scholarly journals Drivers of diversification in a continental radiation of ground beetles (Coleoptera: Carabidae: Lachnophorini) 

2019 ◽  
Vol 2 ◽  
Author(s):  
Laura S. Zamorano ◽  
Terry Erwin ◽  
David Kavanaugh
Keyword(s):  
Evolutionary Biology ◽  
Amazon Basin ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sandy Beaches ◽  
Shape Variation ◽  
Ecological Data ◽  
Molecular Sequence Data ◽  
Geometric Morphometric ◽  
Habitat Occupancy

Understanding the factors responsible for spatial heterogeneity in species diversity is a major challenge in evolutionary biology. The Amazon Basin harbors the highest species richness for a variety of groups, yet whether the Amazon is a cradle or museum of diversity continuous to be an open debate. In this study, we evaluate the phylogenetic relationships of an assemblage of beetles found in seven different habitats within a lowland tropical rainforest in the Ecuadorian Amazon in order to evaluate if the patterns of diversification are consistent with an adaptive radiation or represent the accumulation of species in proportion to time since divergence from a common ancestor. We combined molecular sequence data with morphometric and ecological data to examine the relationship between species diversification and disparity in eco-morphological traits. Phylogenetic analyses identified 8 clades of lachnophorines. A lineage through time analysis revealed a constant rate of divergence. Geometric morphometric analyses based on 46 landmarks revealed significant morphological shape variation among species within clades that correlated with habitat occupancy. Species with a slender pronotum tended to occur in open environments, such as sandy beaches adjacent to water, whereas species with shorter, broader pronotum and elytra inhabited leaf-litter and arboreal habitats. In addition, we found evidence of morphological convergence related to habitat use indicating that Lachnophorini radiation in the Amazon-Basin is accompanied by local ecological adaptation.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

The Cheilosia canicularis group (Diptera: Syrphidae): species delimitation and evolutionary relationships based on wing geometric morphometrics

Zootaxa ◽  
2008 ◽  
Vol 1825 (1) ◽  
pp. 40 ◽  
Author(s):  
JASMINA LUDOŠKI ◽  
LJUBINKA FRANCUSKI ◽  
ANTE VUJIĆ ◽  
VESNA MILANKOV
Keyword(s):  
Sequence Data ◽  
Balkan Peninsula ◽  
Wing Shape ◽  
Canonical Variate ◽  
Wing Size ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Mahalanobis Distances ◽  
Size And Shape ◽  
Upgma Cluster Analysis

A landmark-based geometric morphometric approach was used to assess differences in the size and shape of wing among/within three species of the Cheilosia canicularis group (Diptera: Syrphidae): C. canicularis, C. himantopus and C. orthotricha. Wing size and shape variation was observed from 25, 176 and 41 specimens of C. canicularis, C. himantopus and C. orthotricha, respectively, collected from six localities on the Balkan Peninsula. Significant differences in wing size were obtained among the analysed species and canonical variate analysis showed that wing shape was sufficiently different to allow the correct classification of 73% individuals of C. canicularis, 80% of C. orthotricha and 94% of C. himantopus, and clear delimitation of the species pairs C. canicularis/C. orthotricha and C. himantopus/C. orthotricha. In all analysed species, the consistent sex dimorphism in wing shape was observed indicating that female specimens had shorter and broader wings than males. The UPGMA cluster analysis based on squared Mahalanobis distances revealed close accordance with previously published phylogenetic relationships of these species indicated by allozyme and DNA sequence data analysis. Our results suggested that wing parameters contain useful information in quantification phenotypic variation and identification of species in this challenging group for taxonomy and systematics.

