Optimal sampling strategy for estimation of spatial genetic structure in tree populations

Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms.     

Epigenetics in natural animal populations

Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally‐mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.     

Mathematical studies in animal populations

Zusammenfassung Die vorliegende Arbeit ist eine Fortsetzung derThompson'schen Analysen des Parasitenzyklus bei Insekten, die mit der irrealen Folgerung endeten, dass unter gewissen Voraussetzungen — die wir in der gegenwärtigen Analyse akzeptiert haben —jeder Parasit in relativ kurzer Generationenfolge seinen Wirt, und damit sich selbst, zur Ausrottung bringen muss. Der Einfluss von wiederkehrenden Umwelt-katastrophen wie sie z.B. durch ungünstiges Wetter sehr häufig bedingt sind, wurde untersucht mit dem Ergebnis, dass solche Katastrophen, wenn sie in nicht allzugrossen Intervallen auftreten, völlig genügen, um die Unterbrechung der akkumulativen Parasitierung im Zyklus zu erklären.Die grössere Empfindlichkeit der Parasiten, welche aus allen Beobachtungen und Analysen sich ergibt, ist nicht physiologisch, sondern ökologisch bedingt. Methodisch hat sich gezeigt, dass die Analyse tierischer Populationen weitgehend ohne Anwendung von Integralen möglich ist.Die Ergebnisse, welche die hohe Bedeutung der Feinde bei grosser Wirtsdichte, und ihre minimale Wirksamkeit, wenn letztere niedrig ist, zeigen, sind unabhängig von einem besonderen Dichtefaktor der Feindvermehrung — wie er im allgemeinen besteht und die aufgezeigten Tendenzen noch verstärkt — gewonnen. Der Einfluss des Superparasiten wird unter dem Einfluss wiederkehrender Umwelt-katastrophen minimal. Am Modell einiger beobachteter Gradationen wird die Übereinstimmung mit unserer Analvse demonstriert.

---

Résumé Le travail ci-dessus est la continuation des analyses deThompson des cycles parasitaires chez les insectes, qui l'ont à la conclusion absurde qu'en acceptant certaines suppositions — que nous avons acceptées dans la présente analyse — chaque parasite exterminerait son hôte et par conséquent soi-même. Nous avons étudié l'influence de certains phénomènes catastrophiques récurrents provenant du milieu comme par exemple celle d'un temps défavorable. Ces phénomènes, pourvu qu'ils ne se présentent pas à des intervalles trop grands, suffisent amplement pour expliquer l'interruption de la parasitation accumulative dans les cycles.La sensibilité plus grande des parasites qui est démontrée dans toutes les observations et analyses ne provient pas de causes physiologiques, mais écologiques.La méthodologie a donné comme résultat intéressant le fait que l'analyse des populations animales peut se faire sans l'application des intégrales.Les résultats démontrant la grande importance des ennemis quand les hôtes sont nombreux, mais par contre une activité minimale des ennemis quand les hôtes sont rares, ont été obtenus indépendamment d'une augmentation spéciale des ennemis qui, en général, constitue un facteur important, ce qui renforce encore les tendances que nous avons trouvées. L'influence des superparasites devient minime sous l'action des catastrophes récurrentes dus au milieu. Finalement, au moyen de quelques gradations bien observées, nous avons démontré que notre analyse est conforme aux faits.

     

Modelling animal populations in changing landscapes

Models of Mobile Animal Populations (MAP models) simulate long-term land use changes, population trends and patterns of biological diversity on landscapes of 10³-10⁵ ha. MAP models can incorporate information about past land-use patterns and management practices and can project future patterns based on management plans. We illustrate this approach with an example of how implementation of a U.S. Forest Service management plan at the Savannah River Site in South Carolina, U.S.A., might influence population trends of Bachman's Sparrow Aimophila aestivalis, a relatively rare and declining species in southeastern pine forests. In this case, a management plan, largely designed to improve conditions for an endangered species, Red-cockaded Woodpecker Picoides borealis, may have a negative impact, at least in the short term, on another species of management concern, Bachman's Sparrow.
In a parallel processing version of the MAP models, a single landscape that would ordinarily be too large or detailed to be simulated on a single computer is subdivided into a number of smaller landscapes, and each landscape is simulated in parallel, either on a single multi-tasking machine or on a group of networked machines. With this approach we are attempting to determine just how large a landscape must be before the dynamics of a population within it are more or less independent of factors beyond the landscape boundaries.     

