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2,620 results for “Molecular Phylogeny”
Fig. 7. Male terminalia, ventroposterior view. A in Five new Palaearctic species of Docosia (Diptera: Mycetophilidae), with updated molecular phylogeny of the genus
Fig. 7. Male terminalia, ventroposterior view. A. Docosia anatolica Ševčík sp. nov. B. D. japonica Kurina sp. nov. C. D. polyspina Kurina sp. nov. D. D. peloponnensis Ševčík sp. nov. E. D. svanetica Kurina sp. nov. Scale bars = 0.1 mm.
FIGURE 6 in Morphology and molecular phylogeny of Macrobrachium saengphani sp. nov (Decapoda: Palaemonidae) from Northern Thailand
FIGURE 6. Golden antennules of Macrobrachium saengphani sp. nov.
FIGURE 2 in Morphology and molecular phylogeny of Macrobrachium saengphani sp. nov (Decapoda: Palaemonidae) from Northern Thailand
FIGURE 2. Male (upper and smaller) and female (lower and larger) Macrobrachium saengphani sp. nov.
FIGURE 7 in Morphology and molecular phylogeny of Macrobrachium saengphani sp. nov (Decapoda: Palaemonidae) from Northern Thailand
FIGURE 7. Rostrum of Macrobrachium saengphani sp. nov.
Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: an analysis based on Cetacea
Interest in methods that estimate speciation and extinction rates from molecular phylogenies has increased over the last decade. The application of such methods requires reliable estimates of tree topology and node ages, which are frequently obtained using standard phylogenetic inference combining concatenated loci and molecular dating. However, this practice disregards population-level processes that generate gene tree/species tree discordance. We evaluated the impact of employing concatenation and coalescent-based phylogeny inference in recovering the correct macroevolutionary regime using simulated data based on the well-established diversification rate shift of delphinids in Cetacea. We found that under scenarios of strong incomplete lineage sorting, macroevolutionary analysis of phylogenies inferred by concatenating loci failed to recover the delphinid diversification shift, while the coalescent-based tree consistently retrieved the correct rate regime. We suggest that ignoring microevolutionary processes reduces the power of methods that estimate macroevolutionary regimes from molecular data.
Data from: Consensus and confusion in Molluscan trees: evaluating morphological and molecular phylogenies
Mollusks are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister relationships. Here, we assembled a dataset of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared to a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep-sea class Monoplacophora; but 36.4% of all trees are not significantly different. We also present supertrees derived from 2 data partitions and 3 methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning in order to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in a concerted assessment of potential genetic and anatomical homology, while unequivocally distant taxa will make the most constructive choices for exemplar selection in higher-level phylogenomic analyses.
Data from: Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae)
Background: The Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date. Methods: The relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S. Results: Our results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes. Conclusions: We propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera.
Data from: Integrating fossils with molecular phylogenies improves inference of trait evolution
Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models to phylogenetic comparative data consisting of a molecular phylogeny with branch lengths and trait measurements from extant taxa. These kinds of approaches ignore historical evidence for evolutionary pattern and process contained in the fossil record. In this paper we show through simulation that incorporation of fossil information dramatically improves our ability to distinguish among models of quantitative trait evolution using comparative data. We further suggest a novel Bayesian approach that allows fossil information to be integrated even when explicit phylogenetic hypothesis are lacking for extinct representatives of extant clades. By applying this approach to a comparative dataset comprising body sizes for caniform carnivorans, we show that incorporation of fossil information not only improves ancestral state estimates relative to those derived from extant taxa alone, but also results in preference of a model of evolution with trend towards large body size over alternative models such as Brownian motion or Ornstein-Uhlenbeck processes. Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provided a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists.
Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes
Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including man. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Here we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids. The phylogeny was calibrated using an approach that involves time priors from fossils of the co-evolving hosts, and dates the common ancestor of the Ascaridoidea back to the Early Carboniferous (approximately 360.47–325.27 Ma). The divergence dates and ancestral host types indicated by our study suggest that members of the Ascaridoidea first parasitized terrestrial tetrapods and subsequently extended their host range to elasmobranchs and teleosts. We also propose that the fundamental terrestrial-aquatic switches of these nematodes were affected by changes in sea-level during the Triassic to the Early Cretaceous.
Data from: Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as "Tilapia"
African cichlids formerly referred to as "Tilapia" represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important "Tilapia" or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for "Tilapia" joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.
Data from: Molecular phylogeny of unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of Opisthokontsí
The eukaryotic supergroup known as the Opisthokonta includes animals (Metazoa), fungi, choanoflagellates, as well as some poorly-studied unicellular eukaryotes, such as the Nucleariidea, Fonticula alba, the Ichthyosporea, the Filasterea and Corallochytrium limacisporum. Whereas the evolutionary positions of the well-known opisthokont lineages are mostly resolved, the specific phylogenetic relationships among those neglected opisthokont lineages is unsettled. Moreover, it remains unclear whether Amoebozoa or Apusozoa are the sister group to opisthokonts. Aiming at elucidating the evolutionary tree of the opisthokonts, we have produced a dataset with a large sampling of both organisms and number of genes, including representatives from all known opisthokont lineages. Moreover, we have generated new molecular data from an additional ichthyosporean (Creolimax fragrantissima) and a choanoflagellate (Codosiga botrytis). Our analyses show the Apusozoa as a paraphyletic assemblage with the Apusomonadida as sister group to Opisthokonta. Within the the Holozoa, the Ichthyosporea are shown as the first splitting group, followed by C. limacisporum, the Filasterea, the Choanoflagellata, and the Metazoa. With this taxon-rich opisthokont tree, it is possible to pinpoint the origin and evolution of morphological characters. As an example, we discuss cilia evolution under the evolutionary scenario here presented.
