保护生物学概要

保护生物学的形成是对生物危机的反应和生物科学迅速发展的结果。它是应用科学解决由于人类活动干扰或其它因素引起的物种、群落和生态系统出现的问题的新学科。其”目的是提供保护生物多样性的原理和工具“,其基础科学和应用科学的综合性交叉学科。系统学、生态学、生物地理学和种群生态学的原理和方法是保护生物学重要的理论和实践基础。     

Variation in the rate of convergent evolution: adaptation to a laboratory environment in Drosophila subobscura

Adaptation to novel environments is a central issue in evolutionary biology. One important question is the prevalence of convergence when different populations adapt to the same or similar environments. We investigated this by comparing two studies, 6 years apart, of laboratory adaptation of populations of Drosophila subobscura founded from the same natural location. In both studies several life‐history traits were periodically assayed for the first 14 generations of laboratory adaptation, as well as later generations, and compared with established, laboratory, control populations. The results indicated: (1) a process of convergence for all traits; (2) differences between the two studies in the pattern and rate of convergence; (3) dependence of the evolutionary rates on initial differentiation. The differences between studies might be the result of the differences in the founder populations and/or changes in the lab environment. In either case, the results suggest that microevolution is highly sensitive to genetic and environmental conditions.     

Learning developmental biology has priority in the life sciences curriculum in Singapore

Singapore has embraced the life sciences as an important discipline to be emphasized in schools and universities. This is part of the nation's strategic move towards a knowledge-based economy, with the life sciences poised as a new engine for economic growth. In the life sciences, the area of developmental biology is of prime interest, since it is not just intriguing for students to know how a single cell can give rise to a complex, coordinated, functional life that is multicellular and multifaceted, but more importantly, there is much in developmental biology that can have biomedical implications. At different levels in the Singapore educational system, students are exposed to various aspects of developmental biology. The author has given many guest lectures to secondary (ages 12-16) and high school (ages 17-18) students to enthuse them about topics such as embryo cloning and stem cell biology. At the university level, some selected topics in developmental biology are part of a broader course which caters for students not majoring in the life sciences, so that they will learn to comprehend how development takes place and the significance of the knowledge and impacts of the technologies derived in the field. For students majoring in the life sciences, the subject is taught progressively in years two and three, so that students will gain specialist knowledge in developmental biology. As they learn, students are exposed to concepts, principles and mechanisms that underlie development. Different model organisms are studied to demonstrate the rapid advances in this field and to show the interconnectivity of developmental themes among living things. The course inevitably touches on life and death matters, and the social and ethical implications of recent technologies which enable scientists to manipulate life are discussed accordingly, either in class, in a discussion forum, or through essay writing.     

Defining the landscape of adaptive genetic diversity

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.).     

The limits to biogeographical distributions: insights from the northward range extension of the marine snail, Kelletia kelletii (Forbes, 1852)

Aim The development of accurate models predicting species range shifts in response to climate change requires studies on the population biology of species whose distributional limits are in the process of shifting. We examine the population biology of an example system using the recent northward range expansion of the marine neogastropod Kelletia kelletii (Forbes, 1852). Location This is a marine coastal shelf neogastropod species whose range extends from Isla Asuncion (Baja California, Mexico) to Monterey (CA, USA). Research sites spanned the extent of the range. Methods We examine abundance distributions and size frequency distributions of K. kelletii for evidence of factors determining historic and contemporary distributional patterns. Population studies were supplemented by historic and contemporary hydrographic data, including seawater temperature data from California Cooperative Oceanic Fisheries Investigations (CalCOFI ) and National Data Buoy Center (NDBC), and seawater circulation data. Results The structure of recently established populations varied dramatically from that of historic populations. Markedly low densities and irregular size frequency distributions characterized recently established populations and suggested only occasionally successful recruitment. The point of transition between historic and recently established populations also corresponded to the location of a gradient in seawater temperature and the confluence of two major oceanic currents. The accumulated data suggest that temperature and/or barriers to dispersal could have set both contemporary patterns in population structure as well as the former northern range limit. Main conclusions Early life stages play a critical role in determining distributional patterns of K. kelletii. Dispersal barriers and temperature limitation are two plausible mechanisms that could determine both contemporary and historic distributional patterns. Future studies on this species should attempt to tease apart the relative importance of these factors in maintaining the populations at the northern edge of the range.     

