First detection of an ocellate octopus in the Revillagigedos ecoregion, a biodiversity hotspot located in the Tropical East Pacific Province

The biodiversity of mollusks, particularly cephalopods, has not been exhaustively determined in the Revillagigedos ecoregion, which is a biodiversity hotspot for several marine groups located in the Tropical East Pacific Province. In our study, we detected and examined ocellate octopuses from Socorro and Clarion Islands, and determined their identity using morphological criteria and molecular data from two mitochondrial genes (COIII and COI). The taxon identified was Octopus oculifer, a species considered endemic to the Galapagos Archipelago. In addition, according to our analyses, O. mimus, O. hubbsorum and O. oculifer are very closely related and may represent a species complex comprised of three morphotypes. We found that the evolutionary relationships among octopuses are not determined by the presence of ocelli. This study is the first to report a clade represented by ocellate and non-ocellate species, in addition, the identity of cephalopods in the Revillagigedos was determined with analytical support.

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Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

BMC Genomics ◽

10.1186/s12864-021-08006-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qian Xiong ◽

Yuxin Hu ◽

Wenqi Lv ◽

Qinghua Wang ◽

Guoxiang Liu ◽

...

Keyword(s):

Adaptive Evolution ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Small Variation ◽

Molecular Data ◽

Evolutionary Relationships ◽

Single Family ◽

Chloroplast Genomes ◽

Morphological Criteria ◽

Cp Genome

Abstract Background The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales. Results The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats. Conclusions Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

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Chloroplast Genomes of Five Oedogonium Species: Genome Structure, Phylogenetic Analysis and Adaptive Evolution

10.21203/rs.3.rs-449423/v1 ◽

2021 ◽

Author(s):

xiong qian ◽

Yuxin Hu ◽

Wenqi Lv ◽

Qinghua Wang ◽

Guoxiang Liu ◽

...

Keyword(s):

Adaptive Evolution ◽

Phylogenetic Analyses ◽

Genome Structure ◽

Small Variation ◽

Molecular Data ◽

Evolutionary Relationships ◽

Chloroplast Genomes ◽

Morphological Criteria ◽

The Difference ◽

Cp Genome

Abstract BackgroundThe order Oedogoniales can be divided into three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.ResultsThe five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.ConclusionsOur results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

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Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

Organisms Diversity & Evolution ◽

10.1007/s13127-021-00500-4 ◽

2021 ◽

Author(s):

Antonio Zurita ◽

Cristina Cutillas

Keyword(s):

Taxonomic Status ◽

Molecular Study ◽

Molecular Data ◽

Point Of View ◽

Morphological Data ◽

Molecular Approach ◽

Nuclear Marker ◽

Mitochondrial Markers ◽

Morphological Criteria ◽

Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

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Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

Genome Biology and Evolution ◽

10.1093/gbe/evz209 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2824-2849 ◽

Cited By ~ 6

Author(s):

Paweł Mackiewicz ◽

Adam Dawid Urantówka ◽

Aleksandra Kroczak ◽

Dorota Mackiewicz

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Genes ◽

The Other ◽

Phylogenetic Position ◽

Evolutionary Relationships ◽

Mitochondrial Genomes ◽

Ancestral State ◽

Phylogenetic Information ◽

Long Time ◽

Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

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Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

Invertebrate Systematics ◽

10.1071/is18019 ◽

2018 ◽

Vol 32 (6) ◽

pp. 1298 ◽

Cited By ~ 4

Author(s):

Feng Zhang ◽

Daoyuan Yu ◽

Mark I. Stevens ◽

Yinhuan Ding

Keyword(s):

Species Complex ◽

Instar Larva ◽

Molecular Data ◽

Integrative Taxonomy ◽

Species Level ◽

Integrative Approach ◽

Gene Markers ◽

Late Neogene ◽

Taxonomic Approach ◽

Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

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Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.1999.0605 ◽

1999 ◽

Vol 266 (1414) ◽

pp. 63-73 ◽

Cited By ~ 56

Author(s):

Joachim Schütze ◽

Anatoli Krasko ◽

Marcio Reis Custodio ◽

Sofla M. Efremova ◽

Isabel M. Müller ◽

...

Keyword(s):

Molecular Data ◽

Evolutionary Relationships

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Systematics and phylogeography of the Australasian mangrove crabs Parasesarma semperi and P. longicristatum (Decapoda : Brachyura : Sesarmidae) based on morphological and molecular data

Invertebrate Systematics ◽

10.1071/is17040 ◽

2018 ◽

Vol 32 (1) ◽

pp. 196 ◽

Cited By ~ 2

Author(s):

Adnan Shahdadi ◽

Peter J. F. Davie ◽

Christoph D. Schubart

Keyword(s):

