma Beibei Zheng Chun-Xiang You Da-Gang Hu Richard Espley Kui Lin-Wang Jia-Long Yao Andrew C.allan Awais Khan Schuyler S.Korban Zhangjun Fei Ray Ming Yu-Jin Hao Li Li Yuepeng Han CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Hubei Hongshan LaboratoryWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhan 430074China Agricultural Bioinformatics Key Laboratory of Hubei Province College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhan 430074China University of Chinese Academy of sciences 19A YuquanluBeijing 100049China College of Horticulture Science and Engineering Shandong Agricultural UniversityTai-An 271018China Sino-African Joint Research Center Chinese Academy of SciencesWuhan 430074China The New Zealand Institute for Plant&Food Research Limited AucklandNew Zealand school of biological sciences University of AucklandPrivate Bag 92019Auckland 1142New Zealand Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Department of Natural Resources and Environmental sciences University of Illinois at Urbana-ChampaignUrbanaIL 61801USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA Department of Plant Biology University of Illinois at Urbana-ChampaignUrbanaIL 61801USA

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

关键词： apple fruit taste organic acids soluble sugars fruit size domestication