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Minimum Evolution (minimum + evolution)

Distribution by Scientific Domains

Life Sciences	83%

Selected Abstracts

Molecular phylogeny of Diabrotica beetles (Coleoptera: Chrysomelidae) inferred from analysis of combined mitochondrial and nuclear DNA sequences

INSECT MOLECULAR BIOLOGY, Issue 4 2001
T. L. Clark
Abstract The phylogenetic relationships of thirteen Diabrotica (representing virgifera and fucata species groups) and two outgroup Acalymma beetle species (Coleoptera: Chrysomelidae) were inferred from the phylogenetic analysis of a combined data set of 1323 bp of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and the entire second internal transcribed spacer region (ITS-2) of nuclear ribosomal DNA of 362 characters. Species investigated were D. adelpha, D. balteata, D. barberi, D. cristata, D. lemniscata, D. longicornis, D. porracea, D. speciosa, D. undecimpunctata howardi, D. u. undecimpunctata, D. virgifera virgifera, D. v. zeae, D. viridula, and outgroup A. blandulum and A. vittatum. Maximum parsimony (MP), minimum evolution (ME), and maximum likelihood (ML) analyses of combined COI and ITS-2 sequences clearly place species into their traditional morphological species groups with MP and ME analyses resulting in identical topologies. Results generally confer with a prior work based on allozyme data, but within the virgifera species group, D. barberi and D. longicornis strongly resolve as sister taxa as well as monophyletic with the neotropical species, D. viridula, D. cristata and D. lemniscata also resolve as sister taxa. Both relationships are not in congruence with the prior allozyme-based hypothesis. Within the fucata species group, D. speciosa and D. balteata resolve as sister taxa. Results also strongly supported the D. virgifera and D. undecimpunctata subspecies complexes. Our proposed phylogeny provides some insight into current hypotheses regarding distribution status and evolution of various life history traits for Diabrotica. [source]

New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov.

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2009
R. Guidetti
Abstract Up to few years ago, the phylogenies of tardigrade taxa have been investigated using morphological data, but relationships within and between many taxa are still unresolved. Our aim has been to verify those relationships adding molecular analysis to morphological analysis, using nearly complete 18S ribosomal DNA gene sequences (five new) of 19 species, as well as cytochrome oxidase subunit 1 (COI) mitochondrial DNA gene sequences (15 new) from 20 species, from a total of seven families. The 18S rDNA tree was calculated by minimum evolution, maximum parsimony (MP) and maximum likelihood (ML) analyses. DNA sequences coding for COI were translated to amino acid sequences and a tree was also calculated by neighbour-joining, MP and ML analyses. For both trees (18S rDNA and COI) posterior probabilities were calculated by MrBayes. Prominent findings are as follows: the molecular data on Echiniscidae (Heterotardigrada) are in line with the phylogenetic relationships identifiable by morphological analysis. Among Eutardigrada, orders Apochela and Parachela are confirmed as sister groups. Ramazzottius (Hypsibiidae) results more related to Macrobiotidae than to the genera here considered of Hypsibiidae. Macrobiotidae and Macrobiotus result not monophyletic and confirm morphological data on the presence of at least two large groups within Macrobiotus. Using 18S rDNA and COI mtDNA genes, a new phylogenetic line has been identified within Macrobiotus, corresponding to the ,richtersi-areolatus group'. Moreover, cryptic species have been identified within the Macrobiotus,richtersi group' and within Richtersius. Some evolutionary lines of tardigrades are confirmed, but others suggest taxonomic revision. In particular, the new genus Paramacrobiotus gen. n. has been identified, corresponding to the phylogenetic line represented by the ,richtersi-areolatus group'. Zusammenfassung Die Anzahl der Arten im Phylum Tardigrada ist in den letzten 25 Jahren von 500 Arten auf inzwischen fast 1000 Arten angestiegen. Zurzeit besteht die Gruppe aus zwei Klassen (Heterotardigrada und Eutardigrada), vier Ordnungen, 21 Familien, und 104 Gattungen. Trotz der Häufigkeit der Tardigraden wurde ihnen seit ihrer Entdeckung im Jahr 1773 nur wenig Aufmerksamkeit geschenkt. Bis vor wenigen Jahren wurden ausschließlich morphologische Merkmale verwendet, um die Phylogenie der Tardigrada zu untersuchen. Dennoch sind die Verhältnisse zwischen und innerhalb vieler Arten noch nicht eindeutig geklärt. Das Ziel der vorliegenden Arbeit war es, die bereits bekannten, morphologischen Verhältnisse mit molekularen Ergebnissen zu belegen. Hierzu wurden nur vollständige Sequenzen der ribosomalen 18S rDNA von 19 Arten verwendet. Fünf neue Sequenzen wurden dabei hinzugefügt. Weiterhin wurden von 15 Arten neue mitochrondriale COI Sequenzen verwendet, die mit fünf bekannten COI Sequenzen zu insgesamt sieben Familien gehören. Der 18S rDNA-Baum wurde durch ME, maximum parsimony (MP) and ML Analysen berechnet. Die für COI kodierenden Sequenzen wurden in Aminosäuren übersetzt und der Baum mit NJ, MP and ML Analysen berechnet. Für beide Bäume (18 rDNA und COI) wurden die Wahrscheinlichkeiten durch MrBayes ermittelt. Dabei ergab sich, dass molekulare Daten mit den morphologischen Untersuchungen bei den Echiniscidae (Heterotardigrada) übereinstimmen. Bei Eutardigrada wurden die Ordnungen Apochela und Parachela als Schwestergruppen bestätigt. Ramazzottius (Hypsibiidae) gehört zu der Familie Macrobiotidae und weniger zu Hypsibiidae, zu der die Gattung gegenwärtig gestellt wird. Die molekularen und morphologischen Daten deuten darauf hin, dass es mindestens zwei großer Gruppen innerhalb von Macrobiotus gibt. Durch die 18 rDNA und COI mtDNA Sequenzen konnte eine neue phylogenetische Linie innerhalb von Macrobiotus, der ,richtersi-areolatus Gruppe' zugehörig, identifiziert werden. Weiterhin sind kryptische Arten innerhalb der Macrobiotus richtersi Gruppe' und innerhalb von Richtersius gefunden worden. Die vorliegende Arbeit verifiziert die in vorangegangene Untersuchungen erarbeitete Phylogenie von Tardigraden. Es konnten einige Entwicklungslinien innerhalb den Tardigraden bestätigt werden, andere deuten zukünftige, taxonomische Revisionen an. So wurde die neue Gattung Paramacrobiotus eingeführt, entsprechend der phylogenetischen Linie, die bisher durch die ,richtersi-areolatus Gruppe' vertreten war. [source]

