scholarly journals How did the toad get over the sea to Skye? Tracing the colonisation of Scottish inshore islands by common toads (Bufo bufo)

2021 ◽  
pp. 204-213
Author(s):  
David O'Brien
Keyword(s):  
Native Species ◽  
Clustering Algorithm ◽  
Glacial Refugia ◽  
Bufo Bufo ◽  
Genetic Distances ◽  
Small Islands ◽  
Mt Dna ◽  
Last Glaciation ◽  
Isle Of Skye ◽  
Rule Out

Processes of island colonisation have long been of interest to biologists. Colonisation events themselves are rarely observed, but the processes involved may be inferred using genetic approaches. We investigated possible means of island colonisation by common toads (Bufo bufo) in western Scotland (the Isle of Skye and five neighbouring small islands), using evidence derived from nuclear microsatellites and mitochondrial (mt) DNA. Levels of microsatellite allelic richness for populations on Skye were high and comparable to adjacent mainland populations, but lower for populations on small islands. Pairwise measures of genetic distances between populations and a clustering algorithm were both suggestive of frequent gene flow between Skye and the mainland. For small islands the levels of genetic differentiation were higher, implying stronger isolation and no evidence for inbreeding. The distribution of mtDNA haplotypes broadly mirrored the genetic structure revealed by microsatellites. Reconciled with existing palaeoclimatological evidence, since the last glaciation, our findings rule out the possibility that the B. bufo populations stem from glacial refugia, or that recent anthropogenic transfer of toads is responsible for their current distribution. The most parsimonious explanation of our data is that the studied inshore islands have been repeatedly colonised via rafting from the mainland or neighbouring islands. This may give us insights into the processes likely to take place when ice sheets retreat poleward as a result of climate change. It also has implications for the colonisation of both native and invasive non-native species, and hence the biosecurity of island refugia.

Possibility Clustering Algorithm for Incomplete Data Based on a Deep Computing Model

2021 ◽  
pp. 2141012
Author(s):  
Dongping Li ◽  
Yingchun Yang ◽  
Qiang Yue ◽  
Liqi Cheng ◽  
Jie Song ◽  
...  
Keyword(s):  
Game Theory ◽  
Incomplete Data ◽  
Data Analytics ◽  
Clustering Algorithm ◽  
Fundamental Theory ◽  
Computing Model ◽  
The Game Theory ◽  
The Face ◽  
Experimental Findings ◽  
Rule Out

Clustering is an essential part of data analytics and in Wireless Sensor Networks (WSN). It becomes a problem for causes such as insufficient, unavailable, or compromised data in the face of uncertainties. A solution to tackle the instability of clusters due to missed values has been proposed. The fundamental theory determines whether to incorporate an entity into a group if it is not clear and probable. One of the main issues is identifying requirements for three forms of decision definition, including an entity in a cluster, removing an object from a group, or delaying a decision (defer) to involve or rule out a group. Current studies do not adequately discuss threshold identification and use their fixed values implicitly. This work explores using the game theory-based Possibility Clustering Algorithm for Incomplete Data (PCA-ID) framework to address this problem. In specific, a game theory will be described in which thresholds are determined based on a balance between the groups’ precision and generic characteristics. The points calculated are used to elicit judgments for the grouping of unknown objects. Experimental findings on the deep learning datasets show that the PCA-ID increases the overall quality considerably while maintaining comparable precision levels in competition with similar systems.

DNA barcoding and integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species

Zootaxa ◽  
2011 ◽  
Vol 2997 (1) ◽  
pp. 19 ◽  
Author(s):  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI ◽  
ILARIA GIOVANNINI ◽  
MICHELE CESARI
Keyword(s):  
Dna Barcoding ◽  
Integrative Taxonomy ◽  
Genetic Distances ◽  
Type Locality ◽  
Morphological Data ◽  
New Taxon ◽  
Black Forest ◽  
Mt Dna ◽  
Additional Material ◽  
Starting Point

