Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 585-595
Author(s):  
D.A. Veldkornet ◽  
J.B. Adams ◽  
J.S. Boatwright ◽  
A. Rajkaran
Keyword(s):  
Dna Barcoding ◽  
South African ◽  
Phylogenetic Diversity ◽  
Pairwise Distance ◽  
Closely Related Species ◽  
Phylogenetic Clustering ◽  
Building Community ◽  
Subtropical Estuaries ◽  
Abiotic Interactions ◽  
Conservation Prioritisation

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.

scholarly journals Ability of Current Phylogenetic Clustering to Detect Speciation History

2021 ◽  
Vol 9 ◽  
Author(s):  
Athanasios S. Kallimanis ◽  
Maria Lazarina ◽  
Mariana A. Tsianou ◽  
Aristi Andrikou-Charitidou ◽  
Stefanos Sgardelis
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Common Ancestor ◽  
Pairwise Distance ◽  
Phylogenetic Clustering ◽  
Theoretical Simulation ◽  
Incipient Species ◽  
Evolutionary Relatedness ◽  
History Of ◽  
Game Changer

Phylogenetic diversity aims to quantify the evolutionary relatedness among the species comprising a community, using the phylogenetic tree as the metric of the evolutionary relationships. Could these measures unveil the evolutionary history of an area? For example, in a speciation hotspot (biodiversity cradle), we intuitively expect that the species in the community will be more phylogenetically clustered than randomly expected. Here, using a theoretical simulation model, we estimate the ability of phylogenetic metrics of current diversity to detect speciation history. We found that, in the absence of dispersal, if the incipient species do not coexist in the region of speciation (as expected under allopatric speciation), there was no clear phylogenetic clustering and phylogenetic diversity failed to detect speciation history. But if the incipient species coexisted (sympatric speciation), metrics such as standardized effect size of Faith’s Phylogenetic Diversity (PD) and of Mean Nearest Taxon Distance (MNTD) were able to identify areas of high speciation, while Mean Pairwise Distance (MPD) was a poor indicator. PD systematically outperformed MNTD. Dispersal was a game-changer. It allowed species to expand their range, colonize areas, and led to the coexistence of the incipient species originating from a common ancestor. If speciation gradient was spatially contiguous, dispersal strengthened the associations between phylogenetic clustering and speciation history. In the case of spatially random speciation, dispersal blurred the signal with phylogenetic clustering occurring in areas of low or no speciation. Our results imply that phylogenetic clustering is an indicator of speciation history only under certain conditions.

Morphological description and DNA barcoding of Chaetocladius (Chaetocladius) elisabethae sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Moscow Region

Zootaxa ◽  
2018 ◽  
Vol 4403 (2) ◽  
pp. 378 ◽  
Author(s):  
EUGENYI A. MAKARCHENKO ◽  
MARINA A. MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
DMITRY M. PALATOV
Keyword(s):  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Interspecific Variation ◽  
Instar Larva ◽  
Molecular Data ◽  
Genetic Distances ◽  
Moscow Region ◽  
Morphological Description ◽  
Closely Related Species ◽  
Male Pupa

Illustrated descriptions of the adult male, pupa and fourth instar larva, as well as DNA barcoding results of Chaetocladius (Chaetocladius) elisabethae sp. nov. in comparison with closely related species of Chaetocladius s. str. from the Moscow Region are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between C. (s. str.) elisabethae sp. nov. and other species of the subgenus produced K2P genetic distances of 0.11–0.16, values well associated with interspecific variation. The barcodes of the new species were identical to the Chaetocladius sp. 2ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str. 

Scale dependence in the phylogenetic relatedness of alien and native taxa

2020 ◽  
Vol 13 (5) ◽  
pp. 601-610
Author(s):  
Chris M McGrannachan ◽  
Gillis J Horner ◽  
Melodie A McGeoch
Keyword(s):  
Alien Species ◽  
Spatial Scale ◽  
Native Species ◽  
Spatial Scales ◽  
Pairwise Distance ◽  
Phylogenetic Structure ◽  
Phylogenetic Clustering ◽  
Phylogenetic Relatedness ◽  
Darwin's Naturalization Hypothesis ◽  
Darwin’S Naturalization Hypothesis