A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidae) reveals three cryptic species

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2007
M. Sirna Terranova
Abstract This study examined genetic variation across the range of Brachidontes variabilis to produce a molecular phylogeography. Neighbour joining (NJ), minimum evolution (ME) and maximum parsimony (MP) trees based on partial mitochondrial DNA sequences of 16S-rDNA and cytochrome oxidase (COI) genes revealed three monophyletic clades: (1) Brachidontes pharaonis s.l. from the Mediterranean Sea and the Red Sea; (2) B. variabilis from the Indian Ocean; (3) B. variabilis from the western Pacific Ocean. Although the three clades have never been differentiated by malacologists employing conventional morphological keys, they should be ascribed to the taxonomic rank of species. The nucleotide divergences between Brachidontes lineages (between 10.3% and 23.2%) were substantially higher than the divergence between congeneric Mytilus species (2.3,6.7%) and corresponded to interspecific divergences found in other bivalvia, indicating that they should be considered three different species. Analysis of the 16S-rDNA sequences revealed heteroplasmy, indicating dual uniparental inheritance (DUI) of mtDNA in the species of Brachidontes collected in the Indian Ocean, but not in the species in the Pacific nor in the species in the Red Sea and the Mediterranean Sea. When we employed the conventional estimate of the rate of mitochondrial sequence divergence (2% per million years), the divergence times for the three monophyletic lineages were 6,11 Myr for the Indian Ocean and Pacific Ocean Brachidontes sp. and 6.5,9 Myr for the Red Sea and Indian Ocean Brachidontes sp. Thus, these species diverged from one another during the Miocene (23.8,5.3 Myr). We infer that a common ancestor of the three Brachidontes species probably had an Indo-Pacific distribution and that vicariance events, linked to Pleistocene glaciations first and then to the opening of the Red Sea, produced three monophyletic lineages. Riassunto Lo studio filogeografico è stato condotto su tutto l'areale di Brachidontes variabilis (Krauss, 1848) attraverso l'analisi di sequenze mitocondriali (16S-rDNA e COI) che hanno separato i campioni in tre cladi monofiletici. Diversi algoritmi (NJ, ME e MP) hanno elaborato alberi con la stessa topologia, in cui è possibile riconoscere: (1) Brachidontes pharaonis s.l. dell'area Mar Mediterraneo , Mar Rosso; (2) Brachidontes variabilis dell' Oceano Indiano; (3) Brachidontesvariabilis dell'Oceano Pacifico. Il loro grado di divergenza è sufficientemente alto da potere ascrivere al rango di specie i singoli cladi, nonostante non siano stati ancora individuati i caratteri tassonomici distintivi, a causa della grande variazione morfologica. La divergenza nucleotidica tra le tre linee di Brachidontes era compresa tra 10.3% e 23.2%, in un range di valori superiori a quelli trovati nel confronto tra specie congeneriche di Mytilus sp (2.3,6.7%). Utilizzando il tasso evolutivo, che convenzionalmente viene applicato ai valori di divergenza genetica di geni mitocondriali (2% per milioni di anni), si sono ricavati tempi di divergenza corrispondenti a 6,11 milioni di anni tra Oceano Indiano e Pacifico, e a 6.5,9 milioni di anni tra Mar Rosso e Oceano Indiano. Le tre linee evolutive sembrano essersi separate durante il Miocene. Probabilmente un comune antenato con distribuzione Indo-Pacifica può essere andato incontro a processi di vicarianza e/o di dispersione legati alle glaciazioni pleistoceniche prima e all'apertura del Mar Rosso dopo. [source]