Within the framework of a DNA barcoding project on tardigrade species, a study was carried out on Macrobiotus hufelandi C.A.S. Schultze 1834, the first formally described tardigrade species. We used samples collected from the type locality and additional material from other European sites containing species of the “M. hufelandi group”. The study was performed by integrating morphological, karyological and molecular (mt-DNA cox1) information and comparing these data with morphological data from the type material. Several species from this group were found in the type locality of M. hufelandi (near Freiburg, Black Forest, Germany) and these were all barcoded. One was M. hufelandi, the other two were: Macrobiotus sandrae Bertolani & Rebecchi 1993 (originally described from the same locality), and Macrobiotus vladimiri Bertolani, Biserov, Rebecchi & Cesari in press (type locality Andalo, Italy), all with interspecific genetic distances of more than 19%. A fourth cryptic species, which had the same morphology as M. hufelandi but a genetic distance of 6.7%, was not described as a new taxon but named M. cf. hufelandi sp.1 for this study. Macrobiotus sandrae and M. vladimiri were also present (and barcoded) in Italy (Alps). Additional individuals (animals and eggs) were also found, and barcoded, in Italy (Apennines) and Switzerland that belonged to the haplogroup Macrobiotus cf. hufelandi sp. 1. These data together with other recent studies on tardigrade DNA barcoding represent a starting point for further studies on tardigrade biogeography, phylogeography and diversity.

scholarly journals Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 183-199 ◽  
Author(s):  
Chante Powell ◽  
Virgilio Caleca ◽  
Martina Sinno ◽  
Michaela van Staden ◽  
Simon van Noort ◽  
...  
Keyword(s):  
South Africa ◽  
Native Species ◽  
Fruit Fly ◽  
Genetic Distances ◽  
Sub Saharan Africa ◽  
Olive Fruit Fly ◽  
Western Cape ◽  
Agricultural Pests ◽  
Wasp Species ◽  
Parasitism Rates

Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.

scholarly journals Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrea Chiocchio ◽  
Jan. W. Arntzen ◽  
Iñigo Martínez-Solano ◽  
Wouter de Vries ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Environmental Changes ◽  
Glacial Refugia ◽  
Bufo Bufo ◽  
Genetic Admixture ◽  
Secondary Contact ◽  
Last Interglacial ◽  
Contact Zones ◽  
Genetic Lineages

AbstractGenetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.

scholarly journals Publisher Correction: Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrea Chiocchio ◽  
Jan. W. Arntzen ◽  
Iñigo Martínez‑Solano ◽  
Wouter de Vries ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Glacial Refugia ◽  
Bufo Bufo

scholarly journals The elephant in the room: first record of invasive gregarious species of serpulids (calcareous tube annelids) in Majorca (western Mediterranean)

2021 ◽  
Vol 85 (1) ◽  
pp. 15-28
Author(s):  
Maël Grosse ◽  
Roberto Pérez ◽  
Mateo Juan-Amengual ◽  
Joan Pons ◽  
María Capa
Keyword(s):  
Native Species ◽  
Species Complex ◽  
Sequence Data ◽  
First Record ◽  
Abundant Species ◽  
Molecular Data ◽  
Genetic Distances ◽  
Western Mediterranean ◽  
Morphological Examination ◽  
Nuisance Species

Although there are several nuisance species of serpulids reported worldwide, the present study shows that some of them have been overlooked even in geographic areas that are considered well studied. We report for the first time in Majorca the invasive species Ficopomatus enigmaticus and the first records for the Balearic Islands of the also non-native species Hydroides dianthus, H. dirampha, H. elegans and H. nigra. The most abundant species were F. enigmaticus, found at higher densities in Portixol (with up to 280 ind. m–2), and H. elegans, found at highest densities in the port of Palma (with up to 270 ind. m–2). Species have been identified after morphological examination and corroborated by mitochondrial DNA sequence data: cytochrome c oxidase subunit 1 (COI) and cytochrome b (Cytb). Molecular data show that the same haplotypes have been found in distant and disjoint biogeographic areas worldwide, which is only explicable by unintentional translocation of specimens through vectors (i.e. ship hulls or ballast water). Species delimitation analyses support previous findings that species complexes are common in both Ficopomatus and Hydroides. In fact, only among the Majorcan samples were we able to detect three species of the F. enigmaticus species complex, two of the H. elegans species complex and two of the H. dianthus species complex. The genetic distances between members of the F. enigmaticus species complex are 8.7% to 16.7% in COI sequences. The species of Hydroides hold 5.4% to 47.6 % genetic divergence between species of the same complex.

scholarly journals A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 72
Author(s):  
Lela Urushadze ◽  
George Babuadze ◽  
Mang Shi ◽  
Luis E. Escobar ◽  
Matthew R. Mauldin ◽  
...  
Keyword(s):  
New Species ◽  
Genetic Distances ◽  
Cross Sectional ◽  
New Subgenus ◽  
Sequencing Method ◽  
Positive Rate ◽  
Anal Swab ◽  
Amino Acid Levels ◽  
Three New Species ◽  
Rule Out

Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.

