Present status and future of nematode systematics

Nematology ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 573-582 ◽  
Author(s):  
August Coomans
Keyword(s):  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Molecular Techniques ◽  
Morphological Data ◽  
Future Research ◽  
Correct Identification ◽  
Phylogenetic Systematics ◽  
Data Sets ◽  
Routine Work ◽  
Important Position

AbstractSince phylogenetic systematics became generally accepted and especially since informatics and molecular techniques for phylogenetic analysis were developed, systematics has undergone a conceptual and methodological revolution. Taxonomy, on the contrary, suffered a decline. Poor descriptions, too much routine work and low citation rates hampered it. As a result, the discipline became less attractive to young scientists. With only a small fraction of the biodiversity known, this situation will lead to serious problems in the future in all those fields of nematology depending on a correct identification of species. Phylogenetic analyses of nematodes have been mainly based on morphology, supplemented with developmental characters, but in recent years molecular methods have provided entirely new data sets. Phylogenetic estimates derived from independent data may provide new insights in character homologies through reciprocal illumination. Classifications of nematodes were often biased according to the expertise of the author and were only recently based on the principles of phylogenetic systematics. Recently, molecular and morphological data have been used to support a new overall classification with only (presumably) monophyletic taxa. In this classification plant, as well as animal, parasitic taxa are hierarchically downgraded in accordance with their phylogenetic history. Species occupy an important position in all aspects of biology, therefore the species concept matters. It determines, for example, the outcome of biodiversity assessments, distribution patterns, etc. However, several problems remain to be solved before a consensus will be reached about the choice of a concept. Future research in nematode systematics should comprise well-focused taxonomy based on a combination of classical and modern methods in a way that can raise the interest of young scientists as well as of funding agencies. It should be realised that, with the dwindling present taxonomic expertise, this is a very urgent matter.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Selected Ordovician Trilobites from the Lake St. John District of Quebec and Their Bearing on Systematics

1995 ◽  
Vol 69 (S42) ◽  
pp. 1-19 ◽  
Author(s):  
Pierre J. Lespérance ◽  
Sylvain Desbiens
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Minimal Length ◽  
Large Data Sets ◽  
Morphological Data ◽  
Eye Position ◽  
Data Sets ◽  
Close Relationship ◽  
The Status

The thorax of Hypodicranotus has ten segments and a spine on the eighth. The ages of Erratencrinurus s.l. spicatus and Erratencrinurus (Erratencrinurus?) vigilans in the Lake St. John district do not confirm their temporal roles leading to subgenera of Erratencrinurus, as has been recently suggested. Phylogenetic analyses of large data sets of species previously referred to Encrinuroides and Physemataspis yield a minimal length cladogram containing 18 species. Encrinuroides is restricted to four species, two of which have biogeographic affinities with Iapetus. These results lead to three clades, named the Walencrinuroides n. gen. clade, Frencrinuroides n. gen. clade, and finally the Physemataspis clade, with an enlarged concept of the genus with the erection of Physemataspis (Prophysemataspis) n. subgen. These last three clades are restricted to North America and Scotland, with alternating predominance of one region. Walencrinuroides s.l. gelaisi n. gen. n. sp. is described. New morphological data on Erratencrinurus s.l. spicatus confirm its close relationship with the clades discussed above. Data are insufficient for phylogenetic analysis of selected cheirurine species here surveyed. Eye position, glabellar segmentation, and pygidial shape differentiate the genera Ceraurus and Gabriceraurus; emended diagnoses of these genera are presented. Ceraurus globulobatus and C. matranseris are distinct, but morphologically close to one another. The status of Gabriceraurus dentatus can be stabilized on its extant types.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3516 ◽  
Author(s):  
Sohath Z. Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation forLucilia eximia, Lucilia retroversa, Lucilia ricaandChloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

Integration of morphological and molecular data sets in estimating fungal phytogenies

1995 ◽  
Vol 73 (S1) ◽  
pp. 649-659 ◽  
Author(s):  
François Lutzoni ◽  
Rytas Vilgalys
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Molecular Data ◽  
Morphological Data ◽  
Homogeneity Test ◽  
Data Sets ◽  
Data Set ◽  
Sampling Statistics ◽  
Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

Molecular and morphological phylogenetic analysis and taxonomic revision of the genus Orleanesia (Laeliinae, Epidendroideae, Orchidaceae)

