Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

Agglomerative algorithms iteratively pick a pair of taxa, create a new node that represents the cluster of these taxa, and compute a new distance matrix with reduced size where both taxa are replaced by this node. The cycle is repeated until the number of taxa becomes three (or two for rooted trees). This general scheme was first applied to additive unrooted trees by Sattath and Tversky (ADDTREE method; 1977) in the context of mathematical psychology. The neighbor-joining (NJ) method of Saitou and Nei ( 1987) widely popularized this approach in the phylogenetic study. This method is based on the minimum evolution principle and provides trees with near-minimal sum of branch-length estimates. An alternative formulation of the NJ method with reduced computational complexity was given by Studier and Keppler (SK method; 1988), while Rzhetsky and Nei ( 1992, 1993) clarified the theoretical foundation of the minimum evolution principle. Several simulations (Saitou and Nei 1987; Nei 199 1) have shown a high relative efficiency of ADDTREE and of the NJ method in recovering the true topology. These studies have also shown that ADDTREE and the NJ method, whose principles seem very different, are in fact close and usually provide identical or similar trees. For example, they obtain the same tree with Case’s ( 1978) data. The explanation for this proximity was given by Saitou and Nei ( 1987) for four taxa. In this note, we account for this proximity regardless of the number of taxa, and we show that the minimum evolution principle, as employed in the NJ method, is very close to the neighborliness used by Sattath and Tversky ( 1977) and by Fitch ( 198 1) in a nonagglomerative way. In the following, we recall the principles of the ADDTREE, NJ, and SK methods and explain why they are so close. We will only be concerned with the construction of the tree shape, and not with branch-lengths estimation. For the latter aspect, we refer the reader to the original papers and to

Many popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is {mathbf {N}}{mathbf {P}}-hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although ranked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to {mathbf {N}}{mathbf {P}}-hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

Recombination is an important driving force in evolution. To investigate this evolutionary process in Prune dwarf virus (PDV), 31 accessions retrieved from international databases, supplemented by one Tunisian isolate described here, were analyzed. Two recombination detection programs were used: RDP v3.31β and RECCO. While the first program did not detect any significant recombination events, RECCO detected several breakpoints in partial sequences of the coat protein gene (CP) of fifteen isolates. The Tajima neutrality test implemented in the MEGA4.1β program indicated that there were numerous deletion/insertion events in the sequences. The strongest signal was found in Portuguese isolate 3.12N.14 (accession number AY646846) which had position nt 296–523 in the CP gene. The evolutionary historical relationships between all analyzed isolates were determined by constructing a dendrogram using Neighbor joining (NJ), Minimum evolution (ME), Maximum parsimony (MP), Maximum likelihood (ML), and the Unweighted pair group method with arithmetic mean (UPGMA); all gave similar results. Two main clusters were delineated, one representing recombinant and one nonrecombinant isolates. The recombinant isolates were mostly collected from Portugal, whereas the nonrecombinant isolates originated in eastern Europe.

The phylogeny reconstruction problem is a fundamental problem in computational molecular biology and biochemical physics. Since the number of data sets has grown substantially in recent years, the accuracy and speed of constructing phylogenies become increasingly critical. Numerous studies have demonstrated that the maximum likelihood (ML) method is the most effective method for reconstructing a phylogenetic tree from sequence data. Conversely, tree bisection and reconnection (TBR) is a tree topology rearrangement method that can generate an extensive tree space. In this paper, we propose an enhanced method for reconstructing phylogenetic trees in which the TBR operation is modified and combined with the minimum evolution principle to filter out some unnecessary reconnected positions to reduce the search time. The experiment results demonstrate that the proposed method can assist other algorithms in constructing more accurate trees within a reasonable time.

Molecular phylogeny in Indian Citrus L. (Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA

Sequences of the mitochondrial cytochrome oxidase I (COI) gene of one Greek and 25 Turkish Myzus cerasi (Fabricus) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus were analyzed. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions and the mean of intraspecific divergence was calculated to be 0.3%. Phylogenetic trees were constructed using maximum likelihood, neighbor joining, and minimum evolution. Myzus persicae (Sulzer) and Myzus borealis Ossiannilson were included as outgroups. The population of M. cerasi from Isparta diverged from the rest of the groups and formed a clade (Haplotype B) with Myzus borealis. The rest of the haplotype diversity included Haplotype A and Haplotype C with individuals characterized as Myzus cerasi pruniavium and Haplotype D with Myzus cerasi cerasi. M. cerasi diverged into two subspecies and it must be reevaluated whether this pest is monophagous or oligophagous in terms of plant type dependence. Further studies will be required for a complete barcoding and host-specific status of black cherry aphid.