Genetic variation in the widespread Embothrium coccineum (Proteaceae) endemic to Patagonia: effects of phylogeny and historical events

2007 ◽  
Vol 55 (8) ◽  
pp. 809 ◽  
Author(s):  
Cintia P. Souto ◽  
Andrea C. Premoli
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Life History Traits ◽  
Glacial Refugia ◽  
Genetic Distances ◽  
Species Level ◽  
Historical Events ◽  
Adult Trees ◽  
Cold Tolerant ◽  
Parsimony Trees

Allozyme electrophoresis was used to measure and compare, with other members of the Proteaceae, levels and distribution of genetic diversity in Embothrium coccineum J.R.Forst., a widespread outcrossing species endemic of Andean Patagonian forests. We analysed variation at the species level by sampling 34 populations along its entire range of ~20° latitude. We tested the hypothesis of multiple Pleistocene refugia by phylogeographic methods. We resolved 16 isozyme loci assayed in 934 adult trees. At the species level, total genetic diversity (HT = 0.220) was similar to that of other outcrossed and widespread plant species. Genetic parameters (NA, PSS, HE) were not statistically different from other outcrossed but mostly range-restricted Proteaceae, reflecting a strong phylogenetic imprinting for species sharing life-history traits. Populations are genetically divergent among each other (FST = 0.202). The low correlation between geographic and genetic distances suggests separate histories, i.e. multiple glacial refugia for the cold-tolerant E. coccineum. Phylogeographic trees produced different topologies, although maximum likelihood and parsimony trees shared some elements. Both trees suggest a northern and central clade, and then a separate southern clade. Current processes such as gene flow and selection confound the historic signal. These results seem in contrast to many of the northern hemisphere post-glacial phylogeographic reconstructions which show clear historical tracks of northern range expansion from southern refugia. The present study highlights the importance of phylogenetic imprinting, life-history traits and historical events driving genetic diversity patterns in this widespread Proteaceae from southern South America.

scholarly journals Genetic Structure of Invasive Baby’s Breath (Gypsophila paniculata L.) Populations in a Michigan Dune System

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1123 ◽  
Author(s):  
Hailee B. Leimbach-Maus ◽  
Eric M. McCluskey ◽  
Alexandra Locher ◽  
Syndell R. Parks ◽  
Charlyn G. Partridge
Keyword(s):  
Genetic Structure ◽  
Native Species ◽  
Invasive Plant ◽  
Sand Dunes ◽  
Geographic Distance ◽  
Genetic Distances ◽  
Ecosystem Dynamics ◽  
Dune System ◽  
Chloroplast Microsatellite ◽  
Gypsophila Paniculata

Coastal sand dunes are dynamic ecosystems with elevated levels of disturbance and are highly susceptible to plant invasions. One invasive plant that is of concern to the Great Lakes system is Gypsophila paniculata L. (perennial baby’s breath). The presence of G. paniculata negatively impacts native species and has the potential to alter ecosystem dynamics. Our research goals were to (1) estimate the genetic structure of invasive G. paniculata along the Michigan dune system and (2) identify landscape features that influence gene flow in this area. We analyzed 12 populations at 14 nuclear and two chloroplast microsatellite loci. We found strong genetic structure among populations (global FST = 0.228), and pairwise comparisons among all populations yielded significant FST values. Results from clustering analysis via STRUCTURE and discriminant analysis of principal components (DAPC) suggest two main genetic clusters that are separated by the Leelanau Peninsula, and this is supported by the distribution of chloroplast haplotypes. Land cover and topography better explained pairwise genetic distances than geographic distance alone, suggesting that these factors influence the genetic distribution of populations within the dunes system. Together, these data aid in our understanding of how invasive populations move through the dune landscape, providing valuable information for managing the spread of this species.

scholarly journals Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Abigail Hui En Chan ◽  
Kittipong Chaisiri ◽  
Sompob Saralamba ◽  
Serge Morand ◽  
Urusa Thaenkham
Keyword(s):  
Species Identification ◽  
Genetic Markers ◽  
Molecular Systematics ◽  
Molecular Identification ◽  
Sequence Variation ◽  
Clustering Algorithm ◽  
Mitochondrial Protein ◽  
Genetic Distances ◽  
Rrna Genes ◽  
Universal Primers

Abstract Background Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level. Methods We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the ‘K-means’ clustering algorithm. Results The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes. Conclusion This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the ‘K-means’ clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.

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