Data from: Additional molecular support for the new chordate phylogeny
Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. Despite the inclusion of 25 taxa representing all major lineages, the monophyly of deuterostomes remained poorly supported. The implications of these phylogenetic results for interpreting chordate evolution are discussed in light of recent advances from evolutionary developmental biology and genomics.
Data from: Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography
Antarctic waters represent a unique marine environment delimited by an oceanographic barrier, the Polar Front Zone, and characterized by constant subzero temperatures and presence of sea ice. A group of teleost fish, the Notothenioidei, have adapted to these challenging environmental conditions, undergoing a remarkable diversification. In the present study a total of 798 base pairs, generated from partial sequencing of 16S and 12S mitochondrial ribosomal RNA genes, were examined in 33 notothenioid species representative of all families included in the suborder Notothenioidei. Phylogenetic trees, reconstructed on the basis of sequence data using different methods, indicate that traditional hypotheses on notothenioid systematics and biogeography might be in need of reexamination. Molecular evidence suggests that vicariant speciation could be invoked to explain the early divergence of Eleginops maclovinus, a species previously included in the family Nototheniidae, which is now proposed as the closest sister group to all the rest of notothenioids apart from bovichtids. On the other hand, repeated, independent dispersal through the Polar Front is proposed for the divergence of other subantarctic notothenioid species. Likewise, multiple, independent transitions from benthic to pelagic habit are inferred from molecular data, at variance with the more conservative hypothesis based on cladograms reconstructed from morphological data.
Data from: Using molecular phylogenies in island biogeography: it's about time
Island biogeography aims at inferring the processes that govern the assembly of communities in space and time. Molecular phylogenies can tell us about the timings of island colonisations and diversification, but have rarely been used for the estimation of colonisation, speciation and extinction rates on islands. In this study we illustrate the effects of including phylogenetic information with the Galápagos avifauna. We find that by including colonisation times we obtain much more precise and accurate parameter estimates than if we rely solely on species richness and endemicity status. Inclusion of branching times improves estimates even further. As molecular phylogenies become increasingly available, we urge biogeographers to start using more of the information they contain.
Data from: Combining and Comparing Morphometric Shape Descriptors with a Molecular Phylogeny: The Case of Fruit Type Evolution in Bornean Lithocarpus (Fagaceae)
Fruit type in the genus Lithocarpus (Fagaceae) includes both classic oak acorns and novel modifications. Bornean taxa with modified fruits can be separated into two sections (Synaedrys and Lithocarpus) based on subtle shape differences. Following strict criteria for homology and representation, this variation in shape can be captured and the sections distinguished using elliptic Fourier or eigenshape analysis. Phenograms of fruit shape, constructed using restricted maximum likelihood techniques and these morphometric descriptors, were incorporated into combined and comparative analyses with molecular sequence data from the internal transcribed spacer (ITS) region of the nuclear rDNA using branch-weighted matrix representation. The combined analysis strongly suggested independent derivation of the novel fruit type in the two sections from different acorn-like ancestors, while the comparative analysis indicated frequent decoupling between the molecular and morphological change as inferred at well-supported nodes. The acorn fruit type has undergone little modification between ingroup and outgroup, despite large molecular distance. Greater morphological than molecular change was inferred at critical transitions between acorn and novel fruit types, particularly for section Lithocarpus. The combination of these two different types of data improved our understanding of the macroevolution of fruit type in this difficult group and the comparative analysis highlighted the significant incongruities in evolutionary pattern between the two datasets.
Data from: Phylogeny of digitaria sections Trichachne and Trichophorae (Poaceae, Panicoideae, Paniceae): a morphological and molecular analysis. New circumscription and synopsis
The present study provides evidence for taxonomic delimitation of Digitaria sect. Trichachne based on morphological data (micro- and macromorphology) and molecular data. A phylogenetic analysis was performed using 121 morphological characters and ITS sequences of 22 species and one variety of Digitaria plus three outgroups. In all topologies (based on morphological, molecular, and combined data) Digitaria sect. Trichophorae was non-monophyletic and nested within D. sect. Trichachne. Digitaria sect. Trichophorae is thus synonymized under D. sect. Trichachne and the circumscription of D. sect. Trichachne is emended. Diagnostic morphological characters related to spikelet structure are described and documented with SEM. A key to taxa belonging to D. sect. Trichachne is provided, as well as a synopsis including synonymy, iconography, geographical distribution, and ecology. The neotype of Trichachne sacchariflora Nees is herein designated. Complete illustrations of Digitaria eggersii, D. hitchcockii, and D. patens are provided. The phylogenetic placement of the Australian species D. brownii differed among trees resulting from different data sets, thus it is provisionally not included in D. sect. Trichachne in spite of its morphological similarity. Furthermore, Megaloprotachne albescens is formally transferred to Digitaria, as Digitaria albescens .
FIGURES 9–26 in Molecular phylogeny in ' nano-weevils': description of a new subgenus Nanoacalles and two new species of Calacalles from the Macaronesian Islands (Curculionidae: Cryptorhynchinae)
FIGURES 9–26. Comparison of the endophalli of all known Calacalles species.
FIGURE 5 in Molecular phylogeny of Australian Gehyra (Squamata: Gekkonidae) and taxonomic revision of Gehyra variegata in south-eastern Australia
FIGURE 5. The type specimens of A) Dactyloperus lazelli and B) D. annettae.
FIGURE 6 in Molecular phylogeny and morphological revision of the Ctenotus labillardieri (Reptilia: Squamata: Scincidae) species group and a new species of immediate conservation concern in the southwestern Australian biodiversity hotspot
FIGURE 6. Photographs of the holotype of Ctenotus ora sp. nov. (WAM R131983).
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