scholarly journals Molecular evidence for cryptic species in the common slug eating snake Duberria lutrix lutrix (Squamata, Lamprophiidae) from South Africa

ZooKeys ◽  
2019 ◽  
Vol 838 ◽  
pp. 133-154 ◽  
Author(s):  
Kyle Kullenkampff ◽  
Francois Van Zyl ◽  
Sebastian Klaus ◽  
Savel R. Daniels
Keyword(s):  
South Africa ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Divergence Time ◽  
Total Evidence ◽  
Phylogeographic Structure ◽  
Climatic Fluctuations ◽  
Dna Sequence Data ◽  
The Common

We examined the impact of climatic fluctuations on the phylogeographic structure of the common slug eating snake (Duberrialutrixlutrix) throughout its distribution in South Africa. The evolutionary history within the taxon was examined using partial DNA sequence data for two mitochondrial genes (ND4 + cytb) in combination with a nuclear locus (SPTBN1). Phylogenetic relationships were investigated for both the combined mtDNA and total evidence DNA sequence data. In addition, population and demographic analyses together with divergence time estimations were conducted on the combined mtDNA data. Topologies derived from the combined mtDNA analyses and the total evidence analyses were congruent and retrieved five statistically well-supported clades, suggesting thatDuberrial.lutrixrepresents a species complex. The five clades were generally allopatric, separated by altitudinal barriers and characterised by the absence of shared mtDNA haplotypes suggesting long term isolation. Divergence time estimations indicate that the diversification within theD.l.lutrixspecies complex occurred during the Plio/Pleistocene as a result of climatic fluctuations and habitat shifts for the species. A taxonomic revision of theD.l.lutrixspecies complex may be required to delineate possible species boundaries.

scholarly journals Veterinary Fusarioses within the United States

2016 ◽  
Vol 54 (11) ◽  
pp. 2813-2819 ◽  
Author(s):  
Kerry O'Donnell ◽  
Deanna A. Sutton ◽  
Nathan Wiederhold ◽  
Vincent A. R. G. Robert ◽  
Pedro W. Crous ◽  
...  
Keyword(s):  
United States ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The United States ◽  
Content Type ◽  
Dna Sequence Data ◽  
Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

2011 ◽  
Vol 20 (18) ◽  
pp. 3856-3878 ◽  
Author(s):  
DUSTIN A. WOOD ◽  
A. G. VANDERGAST ◽  
J. A. LEMOS ESPINAL ◽  
R. N. FISHER ◽  
A. T. HOLYCROSS
Keyword(s):  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Dna Sequence Data

scholarly journals Problems related to the taxonomic placement of incompletely preserved amber fossils: transfer of the Paleogene liverwort <i>Cylindrocolea dimorpha</i> (Cephaloziellaceae) to the extant <i>Odontoschisma</i> sect. <i>Iwatsukia</i> (Cephaloziaceae)

Fossil Record ◽  
2017 ◽  
Vol 20 (2) ◽  
pp. 147-157 ◽  
Author(s):  
Kathrin Feldberg ◽  
Jiří Váňa ◽  
Alfons Schäfer-Verwimp ◽  
Michael Krings ◽  
Carsten Gröhn ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Divergence Time ◽  
New Combination ◽  
Crown Group ◽  
Fossil Species ◽  
Dna Sequence Data ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Baltic

Abstract. A revision of the Baltic and Bitterfeld amber fossils assigned to Cylindrocolea dimorpha (Cephaloziellaceae) has yielded evidence of the presence of multicellular, bifid underleaves, which have not previously been reported for this species and conflict with the current circumscription of the family. We transfer the fossil species to Odontoschisma (sect. Iwatsukia) and propose the new combination O. dimorpha of the Cephaloziaceae. Characteristics of the fossil include an overall small size of the plant, entire-margined, bifid leaves and underleaves, more or less equally thickened leaf cell walls, ventral branching that includes stoloniform branches with reduced leaves, and the lack of a stem hyalodermis and gemmae. Placement of the fossil in Cephaloziaceae profoundly affects divergence time estimates for liverworts based on DNA sequence variation with integrated information from the fossil record. Our reclassification concurs with hypotheses on the divergence times of Cephaloziaceae derived from DNA sequence data that provide evidence of a late Early Cretaceous to early Eocene age of the Odontoschisma crown group and an origin of O. sect. Iwatsukia in the Late Cretaceous to Oligocene.