Dual Causality and the Autonomy of Biology

Ernst Mayr’s concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical sciences.     

Do human ‘life history strategies’ exist?

Interest in incorporating life history research from evolutionary biology into the human sciences has grown rapidly in recent years. Two core features of this research have the potential to prove valuable in strengthening theoretical frameworks in the health and social sciences: the idea that there is a fundamental trade-off between reproduction and health; and that environmental influences are important in determining how life histories develop. However, the literature on human life histories has increasingly travelled away from its origins in biology, and become conceptually diverse. For example, there are differences of opinion between evolutionary researchers about the extent to which behavioural traits associate with life history traits to form ‘life history strategies’. Here, I review the different approaches to human life histories from evolutionary anthropologists, developmental psychologists and personality psychologists, in order to assess the evidence for human ‘life history strategies’. While there is precedent in biology for the argument that some behavioural traits, notably risk-taking behaviour, may be linked in predictable ways with life history traits, there is little theoretical or empirical justification for including a very wide range of behavioural traits in a ‘life history strategy’. Given the potential of life history approaches to provide a powerful theoretical framework for understanding human health and behaviour, I then recommend productive ways forward for the field: 1) greater focus on the life history trade-offs which underlie proposed strategies; 2) greater precision when using the language of life history theory and life history strategies; 3) collecting more empirical data, from a diverse range of populations, on linkages between life history traits, behavioural traits and the environment, including the underlying mechanisms which generate these linkages; and 4) greater integration with the social and health sciences.     

Population genetics of Howellia aquatilis (Campanulaceae) in disjunct locations throughout the Pacific Northwest

Howellia aquatilis A.Gray (water howellia) is a federally-listed threatened aquatic plant species with limited distribution in four states: California, Idaho, Montana, and Washington. Previous studies have shown a lack of genetic variation within the species; these studies, however, have excluded samples from one or more states. There have been no published studies on the population biology or genetics of the six known California populations or their evolutionary relationship to the other Pacific Northwest populations. We used Amplified Fragment Length Polymorphisms to identify genetic variation within and among the California populations, and to compare the California populations to the Idaho, Montana, and Washington populations. Analysis of molecular variance of 92 individuals from the six California populations show that 83.8% of genetic variation is found within populations and 16.2% among populations (P < 0.001). All sampled populations from all states provide 83.7% variation within and 16.3% variation among populations (P < 0.001). A UPGMA analysis confirms there is no clear clustering of Howellia aquatilis populations within California, that the Montana populations cluster within the California populations, and, although with limited population sample sizes, the Idaho and Washington populations are distantly related to all other populations. Waterfowl migration patterns support a hypothesis for avian dispersal as a primary factor in gene flow in Howellia aquatilis.     

In the deep end: pooling data and other statistical challenges of zoo and aquarium research

Zoo and aquarium research presents many logistic challenges, including extremely small sample sizes and lack of independent data points, which lend themselves to the misuse of statistics. Pseudoreplication and pooling of data are two statistical problems common in research in the biological sciences. Although the prevalence of these and other statistical miscues have been documented in other fields, little attention has been paid to the practice of statistics in the field of zoo biology. A review of articles published in the journal Zoo Biology between 1999–2004 showed that approximately 40% of the 146 articles utilizing inferential statistics during that span contained some evidence of pseudoreplication or pooling of data. Nearly 75% of studies did not provide degrees of freedom for all statistics and approximately 20% did not report test statistic values. Although the level of pseudoreplication in this dataset is not outside the levels found in other branches of biology, it does indicate the challenges of dealing with appropriate data analysis in zoo and aquarium studies. The standardization of statistical techniques to deal with the methodological challenges of zoo and aquarium populations can help advance zoo research by guiding the production and analysis of applied studies. This study recommends techniques for dealing with these issues, including complete disclosure of data manipulation and reporting of statistical values, checking and control for institutional effects in statistical models, and avoidance of pseudoreplicated observations. Additionally, zoo biologists should seek out other models such as hierarchical or factorial models or randomization tests to supplement their repertoire of t‐tests and ANOVA. These suggestions are intended to stimulate conversation and examination of the current use of statistics in zoo biology in an effort to develop more consistent requirements for publication. Zoo Biol 0:1–14, 2006. © 2006 Wiley‐Liss, Inc.     

