Ecosystem Viable Yields

The World Summit on Sustainable Development (Johannesburg, 2002) encouraged the application of the ecosystem approach by 2010. However, at the same Summit, the signatory States undertook to restore and exploit their stocks at maximum sustainable yield (MSY), a concept and practice without ecosystemic dimension, since MSY is computed species by species, on the basis of a monospecific model. Acknowledging this gap, we propose a definition of "ecosystem viable yields" (EVY) as yields compatible i) with guaranteed biological safety levels for all time and ii) with an ecosystem dynamics. To the difference of MSY, this notion is not based on equilibrium, but on viability theory, which offers advantages for robustness. For a generic class of multispecies models with harvesting, we provide explicit expressions for the EVY. We apply our approach to the anchovy--hake couple in the Peruvian upwelling ecosystem

Riverscape Community Genomics of Ozark Fishes: A Comparative Framework to Infer Ecological and Evolutionary Determinants of Genetic Diversity

Genetic variation is a crucial component of biodiversity and represents the variability and spatial structure of alleles within and among organisms. Evolution modulates this variability over time through mutation, selection, gene flow, and genetic drift. However, our capacity to test foundational theories of population genetics has always been at the mercy of molecular approaches available to quantify patterns of genetic diversity. Initially, techniques for empirical DNA studies were in their infancy and limited by technologies and the price per unit of genetic information. Because of these constraints, our pursuits have generally been limited to investigations of one or a few species simultaneously, hampering our power to draw broadly applicable conclusions. Advances in molecular technologies, e.g., high-throughput sequencing, now provide so much information at so little cost that a multispecies comparative approach to uncovering generalities about evolution is within reach even for applied studies on non-model organisms. Ultimately, genotyping individuals from all species within a community will be feasible and easily replicated across sampling locations and span entire regions. Variability of genetic diversity, within and among species, can be leveraged to explore the relationship between ecology and evolution and between micro- and macroevolution.For my dissertation research, I employed a multispecies framework to link ecological and evolutionary processes driving spatial patterns of biodiversity through comparative analyses of genotypic variability among sympatric species of freshwater fish that inhabit a large sub-basin of the Mississippi River. First, I quantified the extent of admixed ancestry among species within a community by assessing genomic variability among individuals from many species. My analyses uncovered that fish in nature — particularly minnows — have higher than expected hybridization rates. My data even show evidence of hybrid viability and genetic exchange among species (i.e., introgression). I interpret these findings of widespread admixture among distinct species as an indicator that admixture plays a critical role in ecology and evolution – more so than previously considered. Second, I tested for general mechanisms that define spatial genomic variability within species by comparing models of extrinsic drivers of genetic divergence. The river network, or stream hierarchy model, best explained species\u27 genomic variability, as evidenced by the correspondence between genetic divergence and riverine architecture. This general pattern emerged for all species, but the degree of genetic divergence differed widely, indicating that the intrinsic traits of each species may also play an important role. Finally, I further explored how phenotypic traits may modulate species\u27 genetic diversity and ultimately evolutionary trajectories by comparing relationships between traits and metrics of genetic variability among species within a comparative framework. Significant associations between trait values and genetic patterns emerged, allowing me to develop predictive models of genetic diversity using traits alone, without requiring direct genetic assessments. These trait-based models can be applied to prioritize species for conservation and management. My dissertation research demonstrates that modern molecular approaches are uniquely positioned to help unite ecology and evolution, bridging the long-standing dichotomy between these two disciplines. I provide a comparative framework for conservation biology that integrates various temporal and spatial scales and demonstrate with an empirical example how it can be applied to assess thousands of informative genetic markers across entire communities of non-model organisms. My dissertation research elevates population genomics to the community level and outlines how to explore new dimensions in our long-standing inquiry: What drives variation in genetic diversity among species

Cross‐species systems analysis of evolutionary toolkits of neurogenomic response to social challenge

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/1/gbb12502.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/2/gbb12502-sup-0002-TableS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147855/3/gbb12502_am.pd

Marine Protected Areas: Economic and Social Implications

This paper is a guide for citizens, scientists, resource managers, and policy makers, who are interested in understanding the economic and social value of marine protected areas (MPAs). We discuss the potential benefits and costs associated with MPAs as a means of illustrating the economic and social tradeoffs inherent in implementation decisions. In general, the effectiveness of a protected area depends on a complex set of interactions between biological, economic, and institutional factors. While MPAs might provide protection for critical habitats and cultural heritage sites and, in some cases, conserve biodiversity, as a tool to enhance fishery management their impact is less certain. The uncertainty stems from the fact that MPAs only treat the symptoms and not the fundamental causes of overfishing and waste in fisheries.Marine Protected Areas (MPAs), marine reserves, fisheries

The Role of Law in Reducing Barriers to Citizens Participation in Community-Based Natural Resource Management Models