Phytotaxa ◽  
2019 ◽  
Vol 392 (1) ◽  
pp. 1
Author(s):  
GABRIEL F. GONÇALVES ◽  
ANNA VICTORIA S. R. MAUAD ◽  
GIULIANA TAQUES ◽  
ERIC C. SMIDT ◽  
FÁBIO DE BARROS
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Morphological Data ◽  
Data Sets ◽  
New Synonyms ◽  
Nuclear Its

In order to evaluate the monophyly of the genus Orleanesia (Orchidaceae) and to assess its position within Laeliinae, a phylogenetic analysis was performed using molecular (nuclear ITS and plastid matK DNA sequences) and morphological data. A taxonomic revision of Orleanesia was also performed, with a description of the genus and its species using fresh living plants and 115 exsiccates from 31 herbaria. All phylogenetic analyses were highly congruent, and thus the sequence data from all three data sets were combined. The resulting phylogeny corroborated the monophyly of Orleanesia, with two strongly supported clades, and confirmed Caularthron as its sister group. Character analysis was not very informative due to a high degree of homoplasy. Two lectotypifications and three new synonyms were proposed for the genus, thereby reducing the number of accepted species to six. Although none of the species of Orleanesia are considered endangered, it is clear that some populations are threatened with deforestation and habitat reduction.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12713
Author(s):  
Nikolay A. Poyarkov ◽  
Tan Van Nguyen ◽  
Parinya Pawangkhanant ◽  
Platon V. Yushchenko ◽  
Peter Brakels ◽  
...  
Keyword(s):  
Middle Eocene ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Data ◽  
New Subspecies ◽  
Early Oligocene ◽  
Conservation Actions ◽  
Colonization Hypothesis ◽  
High Level

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the “upstream” colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals Norrisanima miocaena, a new generic name and redescription of a stem balaenopteroid mysticete (Mammalia, Cetacea) from the Miocene of California

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7629 ◽  
Author(s):  
Matthew S. Leslie ◽  
Carlos Mauricio Peredo ◽  
Nicholas D. Pyenson
Keyword(s):  
Phylogenetic Analyses ◽  
Original Description ◽  
Type Specimen ◽  
Megaptera Novaeangliae ◽  
Morphological Data ◽  
Humpback Whales ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Baleen Whales ◽  
Size Evolution

Rorqual whales are among the most species rich group of baleen whales (or mysticetes) alive today, yet the monophyly of the traditional grouping (i.e., Balaenopteridae) remains unclear. Additionally, many fossil mysticetes putatively assigned to either Balaenopteridae or Balaenopteroidea may actually belong to stem lineages, although many of these fossil taxa suffer from inadequate descriptions of fragmentary skeletal material. Here we provide a redescription of the holotype of Megaptera miocaena, a fossil balaenopteroid from the Monterey Formation of California, which consists of a partial cranium, a fragment of the rostrum, a single vertebra, and both tympanoperiotics. Kellogg (1922) assigned the type specimen to the genus Megaptera Gray (1846), on the basis of its broad similarities to distinctive traits in the cranium of extant humpback whales (Megaptera novaeangliae (Borowski, 1781)). Subsequent phylogenetic analyses have found these two species as sister taxa in morphological datasets alone; the most recent systematic analyses using both molecular and morphological data sets place Megaptera miocaena as a stem balaenopteroid unrelated to humpback whales. Here, we redescribe the type specimen of Megaptera miocaena in the context of other fossil balaenopteroids discovered nearly a century since Kellogg’s original description and provide a morphological basis for discriminating it from Megaptera novaeangliae. We also provide a new generic name and recombine the taxon as Norrisanima miocaena, gen. nov., to reflect its phylogenetic position outside of crown Balaenopteroidea, unrelated to extant Megaptera. Lastly, we refine the stratigraphic age of Norrisanima miocaena, based on associated microfossils to a Tortonian age (7.6–7.3 Ma), which carries implications for understanding the origin of key features associated with feeding and body size evolution in this group of whales.

scholarly journals Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

2019 ◽  
Vol 186 (4) ◽  
pp. 934-949 ◽  
Author(s):  
Danilo Harms ◽  
J Dale Roberts ◽  
Mark S Harvey
Keyword(s):  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Biodiversity Hotspot ◽  
Molecular Dating ◽  
Environmental Niche ◽  
Ecological Niche Models ◽  
The South ◽  
Niche Modelling ◽  
South West ◽  
Western Division

Abstract The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

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