Abstract
Pedigrees illustrate the genealogical relationships among individuals, and phylogenies do the same for groups of organisms (such as species, genera, etc.). Here, I provide a brief survey of current concepts and methods for calculating and displaying genealogical relationships. These relationships have long been recognized to be reticulating, rather than strictly divergent, and so both pedigrees and phylogenies are correctly treated as networks rather than trees. However, currently most pedigrees are instead presented as “family trees”, and most phylogenies are presented as phylogenetic trees. Nevertheless, the historical development of concepts shows that networks pre-dated trees in most fields of biology, including the study of pedigrees, biology theory, and biology practice, as well as in historical linguistics in the social sciences. Trees were actually introduced in order to provide a simpler conceptual model for historical relationships, since trees are a specific type of simple network. Computationally, trees and networks are a part of graph theory, consisting of nodes connected by edges. In this mathematical context they differ solely in the absence or presence of reticulation nodes, respectively. There are two types of graphs that can be called phylogenetic networks: (1) rooted evolutionary networks, and (2) unrooted affinity networks. There are quite a few computational methods for unrooted networks, which have two main roles in phylogenetics: (a) they act as a generic form of multivariate data display; and (b) they are used specifically to represent haplotype networks. Evolutionary networks are more difficult to infer and analyse, as there is no mathematical algorithm for reconstructing unique historical events. There is thus currently no coherent analytical framework for computing such networks.
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Notes
There is no extant copy of this early biblical pedigree, although we do have two dozen complete or partial copies from the period 950–1250 CE. Jean-Baptiste Piggin has a reconstruction at his Macro-Typography website (http://www.piggin.net/stemmahistoryTOC.htm).
Illustrated in the Open Access paper by Ragan (2009).
Illustrated in the Open Access paper by Morrison (2014a).
Illustrated in the Open Access paper by Ragan (2009).
The original is almost unreadable, but Jean-Baptiste Piggin has digitized a readable copy at his Macro-Typography website (http://www.piggin.net/stemmahist/envelopeM29880.htm).
The original is almost unreadable, but Jean-Baptiste Piggin has digitized a readable copy at his Macro-Typography website (http://www.piggin.net/stemmahist/envelopelambert.htm).
Naudin explicitly rejected a network image (“a disordered tangle of intersecting lines”) as well as a chain (“a linear series”).
Both of these groups have extensive online pedigree databases, which are accessed as treemaps rather than networks.
References
Alexandre, F. (2014). Trees, waves and linkages: Models of language diversification. In C. Bowern & B. Evans (Eds.), Routledge handbook of historical linguistics (pp. 161–189). London: Routledge.
Archibald, J. D. (2014). Aristotle’s ladder, Darwin’s tree: The evolution of visual metaphors for biological order. New York: Columbia University Press.
Arvelakis, A., Reczko, M., Stamatakis, A., Symeonidis, A., & Tollis, I. G. (2005). Using treemaps to visualize phylogenetic trees. Lecture Notes in Computer Science, 3745, 283–293.
Atkinson, Q. D., & Gray, R. D. (2005). Curious parallels, curious connections—Phylogenetic thinking in biology and historical linguistics. Systematic Biology, 54, 513–526.
Auroux, S. (1990). Representation and the place of linguistic change before comparative grammar. In T. De Mauro & L. Formigari (Eds.), Leibniz, Humboldt, and the origins of comparativism (pp. 213–238). Amsterdam: John Bejamins.
Bapteste, E., van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., et al. (2013). Networks: expanding evolutionary thinking. Trends in Genetics, 29, 439–441.
Baroni, M., Semple, C., & Steel, M. (2006). Hybrids in real time. Systematic Biology, 55, 46–56.
Barsanti, G. (1988). Le immagini della natura: Scale, mappe, alberi 1700–1800. Nuncius, 3, 55–125.
Barsanti, G. (1992). La scala, la mappa, l’albero: Immagini e classificazioni della natura fra sei e ottocento. Firenze: Sansoni Editore.
