Frédéric Bouchard

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

Causal Processes, Fitness, and the Differential Persistence of Lineages

Ecological fitness has been suggested to provide a unifying definition of fitness. However, a metric for this notion of fitness was in most cases unavailable except by proxy with differential reproductive success. In this article, I show how differential persistence of lineages can be used as a way to assess ecological fitness. This view is inspired by a better understanding of the evolution of some clonal plants, colonial organisms, and ecosystems. Differential persistence shows the limitation of an ensemblist noncausal understanding of evolution. Causal explanations are necessary to understand the evolution by natural selection of these biological systems.

Subarctic Thermokarst Ponds: Investigating Recent Landscape Evolution and Sediment Dynamics in Thawed Permafrost of Northern Québec (Canada)

Abstract Although widely distributed throughout Arctic and subarctic regions, thermokarst ponds and lakes remain relatively unexplored regarding geomorphological changes in their catchments and their internal properties in relation to climate change over the past decades. This study synthesizes recent landscape evolution and modern sedimentology of limnologically diverse thermokarst ponds near southeastern Hudson Bay, Canada. Spatio-temporal analysis of permafrost mounds, thermokarst ponds, and vegetation surface areas over the past five decades revealed that the recent climate-induced decrease of permafrost-affected areas was not primarily compensated by thermokarst pond development, but rather by a remarkable increase in vegetation cover. These changes appeared to be modulated by topographical and hydrological gradients at the study site, which are associated with east-ward increasing thickness of postglacial marine deposits. At a more contemporary timescale, physico-chemical measurements made on sedimenting materials (sediment traps) and freshly deposited lacustrine sediments of selected thermokarst ponds revealed striking differences both among ponds and between the oxic epilimnion and the oxygen-depleted hypolimnion. These findings underscore the major influence of local landscape properties and oxycline development on pond sedimentology and geochemistry, such as the transport of detritic particles and the concentration of redox-sensitive elements.

EGR-1 activation by EGF inhibits MMP-9 expression and lymphoma growth.

Progression of hematologic malignancies is strongly dependent on bidirectional interactions between tumor cells and stromal cells. Expression of members of the matrix metalloproteinase (MMP) family by stromal cells is a central event during these interactions. However, although several studies have focused on the mechanisms responsible for induction of MMP in stromal cells, the signals that negatively regulate their secretion of in these cells remain largely unknown. Here, we provide evidence that MMP-9 production by stromal cells is suppressed through activation of early growth response protein 1 (EGR-1), thereby inhibiting the growth of thymic lymphoma. We found that EGR-1 expression is induced in stromal cells after contact with lymphoma cells via epidermal growth factor (EGF). Moreover, development of thymic lymphoma was inhibited when induced by lymphoma cells overexpressing EGF compared with control lymphoma cells. Using transgenic mice containing MMP-9 promoter-driven luciferase transgene in its genome, we further demonstrated that EGF/EGR-1 repressed transcriptional activation of the MMP-9 gene by stromal cells. De novo expression of EGR-1 alone by gene transfer or exposure to recombinant human EGF also inhibited MMP-9 expression. Taken together, these results indicate that EGR-1 could be a source of novel targets for therapeutic intervention in lymphoid tumors in which MMP-9 plays a critical role.

Being human is a gut feeling

Some metagenomic studies have suggested that less than 10% of the cells that comprise our bodies are Homo sapiens cells. The remaining 90% are bacterial cells. The description of this so-called human microbiome is of great interest and importance for several reasons. For one, it helps us redefine what a biological individual is. We suggest that a human individual is now best described as a super-individual in which a large number of different species (including Homo sapiens) coexist. New concepts of biological individuality must extend beyond the traditional limitations of our own skin to include our resident microbes. Besides its important contributions to science, microbiome research raises philosophical questions that strike close to home. What is left of Homo sapiens? If most of our cells are not Homo sapiens cells, what does it mean to be an individual human being? In this paper, we argue that the biological individual is determined by the amount of functional integration among its constitutive parts, a definition that applies perfectly to Homo sapiens and its microbiome.