scholarly journals Ecology and seasonality of Pseudo-nitzschia species (Bacillariophyceae) in the northwestern Adriatic Sea over a 30-years period (1988–2020)

2021 ◽  
Vol 22 (3) ◽  
pp. 505
Author(s):  
SONIA GIULIETTI ◽  
TIZIANA ROMAGNOLI ◽  
ALESSANDRA CAMPANELLI ◽  
CECILIA TOTTI ◽  
STEFANO ACCORONI
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Species Complex ◽  
Adriatic Sea ◽  
Sequence Data ◽  
Coastal Station ◽  
Dna Sequence Data ◽  
The Mean ◽  
First Time ◽  
North Western

The ecology and seasonality of Pseudo-nitzschia species and their contribution to phytoplankton community were analysed for the first time at the coastal station of the LTER-Senigallia-Susak transect (north-western Adriatic Sea) from 1988 to 2020. Species composition was addressed using DNA sequence data obtained from 106 monoclonal strains isolated from January 2018 to January 2020. The mean annual cycle of total phytoplankton in the study period (Feb 1988–Jan 2020) showed maximum abundances in winter followed by other peaks in spring and autumn. Diatoms were the main contributors in terms of abundance during the winter and the spring blooms. The autumn peak was due to phytoflagellates and diatoms. In summer phytoflagellates dominated the community, followed by diatoms and dinoflagellates, which in this season reached their annual maximum. Pseudo-nitzschia spp. represented on average 0.4–17.6% of diatom community, but during their blooms they could reach up to up to 90% of the total diatom abundances with 106 cells l-1. By LM, six different taxa were recognized: Pseudo-nitzschia cf. delicatissima and P. cf. pseudodelicatissima were the most abundant, followed by P. cf. fraudulenta, P. pungens, P. multistriata and P. cf. galaxiae. P. cf. fraudulenta and P. pungens were indicator taxa of winter. P. cf. delicatissima and P. cf. pseudodelicatissima were spring and summer taxa, respectively. P. galaxiae showed maximum abundances in autumn. DNA sequences revealed the presence of two species belonging to the ’P. seriata group’ (i.e. P. fraudulenta and P. pungens) and four species belonging to the ‘P. delicatissima group’ (P. calliantha and P. mannii within the P. pseudodelicatissima species complex, and P. delicatissima and P. cf. arenysensis within the P. delicatissima species complex). The presence of several cryptic and pseudo-cryptic species highlights the need to combine LM observations with DNA sequence data when the ecology of Pseudo-nitzschia is investigated. 

scholarly journals Variability in Geminivirus Isolates Associated with Phaseolus spp. in Brazil

1999 ◽  
Vol 89 (3) ◽  
pp. 262-268 ◽  
Author(s):  
Josias C. Faria ◽  
Douglas P. Maxwell
Keyword(s):  
Mosaic Virus ◽  
Dna Sequence ◽  
Sequence Data ◽  
Lima Bean ◽  
Sequence Comparisons ◽  
Dna Sequence Data ◽  
Leonurus Sibiricus ◽  
The Common ◽  
Polymerase Chain ◽  
Lima Beans

Bean golden mosaic geminivirus (BGMV) is the single most devastating virus of common beans in the tropical and subtropical Americas and the Caribbean Basin. The BGMV from Brazil, named BGMV-BZ, is considered distinct from BGMV-PR isolates from Puerto Rico, Guatemala, and the Dominican Republic because of DNA sequence data, the ability to form pseudorecombinants, and mechanical transmissibility properties. In bean-growing areas of Brazil, samples were collected from beans, lima beans, and the weed Leonurus sibiricus displaying typical symptoms of infection by geminiviruses. Viral DNA fragments comprising part of the rep gene, the common region, and part of the cp gene were amplified by polymerase chain reaction, cloned, and sequenced. The bean samples had geminivirus with sequences nearly identical to that of BGMV-BZ collected in Goiânia, state of Goiás, in 1986. The sample from lima bean contained a new species of geminivirus that induces symptoms similar to those induced by BGMV-BZ and was named lima bean golden mosaic virus (LBGMV-BR). While all sequences from bean samples clustered with BGMV-BZ, the sequence from the lima bean isolate stood alone. A mixed infection with abutilon mosaic geminivirus was also found in a single sample from the state of São Paulo. DNA sequence comparisons indicate that the virus isolate from L. sibiricus represents a new geminivirus species, designated here as leonurus mosaic virus.

