Registering the evolutionary history in individual-based models of speciation

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of patterns underlying the processes being modeled, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations and species in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestor–descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance between individuals of extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between trees are performed with metrics describing the overall topology, branch length distribution and imbalance degree. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second.Facultad de Ciencias Naturales y Muse

Association Patterns in Saproxylic Insect Networks in Three Iberian Mediterranean Woodlands and Their Resistance to Microhabitat Loss

The assessment of the relationship between species diversity, species interactions and environmental characteristics is indispensable for understanding network architecture and ecological distribution in complex networks. Saproxylic insect communities inhabiting tree hollow microhabitats within Mediterranean woodlands are highly dependent on woodland configuration and on microhabitat supply they harbor, so can be studied under the network analysis perspective. We assessed the differences in interacting patterns according to woodland site, and analysed the importance of functional species in modelling network architecture. We then evaluated their implications for saproxylic assemblages’ persistence, through simulations of three possible scenarios of loss of tree hollow microhabitat. Tree hollow-saproxylic insect networks per woodland site presented a significant nested pattern. Those woodlands with higher complexity of tree individuals and tree hollow microhabitats also housed higher species/interactions diversity and complexity of saproxylic networks, and exhibited a higher degree of nestedness, suggesting that a higher woodland complexity positively influences saproxylic diversity and interaction complexity, thus determining higher degree of nestedness. Moreover, the number of insects acting as key interconnectors (nodes falling into the core region, using core/periphery tests) was similar among woodland sites, but the species identity varied on each. Such differences in insect core composition among woodland sites suggest the functional role they depict at woodland scale. Tree hollows acting as core corresponded with large tree hollows near the ground and simultaneously housing various breeding microsites, whereas core insects were species mediating relevant ecological interactions within saproxylic communities, e.g. predation, competitive or facilitation interactions. Differences in network patterns and tree hollow characteristics among woodland sites clearly defined different sensitivity to microhabitat loss, and higher saproxylic diversity and woodland complexity showed positive relation with robustness. These results highlight that woodland complexity goes hand in hand with biotic and ecological complexity of saproxylic networks, and together exhibited positive effects on network robustness.The research Projects I+D CGL2011-23658 y CGL2012-31669 of the Spanish Minister of Science provided economic support

Vulnerabilidade das microrregiões da Região Sul do Brasil à pandemia do novo coronavírus (SARS-CoV-2)

This is the first report of the ‘Observatório COVID191 - Grupo: Redes de Contágio – Laboratório de Estudos de Defesa’ for the South region of Brazil. We have combined data of confirmed cases of the new coronavirus (SARS-CoV-2) for the South available up to 17/04/2020, with structural analyses of road networks, from within and between states, to estimate the vulnerability and potential influence of the South micro-regions to propagate the disease.Este é o primeiro relatório do Observatório COVID19 - Grupo: Redes de Contágio – Laboratório de Estudos de Defesa para a região Sul do Brasil. Combinamos dados de casos confirmados do novo coronavírus (SARS-CoV-2) para o Sul, disponíveis até o dia 17/04/2020, com análises estruturais da rede de rotas rodoviárias intra e interestaduais para estimarmos a vulnerabilidade e potencial influência das microrregiões sulinas na propagação da doença

Vulnerabilidade estrutural dos hospitais e cemitérios e crematórios da cidade de São Paulo à COVID-19

This is the first report by the COVID19 Observatory - Group: Contagion Networks analyzing mortality data from the city of São Paulo. In this report, we integrated mortality data for the city of São Paulo between 04/02/2020 and 04/28/2020, with information on the flow of victims between hospitals and cemeteries/crematoriums. We included in our analyzes both confirmed and suspected deaths from COVID-19. The main objectives of this report were: (1) to describe the structure of the flow of victims between locations and (2) to suggest changes in the current flow based on geographical distances in order to avoid a potential overload of the mortuary system. We suggest that the city of São Paulo should plan for a potential overload of the mortuary system (that is, the number of burials), based on the presented results. Thus, our results reinforce the need to adopt specific planning for the management of the extraordinary number of victims of this pandemic. Our predictions are based on the structural analysis of the COVID-19 victim flow network, which shows several hotspots with high vulnerability to system overload. These hotspots concentrate with either the greatest number of deaths (hospital) or of burials (cemetery or crematorium), and therefore have high potential to become overwhelmed by receiving many bodies due to the increase in victims of the pandemic. We recommend special attention to be given to localities on the east side of São Paulo, which has both the most vulnerable hospitals in the city, and also houses cemeteries and crematoriums that have a central role in the network and / or are vulnerable. Based on our optimization analysis, we suggest logistical changes in the current flow of bodies from hospitals to cemeteries/crematoriums so as not to overload the funeral system and minimize transportation costs. In this sense, our results are potentially useful for improving the operational planning of the Municipality of São Paulo, ratifying or rectifying actions underway at the municipal level.Este é o primeiro relatório do Observatório COVID19 - Grupo: Redes de Contágio analisando os dados de óbitos da cidade de São Paulo. Neste relatório, integramos os dados de óbitos da cidade de São Paulo entre os dias 02/04/2020 e 28/04/2020 com informações sobre o fluxo de vítimas entre os hospitais e os cemitérios e crematórios da cidade de São Paulo. Incluímos em nossas análises óbitos confirmados e óbitos suspeitos de COVID-19. Os principais objetivos deste relatório são: (1) descrever a estrutura do fluxo de vítimas entre localidades e (2) sugerir mudanças no fluxo com base em distâncias geográficas de maneira a evitar uma potencial sobrecarga do sistema funerário. Sugere-se à prefeitura da cidade de São Paulo que seja realizado um planejamento para uma potencial sobrecarga do sistema funerário (isto é, número de sepultamentos) da cidade de São Paulo com base nos resultados apresentados. Desta forma, nossos resultados reforçam a necessidade de ser adotado planejamento específico para a gestão dos casos extraordinários visualizados no contexto da pandemia. Esta previsão está baseada na análise estrutural da rede de fluxos de vítimas da COVID-19, que indica a concentração de vários locais com alta vulnerabilidade à sobrecarga do sistema. Tais locais concentram a maior quantidade de óbitos (hospitais) ou a maior concentração de sepultamentos (cemitérios ou crematórios) e tem portanto alto potencial de tornarem-se sobrecarregados por receberem muitos corpos devido ao aumento de vítimas da pandemia. Recomenda-se especial atenção à localidades da zona leste de São Paulo, que apresenta os hospitais mais vulneráveis da cidade e abriga cemitérios e crematórios que possuem papel central na rede e/ou encontram-se vulneráveis. Com base em nossa análise de otimização, sugerimos mudanças logísticas no atual fluxo de corpos de hospitais para cemitérios/crematórios de modo a não sobrecarregar o sistema funerário e minimizar os custos de transporte. Neste sentido, nossos resultados são potencialmente úteis ao aperfeiçoamento do planejamento operacional da Prefeitura Municipal de São Paulo, ratificando ou retificando ações em curso no âmbito municipal

