Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?

Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.

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Phylogenetic studies of eucalypts: fossils, morphology and genomes

Proceedings of the Royal Society of Victoria ◽

10.1071/rs16002 ◽

2016 ◽

Vol 128 (1) ◽

pp. 12 ◽

Cited By ~ 12

Author(s):

Michael J. Bayly

Keyword(s):

Dna Sequencing ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Phylogenetic Studies ◽

Recent Advances ◽

History Of ◽

Morphological And Molecular Data ◽

Economic Use ◽

Insight Into

The eucalypt group includes seven genera: Eucalyptus, Corymbia, Angophora, Eucalyptopsis, Stockwellia, Allosyncarpia and Arillastrum. Knowledge of eucalypt phylogeny underpins classification of the group, and facilitates understanding of their ecology, conservation and economic use, as well as providing insight into the history of Australia’s flora. Studies of fossils and phylogenetic analyses of morphological and molecular data have made substantial contributions to understanding of eucalypt relationships and biogeography, but relationships among some genera are still uncertain, and there is controversy about generic circumscription of the bloodwood eucalypts (genus Corymbia). Relationships at lower taxonomic levels, e.g. among sections and series of Eucalyptus, are also not well resolved. Recent advances in DNA sequencing methods offer the ability to obtain large genomic datasets that will enable improved understanding of eucalypt evolution.

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ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

Jurnal AgroBiogen ◽

10.21082/jbio.v4n1.2008.p35-40 ◽

2016 ◽

Vol 4 (1) ◽

pp. 35 ◽

Cited By ~ 6

Author(s):

Topik Hidayat ◽

Adi Pancoro

Keyword(s):

Dna Sequences ◽

Molecular Phylogenetics ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Biochemical Properties ◽

Intergeneric Hybrids ◽

Basic Knowledge ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Ornamental Crops

Early information resulted from molecular phylogenetic studies of many important ornamental crops is often less attention to many growers and farmers. Phylogenetics is one of the most preferable method in systematics to reconstruct evolutionary relationships of groups of biological organisms in order to understand their biodiversities. This has been revolutionized by DNA sequences data. In this method, a group of organisms that shares many identical characteristics are considered to be closely related; deriving from a common ancestor and is assumed to have similar genetic patterns and biochemical properties. By these basic principles, molecular phylogenetics plays important roles in revealing a basic knowledge on pattern of relationships to which genetic resources can be improved. Over the past decade, botanists have done several thousand phylogenetic analyses based on molecular data of economically and horticulturally important crops. Orchids are the best example for this. There is no doubt that most orchid plants had played roles in horticulture and hybridization. At present, many infrageneric and intergeneric hybrids are available commercially. Successful hybridization can be achieved if two or more individual plants understudy are closely related in respect to their genetics and evolution.

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Phylogeny, evolution, and classification of the ant genus Lasius, the tribe Lasiini, and the subfamily Formicinae (Hymenoptera: Formicidae)

10.1101/2021.07.14.452383 ◽

2021 ◽

Author(s):

Brendon E Boudinot ◽

Marek L Borowiec ◽

Matthew M Prebus

Keyword(s):

Molecular Phylogenetics ◽

Phylogenetic Analyses ◽

Social Parasitism ◽

Molecular Data ◽

Species Group ◽

Total Evidence ◽

Death Process ◽

Ancestral State ◽

Fossil Species

Within the Formicidae, the higher classification of nearly all subfamilies has been recently revised due to the findings of molecular phylogenetics. Here, we integrate morphology and molecular data to holistically address the evolution and classification of the ant genus Lasius, its tribe Lasiini, and their subfamily Formicinae. We accomplish this through a critical re-examination of morphology of extant and fossil taxa, molecular phylogenetic analyses, total-evidence dating under fossilized birth-death process, phylogeography, and ancestral state estimation. We use these results to provide revised taxonomic definitions for the Lasiini and select genera, and we provide a key to the genera of the Lasiini with emphasis on the Lasius genus group. We find that the crown Lasiini originated around the end of the Cretaceous on the Eurasian continent and is divisible into four morphologically distinct clades: Cladomyrma, the Lasius genus group, the Prenolepis genus group, and a previously undetected lineage we name XXXgen. n. The crown of the Lasius genus group is considerably younger than that of the Prenolepis genus group, indicating that extinction has played a major role in the evolution of the former clade. Lasius itself is divided into two well-supported monophyletic groups which are approximately equally speciose. We present evidence that temporary social parasitism and fungiculture arose in Lasius two times independently. Additionally, we recover the paraphyly of three Lasius subgenera and propose replacing all subgenera with an informal species group classification: Lasius = Acanthomyopssyn. rev., = Austrolasiussyn. n., = Cautolasiussyn. n., = Chthonolasius vsyn. n., = Dendrolasiussyn. n. Total-evidence analysis reveals that the Baltic-region amber fossil species Lasius pumilus and Pseudolasius boreus are misplaced to genus; we therefore designate XXXgen. n. for the former and XXXgen. n. for the latter. Further, we transfer XXX and Glaphyromyrmex out of the tribe, considering the former to be incertae sedis in the subfamily, and the latter a member of the Formicini (tribal transfer). Two final taxonomic actions are deemed necessary: synonymy of Lasius escamole Reza, 1925 with Liometopum apiculatum Mayr, 1870 syn. n. (subfamilial transfer), and transfer of Paratrechina kohli to Anoplolepis (tribal transfer, forming A. kohli (Forel, 1916) n. comb.).

