Median-joining networks for inferring intraspecific phylogenies.
TL;DR: A method for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that the MJ method does not resolve ties.
Abstract: Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
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TL;DR: The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help understanding of how organisms were so affected.
Abstract: Global climate has fluctuated greatly during the past three million years, leading to the recent major ice ages. An inescapable consequence for most living organisms is great changes in their distribution, which are expressed differently in boreal, temperate and tropical zones. Such range changes can be expected to have genetic consequences, and the advent of DNA technology provides most suitable markers to examine these. Several good data sets are now available, which provide tests of expectations, insights into species colonization and unexpected genetic subdivision and mixture of species. The genetic structure of human populations may be viewed in the same context. The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help our understanding of how organisms were so affected.
6,341 citations
TL;DR: Popart is presented, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production.
Abstract: Summary
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level.
Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production.
popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining.
The software is open source and freely available for all major operating systems.
3,634 citations
17 Sep 2002
TL;DR: Neighbor-Net is presented, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei and can quickly produce detailed and informative networks for several hundred taxa.
Abstract: We introduce NeighborNet, a network construction and data representation method that combines aspects of the neighbor joining (NJ) and SplitsTree. Like NJ, NeighborNet uses agglomeration: taxa are combined into progressively larger and larger overlapping clusters. Like SPLITSTREE, NeighborNet constructs networks rather than trees, and so can be used to represent multiple phylogenetic hypotheses simultaneously, or to detect complex evolutionary processes like recombination, lateral transfer and hybridization. NeighborNet tends to produce networks that are substantially more resolved than those made with SPLITSTREE. The method is efficient (O(n3) time) and is well suited for the preliminary analyses of complex phylogenetic data. We report results of three case studies: one based on mitochondrial gene order data from early branching eukaryotes, another based on nuclear sequence data from New Zealand alpine buttercups (Ranunculi), and a third on poorly corrected synthetic data.
1,846 citations
Cites methods from "Median-joining networks for inferri..."
...The bestknown network methods in this class are statistical parsimony (Templeton, Crandall, and Sing 1992), median networks (Bandelt et al. 1995), the variants of median networks (Bandelt, Forster, and Röhl 1999; Huber et al. 2001, 2002), and the netting method (Fitch 1997)....
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TL;DR: Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account population-level phenomena.
Abstract: Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena.
1,495 citations
TL;DR: A genotype-phenotype association study in Tanzanians, Kenyans and Sudanese and identified three SNPs that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro, providing a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits.
Abstract: A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470
1,345 citations
References
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01 Feb 1956
TL;DR: Kurosh and Levitzki as discussed by the authors, on the radical of a general ring and three problems concerning nil rings, Bull Amer Math Soc vol 49 (1943) pp 913-919 10 -, On the structure of algebraic algebras and related rings.
Abstract: 7 A Kurosh, Ringtheoretische Probleme die mit dem Burnsideschen Problem uber periodische Gruppen in Zussammenhang stehen, Bull Acad Sei URSS, Ser Math vol 5 (1941) pp 233-240 8 J Levitzki, On the radical of a general ring, Bull Amer Math Soc vol 49 (1943) pp 462^66 9 -, On three problems concerning nil rings, Bull Amer Math Soc vol 49 (1943) pp 913-919 10 -, On the structure of algebraic algebras and related rings, Trans Amer Math Soc vol 74 (1953) pp 384-409
5,104 citations
TL;DR: In this paper, the basic problem of interconnecting a given set of terminals with a shortest possible network of direct links is considered, and a set of simple and practical procedures are given for solving this problem both graphically and computationally.
Abstract: The basic problem considered is that of interconnecting a given set of terminals with a shortest possible network of direct links Simple and practical procedures are given for solving this problem both graphically and computationally It develops that these procedures also provide solutions for a much broader class of problems, containing other examples of practical interest
4,395 citations
TL;DR: The concept of a Wagner Network is formalized and a number of algorithms for calculating such networks are discussed and the rationale for the methods described is discussed.
Abstract: Farris, J. S. (Biol. Sci., State Univ., Stony Brook, N. Y.) 1970. Methods for computing Wagner Trees. Syst. Zool., 19:8342.-The article derives some properties of Wagner Trees and Networks and describes computational procedures for Prim Networks, the Wagner Method, Rootless Wagner Method and optimization of hypothetical intermediates ( HTUs). The Wagner Ground Plan Analysis method for estimating evolutionary trees has been widely employed in botanical studies (see references in Wagner, 1961) and has more recently been employed in zoological evolutionary taxonomy (Kluge, 1966; Kluge and Farris, 1969). Wagner Trees are one possible generalization of the most parsimonious trees of Camin and Sokal (1965). The Wagner technique is of con-siderable interest for quantitative evolution- ary taxonomists because it is readily pro- grammable and because the type of tree produced can tractably be extended to ap- plications in a variety of novel quantitative phyletic techniques. In this paper I shall formalize the concept of a Wagner Network and discuss a number of algorithms for calculating such networks. The rationale for the methods described will not be treated extensively here, as it is published elsewhere (Kluge and Farris, 1969).
1,369 citations
TL;DR: A novel network approach for portraying mtDNA relationships is proposed that reduces the complexity of the network by identifying parallelisms and is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes.
Abstract: Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.
1,092 citations
TL;DR: The conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations, is supported.
Abstract: Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations
904 citations