scholarly journals Capalictus, a new subgenus of Lasioglossum Curtis 1833 from South Africa, with description of three new species (Hymenoptera, Apoidea, Halictidae)

2012 ◽  
Author(s):  
Alain Pauly ◽  
Jason Gibbs ◽  
Michael Kuhlmann
Keyword(s):  
South Africa ◽  
New Species ◽  
South African ◽  
Dna Sequence ◽  
Type Species ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
New Subgenus ◽  
Basal Clade ◽  
Three New Species

Capalictus, a new subgenus of Lasioglossum Curtis, 1833 (Hymenoptera, Apoidea, Halic-tidae), endemic to the South African Cape Province, is described. The type species is Halictus mosselinus Cockerell, 1945. Evylaeus (Sellalictus) fynbosensis (Pauly et al., 2008) is a new junior synonym of L. (C.) mosselinum. Three new species are described: Lasioglossum (Capalictus) hantamense sp. nov., L. (C.) tigrinum sp. nov. and L. (C.) timmermanni sp. nov. DNA sequence data from three nuclear genes support morphologically-determined species limits. Capalictus is a basal clade of the Hemihalictus series of Lasioglossum.

scholarly journals Radiation and divergence in the Rhagoletis Pomonella species complex: inferences from DNA sequence data

2008 ◽  
Vol 21 (3) ◽  
pp. 900-913 ◽  
Author(s):  
X. XIE ◽  
A. P. MICHEL ◽  
D. SCHWARZ ◽  
J. RULL ◽  
S. VELEZ ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Rhagoletis Pomonella ◽  
Dna Sequence Data

Systematics of the Peripatopsis clavigera species complex (Onychophora : Peripatopsidae) reveals cryptic cladogenic patterning, with the description of five new species

2020 ◽  
Author(s):  
Aaron Barnes ◽  
Till Reiss ◽  
Savel R. Daniels
Keyword(s):  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Divergence Time ◽  
Haplotype Network ◽  
Climatic Conditions ◽  
Morphological Data ◽  
Forest Belt ◽  
Mitochondrial Coi ◽  
Velvet Worms

During the present study, DNA sequence data, gross morphology and scanning electron microscopy (SEM) were used to examine cryptic species boundaries in the velvet worm, Peripatopsis clavigera species complex, from the southern Cape Afrotemperate forest belt in South Africa. Sequence data were generated for the mitochondrial COI and the nuclear 18S rRNA loci and phylogenetically analysed using both a Bayesian inference and a maximum-likelihood approach. Both the COI data and the combined DNA sequence topology (COI+18S) revealed the presence of five clades within the Peripatopsis clavigera species complex, and revealed that specimens from Tulbagh were distantly related and represented a sixth clade. The evolutionary distinction of the five clades was corroborated to varying degrees by the four species-delimitation methods (ABGD, PTP, GMYC and STACEY); however, both the gross morphological data and the SEM provided limited diagnostic differences between the five clades. Furthermore, the COI haplotype network and phylogeographic analyses provided evidence of genetic isolation between lineages that are currently syntopic. The distribution of genealogically exclusive and widespread maternal lineages was atypical among velvet worms and did not reflect the general trend of genetic and geographical isolation. Instead, lineages exhibited admixture among localities, a result most likely due to fluctuations in climatic conditions affecting the southern Cape Afrotemperate forest during the Pliocene–Pleistocene period as evident from our divergence time estimations. Four novel, narrow-range endemic species – P. ferox, sp. nov., P. mellaria, sp. nov., P. edenensis, sp. nov. and P. mira, sp. nov. – are described within the P. clavigera species complex, whereas the Tulbagh specimens are described as P. tulbaghensis, sp. nov. Collectively, these results demonstrate that Peripatopsis likely contains several undescribed species.

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