The minimum evolution problem: Overview and classification

NETWORKS: AN INTERNATIONAL JOURNAL, Issue 2 2009
Daniele Catanzaro
Abstract Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data. These relationships are typically described by means of weighted trees, or phylogenies, whose leaves represent the observed organisms, internal vertices the intermediate ancestors, and edges the evolutionary relationships between pairs of organisms. Molecular phylogenetics provides several criteria for selecting one phylogeny from among plausible alternatives. Usually, such criteria can be expressed in terms of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important criteria is the minimum evolution (ME) criterion, which states that the optimal phylogeny for a given set of organisms is the one whose sum of edge weights is minimal. Finding the phylogeny that satisfies the ME criterion involves solving an optimization problem, called the minimum evolution problem (MEP), which is notoriously -Hard. This article offers an overview of the MEP and discusses the different versions of it that occur in the literature. © 2008 Wiley Periodicals, Inc. NETWORKS, 2009 [source]

Systematics and phylogeography of a threatened tortoise, the speckled padloper

ANIMAL CONSERVATION, Issue 3 2010
S. R. Daniels
Abstract This study investigated the systematics and phylogeography of a threatened tortoise of South Africa, the speckled padloper Homopus signatus. Sixty three specimens were collected from 17 localities that covered the distributional range of the two subspecies in western South Africa and a north-eastern population that was recently discovered near Pofadder. The Pofadder sample could not be assigned to either subspecies based on morphology. The samples were sequenced for two partial mtDNA fragments, nicotinamide adenine dinucleotide dehydrogenase component four and cytochrome b, which yielded ,1.1 kb, while a subset of the samples were sequenced for a 390 bp nuclear DNA (nDNA) fragment of prolactin. Phylogenetic analyses of mtDNA using minimum evolution, maximum parsimony and Bayesian inferences supported the monophyly of H. signatus and revealed that the Pofadder specimen was basal in the topology and sister to the remainder. The phylogenetic analyses did not support the recognition of two subspecies; there was statistical support for a Homopus signatus signatus clade but Homopus signatus cafer was not monophyletic. The nDNA analysis showed no difference between the subspecies and placed the Pofadder sample distant but not distinct from H. s. signatus. The mtDNA and the nDNA data suggest that the subspecies are invalid taxonomic units. The structure of the mtDNA network corresponded to the geographical distribution of populations. The north-western populations formed one haplocluster, corresponding to H. s. signatus, whereas the south-western populations formed three haploclusters, corresponding to H. s. cafer. The Pofadder sample was unconnected to the network. The morphology of the northern and southern morphotypes probably reflects selection for crypsis on the different substrate types of the regions, granites and sedimentary rocks, respectively. These results highlight that subspecies designations should be authenticated by molecular techniques because morphological plasticity can obfuscate phylogenetic relationships. We consider the western H. signatus populations as one taxonomic unit and recommend wider sampling of the Pofadder locality to clarify the taxonomic status of this lineage. [source]

Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciation

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009
SAVEL R. DANIELS
The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two-fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly-identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97, 200,216. [source]