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Cold Spring Harbor Perspectives in... Apr 2016Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has... (Review)
Review
Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.
Topics: Adaptation, Biological; Bacteria; Biological Evolution; Gene Transfer, Horizontal; Phylogeny; Prokaryotic Cells
PubMed: 26801681
DOI: 10.1101/cshperspect.a018036 -
Current Biology : CB Oct 2019Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content... (Review)
Review
Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve.
Topics: Biological Evolution; Evolution, Molecular; Genome, Bacterial; Metagenome; Phylogeny
PubMed: 31639358
DOI: 10.1016/j.cub.2019.08.012 -
Current Biology : CB Oct 2021The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely...
The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s. These methods depend on our understanding of how nucleotide or amino acid sequences evolve through time and in different lineages. Armed with this knowledge, researchers can make inferences about the relationships and amount of genomic divergence among species.
Topics: Biological Evolution; Evolution, Molecular; Genome; Genomics; Phylogeny
PubMed: 34637727
DOI: 10.1016/j.cub.2021.07.039 -
International Journal of Environmental... Jan 2020Aspects of human evolutionary biology and prehistory are discussed in relation to vitamin D. The evolution of hairlessness, combined with the need for efficient eccrine... (Review)
Review
Aspects of human evolutionary biology and prehistory are discussed in relation to vitamin D. The evolution of hairlessness, combined with the need for efficient eccrine sweat production for cooling, provided evolutionary pressure to protect the skin from ultraviolet damage by developing cutaneous pigmentation. There was a subsequent loss of pigmentation as humans journeyed to northern latitudes. Their increasing mastery of technology outstripped evolution's finite pace as further dispersal occurred around the globe. A timeline for the development of clothing to provide warmth, and the consequent shielding from ultraviolet light, which diminished vitamin D synthesis, can be inferred by an examination of mutations in the human louse.
Topics: Animals; Biological Evolution; Humans; Skin; Vitamin D; Vitamins
PubMed: 31963858
DOI: 10.3390/ijerph17020646 -
Current Biology : CB Oct 2020Florian Maderspacher introduces the microbiology special issue and asks how the study of microbes has shaped our understanding of evolution.
Florian Maderspacher introduces the microbiology special issue and asks how the study of microbes has shaped our understanding of evolution.
Topics: Bacteria; Biodiversity; Biological Evolution; Ecology; Environmental Microbiology; Microbial Interactions; Phylogeny
PubMed: 33022245
DOI: 10.1016/j.cub.2020.09.010 -
Proceedings. Biological Sciences Jul 2023The evolutionary history of animal cognition appears to involve a few major changes that opened up new phylogenetic possibilities for cognition. Here, we review and... (Review)
Review
The evolutionary history of animal cognition appears to involve a few major changes that opened up new phylogenetic possibilities for cognition. Here, we review and contrast current transitional accounts of cognitive evolution. We discuss how an important feature of an evolutionary transition should be that it changes what is evolvable, so that the possible phenotypic spaces before and after a transition are different. We develop an account of cognitive evolution that focuses on how selection might act on the computational architecture of nervous systems. Selection for operational efficiency or robustness can drive changes in computational architecture that then make new types of cognition evolvable. We propose five major transitions in the evolution of animal nervous systems. Each of these gave rise to a different type of computational architecture that changed the evolvability of a lineage and allowed the evolution of new cognitive capacities. Transitional accounts have value in that they allow a big-picture perspective of macroevolution by focusing on changes that have had major consequences. For cognitive evolution, however, we argue it is most useful to focus on evolutionary changes to the nervous system that changed what is evolvable, rather than to focus on specific cognitive capacities.
Topics: Animals; Biological Evolution; Phylogeny; Cognition
PubMed: 37403503
DOI: 10.1098/rspb.2023.0671 -
Current Biology : CB Apr 2023Neuroplasticity and evolutionary biology have been prominent fields of study for well over a century. However, they have advanced largely independently, without...
Neuroplasticity and evolutionary biology have been prominent fields of study for well over a century. However, they have advanced largely independently, without consideration of the benefits of integration. We propose a new framework by which researchers can begin to examine the evolutionary causes and consequences of neuroplasticity. Neuroplasticity can be defined as changes to the structure, function or connections of the nervous system in response to individual experience. Evolution can alter levels of neuroplasticity if there is variation in neuroplasticity traits within and between populations. Neuroplasticity may be favored or disfavored by natural selection depending on the variability of the environment and the costs of neuroplasticity. Additionally, neuroplasticity may affect rates of genetic evolution in many ways: for example, decreasing rates of evolution by buffering against selection or increasing them via the Baldwin effect, by increasing genetic variation or by incorporating evolved peripheral changes to the nervous system. These mechanisms can be tested using comparative and experimental approaches and by examining patterns and consequences of variation in neuroplasticity among species, populations and individuals.
Topics: Humans; Biological Evolution; Evolution, Molecular; Phenotype; Neuronal Plasticity
PubMed: 37098327
DOI: 10.1016/j.cub.2023.03.002 -
Biology Letters May 2021A widespread and popular belief posits that humans possess a cognitive capacity that is limited to keeping track of and maintaining stable relationships with...
A widespread and popular belief posits that humans possess a cognitive capacity that is limited to keeping track of and maintaining stable relationships with approximately 150 people. This influential number, 'Dunbar's number', originates from an extrapolation of a regression line describing the relationship between relative neocortex size and group size in primates. Here, we test if there is statistical support for this idea. Our analyses on complementary datasets using different methods yield wildly different numbers. Bayesian and generalized least-squares phylogenetic methods generate approximations of average group sizes between 69-109 and 16-42, respectively. However, enormous 95% confidence intervals (4-520 and 2-336, respectively) imply that specifying any one number is futile. A cognitive limit on human group size cannot be derived in this manner.
Topics: Animals; Bayes Theorem; Biological Evolution; Phylogeny; Primates
PubMed: 33947220
DOI: 10.1098/rsbl.2021.0158 -
Trends in Plant Science Mar 2023Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics,... (Review)
Review
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
Topics: Biological Evolution; Plants; Phylogeny; Ecology; Genomics; Evolution, Molecular
PubMed: 36328872
DOI: 10.1016/j.tplants.2022.09.009 -
Current Biology : CB Jul 2020A groundbreaking study of brain evolution across birds and dinosaurs reveals potential drivers of increased brain size including biogeography and ecology. The most...
A groundbreaking study of brain evolution across birds and dinosaurs reveals potential drivers of increased brain size including biogeography and ecology. The most dramatic change occurred in the Neoaves after the Cretaceous-Paleogene extinction rather than earlier in bird evolution.
Topics: Animals; Biological Evolution; Birds; Brain; Dinosaurs; Fossils; Organ Size; Phylogeny
PubMed: 32634422
DOI: 10.1016/j.cub.2020.05.025