Optimal harvesting of stochastically fluctuating populations

 We obtain the optimal harvesting plan to maximize the expected discounted number of individuals harvested over an infinite future horizon, under the most common (Verhulst-Pearl) logistic model for a stochastically fluctuating population. We also solve the problem for the standard variants of the model where there are constraints on the admissible harvesting rates. We use stochastic calculus to derive the optimal population threshold at which individuals are harvested as well as the overall value of the population in the sense of the model. We show that except under extreme conditions, the population is never depleted in finite time, but remains in a stationary distribution which we find explicitly. Needless to say, our results prove that any strategy which totally depletes the population is sub-optimal. These results are much more precise than those previously obtained for this problem. Received 24 June 1996; received in revised form 7 April 1997     

Recovery of marine animal populations and ecosystems

Many marine populations and ecosystems have experienced strong historical depletions, yet reports of recoveries are increasing. Here, we review the growing research on marine recoveries to reveal how common recovery is, its magnitude, timescale and major drivers. Overall, 10-50% of depleted populations and ecosystems show some recovery, but rarely to former levels of abundance. In addition, recovery can take many decades for long-lived species and complex ecosystems. Major drivers of recovery include the reduction of human impacts, especially exploitation, habitat loss and pollution, combined with favorable life-history and environmental conditions. Awareness, legal protection and enforcement of management plans are also crucial. Learning from historical recovery successes and failures is essential for implementing realistic conservation goals and promising management strategies.     

Optimal lineage principle for age-structured populations

We present a formulation of branching and aging processes that allows age distributions along lineages to be studied within populations, and provides a new interpretation of classical results in the theory of aging. We establish a variational principle for the stable age distribution along lineages. Using this optimal lineage principle, we show that the response of a population's growth rate to age-specific changes in mortality and fecundity--a key quantity that was first calculated by Hamilton--is given directly by the age distribution along lineages. We apply our method also to the Bellman-Harris process, in which both mother and progeny are rejuvenated at each reproduction event, and show that this process can be mapped to the classic aging process such that age statistics in the population and along lineages are identical. Our approach provides both a theoretical framework for understanding the statistics of aging in a population, and a new method of analytical calculations for populations with age structure. We discuss generalizations for populations with multiple phenotypes, and more complex aging processes. We also provide a first experimental test of our theory applied to bacterial populations growing in a microfluidics device.     

Optimal sex ratios in structured populations

In this paper, we develop a general method to determine evolutionary equilibrium sex ratios and to check evolutionary stability, continuous stability and invadability in exact genetic models with or without dominance. This method is then applied to three kinds of models for structured populations: the first one concerns Hamilton's LMC model, except that only a fraction beta of female offspring mate with male offspring born in the same colonies, while a fraction 1-beta mate with male offspring chosen at random within the whole population; in the second model, it is assumed that partial dispersal of inseminated females occurs after mating; in the third model, partial dispersal of male and female offspring occurs before mating. In the first model, the effect of population regulation is studied while, in the other models, two kinds of dispersal are considered: proportional and uniform.     

The statistical analysis of survival in animal populations

Estimating, comparing and modelling survival rates are central to population biology. However, there are many difficulties in measuring these rates in animal populations in the wild. The most relevant information is based on samples of marked individuals, i.e. capture-recapture data. In recent years, a number of new statistical approaches to the analysis of such data have been developed, permitting more sophisticated and precise measurement of survival rates.     

Genetic effects of harvest on wild animal populations

Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.     

Optimal open-loop desynchronization of neural oscillator populations

Deep brain stimulation (DBS) is an increasingly used medical treatment for various neurological disorders. While its mechanisms are not fully understood, experimental evidence suggests that through application of periodic electrical stimulation DBS may act to desynchronize pathologically synchronized populations of neurons resulting desirable changes to a larger brain circuit. However, the underlying mathematical mechanisms by which periodic stimulation can engender desynchronization in a coupled population of neurons is not well understood. In this work, a reduced phase-amplitude reduction framework is used to characterize the desynchronizing influence of periodic stimulation on a population of coupled oscillators. Subsequently, optimal control theory allows for the design of periodic, open-loop stimuli with the capacity to destabilize completely synchronized solutions while simultaneously stabilizing rotating block solutions. This framework exploits system nonlinearities in order to strategically modify unstable Floquet exponents. In the limit of weak neural coupling, it is shown that this method only requires information about the phase response curves of the individual neurons. The effects of noise and heterogeneity are also considered and numerical results are presented. This framework could ultimately be used to inform the design of more efficient deep brain stimulation waveforms for the treatment of neurological disease.