The friendship paradox in species-rich ecological networks: implications for conservation and monitoring

FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPA great challenge in ecology and conservation biology is to deal with the inherent complexity of ecological systems. Because species are embedded in species-rich systems characterized by multiple interactions, it is often hard to identify which species are really important for ecological processes such as pollination. Here we show that species-rich networks describing plant-pollinator interactions share a property with networks depicting social relationships, the friendship paradox, which allows identifying highly-connected species without detailed information on the whole network of interactions. Numerical simulations support that the identified species are those more likely to affect community structure and ecological dynamics. A sampling protocol taking into account the friendship paradox property could be adapted to field studies, helping in the search for conservation surrogates or to monitor changes in the communities, such as functional extinction or the increase in ecological importance of invasive species. We hypothesize that the friendship paradox is likely to arise in networks describing other types of ecological interactions. Besides being useful for conservation and ecosystem management, the friendship paradox may have relevant implications in other areas of biology as well.209245252FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP2009/54567-62015/11985-32016/00635-

Persistence of Pollination Systems

Pollination systems are composed of flowering plants and flower visitors, en- gaging into mutualistic interactions. However, the flower visitors include true pollinators, which pollinate the flower by visiting it through the legitimate way, and also by cheaters, which use the flower′s resources (e.g. nectar and pollen) without pollinating it or been just marginally efficient on pollination. On the one hand, plants have different flower structures, as shallow and tubu- lar flowers, which can provide some protection agains the cheaters effects or higher efficiency when visited by pollinators. Even though cheaters can dam- age flowers, there is evidence that cheaters can have a positive effect on the pollination service. In fact, the existence of cheaters decreases the amount of reward provided by plants in a given environment. Therefore, pollinators travel further in order to visit more flowers or even spend a longer time in each flower to collect enough resources. It increases the cross-pollination rate and the pollination success, especially to auto-incompatible plant species. The presence of cheaters in these systems represent a delicate trade-off when mutualistic interactions when cheaters effects are taken into account. In this work, we are interested to understand how pollination systems allow the per- sistent coexistence of the two types of visitors and plants. We developed a mean field analytical model relying on game theory, with a bipartite network of two kinds of plants (shallow and tubular flowers) and two kinds of visitors (pollinators and cheaters). Our analytical and numerical results confirm the presence of metastable states of persistent coexistence of the above-mentioned visitors and plants. In order to better describe additional real-world features of pollination systems (i.e. the spatial distribution of flowers, the depletion of resources, and the crossing pollination effect) we also implement an agent- based model. In this case, we observed coexistence of the two visitors and two plants when we included the space. We are still studying the agent- based mode approach to understand, for instance, how spatial structures (as the ones resulting from mankind actions) can affect pollination systems

Registering the evolutionary history in individual-based models of speciation

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of patterns underlying the processes being modeled, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations and species in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestor–descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance between individuals of extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between trees are performed with metrics describing the overall topology, branch length distribution and imbalance degree. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second.Fil: Costa, Carolina L. N.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Marquitti, Flavia M. D.. Universidade Estadual de Campinas; BrasilFil: Perez, Sergio Ivan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidade Estadual de Campinas; Brasil. Universidad Nacional de La Plata. Facultad de Cienicas Naturales y Museo. División Antropología; ArgentinaFil: Schneider, David Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidade Estadual de Campinas; BrasilFil: Ramos, Marlon F.. Universidade Estadual de Campinas; BrasilFil: Aguiar, Marcus A. M. de. Universidade Estadual de Campinas; Brasi

Registering the evolutionary history in individual-based models of speciation

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL E NÍVEL SUPERIORUnderstanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of patterns underlying the processes being modeled, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations and species in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestor-descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance between individuals of extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between trees are performed with metrics describing the overall topology, branch length distribution and imbalance degree. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second.510114FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL E NÍVEL SUPERIORFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL E NÍVEL SUPERIOR2015/11985-32016/01343-72016/06054-3302049/2015-0152885/2016-1sem informaçã

input

An example of input data to run the ibm.f90 code

Individual-based model

The code for run simulations based on the model presented in the paper