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In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.
A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.
Panarthropoda is a proposed animal clade containing the extant phyla Arthropoda, Tardigrada and Onychophora. Panarthropods also include extinct marine legged worms known as lobopodians ("Lobopodia"), a paraphyletic group where the last common ancestor and basal members (stem-group) of each extant panarthropod phylum are thought to have risen. However the term "Lobopodia" is sometimes expanded to include tardigrades and onychophorans as well.
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in the context of, for example, phenotypic evolution or population genetics.
Robin Ian MacDonald Dunbar is a British biological anthropologist, evolutionary psychologist, and specialist in primate behaviour. Dunbar is professor emeritus of evolutionary psychology of the Social and Evolutionary Neuroscience Research Group in the Department of Experimental Psychology at the University of Oxford. He is best known for formulating Dunbar's number, a measurement of the "cognitive limit to the number of individuals with whom any one person can maintain stable relationships".
Richard Walter Wrangham is an English anthropologist and primatologist; he is Professor of Biological Anthropology at Harvard University. His research and writing have involved ape behavior, human evolution, violence, and cooking.
Dual inheritance theory (DIT), also known as gene–culture coevolution or biocultural evolution, was developed in the 1960s through early 1980s to explain how human behavior is a product of two different and interacting evolutionary processes: genetic evolution and cultural evolution. Genes and culture continually interact in a feedback loop: changes in genes can lead to changes in culture which can then influence genetic selection, and vice versa. One of the theory's central claims is that culture evolves partly through a Darwinian selection process, which dual inheritance theorists often describe by analogy to genetic evolution.
Ancestral reconstruction is the extrapolation back in time from measured characteristics of individuals, populations, or specie to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence, the amino acid sequence of a protein, the composition of a genome, a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species. This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the evolutionary history of the species in the tree. Since modern genetic sequences are essentially a variation of ancient ones, access to ancient sequences may identify other variations and organisms which could have arisen from those sequences. In addition to genetic sequences, one might attempt to track the changing of one character trait to another, such as fins turning to legs.
Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent. This realization inspired the development of explicitly phylogenetic comparative methods. Initially, these methods were primarily developed to control for phylogenetic history when testing for adaptation; however, in recent years the use of the term has broadened to include any use of phylogenies in statistical tests. Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.
Paul H. Harvey is a British evolutionary biologist. He is Professor of Zoology and was head of the zoology department at the University of Oxford from 1998 to 2011 and Secretary of the Zoological Society of London from 2000 to 2011, holding these posts in conjunction with a professorial fellowship at Jesus College, Oxford.
Quantitative comparative linguistics is the use of quantitative analysis as applied to comparative linguistics. Examples include the statistical fields of lexicostatistics and glottochronology, and the borrowing of phylogenetics from biology.
Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.
The term phylogenetic niche conservatism has seen increasing use in recent years in the scientific literature, though the exact definition has been a matter of some contention. Fundamentally, phylogenetic niche conservatism refers to the tendency of species to retain their ancestral traits. When defined as such, phylogenetic niche conservatism is therefore nearly synonymous with phylogenetic signal. The point of contention is whether or not "conservatism" refers simply to the tendency of species to resemble their ancestors, or implies that "closely related species are more similar than expected based on phylogenetic relationships". If the latter interpretation is employed, then phylogenetic niche conservatism can be seen as an extreme case of phylogenetic signal, and implies that the processes which prevent divergence are in operation in the lineage under consideration. Despite efforts by Jonathan Losos to end this habit, however, the former interpretation appears to frequently motivate scientific research. In this case, phylogenetic niche conservatism might best be considered a form of phylogenetic signal reserved for traits with broad-scale ecological ramifications. Thus, phylogenetic niche conservatism is usually invoked with regards to closely related species occurring in similar environments.
The phylogenetic split of Hominidae into the subfamilies Homininae and Ponginae is dated to the middle Miocene, roughly 18 to 14 million years ago. This split is also referenced as the "orangutan–human last common ancestor" by Jeffrey H. Schwartz, professor of anthropology at the University of Pittsburgh School of Arts and Sciences, and John Grehan, director of science at the Buffalo Museum.