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Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification

The Auk ◽

10.1093/ornithology/ukab042 ◽

2021 ◽

Author(s):

Jeremy J Kirchman ◽

Nancy Rotzel McInerney ◽

Thomas C Giarla ◽

Storrs L Olson ◽

Elizabeth Slikas ◽

...

Keyword(s):

Confidence Intervals ◽

Geographic Distribution ◽

Molecular Phylogenetics ◽

Phylogenetic Analyses ◽

Nucleotide Sequences ◽

Museum Specimens ◽

Multispecies Coalescent ◽

Evolutionary Studies ◽

Age Estimates

Abstract The rails (Family Rallidae) are the most diverse and widespread group in the Gruiformes. Their extensive fossil history, global geographic distribution, and tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but the rarity of modern museum specimens of so many rail species has, until recently, limited the scope of molecular phylogenetics studies. As a result, the classification of rails remains one of the most unsettled among major bird radiations. We extracted DNA from museum specimens of 82 species, including 27 from study skins collected as long ago as 1875, and generated nucleotide sequences from thousands of homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation and multispecies coalescent approaches, resulted in well-supported and highly congruent phylogenies that resolve the major lineages of rails and reveal several currently recognized genera to be polyphyletic. A fossil-calibrated time tree is well-resolved and supports the hypothesis that rails split into 2 major lineages (subfamilies Himantornithinae and Rallinae) ~34 mya, but clade age estimates have wide confidence intervals. Our results, combined with results of other recently published phylogenomics studies of rails and other Gruiformes, form the basis for a proposed classification of the Rallidae that recognizes 40 genera in 9 tribes.

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Phylogenetic taxonomy and classification of the Crinoidea (Echinodermata)

Journal of Paleontology ◽

10.1017/jpa.2016.142 ◽

2017 ◽

Vol 91 (4) ◽

pp. 829-846 ◽

Cited By ~ 38

Author(s):

David F. Wright ◽

William I. Ausich ◽

Selina R. Cole ◽

Mark E. Peter ◽

Elizabeth C. Rhenberg

Keyword(s):

Phylogenetic Relationships ◽

Fossil Record ◽

Phylogenetic Analyses ◽

Major Goal ◽

Evolutionary Patterns ◽

Phylogenetic Taxonomy ◽

Phylogenetic Perspective ◽

Phylogenetic Hypotheses ◽

Patterns And Processes

AbstractA major goal of biological classification is to provide a system that conveys phylogenetic relationships while facilitating lucid communication among researchers. Phylogenetic taxonomy is a useful framework for defining clades and delineating their taxonomic content according to well-supported phylogenetic hypotheses. The Crinoidea (Echinodermata) is one of the five major clades of living echinoderms and has a rich fossil record spanning nearly a half billion years. Using principles of phylogenetic taxonomy and recent phylogenetic analyses, we provide the first phylogeny-based definition for the Clade Crinoidea and its constituent subclades. A series of stem- and node-based definitions are provided for all major taxa traditionally recognized within the Crinoidea, including the Camerata, Disparida, Hybocrinida, Cladida, Flexibilia, and Articulata. Following recommendations proposed in recent revisions, we recognize several new clades, including the Eucamerata Cole 2017, Porocrinoidea Wright 2017, and Eucladida Wright 2017. In addition, recent phylogenetic analyses support the resurrection of two names previously abandoned in the crinoid taxonomic literature: the Pentacrinoidea Jaekel, 1918 and Inadunata Wachsmuth and Springer, 1885. Last, a phylogenetic perspective is used to inform a comprehensive revision of the traditional rank-based classification. Although an attempt was made to minimize changes to the rank-based system, numerous changes were necessary in some cases to achieve monophyly. These phylogeny-based classifications provide a useful template for paleontologists, biologists, and non-experts alike to better explore evolutionary patterns and processes with fossil and living crinoids.

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A new predatory leech from Vietnam (Hirudinida : Arhynchobdellida : Salifidae): its phylogenetic position with comments on the classification of the family

Invertebrate Systematics ◽

10.1071/is15008 ◽

2015 ◽

Vol 29 (5) ◽

pp. 473 ◽

Cited By ~ 1

Author(s):

Takafumi Nakano ◽

Son Truong Nguyen

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Molecular Data ◽

Phylogenetic Position ◽

12S Rrna ◽

The Family ◽

Morphological And Molecular Data ◽

First Time

The family Salifidae is a predaceous leech taxon in the suborder Erpobdelliformes. Although Salifidae is widely distributed in the African, Oriental, Indo-Malayan, Sino-Japanese and Australasian regions, the phylogenetic relationships of the family Salifidae have never been tested using molecular data obtained from leeches collected from the family distributional range. A salifid species was collected for the first time in Vietnam, and relevant morphological and molecular data are presented here. Because the Vietnamese salifid species possesses unique morphological characteristics among the known salifid species, this species is herein described as a new species, Salifa motokawai, sp. nov. Phylogenetic analyses based on nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers demonstrate that the Vietnamese salifid species is a close congener with the African Salifa perspicax and the Malagasy Linta be. Furthermore, molecular data revealed non-monophyly of the Asian salifid leeches. According to the observed phylogenetic relationships and morphological characteristics of the Vietnamese Salifa motokawai, sp. nov., the current classification of salifid taxa should be revised.