Heuristics for unrooted, unranked, and ranked anomaly zones under birth-death models

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the neighborhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighborhood of a tree have been well-studied; however, little is known about the number of trees at distance two, three, or (more generally) $k$ from a given tree. In this paper we provide a number of exact and asymptotic results concerning these quantities and identify some key aspects of tree shape that play a role in determining these quantities. We obtain several new results for two of the main tree rearrangement operations---nearest neighbor interchange and subtree prune and regraft---as well as for the Robinson--Foulds metric on trees.

Since 2020, the SARS-CoV-2 virus has infected billions of people and spread to 185 countries. The virus spreads by making new copies of its genome inside human cells and exploits the cells’ machinery to synthesise viral proteins it needs to infect further cells. Each time the virus copies its genetic material there’s a chance that the replication process introduces an error to the genetic sequence. Over time, these mutations accumulate which can give rise to new variants with different properties. These new variants, originating from a common ancestor, may spread faster or be able to evade immune systems that have learnt to recognise previous variants. To understand where new variants of SARS-CoV-2 come from and how related they are to each other, scientists build family trees called ‘phylogenetic trees’ based on similarities in the genetic sequences of different variants of the virus. Looking at these trees researchers can track how a variant spreads geographically, and also attempt to identify new worrying variants that might lead to a new wave of infections. The scale of the COVID-19 pandemic together with the global effort by clinicians and researchers to sequence SARS-CoV-2 genetic material means a library of over 13 million SARS-CoV-2 genomes now exists, making it the largest such collection for any organism. Although phylogenetic trees of viruses have been studied for a long time, exploring the SARS-CoV-2 library presents technical and practical challenges due to its sheer size. Sanderson has developed an open-source web tool called Taxonium that allows users to explore phylogenetic trees with millions of sequences. With help from collaborators at the University of California, Santa Cruz, Sanderson built a website called Cov2Tree, that uses the Taxonium platform to allow immediate access to an expansive tree of all publicly available SARS-CoV-2 sequences. Cov2Tree enables users to visualise all SARS-CoV-2 genomes in a birds-eye view akin to a ‘Google Earth for virus sequences’ where anyone can zoom in on a related family of viruses down to the level of individual sequences. This can be used to compare variants and follow geographic spread. Using Taxonium, scientists can explore how virus sequences are related to each other. They can also see the individual mutations that have occurred at each branch of the tree, and can search for sequences based on mutation, geographical location, or other factors. Interestingly, a trend appearing in the SARS-CoV-2 phylogenetic tree is the emergence of identical mutations at different branches of the tree without a common origin. These mutations may be a result of convergent evolution, a phenomenon that occurs when a mutation appears independently in different variants as it confers an advantage to the virus making such mutations more likely to persist. This means that scientists may be able to expect certain mutations to appear in more distantly related variants if they have appeared independently in several different variants already. Overall, Taxonium is an important tool for monitoring SARS-CoV-2 genomes, but it also has broader applications. The tool can be used to browse phylogenetic trees of other viruses and organisms. Furthermore, the Taxonium website offers a way to browse a tree of life, with images and links to Wikipedia. The SARS-CoV-2 library might be the largest now, but in the future even bigger datasets will likely be available, highlighting the importance of tools like Taxonium.

A note on the relaxation time of two Markov chains on rooted phylogenetic tree spaces

In this article, we review (1) statistical tests of DNA phylogenies inferred by the maximum- parsimony method, including tests that take into account the effect of different base compositions among lineages, (2) statistical tests based on the minimum-evolution criterion, i.e., the best tree is the tree with the smallest sum of branch-length estimates, and (3) the bootstrap technique for estimating the confidence level of a phylogenetic hypothesis based on either the maximum-parsimony or the neighbor-joining method. We explain why the bootstrap technique usually gives biased estimates and how to correct the bias. (DNA phylogenies; parsimony; neighbor joining; minimum evolution; statis? tical tests; bootstrap; bias correction.)