Genetic Data ◽

Morphological Characters ◽

Molecular Data ◽

Geographic Range ◽

The Philippines ◽

Mitochondrial Genes ◽

Width Ratio ◽

Sister Relationship ◽

Mangrove Crabs ◽

Morphological And Molecular Data

Parasesarma semperi (Bürger, 1893) was first described from Bohol in the Philippines and is considered to be widely distributed in Southeast Asia. Parasesarma longicristatum (Campbell, 1967) was originally described as a subspecies of P. semperi from Queensland, Australia, and later recognised as a full species. In this study, we re-examine specimens of the two species from across their entire geographic range using genetic markers, a morphometric analysis, and traditional morphological characters. Previous taxonomic species diagnoses were found to be unreliable, but morphometric principle component analyses consistently separate the two species, with the length to width ratio of the propodus of the fourth pereiopod being of particular importance. Genetic data corresponding to the mitochondrial genes COI, ND1 and 16S confirmed a close sister relationship between the two species, forming reciprocally monophyletic groups. Both species have high haplotype diversities and high intraspecific gene flow.

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A new Gonatocerus (Hymenoptera: Mymaridae) from Argentina, with taxonomic notes and molecular data on the G. tuberculifemur species complex

Zootaxa ◽

10.11646/zootaxa.1949.1.1 ◽

2008 ◽

Vol 1949 (1) ◽

pp. 1-29 ◽

Cited By ~ 13

Author(s):

SERGUEI V. TRIAPITSYN ◽

GUILLERMO A. LOGARZO ◽

JESSE H. DE LEÓN ◽

EDUARDO G. VIRLA

Keyword(s):

New Species ◽

Species Complex ◽

Reciprocal Cross ◽

Molecular Data ◽

Species Group ◽

Host Association ◽

Cross Breeding ◽

Association Data ◽

Distinguishing Features ◽

Distinct Taxon

Gonatocerus deleoni Triapitsyn, Logarzo & Virla sp. n., reared from sentinel eggs of Tapajosa rubromarginata (Signoret) (Cicadellidae: Cicadellinae: Proconiini) on citrus plants, a new member of the ater species group of Gonatocerus Nees (Mymaridae), is described from the state of Mendoza, Argentina. Taxonomic notes and host association data are provided to help differentiate this new species from the morphologically similar but genetically distinct taxon, G. tuberculifemur (Ogloblin). The female of the latter is redescribed and the male is newly described. Gonatocerus deleoni, G. tuberculifemur, and three forms (different molecular clades) comprise the G. tuberculifemur complex. These forms are identified but not formally described because of lack of morphologically distinguishing features. The taxonomic conclusions are supported by molecular data, and by results of reciprocal cross-breeding experiments between most of them.

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Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus

Contributions to Zoology ◽

10.1163/18759866-20191421 ◽

2020 ◽

Vol 89 (2) ◽

pp. 188-209

Author(s):

Yutaro Oku ◽

Kenji Iwao ◽

Bert W. Hoeksema ◽

Naoko Dewa ◽

Hiroyuki Tachikawa ◽

...

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Scleractinian Corals ◽

Type Specimens ◽

Mitochondrial Coi ◽

Clade B ◽

Unknown Species ◽

Molecular Phylogenetic ◽

Morphological Differences

Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.

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Molecular phylogeny of the weevil genus Kyklioacalles Stüben, with descriptions of a new subgenus Glaberacalles and two new species (Curculionidae: Cryptorhynchinae)

Zootaxa ◽

10.11646/zootaxa.2662.1.2 ◽

2010 ◽

Vol 2662 (1) ◽

pp. 28 ◽

Cited By ~ 1

Author(s):

PETER E. STÜBEN ◽

JONAS J. ASTRIN

Keyword(s):

New Species ◽

Molecular Phylogeny ◽

Bayesian Analysis ◽

Morphological Differentiation ◽

Molecular Data ◽

Mitochondrial Genes ◽

Morphological Evidence ◽

New Subgenus ◽

Western Palearctic ◽

Two New Species

A molecular phylogeny of the western Palearctic weevil genus Kyklioacalles Stüben, 1999 is presented, combining two mitochondrial genes (CO1 and 16S) in a Bayesian analysis. Based on molecular data, the validity of the subspecies Kyklioacalles punctaticollis punctaticollis (Lucas, 1849) and Kyklioacalles punctaticollis meteoricus (Meyer, 1909) is discussed and the morphological differentiation of the endophalli and known distributions of both subspecies are verified. Glaberacalles subg. n. (formerly Kyklioacalles punctaticollis-group) and two new species are described, Kyklioacalles atlasicus sp.n. from Morocco and Kyklioacalles plantapilosus sp.n. from Spain. Kyklioacalles berberi (Stüben, 2005), comb. n. and Kyklioacalles olcesei (Tournier, 1873) comb. n. are transferred from Acalles Schoenherr. The molecular results further advocate a transfer of Onyxacalles pyrenaeus (Boheman, 1844) to Kyklioacalles; however this is not supported by morphological evidence. Kyklioacalles almadensis Stüben, 2004 syn. n. (Spain) is synonymized with Kyklioacalles bupleuri Stüben, 2004 (Tunisia). A catalogue of all 40 (sub-)species of Kyklioacalles is given and a key of the species of the subgenus Glaberacalles is presented.

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