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Phylogeny and classification of the genus-group taxa of Loxandrina (Coleoptera, Carabidae, Abacetini)

Deutsche Entomologische Zeitschrift ◽

10.3897/dez.67.55985 ◽

2020 ◽

Vol 67 (2) ◽

pp. 151-182

Author(s):

Kipling Will

Keyword(s):

North American ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Historical Biogeography ◽

North American Species ◽

Diagnostic Features ◽

Genus Level

Bayesian and parsimony phylogenetic analyses of combined and partitioned datasets of molecular (partial sequences of 28S, wg, COI, and CAD) and morphological (51 characters of adults) data for exemplar taxa of five outgroup and 76 ingroup abacetine carabids resulted in a monophyletic Loxandrina Erwin & Sims, 1984 that is split into Australian and American clades. The genus Loxandrus LeConte, 1853 as previously delimited is not monophyletic relative to numerous genus-level taxa in Abacetini Chaudoir, 1873 and is restricted to a subgenus of North American species. A reclassification and nomenclatural changes for the subtribe that are consistent with the phylogeny are provided. Three genera are removed from Loxandrina: Aulacopodus Britton, 1940 moved to Pterostichini Bonelli, 1810; Cosmodiscus Sloane, 1907 and Tiferonia Darlington, 1962 moved to Abacetina. Based on the phylogenetic relationships and nomenclatural priority only four genera are recognized in Loxandrina: Cerabilia Laporte, 1867, Zeodera Laporte, 1867, Pediomorphus Chaudoir, 1878, and Oxycrepis Reiche, 1843. All other previously recognized genera are treated as subgenera. The classification change created eight secondary homonyms that are resolved by the proposal of the following: Oxycrepis gebi, replacement name for O. balli (Straneo, 1993); O. amatona, replacement name for O. matoana (Straneo, 1993); O. xiproma, replacement name for O. proxima (Straneo, 1993); O. rasutulis, replacement name for O. suturalis (Straneo, 1993); O. laevinota, replacement name for O. laevicollis (Bates, 1871); O. arvulap, replacement name for O. parvula (Straneo, 1951); O. noaffine, replacement name for O. affinis (Straneo, 1991); O. alutona, replacement name for O. notula (Tschitschérine, 1901). An overview of the morphological characteristics and diagnostic features of Loxandrina taxa is provided. A key and habitus images are provided for identification of genera and subgenera. The possible historical biogeography of the group is discussed in light of their phylogenetic relationships and past geological events.

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A Phylogenetic Investigation of the New Zealand Pteridaceae Ferns

10.26686/wgtn.16934449.v1 ◽

2021 ◽

Author(s):

◽

Whitney L M Bouma

Keyword(s):

New Zealand ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Native Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Taxonomic Confusion ◽

Species Specific

The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.

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Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

Scientia Marina ◽

10.3989/scimar.05067.28a ◽

2020 ◽

Vol 84 (4) ◽

pp. 317-330

Author(s):

Francisco J. García-Cárdenas ◽

Mónica Núñez-Flores ◽

Pablo J. López-González

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Nuclear Markers ◽

Divergence Time Estimates ◽

Time Estimates ◽

Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

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Data analytics for smart buildings: a classification method for anomaly detection for measured data

Journal of Physics Conference Series ◽

10.1088/1742-6596/2042/1/012015 ◽

2021 ◽

Vol 2042 (1) ◽

pp. 012015

Author(s):

Enguerrand de Rautlin de la Roy ◽

Thomas Recht ◽

Akka Zemmari ◽

Pierre Bourreau ◽

Laurent Mora

Keyword(s):

Energy Consumption ◽

Anomaly Detection ◽

Data Quality ◽

Data Analytics ◽

Measured Data ◽

Detection Techniques ◽

Frequent Use ◽

Different Types ◽

User Comfort

Abstract Data generated by the increasingly frequent use of sensors in housing provide the opportunity to monitor, manage and optimize the energy consumption of a building and the user comfort. These data are often strewn with rare or anomalous events, considered as anomalies (or outliers), that must be detected and ultimately corrected in order to improve the data quality. However, many approaches are used or might be used (for the most recent ones) to achieve this purpose. This paper proposes a classification methodology of anomaly detection techniques applied to building measurements. This classification methodology uses a well-suited anomaly typology and measurement typology in order to provide, in the future, a classification of the most adapted anomaly detection techniques for different types of building measurements, anomalies and needs.

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