A revision of the planthopper genus Chionomus Fennah (Hemiptera: Fulgoroidea: Delphacidae)

Zootaxa ◽  
2020 ◽  
Vol 4811 (1) ◽  
pp. 1-63
Author(s):  
KATHRYN M. WEGLARZ ◽  
CHARLES R BARTLETT
Keyword(s):  
Mixed Model ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Molecular Evidence ◽  
Additional Species ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Original Definition ◽  
Definition Of

The planthopper genus Chionomus Fennah, 1971 (Hemiptera: Fulgoroidea: Delphacidae) currently includes three Neotropical species, removed from the polyphyletic genus Delphacodes Fieber, 1866. Morphological and molecular evidence further redefine Chionomus to include ten additional species (eight species removed from Delphacodes, two described as new, viz. Chionomus dolonus n. sp. and C. herkos n. sp.), with another four species synonymized. Phylogenetic analyses of morphological and molecular sequence data of the mitochondrial gene Cytochrome Oxidase I provide support for the monophyly of Chionomus. We use a mixed model Bayesian optimality criterion to define phylogenetic relationships among Chionomus and support paraphyly of the original definition of Chionomus (with respect to Delphacodes) and monophyly of the revised genus. 

Across Lydekker's Line - first report of mite harvestmen (Opiliones : Cyphophthalmi : Stylocellidae) from New Guinea

2007 ◽  
Vol 21 (3) ◽  
pp. 207 ◽  
Author(s):  
Ronald M. Clouse ◽  
Gonzalo Giribet
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Single Male ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
Biogeographic Region ◽  
Molecular Phylogenetic ◽  
History Of

Opiliones (harvestmen) in the suborder Cyphophthalmi are not known to disperse across oceans and each family in the suborder is restricted to a clear biogeographic region. While undertaking a revisionary study of the South-east Asian family Stylocellidae, two collections of stylocellids from New Guinea were noted. This was a surprising find, since the island appears never to have had a land connection with Eurasia, where the rest of the family members are found. Here, 21 New Guinean specimens collected from the westernmost end of the island (Manokwari Province, Indonesia) are described and their relationships to other cyphophthalmids are analysed using molecular sequence data. The specimens represent three species, Stylocellus lydekkeri, sp. nov., S. novaguinea, sp. nov. and undescribed females of a probable third species, which are described and illustrated using scanning electron microscope and stereomicroscope photographs. Stylocellus novaguinea, sp. nov. is described from a single male and it was collected with a juvenile and the three females of the apparent third species. Molecular phylogenetic analyses indicate that the new species are indeed in the family Stylocellidae and they therefore reached western New Guinea by dispersing through Lydekker’s line – the easternmost limit of poor dispersers from Eurasia. The New Guinean species may indicate at least two episodes of oceanic dispersal by Cyphophthalmi, a phenomenon here described for the first time. Alternatively, the presence in New Guinea of poor dispersers from Eurasia may suggest novel hypotheses about the history of the island.

scholarly journals The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 108 ◽  
Author(s):  
Nan Song ◽  
Xin-xin Li ◽  
Qing Zhai ◽  
Hakan Bozdoğan ◽  
Xin-ming Yin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Genomic Data ◽  
Considerable Progress ◽  
Mitochondrial Genomes ◽  
Special Focus ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Taxonomic Sampling ◽  
Inference Methods

The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.

scholarly journals Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 75-100 ◽  
Author(s):  
C.G. Boluda ◽  
V.J. Rico ◽  
P.K. Divakar ◽  
O. Nadyeina ◽  
L. Myllys ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Species Delimitation ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Haplotype Network ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Molecular Sequence Data

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

scholarly journals Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

2014 ◽  
Vol 28 (1) ◽  
pp. 32 ◽  
Author(s):  
Rüdiger Bieler ◽  
Paula M. Mikkelsen ◽  
Timothy M. Collins ◽  
Emily A. Glover ◽  
Vanessa L. González ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Analytical Framework ◽  
Morphological Characters ◽  
Molecular Data ◽  
Probabilistic Methods ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Protein Encoding ◽  
Encoding Genes

