Median-joining networks for inferring intraspecific phylogenies

Bandelt, H. J.; Forster, P.; Rohl, A.

doi:10.1093/oxfordjournals.molbev.a026036

Cited by 11,742Genomics and Phylogenetic StudiesGenetic diversity and population structureForensic and Genetic Research

Median-joining networks for inferring intraspecific phylogenies

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Bandelt, H. J., Forster, P., Rohl, A.·1999·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a026036

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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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Haplogroup H1 contains the majority of the Southwest samples, and its haplotypes are closely related (although not identical) to those occurring in present-day Eastern (M. g. silvestris), Rio Grande (M. g. intermedia), and Florida (M. g. osceola) wild turkey populations that currently occur outside the Southwest.
“Haplogroup H1 contains the majority of the Southwest samples, and its haplotypes are closely related (although not identical) to those occurring in present-day Eastern (M. g. silvestris), Rio Grande (M. g. intermedia), and Florida (M. g. osceola) wild turkey populations that currently occur outside the Southwest (Fig. 4 and Fig. S1) (15, 16).”
From Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication (2010) · cites this paper as [16]
Even 'relic' populations of wild turkeys, with no history of extirpation or human-mediated reintroductions, show limited phylogeographic subspecies patterning.
“However, even “relic” populations of wild turkeys, with no history of extirpation or human-mediated reintroductions, show limited phylogeographic subspecies patterning (15, 16), which may also reflect a postglacial colonization into a relatively continuous habitat, especially for the Eastern and Rio Grande subspecies (15).”
From Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication (2010) · cites this paper as [16]

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Median-Joining Networks
(2008) · Springer eBooks · doi:10.1007/978-1-4020-6754-9_10040
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Authors: Bandelt, H. J., Forster, P., & Rohl, A.
Affiliations: Universität Hamburg (DE)
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 1999-01-01
Volume: 16
Issue: 1
Pages: 37-48
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a026036
OpenAlex: W2096420865
Cited by: 11,742
References: 14
Citations by year: 2026: 408 · 2025: 515 · 2024: 600 · 2023: 660 · 2022: 738 · 2021: 799 · 2020: 794 · 2019: 675 · 2018: 664 · 2017: 690 · 2016: 691 · 2015: 662 · 2014: 623 · 2013: 593 · 2012: 514
FWCI: 9.76
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords: median-joining network, intraspecific phylogeny, phylogenetic networks, maximum parsimony, homoplasy, multistate characters, mitochondrial DNA, Kruskal's algorithm
MeSH terms: Algorithms, DNA, Mitochondrial, Humans, Models, Genetic, Phylogeny, Genome, Human

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Median-joining networks for inferring intraspecific phylogenies

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