A persistence enhancing propensity account of ecological function to explain ecosystem evolution

We argue that ecology in general and biodiversity and ecosystem function (BEF) research in particular need an understanding of functions which is both ahistorical and evolutionarily grounded. A natural candidate in this context is Bigelow and Pargetter’s (1987) evolutionary forward-looking account which, like the causal role account, assigns functions to parts of integrated systems regardless of their past history, but supplements this with an evolutionary dimension that relates functions to their bearers’ ability to thrive and perpetuate themselves. While Bigelow and Pargetter’s account focused on functional organization at the level of organisms, we argue that such an account can be extended to functional organization at the community and ecosystem levels in a way that broadens the scope of the reconciliation between ecosystem ecology and evolutionary biology envisioned by many BEF researchers (e.g. Holt 1995; Loreau 2010a). By linking an evolutionary forward-looking account of functions to the persistence-based understanding of evolution defended by Bouchard (2008, 2011) and others (e.g. Bourrat 2014; Doolittle 2014), and to the theoretical research on complex adaptive systems (Levin 1999, 2005; Norberg 2004), we argue that ecosystems, by forming more or less resilient assemblages, can evolve even while they do not reproduce and form lineages. We thus propose a Persistence Enhancing Propensity (PEP) account of role functions in ecology to account for this overlap of evolutionary and ecological processes.

Hidden biofilms in a far northern lake and implications for the changing Arctic

Shallow lakes are common across the Arctic landscape and their ecosystem productivity is often dominated by benthic, cyanobacterial biofilms. Many of these water bodies freeze to the bottom and are biologically inactive during winter, but full freeze-up is becoming less common with Arctic warming. Here we analyzed the microbiome structure of newly discovered biofilms at the deepest site of a perennially ice-covered High Arctic lake as a model of polar microbial communities that remain unfrozen throughout the year. Biofilms were also sampled from the lake’s shallow moat region that melts out and refreezes to the bottom annually. Using high throughput small subunit ribosomal RNA sequencing, we found more taxonomic richness in Bacteria, Archaea and microbial eukaryotes in the perennially unfrozen biofilms compared to moat communities. The deep communities contained both aerobic and anaerobic taxa including denitrifiers, sulfate reducers, and methanogenic Archaea. The water overlying the deep biofilms was well oxygenated in mid-summer but almost devoid of oxygen in spring, indicating anoxia during winter. Seasonally alternating oxic-anoxic regimes may become increasingly widespread in polar biofilms as fewer lakes and ponds freeze to the bottom, favoring prolonged anaerobic metabolism and greenhouse gas production during winter darkness.

Paleolimnology of thermokarst lakes: a window into permafrost landscape evolution

Widespread across northern permafrost landscapes, thermokarst ponds and lakes provide vital wildlife habitat and play a key role in biogeochemical processes. Stored in the sediments of these typically shallow and dynamic waterbodies are rich sources of paleoenvironmental information whose potential has not yet been fully exploited, likely because of concerns over stratigraphic preservation and challenges to develop reliable sediment core chronologies. Here, we present an overview of recently derived informative paleolimnological reconstructions based on multiparameter analysis of sediment archives from permafrost aquatic basins. We include examples from across the Canadian North, Alaska, and Siberia that illustrate their value for providing insights into temporal patterns of lake inception, catchment erosion, aquatic productivity, hydrological evolution, and landscape disturbances. Although not captured in our survey, emerging research directions focused on carbon accumulation, storage, and balance hold m...

Distribution and diversity of diatom assemblages in surficial sediments of shallow lakes in Wapusk National Park (Manitoba, Canada) region of the Hudson Bay Lowlands

Abstract The hydrology of shallow lakes (and ponds) located in the western Hudson Bay Lowlands (HBL) is sensitive to climate warming and associated permafrost thaw. However, their biological characteristics are poorly known, which hampers effective aquatic ecosystem monitoring. Located in northern Manitoba along the southwestern coast of Hudson Bay, Wapusk National Park (WNP) encompasses numerous shallow lakes representative of the subarctic zone. We analyzed the distribution and diversity of diatom (microscopic algae; class Bacillariophyceae) assemblages in surficial sediments of 33 lakes located in three different ecozones spanning a vegetation gradient, from NE to SW: the Coastal Fen (CF), the Interior Peat Plateau (IPP), and the Boreal Spruce Forest (BSF). We found significant differences (P < 0.05) in diatom community composition between CF and IPP lakes, and CF and BSF lakes, but not between IPP and BSF lakes. These results are consistent with water chemistry measurements, which indicated distinct limnological conditions for CF lakes. Diatom communities in CF lakes were generally dominated by alkaliphilous taxa typical of waters with medium to high conductivity, such as Nitzschia denticula. In contrast, several IPP and BSF lakes were dominated by acidophilous and circumneutral diatom taxa with preference for low conductivity (e.g., Tabellaria flocculosa, Eunotia mucophila, E. necompacta var. vixcompacta). This exploratory survey provides a first detailed inventory of the diatom assemblages in the WNP region needed for monitoring programs to detect changes in shallow lake ecosystems and ecozonal shifts in response to climate variations.

A synthesis of thermokarst lake water balance in high-latitude regions of North America from isotope tracers

Numerous studies utilizing remote sensing imagery and other methods have documented that thermokarst lakes are undergoing varied hydrological transitions in response to recent climate changes, from...