[Extract] Environmental protection and natural resource management are highly complicated, dynamic processes intersecting natural and social systems. Policies related to these issues involve a broad array of inputs, including, among others, scientific data, legal information, value judgments, philosophical perspectives, and economic decisions, and they can have momentous consequences not only at international, national, and state levels, but also for communities and individuals. In recognition of these impacts, policy and lawmakers in 50+ countries are pursuing community-based approaches to environmental protection and natural resource management by delegating some degree of management and decision-making authority over parks or other protected areas; forests; water, coastal resources, and fisheries; wildlife; and other natural resources to community user groups.One framework for promoting citizen participation in the management of public natural resources is the Community-Based Natural Resource Management Model (CBNRM). This model adopts a socio-ecological approach that integrates local institutions, customary practices, and community knowledge structures into natural adaptive systems protection and administration. It is believed that consideration of these factors and that involvement of local stakeholders in management, regulatory, and enforcement processes will result in improved resource management outcomes.This paper will briefly describe the CBNRM model and will review its use in relation to various levels and categories of legal obligations in two very different contexts. It also will consider barriers that have been identified to citizen participation in these CBNRM models and will explore how law or other instruments might be utilized to respond to these challenges.[Extract] Environmental protection and natural resource management are highly complicated, dynamic processes intersecting natural and social systems. Policies related to these issues involve a broad array of inputs, including, among others, scientific data, legal information, value judgments, philosophical perspectives, and economic decisions, and they can have momentous consequences not only at international, national, and state levels, but also for communities and individuals. In recognition of these impacts, policy and lawmakers in 50+ countries are pursuing community-based approaches to environmental protection and natural resource management by delegating some degree of management and decision-making authority over parks or other protected areas; forests; water, coastal resources, and fisheries; wildlife; and other natural resources to community user groups.One framework for promoting citizen participation in the management of public natural resources is the Community-Based Natural Resource Management Model (CBNRM). This model adopts a socio-ecological approach that integrates local institutions, customary practices, and community knowledge structures into natural adaptive systems protection and administration. It is believed that consideration of these factors and that involvement of local stakeholders in management, regulatory, and enforcement processes will result in improved resource management outcomes.This paper will briefly describe the CBNRM model and will review its use in relation to various levels and categories of legal obligations in two very different contexts. It also will consider barriers that have been identified to citizen participation in these CBNRM models and will explore how law or other instruments might be utilized to respond to these challenges

Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research

Evolutionary history of sympatric rainbow skinks from the australian monsoonal tropics

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2018How speciation, range shifting and reticulation through climatic oscillations combine to shape current patterns of local and regional diversity remains a key question in evolutionary biology. This can be investigated by using multi-scale analyses of closely related species assemblages in diverse communities, such as the lizards of Australia’s tropical savannas. An example of these is the understudied group of rainbow skinks (Carlia) that are broadly co-distributed across the Australian Monsoonal Tropics (AMT) region, and that stands out from most well-studied Carlia species occurring along the Australian east coast. The aims of this thesis were to: i) identify lineage diversity between two sympatric and closely related skinks and to use an integrative taxonomic approach to statistically test major lineages as species; ii) compare past responses of species with different climatic niche breadth that experienced the same climatic fluctuations; iii) infer the phylogenetic relationships of the rainbow skinks in a collaborative study; and iv) explore the occurrence of introgression in a group of six species that broadly cooccur in the AMT, using a dataset by target exon capture (>1000 loci). The investigation of lineage diversity discovered cryptic lineages mostly in the Kimberley region (north west of Australia). In an integrative taxonomic approach, these lineages were then statistically validated as new species using multispecies coalescent methods and morphological analyses, and subsequently described as C. insularis sp. nov and C. isostriacantha sp. nov. with genetic and morphological characters. The exploration of how concordant were the species responses with late Pleistocene climatic changes, identified contrasting responses by species with different climatic niches, suggesting that the narrow climatic specialist species was more sensitive to these changes. In addition, using multiple phylogenomic approaches, it contributed to a much improved and well-supported phylogeny for the rainbow skinks in comparison with a previous, poorly resolved tree. The new tree showed that the six Carlia species that co-occur in the AMT are actually closely related. Lastly, the analysis for the presence of introgression between the AMT sympatric species did not detect evidence of recent admixture, but identified patterns of ancestral introgression before the divergence of sister species, and some instances of introgression in the more climatic unstable Kimberley region. It also showed that by accounting for reticulated evolution with phylogenetic networks methods, a distinct topology from the overall well supported species tree can be observed, in this case with the clade inferred as introgressed appearing as more ancestral in the phylogeny. The results of this thesis have implications for the understanding of the processes driving cryptic species diversity and responses to past climatic change across this richm and understudied Australian Monsoonal Tropics biome