There are two main approaches currently used to analyze archaeological remains from an evolutionary perspective: evolutionary archaeology and behavioral ecology. The former assumes that cultural change observed in the archaeological record can be best explained by the direct action of natural selection and other Darwinian processes on heritable variation in artifacts and behavior. The latter assumes that cultural and behavioral change results from phenotypic adaptations to varying social and ecological environments.
Ruth Mace FBA is a British anthropologist, biologist, and academic. She specialises in the evolutionary ecology of human demography and life history, and phylogenetic approaches to culture and language evolution. Since 2004, she has been Professor of Evolutionary Anthropology at University College London.
Laura Fortunato is an evolutionary anthropologist whose research investigates the evolution of human social and cultural behavior. She investigates topics such as the evolution of kinship and marriage systems, social complexity and culture.
Phylogenetic signal is an evolutionary and ecological term, that describes the tendency or the pattern of related biological species to resemble each other more than any other species that is randomly picked from the same phylogenetic tree.
References
- 1 2 3 4 5 6 "PAGEL, Prof. Mark". Who's Who 2014, A & C Black, an imprint of Bloomsbury Publishing plc, 2014; online edn, Oxford University Press.(subscription required)
- ↑ Staff Profile: Professor Mark Pagel School of Biological Sciences, University of Reading. 24 August 2012. Retrieved 25 August 2012. Archived here Archived 3 February 2014 at the Wayback Machine
- ↑ Mark Pagel's publications indexed by the Scopus bibliographic database. (subscription required)
- ↑ Reading Evolutionary Biology Group – Home. Archived here. Archived 11 November 2017 at the Wayback Machine
- ↑ Pagel, Mark (2014). Determinants of the Success and Failure of Ridge Regression (PhD thesis). University of Washington. ProQuest 303081403.
- ↑ Smith, Kerri (26 June 2014). "Love in the lab: Close collaborators". Nature. 160 (510): 458–460. Bibcode:2014Natur.510..458S. doi: 10.1038/510458a . PMID 24965634.
- ↑ English language 'originated in Turkey' by Jonathan Ball, BBC News, 25 August 2012. Retrieved 25 August 2012.
- ↑ Pagel, M. (1999). "Inferring the historical patterns of biological evolution". Nature. 401 (6756): 877–84. Bibcode:1999Natur.401..877P. doi:10.1038/44766. hdl: 2027.42/148253 . PMID 10553904. S2CID 205034365.
- ↑ Freckleton, R. P.; Harvey, P. H.; Pagel, M. (2002). "Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence". The American Naturalist. 160 (6): 712–26. doi:10.1086/343873. PMID 18707460. S2CID 19796539.
- ↑ Pagel, M. (1997). "Inferring evolutionary processes from phylogenies". Zoologica Scripta. 26 (4): 331–348. doi:10.1111/j.1463-6409.1997.tb00423.x. S2CID 53486234.
- ↑ Pagel, M.; Meade, A.; Barker, D. (2004). "Bayesian Estimation of Ancestral Character States on Phylogenies". Systematic Biology. 53 (5): 673–84. doi: 10.1080/10635150490522232 . PMID 15545248.
- 1 2 Mace, Ruth; Pagel, Mark (1994). "The Comparative Method in Anthropology". Current Anthropology. 35 (5): 549. doi:10.1086/204317. S2CID 146297584.
- ↑ Mark Pagel at TED
- ↑ Encyclopedia of Evolution. Vol. 2 volume set. USA: OUP. 2002. ISBN 978-0-19-512200-8 . Retrieved 24 March 2013.
- ↑ Wired for Culture: The Natural History of Human Cooperation ISBN 1846140153
- ↑ Julian Baggini (23 February 2012). "Wired for Culture by Mark Pagel – review". The Guardian . Retrieved 24 July 2012.
- 1 2 Professor Mark Pagel FRS, The Royal Society of London for Improving Natural Knowledge
- ↑ "The Glasgow Gifford Lectures". gla.ac.uk. University of Glasgow.
- ↑ Smith, K. (2014). "Love in the lab: Close collaborators". Nature. 510 (7506): 458–460. Bibcode:2014Natur.510..458S. doi: 10.1038/510458a . PMID 24965634.