     

Studies of animal populations from Lamarck to Darwin

Summary and conclusions Darwin's theory of evolution brought to an end the static view of nature. It was no longer possible to think of species as immortal, with secure places in nature. Fluctuation of population could no longer be thought of as occurring within definite limits which had been set at the time of creation. Nor was it any longer possible to generalize from the differential reproductive potentials, or from a few cases of mutualism between species, that everything in nature was fitted to produce general ends, and reciprocal uses. ¹³⁴ The appeal to design could no longer be substituted for answers to questions concerning animal demography. Instead, the dynamics of a population had to be viewed as the outcome of species' struggle against animate and inanimate factors in the environment. Both the members of a species and the environmental factors tend to vary randomly, and therefore neither evolution nor population dynamics could be fully understood alone. For this reason Darwin's linking of the two subjects was inevitable and not merely an historical accident. Since Darwin had shown that no automatic equilibrium existed, he demonstrated the importance of closer study of the causes of population dynamics and extinction. He also indicated that an understanding of population depends upon the development of a broad knowledge in ecology.Viewed from another direction, Darwin's work ended the early modern era of population studies by clarifying three interrelated problems which were important for understanding population: extinction, distribution, and the nature of species. The components of his answer had been discussed in the eighteenth century, but there had not existed enough evidence for the completion of the revolution in thought which had then begun. At the beginning of the nineteenth century, Playfair found the evidence for extinction conclusive, and, in spite of Lamarck, Curvier convinced the scientific world that there could no longer be any doubt about it. This was a step the importance of which, with his limited knowledge of biogeography and population, Cuvier could not have fully realized. Lamarck attempted, with his evolutionary theory, to circumvent the necessity for admitting extinction, but he overestimated the adaptability of organisms and in doing so he underestimated the importance of competition and the whole field of ecology. On the other hand, he was not willing to let questions such as the origin of species remain taboo to science. The origin of species was a biogeographical as well as a paleontological question. Humboldt correlated environment with the distribution of species and conveyed the impression that plant communities are subject to change. De Candolle, following the lead of Linnaeus and Humboldt, emphasized the ecological aspects of biogeography, not only the importance of habitat and range, clearly showing the ecological effects of competition. The entomologists Kirby and Spence took a faltering step toward understanding the relationship between population and ecological role, but they fell short of any significant new conclusions. Neither they nor Swainson could fully comprehend the new perspective of De Candolle.Lyell was able to bring together the evidence from these three lines of investigation and weave them into an important synthesis that almost accomplished that Darwin later did. Although opposing Lamarck's theory of evolution, Lyell had a dynamic view of ecology. He realized that population dynamics offered an important key to the understanding of biogeography. Since he knew that species become extinct, he investigated closely the factors which could either preserve or extinguish species. While explaining these factors, he described the interrelationships of species in greater detail than had ever been done before. Forbes continued to develop Lyell's ecological concepts, and his first-hand field experience enabled him to describe biotic communities more concretely than Lyell had.Having the advantages of Lyell's understanding and his own experience from a global voyage, Darwin could take the final step from the static to the dynamic concept of life. He had seen populations fluctuating and also fossil species in South America, and on the Galapagos Islands he had encountered a biogeographical problem that could not be credibly solved without the idea of evolution. However, the bare idea of evolution did not fully answer his questions. He sought physiological causes of extinction before he read Malthus and realized that De Candolle and Lyell had correctly emphasized the importance of competition. Darwin found that, in order to understand evolution, he needed to improve his understanding of ecology. He wanted to know when populations were most easily decimated, how extensive were competition and cooperation, what effects parasites have upon populations, and what changes occur in biotic communities when a species is either added or subtracted. He contributed to some extent to answering these questions. Though there remained much for others to do, there was now a new and more secure theoretical framework within which later studies could be interpreted. As Ernst Mayr has observed, Darwin's consistent thinking in terms of population has had an impact on biological theory and practice which is second only to his sponsorship of natural selection as the mechanism of evolution. ¹³⁵     