Baum, D. A., & Smith, S. D. (2012). Tree thinking: An introduction to phylogenetic biology. Greenwood Village CO: Roberts and Co.
Benveniste, R. E., & Todaro, G. J. (1974). Evolution of C-type viral genes: Inheritance of exogenously acquired viral genes. Nature, 252, 456–459.
Bertrand, Y. J., Scheen, A. C., Marcussen, T., Pfeil, B. E., de Sousa, F., & Oxelman B. (2015). Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae). Systematic Biology, 64, 448–471.
Bokhari, S. H., & Janies, D. A. (2010). Reassortment networks for investigating the evolution of segmented viruses. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7, 288–298.
Brace, C. L. (1981). Tales of the phylogenetic woods: The evolution and significance of evolutionary trees. American Journal of Physical Anthropology, 56, 411–429.
Cavalli-Sforza, L. L., & Feldman, M. W. (1981). Cultural transmission and evolution. Princeton: Princeton University Press.
Cayley, A. (1857). On the theory of the analytical forms called trees. Philosophical Magazine, 13, 172–176.
Clark, C. A. (2001). Evolution for John Doe: Pictures, the public, and the Scopes trial debate. Journal of American History, 87, 1275–1303.
Dagan, T. (2011). Phylogenomic networks. Trends in Microbiology, 19, 483–491.
Darwin, C. (1859). On the origin of species by means of natural selection. London: John Murray.
Degnan, J. H., & Rosenberg, N. A. (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution, 24, 332–340.
Drinkwater, B., & Charleston, M. A. (2014). An improved node mapping algorithm for the cophylogeny reconstruction problem. Coevolution, 2, 1–17.
Estabrook, A. H., & Davenport, C. B. (1912). The Nam family: A study in cacogenics (p. 2). Cold Spring Harbor, NY: Eugenics Record Office Memoir No.
Fisler, M., & Lecointre, G. (2013). Categorizing ideas about trees: A tree of trees. PLoS ONE, 8, e68814.
Francis, A., & Steel, M. (2015). Which phylogenetic networks are merely trees with additional arcs? Systematic Biology, 64, 768–777.
García-Pereira, M. J., Carvajal-Rodríguez, A., Whelan, S., Caballero, A., & Quesada, H. (2014). Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers. Molecular Phylogenetics and Evolution, 76, 102–109.
Geisler, H., & List, J.-M. (2013). Do languages grow on trees? The tree metaphor in the history of linguistics. In H. Fangerau, H. Geisler, T. Halling, & W. Martin (Eds.), Classification and evolution in biology, linguistics and the history of science: Concepts, methods, visualization (pp. 111–124). Stuttgart: Franz Steiner Verlag.
Glaubrecht, M. (2012). Franz Hilgendorf’s dissertation “Beiträge zur Kenntnis des Süßwasserkalks von Steinheim” from 1863: Transcription and description of the first Darwinian interpretation of transmutation. Zoosystematics and Evolution, 88, 231–259.
Gontier, N. (2011). Depicting the tree of life: The philosophical and historical roots of evolutionary tree diagrams. Evolution: Education and Outreach, 4, 515–538.
Grant, V. (1953). The role of hybridization in the evolution of the leafy-stemmed gillias. Evolution, 7, 51–64.
Gusfield, D. (2014). Recombinatorics: The algorithmics of ancestral recombination graphs and explicit phylogenetic networks. Cambridge: MIT Press.
Hellström, N. P. (2011). The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History, 38, 1–17.
Hilgendorf, F. (1866). Planorbis multiformis im Steinheimer Süßwasserkalk: ein beispiel von gestaltveränderung im laufe der zeit. Berlin: Buchhandlung von W. Weber.
Holder, M. T., Anderson, J. A., & Holloway, A. K. (2001). Difficulties in detecting hybridization. Systematic Biology, 50, 978–982.
