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Current Biology : CB May 2017Phylogenetic comparative methods (PCMs) enable us to study the history of organismal evolution and diversification. PCMs comprise a collection of statistical methods for...
Phylogenetic comparative methods (PCMs) enable us to study the history of organismal evolution and diversification. PCMs comprise a collection of statistical methods for inferring history from piecemeal information, primarily combining two types of data: first, an estimate of species relatedness, usually based on their genes, and second, contemporary trait values of extant organisms. Some PCMs also incorporate information from geological records, especially fossils, but also other gradual and episodic events in the Earth's history (for example, trait data from fossils or the global oxygen concentration as an independent variable). It is important to note at the outset that PCMs are not concerned with reconstructing the evolutionary relationships among species; this has to do with estimating the phylogeny from genetic, fossil and other data, and a separate set of methods for this process makes up the field of phylogenetics. PCMs as a set of methods are distinct from, but are not completely independent of, phylogenetics. PCMs are used to address the questions: how did the characteristics of organisms evolve through time and what factors influenced speciation and extinction?
Topics: Animals; Biological Evolution; Fossils; Genetic Speciation; Models, Genetic; Phylogeny
PubMed: 28486113
DOI: 10.1016/j.cub.2017.03.049 -
Trends in Ecology & Evolution Oct 2012Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research... (Review)
Review
Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vaccine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed understanding of the genomic and molecular basis of experimental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limitations, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.
Topics: Adaptation, Physiological; Animals; Biological Evolution; Evolution, Molecular; Humans; Models, Biological
PubMed: 22819306
DOI: 10.1016/j.tree.2012.06.001 -
Heredity Oct 2015
Topics: Adaptation, Biological; Biological Evolution; Genetic Fitness; Genetic Speciation; Genetic Variation; Phenotype
PubMed: 26350631
DOI: 10.1038/hdy.2015.64 -
Proceedings of the National Academy of... Jul 1998Evolvability is an organism's capacity to generate heritable phenotypic variation. Metazoan evolution is marked by great morphological and physiological diversification,... (Review)
Review
Evolvability is an organism's capacity to generate heritable phenotypic variation. Metazoan evolution is marked by great morphological and physiological diversification, although the core genetic, cell biological, and developmental processes are largely conserved. Metazoan diversification has entailed the evolution of various regulatory processes controlling the time, place, and conditions of use of the conserved core processes. These regulatory processes, and certain of the core processes, have special properties relevant to evolutionary change. The properties of versatile protein elements, weak linkage, compartmentation, redundancy, and exploratory behavior reduce the interdependence of components and confer robustness and flexibility on processes during embryonic development and in adult physiology. They also confer evolvability on the organism by reducing constraints on change and allowing the accumulation of nonlethal variation. Evolvability may have been generally selected in the course of selection for robust, flexible processes suitable for complex development and physiology and specifically selected in lineages undergoing repeated radiations.
Topics: Animals; Biological Evolution; Phylogeny; Selection, Genetic
PubMed: 9671692
DOI: 10.1073/pnas.95.15.8420 -
Journal of Anatomy Apr 2016Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the... (Review)
Review
Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins.
Topics: Adaptation, Biological; Animals; Biological Evolution; Ecosystem; Fossils; Phylogeny; Primates
PubMed: 26830706
DOI: 10.1111/joa.12441 -
Proceedings. Biological Sciences Jan 2016The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable... (Review)
Review
The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.
Topics: Adaptation, Biological; Biological Evolution; Fossils; Genetic Speciation; Genetic Variation; Genome
PubMed: 26763705
DOI: 10.1098/rspb.2015.2547 -
Journal of the Royal Society, Interface Jun 2017Scientists are always on the lookout for new modalities of information which could reveal new biological features that are useful for deciphering the complexity of... (Review)
Review
Scientists are always on the lookout for new modalities of information which could reveal new biological features that are useful for deciphering the complexity of biological systems. Here, we introduce Raman spectroscopy as a prime candidate for ecology and evolution. To encourage the integration of this microscopy technique in the field of ecology and evolution, it is crucial to discuss first how Raman spectroscopy fits within the conceptual, technical and pragmatic considerations of ecology and evolution. In this paper, we show that the spectral information holds reliable indicators of intra- and interspecies variations, which can be related to the environment, selective pressures and fitness. Moreover, we show how the technical and pragmatic aspects of this modality (non-destructive, non-labelling, speed, relative low cost, etc.) enable it to be combined with more conventional methodologies. With this paper, we hope to open new avenues of research and extend the scope of available methodologies used in ecology and evolution.
Topics: Animals; Biological Evolution; Ecology; Ecosystem; Species Specificity; Spectrum Analysis, Raman
PubMed: 28592661
DOI: 10.1098/rsif.2017.0174 -
Journal of Evolutionary Biology Dec 2023When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify),... (Review)
Review
When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.
Topics: Phylogeny; Biological Evolution; Microbiota; Evolution, Molecular; Genome; Symbiosis
PubMed: 37750599
DOI: 10.1111/jeb.14221 -
Comptes Rendus Biologies May 2023Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted... (Review)
Review
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
Topics: Eukaryotic Cells; Symbiosis; Phylogeny; Archaea; Eukaryota; Biological Evolution
PubMed: 37254790
DOI: 10.5802/crbiol.118 -
Current Opinion in Genetics &... Aug 2016The Xenacoelomorpha, with its phylogenetic position as sister group of the Nephrozoa (Protostomia+Deuterostomia), plays a key-role in understanding the evolution of... (Review)
Review
The Xenacoelomorpha, with its phylogenetic position as sister group of the Nephrozoa (Protostomia+Deuterostomia), plays a key-role in understanding the evolution of bilaterian cell types and organ systems. Current studies of the morphological and developmental diversity of this group allow us to trace the evolution of different organ systems within the group and to reconstruct characters of the most recent common ancestor of Xenacoelomorpha. The disparity of the clade shows that there cannot be a single xenacoelomorph 'model' species and strategic sampling is essential for understanding the evolution of major traits. With this strategy, fundamental insights into the evolution of molecular mechanisms and their role in shaping animal organ systems can be expected in the near future.
Topics: Animals; Biological Evolution; Phylogeny
PubMed: 27322587
DOI: 10.1016/j.gde.2016.05.019