中国斑马鱼研究发展历程及现状

斑马鱼作为重要的脊椎动物模式系统之一, 由于其多方面的优势, 在生命科学研究领域发挥着越来越重要的作用。目前, 斑马鱼已被广泛地用于发育生物学、分子生物学、细胞生物学、遗传学、神经生物学、肿瘤学、免疫学、海洋生物学、药物学、毒理与环保等诸多方面的研究, 一些重要的成果不断涌现, 为现代生命科学的发展做出了重要贡献。我国20世纪90年代后期引入斑马鱼模式系统, 此后研究队伍扩大很快, 有影响的研究成果不断涌现, 促进了多个学科的发展。文章重点综述了我国内地与香港地区在斑马鱼研究方面的发展历程以及所取得的代表性成果, 以期促进该模式系统更广泛地用于开展高水平研究。     

Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere

Phylogeography is a young, vigorous and integrative field of study that uses genetic data to understand the history of populations. This field has recently expanded into many areas of biology and also into several historical disciplines of Earth sciences. In this review, I present a numerical synthesis of the phylogeography literature based on an examination of over 3000 articles published during the first 20 years of the field (i.e. from 1987 to 2006). Information from several topics needed to evaluate the progress, tendencies and deficiencies of the field is summarized for 10 major groups of organisms and at a global scale. The topics include the geography of phylogeographic surveys, comparative nature of studies, temporal scales and major environments investigated, and genetic markers used. I also identify disparities in research productivity between the developing and the developed world, and propose ways to reduce some of the challenges faced by phylogeographers from less affluent countries. Phylogeography has experienced explosive growth in recent years fuelled by developments in DNA technology, theory and statistical analysis. I argue that the intellectual maturation of the field will eventually depend not only on these recent developments, but also on syntheses of comparative information across different regions of the globe. For this to become a reality, many empirical phylogeographic surveys in regions of the Southern Hemisphere (and in developing countries of the Northern Hemisphere) are needed. I expect the information and views presented here will assist in promoting international collaborative work in phylogeography and in guiding research efforts at both regional and global levels.     

Tracing the invasion history of mealy plum aphid, Hyalopterus pruni (Hemiptera: Aphididae), in North America: a population genetics approach

Biological invasions are typically the outcome of complex patterns of introduction, establishment, and spread, and genetic methods are excellent tools to resolve such histories for non-native organisms. The mealy plum aphid, Hyalopterus pruni, is an invasive pest of dried plum in California. We examined nine microsatellite loci and DNA sequences from three mitochondrial genes (1,148 bp) in populations throughout the native and invaded ranges of H. pruni to assess key invasion parameters, including geographic origins of invasive populations, number of introductions, and levels of genetic diversity and gene flow. Our results provide evidence for multiple invasions of H. pruni into North America, suggesting that aphids in California may have been introduced from Spain, and aphids in the eastern United States and Vancouver, Canada were likely introduced from central or northern Europe. H. pruni populations in California were characterized by low genetic diversity relative to native populations, while the two other North American populations were less genetically impoverished. Gene flow among introduced populations was low, but does appear to occur with some regularity. These findings provide a framework for more detailed studies of H. pruni, but also represent a model for how population genetics approaches can be used to study invasion biology and aid the development of optimized management methods for agricultural pests. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Habitat connectivity, more than species’ biology, influences genetic differentiation in a habitat specialist, the short-eared rock-wallaby (Petrogale brachyotis)

It is difficult to assess the relative influence of anthropogenic processes (e.g., habitat fragmentation) versus species’ biology on the level of genetic differentiation among populations when species are restricted in their distribution to fragmented habitats. This issue is particularly problematic for Australian rock-wallabies (Petrogale sp.), where most previous studies have examined threatened species in anthropogenically fragmented habitats. The short-eared rock-wallaby (Petrogale brachyotis) provides an opportunity to assess natural population structure and gene flow in relatively continuous habitat across north-western Australia. This region has reported widespread declines in small-to-medium sized mammals, making data regarding the influence of habitat connectivity on genetic diversity important for broad-scale management. Using non-invasive and standard methods, 12 microsatellite loci and mitochondrial DNA were compared to examine patterns of population structure and dispersal among populations of P. brachyotis in the Kimberley, Western Australia. Low genetic differentiation was detected between populations separated by up to 67?km. The inferred genetic connectivity of these populations suggests that in suitable habitat P. brachyotis can potentially disperse far greater distances than previously reported for rock-wallabies in more fragmented habitat. Like other Petrogale species male-biased dispersal was detected. These findings suggest that a complete understanding of population biology may not be achieved solely by the study of fragmented populations in disturbed environments and that management strategies may need to draw on studies of populations (or related species) in undisturbed areas of contiguous habitat.     

