Genetic differentiation in the nearly extinct harlequin frogs (Bufonidae: Atelopus), with emphasis on the Andean Atelopus ignescens and A. bomolochos species complexes

Zootaxa ◽  
2010 ◽  
Vol 2574 (1) ◽  
pp. 55 ◽  
Author(s):  
JUAN M. GUAYASAMIN ◽  
ELISA BONACCORSO ◽  
WILLIAM E. DUELLMAN ◽  
LUIS A. COLOMA
Keyword(s):  
Maximum Likelihood ◽  
Genetic Differentiation ◽  
Evolutionary Relationships ◽  
Undescribed Species ◽  
Geographic Isolation ◽  
Field Surveys ◽  
Species Complexes ◽  
Unidentified Species ◽  
Two Populations ◽  
Mitochondrial Fragment

The evolutionary relationships of Andean harlequin frogs were studied, with emphasis on the Atelopus ignescens and A. bomolochos species complexes. Sampling included 53 individuals belonging to eight taxa and several unidentified species, for which a mitochondrial fragment (16S, tRNA-Leu, ND1, and tRNA-Ile; 1294 bp) was amplified. Bayesian and Maximum Likelihood analyses were used to obtain hypotheses of relationships. The resulting phylogeny indicates that the species complexes are non-monophyletic. Additionally, analyses support the presence of four or five undescribed species. Most of these populations and newly discovered lineages have not been recorded in several years and are presumed extinct, the exception being two populations of probably new taxa from mid-elevations in southeastern Ecuador found during recent field surveys. Although sampling is limited, geographic isolation is the most plausible cause of differentiation among populations and taxa.

scholarly journals Ongoing revision of Echiniscoididae (Heterotardigrada: Echiniscoidea), with the description of a new interstitial species and genus with unique anal structures

2019 ◽  
Vol 188 (3) ◽  
pp. 663-680 ◽  
Author(s):  
Nadja Møbjerg ◽  
Aslak Jørgensen ◽  
Reinhardt M Kristensen
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Undescribed Species ◽  
Intertidal Sediments ◽  
Species Complexes ◽  
Close Relationship ◽  
Unidentified Species ◽  
Coi Sequences

Abstract Marine tidal heterotardigrades (Echiniscoididae) have gained increasing interest owing to their unique adaptations and evolutionary position, bridging marine and limnoterrestrial taxa. Echiniscoididae was established to accommodate the marine genera Anisonyches and Echiniscoides. However, it has become apparent that Anisonyches, with its claw configuration, median cirrus and seminal receptacles, clearly has little or no affinity to tidal echiniscoidids with supernumerary claws. Consequently, we establish Anisonychidae fam. nov. to accommodate Anisonyches in a paraphyletic Arthrotardigrada and discuss its affinity to other heterotardigrade taxa. We recently split Echiniscoides into Isoechiniscoides and Echiniscoides s.l. The latter remains a miscellany of species complexes and undescribed genera, and it has become evident that a larger number of echiniscoidids belonging to Echiniscoides, Isoechiniscoides and undescribed genera coexist in intertidal sediments. Here, we erect Neoechiniscoides aski gen. nov., sp. nov. from Roscoff, France, which has a unique anal system, characterized by prominent lateral lobes with a set of wing-like structures. Phylogenetic analyses based on COI sequences infer a close relationship between N. aski, an undescribed species from Roscoff and unidentified species from Maine, USA. We propose that the new genus includes the former Echiniscoides species Echiniscoides pollocki and Echiniscoides horningi, which we hereby transfer.