Holm, G. (1972). Carl Johan Schlyter and textual scholarship. Kungliga Gustav Adolfs Akademiens Årsbok, 1972, 48–80.
Howe, C. J., & Windram, H. F. (2011). Phylomemetics—Evolutionary analysis beyond the gene. PLoS Biology, 9, e1001069.
Huber, K. T., Oxelman, B., Lott, M., & Moulton, V. (2006). Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular Biology and Evolution, 23, 1784–1791.
Huson, D. H., Rupp, R., & Scornavacca, C. (2011). Phylogenetic networks: Concepts, algorithms and applications. Cambridge: Cambridge University Press.
Huson, D. H., & Scornavacca, C. (2011). A survey of combinatorial methods for phylogenetic networks. Genome Biology and Evolution, 3, 23–35.
Johnson, J., Roberts, T. L., Verplank, W., Smith, D. C., Irby, C., Beard, M., & Mackey, K. (1989). The Xerox “Star”: A retrospective. IEEE Computer, 22, 11–29.
Jones, G., Sagitov, S., & Oxelman, B. (2013). Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology, 62, 467–478.
Jones, D., & Sneath, P. H. (1970). Genetic transfer and bacterial taxonomy. Bacteriology Reviews, 34, 40–81.
Klapisch-Zuber, C. (1991). The genesis of the family tree. I Tatti Studies in the Italian Renaissance, 4, 105–129.
Klapisch-Zuber, C. (2000). L’Ombre des ancêtres: Essai sur l’imaginaire médiéval de la parenté. Paris: Fayard.
Kück, P., Misof, B., & Wägele, J.-W. (2014). Systematic errors in maximum-likelihood tree inference. In J.-W. Wägele & T. Bartolomaeus (Eds.), Deep Metazoan phylogeny: The backbone of the Tree of Life (pp. 563–583). Berlin: De Gruyter.
Kull, K. (2003). Ladder, tree, web: The ages of biological understanding. Sign Systems Studies, 31, 589–603.
Lanier, H. C., & Knowles, L. L. (2015). Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies. Molecular Phylogenetics and Evolution, 83, 191–199.
Lipson, M., Loh, P.-R., Levin, A., Reich, D., Patterson, N., & Berger, B. (2013). Efficient moment-based inference of population admixture parameters and sources of gene flow. Molecular Biology and Evolution, 30, 1788–1802.
List, J.-M., Nelson-Sathi, S., Geisler, H., & Martin, W. (2013). Networks of lexical borrowing and lateral gene transfer in language and genome evolution. BioEssays, 36, 141–150.
Marcussen, T., Heier, L., Brysting, A. K., Oxelman, B., & Jakobsen, K. S. (2015). From gene trees to a dated allopolyploid network: Insights from the angiosperm genus Viola (Violaceae). Systematic Biology, 64, 84–101.
Marcussen, T., Jakobsen, K. S., Danihelka, J., Ballard, H. E., Blaxland, K., Brysting, A. K., & Oxelman, B. (2012). Inferring species networks from gene trees in high-polyploid north American and Hawaiian violets (Viola, Violaceae). Systematic Biology, 61, 107–126.
Mardulyn, P. (2012). Trees and/or networks to display intraspecific DNA sequence variation? Molecular Ecology, 21, 3385–3390.
Martin, W. F. (2011). Early evolution without a tree of life. Biology Direct, 36, 6.
Mereschkowsky, C. (1910). Theorie der zwei Plasmaarten als Grundlage der Symbiogenese, einer neuen Lehre von der Entstehung der Organismen. Biologisches Centralblatt, 30, 278–303, 321–347, 353–367.
Minaka, N., & Sugiyama, K. (2012). Phylogeny mandala: Chain, tree, and network. Tokyo: NTT.
Mindell, D. P. (2013). The tree of life: Metaphor, model, and heuristic device. Systematic Biology, 62, 479–489.
Mivart, S. G. (1865). Contributions towards a more complete knowledge of the axial skeleton in the primates. Proceedings of the Zoological Society of London, 33, 545–592.