生境破碎化对动物种群存活的影响

生境破碎是生物多样性下降的主要原因之一。通常以岛屿生物地理学、异质种群生物学和景观生态学的理论来解释不同空间尺度中生境破碎化的生态学效应。生境破碎化引起面积效应、隔离效应和边缘效应。这些效应通过影响动物种群的绝灭阈值、分布和多度、种间关系以及生态系统过程,最终影响动物种群的存活。野外研究表明,破碎化对动物的影响,因物种、生境类型和地理区域不同而有所变化,因此,预测物种在破碎生境中的存活比较困难。研究热点集中于：确定生境面积损失和生境斑块的空间格局对破碎景观中物种绝灭的相对影响,破碎景观中物种的适宜生境比例和绝灭阈值,异质种群动态以及生态系统的生态过程。随着3S技术的发展,生境破碎化模型趋于复杂,而发展有效的模型和验证模型将成为一项富有挑战性的任务。     

Management of genetic diversity in small farm animal populations

Many local breeds of farm animals have small populations and, consequently, are highly endangered. The correct genetic management of such populations is crucial for their survival. Managing an animal population involves two steps: first, the individuals who will be permitted to leave descendants are to be chosen and the number offspring they will be permitted to produce has to be determined; second, the mating scheme has to be identified. Strategies dealing with the first step are directed towards the maximisation of effective population size and, therefore, act jointly on the reduction in the loss of genetic variation and in the increase of inbreeding. In this paper, the most relevant methods are summarised, including the so-called 'Optimum Contribution' methodology (contributions are proportional to the coancestry of each individual with the rest), which has been shown to be the best. Typically, this method is applied to pedigree information, but molecular marker data can be used to complete or replace the genealogy. When the population is subjected to explicit selection on any trait, the above methodology can be used by balancing the response to selection and the increase in coancestry/inbreeding. Different mating strategies also exist. Some of the mating schemes try to reduce the level of inbreeding in the short term by preventing mating between relatives. Others involve regular (circular) schemes that imply higher levels of inbreeding within populations in the short term, but demonstrate better performance in the long term. In addition, other tools such as cryopreservation and reproductive techniques aid in the management of small populations. In the future, genomic marker panels may replace the pedigree information in measuring the coancestry. The paper also includes the results of several experiments and field studies on the effectiveness and on the consequences of the use of the different strategies.     

Passive acoustic monitoring of animal populations with transfer learning

Progress in deep learning, more specifically in using convolutional neural networks (CNNs) for the creation of classification models, has been tremendous in recent years. Within bioacoustics research, there has been a large number of recent studies that use CNNs. Designing CNN architectures from scratch is non-trivial and requires knowledge of machine learning. Furthermore, hyper-parameter tuning associated with CNNs is extremely time consuming and requires expensive hardware. In this paper we assess whether it is possible to build good bioacoustic classifiers by adapting and re-using existing CNNs pre-trained on the ImageNet dataset – instead of designing them from scratch, a strategy known as transfer learning that has proved highly successful in other domains. This study is a first attempt to conduct a large-scale investigation on how transfer learning can be used for passive acoustic monitoring (PAM), to simplify the implementation of CNNs and the design decisions when creating them, and to remove time consuming hyper-parameter tuning phases. We compare 12 modern CNN architectures across 4 passive acoustic datasets that target calls of the Hainan gibbon Nomascus hainanus, the critically endangered black-and-white ruffed lemur Varecia variegata, the vulnerable Thyolo alethe Chamaetylas choloensis, and the Pin-tailed whydah Vidua macroura. We focus our work on data scarcity issues by training PAM binary classification models very small datasets, with as few as 25 verified examples. Our findings reveal that transfer learning can result in up to 82% F1 score while keeping CNN implementation details to a minimum, thus rendering this approach accessible, easier to design, and speeding up further vocalisation annotations to create PAM robust models.     

Passive uplift of plant and animal populations during mountain-building

If a community and its substrate are raised by tectonic uplift, the species present can either die out in the area, survive in situ unchanged, or survive in situ with adaptation and differentiation. The large-scale passive uplift of plant and animal populations during mountain-building is accepted in a growing number of studies, but the idea has seldom been examined critically. If passive uplift does occur, it has implications for interpreting community structure and speciation in some of the most biodiverse places on Earth, tropical mountains. It would also provide a simple explanation for many altitudinal anomalies, such as the occurrence of typical coastal elements at unusually high altitudes in certain localities. Examples include the coastal saltmarsh plant Salicornia at 4200 m altitude in the rapidly uplifted Andes, coastal frogs and ferns in African mountains, and inland mangroves in New Guinea. The first aim of this paper is to review previous work on passive uplift worldwide and the main ideas that have been discussed. A second goal is to discuss possible tests of passive uplift.