Tersilochinae of South, Southeast and East Asia, excluding Mongolia and Japan (Hymenoptera: Ichneumonidae)

2011 ◽  
Vol 20 (1) ◽  
pp. 96-148 ◽  
Author(s):  
A.I. Khalaim
Keyword(s):  
Sri Lanka ◽  
South Korea ◽  
East Asia ◽  
Far East ◽  
New Combination ◽  
East China ◽  
Far East Of Russia ◽  
Undescribed Species ◽  
Oriental Region ◽  
Unidentified Species

Tersilochines of South, Southeast and East Asia (excluding Mongolia and Japan) have been studied. Eight genera and 60 species are recorded in the region: Allophrys (2 species), Barycnemis (5 species), Diaparsis (29 species), Phradis (2 species, including 1 unidentified species), Probles (12 species, including 1 unidentified and 6 undescribed species), Sathropterus (2 species), Slonopotamus gen. nov. (2 species) and Tersilochus (6 species, including one species of the obscure status). One genus and 26 species are described as new: Allophrys bruneiensis sp. nov. (Brunei), A. occipitata sp. nov. (Vietnam, India), Diaparsis absista sp. nov. (Brunei), D. bannapeana sp. nov. (Laos), D. bolikhamsaica sp. nov. (Laos, Thailand), D. brunnea sp. nov. (Brunei), D. crenulator sp. nov. (Brunei), D. dediticia sp. nov. (Vietnam, Brunei), D. hilaris sp. nov. (Vietnam), D. karnatakana sp. nov. (India), D. labiensis sp. nov. (Brunei), D. mandibulator sp. nov. (Laos), D. minuta sp. nov. (Vietnam), D. monstrosa sp. nov. (Brunei), D. morleyi sp. nov. (Sri Lanka), D. propodeator sp. nov. (Brunei, Sarawak State of Malaysia, southern Indonesia, Laos), D. pulchra sp. nov. (South Korea), D. sarawakiensis sp. nov. (Sarawak and Pahang states of Malaysia), D. viela sp. nov. (Vietnam, Laos), D. vietnamica sp. nov. (Vietnam), D. zispina sp. nov. (Vietnam), Probles vietnamica sp. nov. (Vietnam, probably East China and south of Far East of Russia), Sathropterus secundus sp. nov. (Vietnam), Slonopotamus elephantoides sp. nov. (Laos), S. indianus sp. nov. (India) and Tersilochus granulatus sp. nov. (South Korea). Generic assignment of two species are changed: Barycnemis sanctijohanni (Rao & Kurian, 1951), new combination, and Probles (Microdiaparsis) caudate (Morley, 1913), new combination. Barycnemis dissimilis and B. tobiasi from Nepal, Diaparsis convexa from Vietnam, D. niphadoctona from Laos, and Sathropterus pumilus from India and Nepal are newly recorded from the countries. The genus Diaparsis comprises almost half of species of the tersilochine fauna of the studied region (29 species, 48%), and is a dominant genus in the Oriental Region. Keys to genera and species of Tersilochinae of South, Southeast and East Asia (excluding Mongolia and Japan) are provided.

scholarly journals Annelid Diversity: Historical Overview and Future Perspectives

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 129
Author(s):  
María Capa ◽  
Pat Hutchings
Keyword(s):  
State Of The Art ◽  
Molecular Taxonomy ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Future Perspectives ◽  
Special Issue ◽  
Species Numbers ◽  
Species Complexes ◽  
Taxonomic Groups ◽  
A New Species

Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.

Phylogeny of Criconematina Siddiqi, 1980 (Nematoda: Tylenchida) based on morphology and D2-D3 expansion segments of the 28S-rRNA gene sequences with application of a secondary structure model

Nematology ◽  
2005 ◽  
Vol 7 (6) ◽  
pp. 927-944 ◽  
Author(s):  
Renato Crozzoli ◽  
Franco Lamberti ◽  
Nicola Vovlas ◽  
James Baldwin ◽  
Sergei Subbotin ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Secondary Structure ◽  
Sequence Divergence ◽  
Complex Model ◽  
Rrna Gene ◽  
28S Rrna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Loop Region ◽  
Unidentified Species