Moret, B. M. E., Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., et al. (2004). Phylogenetic networks: Modeling, reconstructibility, and accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 13–23.
Morrison, D. A. (2005). Networks in phylogenetic analysis: New tools for population biology. International Journal for Parasitology, 35, 567–582.
Morrison, D. A. (2011). Introduction to phylogenetic networks. Uppsala: RJR Productions.
Morrison, D. A. (2013a). [Book review of] “Tree thinking: An introduction to phylogenetic biology”. Systematic Biology, 62, 634–637.
Morrison, D. A. (2013b). Phylogenetic networks are fundamentally different from other kinds of biological networks. In W. J. Zhang (Ed.), Network biology: Theories, methods and applications (pp. 23–68). New York: Nova Science.
Morrison, D. A. (2014a). Phylogenetic networks: A review of methods to display evolutionary history. Annual Research and Review in Biology, 4, 1518–1543.
Morrison, D. A. (2014b). Is the tree of life the best metaphor, model or heuristic for phylogenetics? Systematic Biology, 63, 628–638.
Morrison, D. A. (2014c). Phylogenetic networks—A new form of multivariate data summary for data mining and exploratory data analysis. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 4, 296–312.
Morrison, D. A. (2015a). [Book review of] ‘The tree of life: Evolution and classification of living organisms’. Systematic Biology, 64, 546–548.
Morrison, D. A. (2015b). Pattern recognition in phylogenetics: Trees and networks. In M. Elloumi, C. S. Iliopoulos, J. T. L. Wang, & A. Y. Zomaya (Eds.), Pattern recognition in computational molecular biology: Techniques and approaches (pp. 417–436). New York: Wiley.
Müller, F. (1864). Für Darwin. Leipzig: Verlag von Wilhelm Engelman.
Nakhleh, L. (2013). Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution, 28, 719–728.
Naudin, C. (1852). Considérations philosophiques sur l’espèce et la variété. Revue Horticole, 1(4), 102–109.
O’Hara, R. J. (1992). Telling the tree: Narrative representation and the study of evolutionary history. Biology and Philosophy, 7, 135–160.
Patterson, N. J., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., et al. (2012). Ancient admixture in human history. Genetics, 192, 1065–1093.
Pax, F. A. (1888). Monographische übersicht über die arten der gattung Primula. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie, 10, 75–241.
Penny, D. (2011). Darwin’s theory of descent with modification, versus the biblical tree of life. PLoS Biology, 9, e1001096.
Pickrell, J. K., & Pritchard, J. K. (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics, 8, e1002967.
Pietsch, T. W. (2012). Trees of life: A visual history of evolution. Baltimore: Johns Hopkins University Press.
Piggin, J.-B. (2013). The great stemma: A Late Antique diagrammatic chronicle of pre-Christian time. Studia Patristica, 62, 259–278.
Platnick, N. I., & Cameron, H. D. (1977). Cladistic methods in textual, linguistic, and phylogenetic analysis. Systematic Zoology, 26, 380–385.
Popa, O., Hazkani-Covo, E., Landan, G., Martin, W., & Dagan, T. (2011). Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Research, 21, 599–609.
Posada, D., & Crandall, K. A. (2001). Intraspecific gene genealogies: Trees grafting into networks. Trends in Ecology & Evolution, 16, 37–45.
Priestly, T. M. S. (1975). Schleicher, Éelakovsk˝, and the family-tree diagram: A puzzle in the history of linguistics. Historiographica Linguistica, 2, 299–333.
Ragan, M. (2009). Trees and networks before and after Darwin. Biology Direct, 4, 43.
Reif, W.-E. (1983). Hilgendorf’s (1863) dissertation on the Steinheim planorbids (Gastropoda; Miocene): The development of a phylogenetic research program for paleontology. Paläontologische Zeitschrift, 57, 7–20.
