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Register a new userSeed balancing selection: Coexistence in seedbank models
اختيار موازنة البذور: التعايش في نماذج بنوك البذور
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Jos\\'e Luis P\\'erez J.L. P\\'erez
Publication date
2021
fields
Biology
and research's language is
English
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نحن نعتبر مجموعة سكانية مكونة من نوعين من الأفراد ؛ كل من يمكن أن ينتج ذرية في جزيرتين مختلفتين (كحالة معينة يمكن تفسير الجزر على أنها أفراد نشيطون أو نائمون). نقوم بنمذجة تطور السكان من كل نوع باستخدام انتشار من نوعين Feller مع الهجرة ، وندرس تكرار أحد الأنواع ، في كل جزيرة ، عندما يتم فرض الحجم الكلي للسكان في كل جزيرة ثابت في مجموعة مرات كثيفة. هذا يؤدي إلى حل SDE الذي نسميه nanymmetric ثنائي الجزيرتين عملية التردد. نحن نشتق خصائص هذه العملية ونحصل على حد كبير من السكان عندما يميل الحجم الإجمالي لكل جزيرة إلى اللانهاية. بالإضافة إلى ذلك ، نحسب تقلبات العملية حول حدها التعريفي. نحن نؤسس الظروف التي بموجبها تكون عملية التردد غير المتماثل ثنائية الجزيرتين. الثنائي عبارة عن سلسلة ماركوف ذات بعدين مستمر يمكن تفسيرها من حيث الطفرة ، التفرع ، التفرع المزدوج ، الاندماج ، ومصطلح جديد مختلط لترحيل التحديد. أيضًا ، نجري تحليل استقرار للنظام الديناميكي المحدد ونقدم بعض النتائج العددية لدراسة التثبيت وشكل جديد من تحديد الموازنة. عند التقييد على نموذج بنك البذور ، نلاحظ أن بعض مجموعات المعلمات تؤدي إلى تحديد التوازن. إلى جانب إيجاد طريقة أخرى تزيد بها الخزانات الجينية من التباين الجيني ، نجد أنه إذا تنافست مجموعة تضم بنكًا للبذور مع مجموعة لا تقوم بذلك ، فسيتمتع منتجو البذور بميزة انتقائية إذا كانوا يتكاثرون بشكل أسرع ، لكنهم لن يحصلوا عليها لها عيب انتقائي إذا كانت تتكاثر بشكل أبطأ: سيناريو الحالة الأسوأ هو موازنة التحديد.
We consider a population constituted by two types of individuals; each of them can produce offspring in two different islands (as a particular case the islands can be interpreted as active or dormant individuals). We model the evolution of the population of each type using a two-type Feller diffusion with immigration, and we study the frequency of one of the types, in each island, when the total population size in each island is forced to be constant at a dense set of times. This leads to the solution of a SDE which we call the asymmetric two-island frequency process. We derive properties of this process and obtain a large population limit when the total size of each island tends to infinity. Additionally, we compute the fluctuations of the process around its deterministic limit. We establish conditions under which the asymmetric two-island frequency process has a moment dual. The dual is a continuous-time two-dimensional Markov chain that can be interpreted in terms of mutation, branching, pairwise branching, coalescence, and a novel mixed selection-migration term. Also, we conduct a stability analysis of the limiting deterministic dynamical system and present some numerical results to study fixation and a new form of balancing selection. When restricting to the seedbank model, we observe that some combinations of the parameters lead to balancing selection. Besides finding yet another way in which genetic reservoirs increase the genetic variability, we find that if a population that sustains a seedbank competes with one that does not, the seed producers will have a selective advantage if they reproduce faster, but will not have a selective disadvantage if they reproduce slower: their worst case scenario is balancing selection.
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We introduce a new Wright-Fisher type model for seed banks incorporating simultaneous switching, which is motivated by recent work on microbial dormancy. We show that the simultaneous switching mechanism leads to a new jump-diffusion limit for the scaled frequency processes, extending the classical Wright-Fisher and seed bank diffusion limits. We further establish a new dual coalescent structure with multiple activation and deactivation events of lineages. While this seems reminiscent of multiple merger events in general exchangeable coalescents, it actually leads to an entirely new class of coalescent processes with unique qualitative and quantitative behaviour. To illustrate this, we provide a novel kind of condition for coming down from infinity for these coalescents using recent results of Griffiths.
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenskis long-term evolution experiment with Escherichia coli, where models aim at explaining the observed curve of the evolution of the mean fitness. The second part describes a model of a host-pathogen system where the population of pathogenes experiences balancing selection, migration, and mutation, as motivated by observations of the genetic diversity of HCMV (the human cytomegalovirus) across hosts.
While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates.
Recently, the selection-recombination equation with a single selected site and an arbitrary number of neutral sites was solved by means of the ancestral selection-recombination graph. Here, we introduce a more accessible approach, namely the ancestral initiation graph. The construction is based on a discretisation of the selection-recombination equation. We apply our method to systematically explain a long-standing observation concerning the dynamics of linkage disequilibrium between two neutral loci hitchhiking along with a selected one. In particular, this clarifies the nontrivial dependence on the position of the selected site.
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