The systematics and phylogeny of flatfish is investigated on the basis of an incomplete nucleotide sequence of 16S rRNA and the complete Co-1 and Cyt-b sequences. In total 62 specimens of 14 species of our own collections were submitted to the GenBank/BOLD repositories and studied. Four types of gene trees were reconstructed: Bayesian (BA), maximum likelihood (ML), minimum evolution (ME), and neighbor joining (NJ). These trees showed basically similar topology. Two separate branches on the trees support the previously identified subfamilies Hippoglossoidinae and Pleuronectinae with the monophyletic status of these taxa. The subfamily Pleuronectinae can be considered monophyletic if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Three sets of nucleotide sequences were formed and independently studied. One set included all the obtained 16S rRNA gene sequences (291 bp), the second set included a sample of longer 16S rRNA sequences (617 bp), and the third set consisted of three gene sequences: 16S rRNA, Co-1, and Cyt-b (2926 bp). All three data sets gave a similar phylogenetic signal, which is consistent with the traditional concept of the taxonomy of the Pleuronectiformes order; however, the second and third sets provided better resolution of topology.

Nuclear DNA is widely used to estimate phylogenetic and phylogeographic relationships. Nuclear gene variants may be present in an individual's genome, and these result in Intra-Individual Site Polymorphisms (2ISP; pronounced "twisp") in direct-PCR or individual-consensus sequences based on a sample of clones or fragment sequences from next generation sequencing (NGS). 2ISPs can occur fairly often, especially within, but not restricted to, high-copy-number regions such as the widely used internal transcribed spacers of the nuclear ribosomal cistron. Dealing with 2ISPs has been problematic as phylogeny reconstruction optimality criteria generally do not take account of this variation. Here we test whether an approach that treats 2ISPs as additional (termed "informative"), rather than ambiguous, characters offers improved support in three common criteria used for phylogenetic inference: Minimum Evolution (via Neighbour Joining), Maximum Parsimony, and Maximum Likelihood. We demonstrate significant improvements using the 2ISP-informative treatment with simulated, real-world, and case-study data sets. We envisage that this 2ISP-informative approach will greatly aid phylogenetic inference using any nuclear DNA regions that contain polymorphisms within individuals (including consensus sequences generated from NGS), especially at the intrageneric or intraspecific level.

The current study is the first phylogenetic and secondary RNA structure analysis of Dactylogyrus species parasitising gill filaments of Iraqi cyprinid fishes. Most previous phylogenetic studies have targeted on primary DNA sequence data. Nevertheless, RNA secondary configuration is principally helpful in systematics since they comprise features that do not appear in the primary sequence and provide morphological information. The primary objective was molecular-based identification of Dactylogyrids species using evolutionary tree and secondary RNA structure prediction. A total of 681 fish were collected from the Lesser Zab River in the northeast of Iraq in the sub-district of Altun-Kopru from August 2016 to September 2017 and brought to the Zoology Research Laboratory, Salahaddin University-Erbil, Iraq. All fish were classified as 18 cyprinid species. The species of Dactylogyrus were identified by the 28S rDNA subunit using PCR and sequencing methods, and the obtained nucleotide sequences were then compared with the available GenBank sequences. Phylogenetic relationships were concluded using Neighbour-Joining (NJ), Maximum Likelihood (ML), and Minimum Evolution (ME) methods. The results justify the validation of 11 Dactylogyrus species (three of them were newly recorded in Iraq). Additionally, out of nine infected fish species, seven of them were regarded as a new host for Dactylogyrus species. Secondary RNA configuration prediction using minimum free energy was considered as a hopeful tool for species identification. This was considered the first comprehensive phylogenetic study in the area. It was concluded that PCR sequencing, phylogenetic and secondary RNA analysis were proper molecular methods for identifying Dactylogyrids species on the gills of fishes.

Short phylogenetic distances between taxa occur, for example, in studies on ribosomal RNA-genes with slow substitution rates. For consistently short distances, it is proved that in the completely singular limit of the covariance matrix ordinary least squares (OLS) estimates are minimum variance or best linear unbiased (BLU) estimates of phylogenetic tree branch lengths. Although OLS estimates are in this situation equal to generalized least squares (GLS) estimates, the GLS chi-square likelihood ratio test will be inapplicable as it is associated with zero degrees of freedom. Consequently, an OLS normal distribution test or an analogous bootstrap approach will provide optimal branch length tests of significance for consistently short phylogenetic distances. As the asymptotic covariances between branch lengths will be equal to zero, it follows that the product rule can be used in tree evaluation to calculate an approximate simultaneous confidence probability that all interior branches are positive.