Rieppel, O. (2010). The series, the network and the tree: Changing metaphors of order in nature. Biology and Philosophy, 25, 475–496.
Ritschl, F. (1832). Thomae Magistri sive theoduli monachi ecloga vocum Atticarum. Halle: Orphanotrophei.
Salzburger, W., Ewing, G. B., & von Haeseler, A. (2011). The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Molecular Ecology, 20, 1952–1963.
Sang, T., & Zhong, Y. (2000). Testing hybridization hypotheses based on incongruent gene trees. Systematic Biology, 49, 422–434.
Schleicher, A. (1853). Die ersten Spaltungen des Indogermanischen Urvolkes. Allgemeine Monatsschrift für Wissenschaft und Literatur, 1853, 786–787.
Schmidt, J. (1872). Die werwandtschaftsverhältnisse de indogermanischen sprachen. Weimar: Hermann Böhlau.
Simmons, M. P., & Gatesy, J. (2015). Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Molecular Phylogenetics and Evolution, 91, 98–122.
Southworth, F. C. (1964). Family-tree diagrams. Language, 40, 557–565.
Springer, M. S. & Gatesy, J. (2016). The gene tree delusion. Molecular Phylogenetics and Evolution, 94, 1–33.
Stevens, P. F. (1984). Metaphors and typology in the development of botanical systematics 1690–1960, or the art of putting new wine in old bottles. Taxon, 33, 169–211.
Stevens, P. F. (1994). The development of biological systematics: Antoine-Laurent de Jussieu, nature, and the natural system. New York: Columbia University Press.
Sutrop, U. (2000). From the ‘Language Family Tree’ to the ‘Tangled Web of Languages’. In: A. Nurk, T. Palo & T. Seilenthal (Eds.), Congressus nonus internationales Fenno-Ugristarum 7–13.8.2000. Part I: orationes plenariae & orationes publicae (pp. 197–219). Tartu, Estonia: Eesti Fennougristide Komitee.
Sutrop, U. (2012). Estonian traces in the tree of life concept and in the language family tree theory. Journal of Estonian and Finno-Ugric Linguistics, 3, 297–326.
Szöllösi, G. J., Tannier, E., Daubin, V., & Boussau, B. (2015). The inference of gene trees with species trees. Systematic Biology, 64, e42–e62.
Tassy, P. (1991). L’arbre à remonter le temps. Paris: Christian Bourgois Éditeur.
Tassy, P. (2011). Trees before and after Darwin. Journal of Zoological Systematics and Evolutionary Research, 49, 89–101.
Wallace, A. R. (1855). On the law which has regulated the introduction of new species. Annals and Magazine of Natural History, 16(2), 184–196.
Xi, Z., Liu, L., & Davis, C. C. (2015). Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Molecular Phylogenetics and Evolution, 92, 63–71.
Yu, Y., Barnett, R. M., & Nakhleh, L. (2013a). Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology, 62, 738–751.
Yu, Y., Degnan, J. H., & Nakhleh, L. (2012). The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics, 8, e1002660.
Yu, Y., Dong, J., Liu, K. J., & Nakhleh, L. (2014). Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences of the USA, 111, 16448–16453.
Yu, Y., Ristic, N., & Nakhleh, L. (2013b). Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinformatics, 14, S6.
Yu, Y., Than, C., Degnan, J. H., & Nakhleh, L. (2011). Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology, 60, 138–149.
Yutin, N., Raoult, D., & Koonin, E. V. (2013). Virophages, polintons, and transpovirons: A complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virology Journal, 10, 158.
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Thanks to Akademikernas A-kassa and Trygghetsstiftelsen for funding, and to Luay Nakhleh and an anonymous referee for comments.
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Morrison, D.A. Genealogies: Pedigrees and Phylogenies are Reticulating Networks Not Just Divergent Trees. Evol Biol 43, 456–473 (2016). https://doi.org/10.1007/s11692-016-9376-5
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DOI: https://doi.org/10.1007/s11692-016-9376-5