Abstract Aims Darwin’s naturalization hypothesis proposes that successfully established alien species are less closely related to native species due to differences in their ecological niches. Studies have provided support both for and against this hypothesis. One reason for this is the tendency for phylogenetic clustering between aliens and natives at broad spatial scales with overdispersion at fine scales. However, little is known about how the phylogenetic relatedness of alien species alters the phylogenetic structure of the communities they invade, and at which spatial scales effects may manifest. Here, we examine if invaded understorey plant communities, i.e. containing both native and alien taxa, are phylogenetically clustered or overdispersed, how relatedness changes with spatial scale and how aliens affect phylogenetic patterns in understorey communities. Methods Field surveys were conducted in dry forest understorey communities in south-east Australia at five spatial scales (1, 20, 500, 1500 and 4500 m2). Standardized effect sizes of two metrics were used to quantify phylogenetic relatedness between communities and their alien and native subcommunities, and to examine how phylogenetic patterns change with spatial scale: (i) mean pairwise distance and (ii) mean nearest taxon distance (MNTD). Important Findings Aliens were closely related to each other, and this relatedness tended to increase with scale. Native species and the full community exhibited either no clear pattern of relatedness with increasing spatial scale or were no different from random. At intermediate spatial scales (20–500 m2), the whole community tended towards random whereas the natives were strongly overdispersed and the alien subcommunity strongly clustered. This suggests that invasion by closely related aliens shifts community phylogenetic structure from overdispersed towards random. Aliens and natives were distantly related across spatial scales, supporting Darwin’s naturalization hypothesis, but only when phylogenetic distance was quantified as MNTD. Phylogenetic dissimilarity between aliens and natives increased with spatial scale, counter to expected patterns. Our findings suggest that the strong phylogenetic clustering of aliens is driven by human-mediated introductions involving closely related taxa that can establish and spread successfully. Unexpected scale-dependent patterns of phylogenetic relatedness may result from stochastic processes such as fire and dispersal events and suggest that competition and habitat filtering do not exclusively dominate phylogenetic relationships at fine and coarse spatial scales, respectively. Distinguishing between metrics that focus on different evolutionary depths is important, as different metrics can exhibit different scale-dependent patterns.

scholarly journals DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae)

2007 ◽  
Vol 274 (1619) ◽  
pp. 1731-1739 ◽  
Author(s):  
T.L Whitworth ◽  
R.D Dawson ◽  
H Magalon ◽  
E Baudry
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Introgressive Hybridization ◽  
Species Number ◽  
Closely Related Species ◽  
Endosymbiotic Bacteria ◽  
Limited Success ◽  
Mtdna Introgression ◽  
Mtdna Haplotype

In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora , known to be infected with the endosymbiotic bacteria Wolbachia . We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia -associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.

DNA barcoding reveals a high incidence of fish species misrepresentation and substitution on the South African market

2012 ◽  
Vol 46 (1) ◽  
pp. 30-40 ◽  
Author(s):  
Donna-Mareè Cawthorn ◽  
Harris Andrew Steinman ◽  
R. Corli Witthuhn
Keyword(s):  
Dna Barcoding ◽  
South African ◽  
Fish Species ◽  
The South ◽  
High Incidence

Cladocerans of the Alona affinis (Leydig, 1860) group from South Africa

Zootaxa ◽  
2009 ◽  
Vol 1990 (1) ◽  
pp. 41-54 ◽  
Author(s):  
ARTEM YU SINEV
Keyword(s):  
South Africa ◽  
South African ◽  
Morphological Characters ◽  
Sensu Stricto ◽  
Closely Related Species ◽  
Unknown Species ◽  
Kwazulu Natal ◽  
African Populations ◽  
Alona Affinis ◽  
The Republic

Study of South African populations of chydorid cladocerans in the Alona affinis-group (Anomopoda: Chydoridae) revealed two closely related species, Alona affinis (Leydig, 1860) and a second, previously unknown, species A. martensi sp. n. No significant differences were seen between South African and Eurasian populations of A. affinis sensu stricto. A. martensi sp. n. differs from other species of the affinis-group by a shorter spine on the basal segment of antennal exopodite, and can be distinguished from A. affinis by a number of additional morphological characters. A. affinis is distributed mainly in the East and South regions of the Republic of South Africa, and is less frequented in this region. Confined mainly to artificial water bodies its presence may be human-mediated. A. martensi sp. n. sems to be endemic to the Drakensberg mountains within the borders of the KwaZulu-Natal Province and Lesotho.

Sign in / Sign up

Export Citation Format

Share Document