AFLP and breeding system studies indicate vicariance origin for scattered populations and enigmatic low fecundity in the Moroccan endemic Hypochaeris angustifolia (Asteraceae), sister taxon to all of the South American Hypochaeris species

We used Amplified Fragment Length Polymorphism markers (AFLP) and breeding system studies to investigate the population structure and reproductive biology of Hypochaeris angustifolia (Asteraceae: Cichorieae). This species is endemic to altiplanos of the Atlas Mountains (Morocco) where it occurs in scattered populations, and it is the sister species to c. 40 species of this genus in South America. PCoA, NJ, and Bayesian clustering, revealed that the populations are very isolated whilst AFLP parameters show that almost all populations have marked genetic divergence. We contend that these features are more in accord with a vicariance origin for the scattered populations of H. angustifolia, rather than establishment by long-distance dispersal. The breeding system studies revealed that H. angustifolia is a self-incompatible species, with low fecundity in natural and in experimental crosses, probably due to a low frequency of compatible phenotypes within and between the populations.     

On applications of landscape genetics

Recent assertions in the literature (e.g., Keller et al. 2015) suggest that landscape genetic research has been infrequently applied by practitioners. We were interested to test this assertion, which is difficult to assess, since applications may not be detectable through searches of peer-reviewed literature. Producing publications may not be a goal of practitioners. We developed a method to search the internet for evidence of research applications and evaluated 25 different research fields in the natural sciences. We found that fields with more publications also had more applications, but the field of landscape genetics was less applied than expected based on the number of peer-reviewed publications—only about 4 % of landscape genetics articles were applied. In fact, all research fields in genetics or evolutionary biology were under-applied compared to ‘whole organism’, ecological research fields. This result suggests the lack of applications in landscape genetics may be due to a systemic under-application of genetics research, perhaps related to a lack of understanding of genetics by practitioners. We did find some evidence of landscape genetic applications however, which we sorted into 5 categories: (1) identification of evolutionarily significant units for conservation, (2) managing pathogens and invasive species, (3) natural heritage systems planning, (4) assessing population status, and (5) restoration of populations.     

Comparison of synchronized Chinese hamster ovary cells obtained by mitotic shake-off, hydroxyurea, aphidicolin, or methotrexate

Synchronized cell populations are necessary to study many aspects of cell biology. We have developed a method to obtain highly synchronized Chinese hamster ovary cell populations in S phase or G2 phase by utilizing mitotic selection followed by incubation with either hydroxyurea, aphidicolin, or methotrexate for 12 h. Flow cytometry analysis shows that the coefficient of variation in the spread of the cell population in S phase is as low as 6%. Drug toxicity studies compare the effects of the various drugs on G1 and S phase cells. The use of aphidicolin or hydroxyurea results in the most highly synchronized cell populations, but methotrexate yields inadequate synchronization. These results demonstrate that both aphidicolin and hydroxyurea are useful drugs for obtaining highly synchronized cell populations after an initial synchrony in mitosis. Aphidicolin is perhaps the best choice because of less toxicity to S phase cells when used in low concentrations.     

On the Long-Term Fitness of Cells in Periodically Switching Environments

Because all the cell populations are capable of making switches between different genetic expression states in response to the environmental change, Thattai and van Oudenaarden (Genetics 167, 523–530, 2004) have raised a very interesting question: In a constantly fluctuating environment, which type of cell population (heterogeneous or homogeneous) is fitter in the long term? This problem is very important to development and evolution biology. We thus take an extensive analysis about how the cell population evolves in a periodically switching environment either with symmetrical time-span or asymmetrical time-span. A complete picture of the phase diagrams for both cases is obtained. Furthermore, we find that the systems with time-dependent cellular transitions all collapse to the same set of dynamical equations with the modified parameters. Furthermore, we also explain in detail how the fitness problem bears much resemblance to the phenomenon, stochastic resonance, in physical sciences. Our results could be helpful for the biologists to design artificial evolution experiments and unveil the mystery of development and evolution.