AbstractThe suborder Criconematina is a large group of ecto- and endoparasitic nematodes, including several species of major agricultural importance. The D2-D3 expansion segments of the 28S nuclear ribosomal RNA gene were amplified and sequenced from 23 nominal and six unidentified species from the genera Mesocriconema, Criconemoides, Ogma, Criconema, Xenocriconemella, Hemicriconemoides, Hemicycliophora, Paratylenchus, Tylenchulus, Trophonema and Sphaeronema, together with outgroup taxa from Tylenchidae (Aglenchus) and Atylenchidae (Eutylenchus). A sequence alignment optimised using the secondary structure model was analysed using maximum parsimony, maximum likelihood and Bayesian inference approaches under two models. All analyses yielded a similar topology with differences primarily in the position of poorly supported clades. Although some molecular trees differ from the previous morphologically based hypotheses of criconematid phylogeny, maximum likelihood tests did not yield statistically significant differences between some of the tested classical morphological and molecular topologies. DNA data support monophyly for the genera Mesocriconema, Hemicriconemoides and Criconema and reject the hypothesis of a single origin of criconematids with a cuticular sheath or 'double cuticle'. Application of the complex model of rRNA evolution, considering paired nucleotides for the stem and unpaired nucleotides for the loop region, resulted in a majority rule consensus Bayesian tree with unresolved relationships between main clades. This lack of resolution is expected by the low number of independently evolving nucleotides. Sequence divergence in this DNA segment between populations of Mesocriconema xenoplax, M. sphaerocephalum and Hemicriconemoides cocophillus suggest the presence of several sibling species under these taxa names.

scholarly journals High Genetic Differentiation among European White Oak Species (Quercus spp.) at a Dehydrin Gene

2015 ◽  
Vol 43 (2) ◽  
pp. 582-588 ◽  
Author(s):  
Iacob CRĂCIUNESC ◽  
Barbara VORNAM ◽  
Ludger LEINEMANN ◽  
Reiner FINKELDEY ◽  
Neculae ȘOFLETEA ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Related Species ◽  
Population Level ◽  
Quercus Petraea ◽  
White Oak ◽  
Closely Related Species ◽  
Significant Differentiation ◽  
Dehydrin Gene ◽  
First Time ◽  
Two Populations

Dehydryn genes are involved in plant response to environmental stress and may be useful to examine functional diversity in relation to adaptive variation. Recently, a dehydrin gene (DHN3) was isolated in Quercus petraea and showed little differentiation between populations of the same species in an altitudinal transect. In the present study, inter- and intraspecific differentiation patterns in closely related and interfertile oaks were investigated for the first time at the DHN3 locus. A four-oak-species stand (Quercus frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L.) and two populations for each of five white oak species (Q. frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L. and Q. pedunculiflora K. Koch) were analyzed. Three alleles shared by all five oak species were observed. However, only two alleles were present in each population, but with different frequencies according to the species. At population level, all interspecific pairs of populations showed significant differentiation, except for pure Q. robur and Q. pedunculiflora populations. In contrast, no significant differentiation (p > 0.05) was found among conspecific populations. The DHN3 locus proved to be very useful to differentiate Q. frainetto and Q. pubescens from Q. pedunculiflora (FST = 0.914 and 0.660, respectively) and Q. robur (FST = 0.858 and 0.633, respectively). As expected, the lowest level of differentiation was detected between the most closely related species, Q. robur and Q. pedunculiflora (FST = 0.020). Our results suggest that DHN3 can be an important genetic marker for differentiating among European white oak species.

A reassessment of apheloriine millipede phylogeny: additional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmidae)

Zootaxa ◽  
2007 ◽  
Vol 1610 (1) ◽  
pp. 27-39 ◽  
Author(s):  
PAUL E. MAREK ◽  
JASON E. BOND
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Bayes Factor ◽  
Appalachian Mountains ◽  
Deciduous Forests ◽  
Eastern United States ◽  
Undescribed Species ◽  
Direct Optimization ◽  
Species List ◽  
Phylogenetic Hypotheses