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

scholarly journals The limitations of ontogenetic data in phylogenetic analyses

2002 ◽  
Vol 71 (1-3) ◽  
pp. 47-65 ◽  
Author(s):  
Stefan Koenemann ◽  
Frederick R. Schram
Keyword(s):  
Maximum Parsimony ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Real Data ◽  
Linear Type ◽  
Molecular Sequence Data ◽  
Event Sequences ◽  
Coding Method

The analysis of consecutive ontogenetic stages, or events, introduces a new class of data to phylogenetic systematics that are distinctly different from traditional morphological characters and molecular sequence data. Ontogenetic event sequences are distinguished by varying degrees of both a collective and linear type of dependence and, therefore, violate the criterion of character independence. We applied different methods of phylogenetic reconstruction to ontogenetic data including maximum parsimony and distance (cluster) analyses. Two different data sets were investigated: (1) four simulated ontogenies with defined phylogenies of six hypothetical taxa, and (2) a set of “real” data comprising sequences of 29 ontogenetic events from 11 vertebrate taxa. We confirm that heterochronic event sequences do contain a phylogenetic signal. However, based on our results we argue that maximum parsimony is a biased method to analyze such developmental sequence data. Ontogenetic events require a special analytical algorithm that would not neglect instances of chronological (horizontal) dependence of this type of data. One coding method, “event-pairing”, appeared to fulfill this requirement in the vertebrate analyses. However, to accurately analyze ontogenetic sequence data, a more sophisticated coding method and algorithm are needed, for example, measuring distances of dependent events.

Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)

2013 ◽  
Vol 87 (2) ◽  
pp. 211-216 ◽  
Author(s):  
Bernard L. Cohen ◽  
Maria Aleksandra Bitner
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequences ◽  
Relaxed Clock

We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cannot directly illuminate the systematics of fossils, the independent, genealogical evidence and phylogenetic inferences about extant forms that they make possible are highly relevant to paleontological systematics because they highlight the limitations of evolutionary inference from morphology. Parsimony, distance, maximum likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a tree topology that disagrees strongly with the existing superfamily classification. All tested phylogenetic reconstructions agree that the taxa analyzed fall into three clades designated A1, A2, and B that reflect two major divergence events. The relaxed-clock analysis indicates that clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect Permo-Triassic (and later) events. Morphological homoplasy and possible gene co-option are suggested as the main sources for the discord between the morpho-classification, the results of cladistic analyses of morphology, and the relationships reconstructed from molecular sequences. The origin, function and evolutionary implications of the deletion-bearing rhynchonellide SSU rDNA sequences are briefly discussed in relation to pseudogenes and concerted evolution in the rDNA genomic region.

scholarly journals Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

2021 ◽  
Author(s):  
Vanina Tonzo ◽  
AdriÀ Bellvert ◽  
Joaquín Ortego
Keyword(s):  
Gene Flow ◽  
Biological Diversity ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Secondary Contact ◽  
Lineage Sorting ◽  
Glacial Cycles ◽  
Reciprocal Monophyly ◽  
Geometric Morphometric

AbstractInferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression. In this study, we combined high throughput sequence data (ddRADseq), geometric morphometric information, and novel phylogenetic inference methods that explicitly account for gene flow to infer the evolutionary relationships and the timing and mode of diversification in a complex of Ibero-Maghrebian montane grasshoppers of the subgenus Dreuxius (genus Omocestus). Our analyses supported the phenotypic distinctiveness of most sister taxa, two events of historical introgression involving lineages at different stages of the diversification continuum, and the recent Pleistocene origin (< 1 Ma) of the complex. Phylogenetic analyses did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting overseas migration between the two continents during the Pleistocene. Collectively, these results indicate that periods of isolation and secondary contact linked to Pleistocene glacial cycles likely contributed to both allopatric speciation and post divergence gene flow in the complex. This study exemplifies how the integration of multiple lines of evidence can help to reconstruct complex histories of reticulated evolution and highlights the important role of Quaternary climatic oscillations as a diversification engine in the Ibero-Maghrebian biodiversity hotspot.

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