Millipedes in the tribe Apheloriini occur throughout the eastern United States, predominately in the deciduous forests of the Appalachian Mountains. Herein we present a reassessment of apheloriine millipede phylogeny using mitochondrial DNA sequences and an additional 29 exemplar taxa (including 15 undescribed species and all of the species in the genus Brachoria, except one). In this study, first we check the results of the previous phylogeny of the tribe (Marek and Bond, 2006) with different alignment and phylogenetic techniques (direct optimization and maximum likelihood), and second reconstruct a new phylogeny evaluating it in the same way with Bayesian, maximum likelihood, and direct optimization. Using this updated and expanded phylogeny, we tested historical classifications with Bayes factor and Shimodaira-Hasegawa hypothesis testing, consistently finding very strong evidence against their implied phylogenetic hypotheses. Lastly, using the new phylogeny as a foundation, we make taxonomic modifications and provide an updated species list of Apheloriini (106 species/17 genera).

scholarly journals Evolutionary relationships of completely sequenced Clostridia species and close relatives

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4276-4283 ◽  
Author(s):  
Takashi Kunisawa
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Gene Arrangement ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bayesian Tree ◽  
Maximum Likelihood Methods ◽  
Genome Sequence Information ◽  
Close Relatives

The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

Systematics of the Boana semilineata species group (Anura: Hylidae), with a description of two new species from Amazonian Ecuador

2020 ◽  
Vol 190 (1) ◽  
pp. 149-180
Author(s):  
Marcel A Caminer ◽  
Santiago R Ron
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Species Group ◽  
Valid Species ◽  
Undescribed Species ◽  
Phenotypic Characters ◽  
Species Complexes ◽  
Candidate Species ◽  
Amazonian Ecuador ◽  
First Time

Abstract The combination of genetic and phenotypic characters for species delimitation has allowed the discovery of many undescribed species of Neotropical amphibians. In this study, we used DNA sequences (genes 12S, 16S, ND1 and COI) and morphologic, bioacoustic and environmental characters of the Boana semilineata group to evaluate their phylogenetic relationships and assess their species limits. In addition, we included DNA sequences of several species of Boana to explore cryptic diversity in other groups. We found three Confirmed Candidate Species (CCS) within the B. semilineata group. Holotype examination of Hyla appendiculata shows that it is a valid species that corresponds to one of the CCS, which is here transferred to Boana. We describe the two remaining CCS. Our phylogeny highlights a number of secondary but meaningful observations that deserve further investigation: (1) populations of B. pellucens from northern Ecuador are more closely related to B. rufitela from Panama than to other Ecuadorian populations of B. pellucens; (2) we report, for the first time, the phylogenetic relationships of B. rubracyla showing that it is closely related to B. rufitela and B. pellucens; and (3) B. cinerascens and B. punctata form two species complexes consisting of several unnamed highly divergent lineages. Each of these lineages likely represents an undescribed species.

Genetic differences within natural and planted stands of Quercus petraea

2011 ◽  
Vol 6 (4) ◽  
pp. 597-605 ◽  
Author(s):  
Jiří Dostálek ◽  
Tomáš Frantík ◽  
Miroslava Lukášová
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Genetic Structure ◽  
Quercus Petraea ◽  
Genetic Differences ◽  
Sessile Oak ◽  
Population Structures ◽  
Nuclear Microsatellite ◽  
The Impact ◽  
Two Populations

AbstractFive sessile oak [Quercus petraea (Matt.) Liebl.] stands from the Czech Republic were studied to learn about the impact of different types of forest management regimes on the genetic differences among tree populations and on population structures. One population had not been markedly affected by human activity, two populations represented unplanted stands that were extensively managed for a long period of time using the coppice system, and two populations were planted stands. Approximately 100 trees from each stand were mapped and subsequently genotyped using 10 nuclear microsatellite loci. We determined the spatial genetic structure of each population and the genetic differentiation among the populations. We found that: (i) the populations were genetically differentiated, but the differences between the unplanted and planted stands were not markedly significant; (ii) the genetic differentiation among the populations depended on the geographical distribution of the populations; (iii) within unplanted stands, a strong spatial genetic structure was seen; and (iv) within planted stands, no spatial genetic structure was observed. Our findings implies that the analysis of spatial genetic structure of the sessile oak forest stand can help reveal and determine its origin.

Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 125-138
Author(s):  
Sohrab Mirzaei ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
28S Rdna ◽  
Molecular Characterisation ◽  
Morphometric Data ◽  
Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

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