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Journal articles on the topic 'Diversità intraspecifica'

Author: Grafiati

Published: 11 March 2023

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1

Anisimov, Andrey P., Luther E. Lindler, and Gerald B. Pier. "Intraspecific Diversity of Yersinia pestis." Clinical Microbiology Reviews 17, no. 2 (April 2004): 434–64. http://dx.doi.org/10.1128/cmr.17.2.434-464.2004.

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SUMMARY Increased interest in the pathogenic potential of Yersinia pestis has emerged because of the potential threats from bioterrorism. Pathogenic potential is based on genetic factors present in a population of microbes, yet most studies evaluating the role of specific genes in virulence have used a limited number of strains. For Y. pestis this issue is complicated by the fact that most strains available for study in the Americas are clonally derived and thus genetically restricted, emanating from a strain of Y. pestis introduced into the United States in 1902 via marine shipping and subsequent spread of this strain throughout North and South America. In countries from the former Soviet Union (FSU), Mongolia, and China there are large areas of enzootic foci of Y. pestis infection containing genetically diverse strains that have been intensely studied by scientists in these countries. However, the results of these investigations are not generally known outside of these countries. Here we describe the variety of methods used in the FSU to classify Y. pestis strains based on genetic and phenotypic variation and show that there is a high level of diversity in these strains not reflected by ones obtained from sylvatic areas and patients in the Americas.

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2

Anisimov, Andrey P., Luther E. Lindler, and Gerald B. Pier. "Intraspecific Diversity of Yersinia pestis." Clinical Microbiology Reviews 17, no. 3 (July 2004): 695. http://dx.doi.org/10.1128/cmr.17.3.695.2004.

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3

Ceccarelli, M., V. Sarri, M. E. Caceres, and P. G. Cionini. "Intraspecific genotypic diversity in plants." Genome 54, no. 9 (September 2011): 701–9. http://dx.doi.org/10.1139/g11-039.

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Variations in the nuclear DNA, mainly as a result of quantitative modulations of DNA repeats belonging to different sequence families of satellite DNA and to the activity of transposable elements, have been assessed within several angiosperm species. These variations alter the amount and organization of the DNA and therefore the genotype, rather than the genome proper. They take place on an evolutionary time scale as the result of selection processes after the occurrence of uncontrolled events in the genome or may be due to direct responses of plant genomes to environmental stimuli that occur under plant-level control within a short developmental period of a single generation. These DNA changes are correlated to changes in the developmental dynamics and phenotypic characteristics of the plants, and the capability to carry out genotypic variation is an evolutionary trait that allows plant species to adapt to different environmental conditions, as well as to the variability of conditions in a given environment. The link between developmental and environmental stimuli and repetitive DNA that elicits the intraspecific diversity of plant genotypes may provide models of evolutionary change that extend beyond the conventional view of evolution by allelic substitution and take into account epigenetic effects of the genome structure.

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4

Cantone, Frank A., and John D. Vandenberg. "Intraspecific diversity in Paecilomyces fumosoroseus." Mycological Research 102, no. 2 (February 1998): 209–15. http://dx.doi.org/10.1017/s0953756297004590.

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5

Batasheva, B. A., and A. A. Al’derov. "Intraspecific diversity of common barley precocity." Russian Agricultural Sciences 35, no. 1 (February 2009): 15–17. http://dx.doi.org/10.3103/s1068367409010054.

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6

Talukdar, K., and S. Sen. "INTRASPECIFIC GENETIC DIVERSITY IN ALLIUM ASCALONICUM." Acta Horticulturae, no. 433 (May 1997): 215–22. http://dx.doi.org/10.17660/actahortic.1997.433.22.

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7

Cianciaruso, M. V., M. A. Batalha, K. J. Gaston, and O. L. Petchey. "Including intraspecific variability in functional diversity." Ecology 90, no. 1 (January 2009): 81–89. http://dx.doi.org/10.1890/07-1864.1.

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8

Sanz-Cortés, F., D. E. Parfitt, C. Romero, D. Struss, G. Llacer, and M. L. Badenes. "Intraspecific olive diversity assessed with AFLP." Plant Breeding 122, no. 2 (April 2003): 173–77. http://dx.doi.org/10.1046/j.1439-0523.2003.00808.x.

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9

Araújo, Márcio S., and Raul Costa-Pereira. "Latitudinal gradients in intraspecific ecological diversity." Biology Letters 9, no. 6 (December 23, 2013): 20130778. http://dx.doi.org/10.1098/rsbl.2013.0778.

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The increase in the number of species with decreasing latitude is a striking pattern of global biodiversity. An important feature of studies of this pattern up to now has been the focus on species as the fundamental unit of interest, neglecting potential within-species ecological diversity. Here, we took a new perspective on this topic by measuring the degree to which individuals within populations differ in niche attributes across a latitudinal gradient (range: 54.01° S to 69.12° N). We show that 156 populations of 76 species across a wide range of vertebrate and invertebrate animal taxa contain more ecologically diverse assemblages of individuals towards lower latitudes. Our results add a new level of complexity to our understanding of global patterns of biodiversity and suggest the possibility that niche variation is partly responsible for the latitudinal gradients of species diversity.

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10

Lin, Meilan, Deborah A. Payne, and John R. Schwarz. "Intraspecific Diversity of Vibrio vulnificus in Galveston Bay Water and Oysters as Determined by Randomly Amplified Polymorphic DNA PCR." Applied and Environmental Microbiology 69, no. 6 (June 2003): 3170–75. http://dx.doi.org/10.1128/aem.69.6.3170-3175.2003.

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ABSTRACT Randomly amplified polymorphic DNA (RAPD) PCR was used to analyze the temporal and spatial intraspecific diversity of 208 Vibrio vulnificus strains isolated from Galveston Bay water and oysters at five different sites between June 2000 and June 2001. V. vulnificus was not detected during the winter months (December through February). The densities of V. vulnificus in water and oysters were positively correlated with water temperature. Cluster analysis of RAPD PCR profiles of the 208 V. vulnificus isolates revealed a high level of intraspecific diversity among the strains. No correlation was found between the intraspecific diversity among the isolates and sampling site or source of isolation. After not being detected during the winter months, the genetic diversity of V. vulnificus strains first isolated in March was 0.9167. Beginning in April, a higher level of intraspecific diversity (0.9933) and a major shift in population structure were observed among V. vulnificus isolates. These results suggest that a great genetic diversity of V. vulnificus strains exists in Galveston Bay water and oysters and that the population structure of this species is linked to changes in environmental conditions, especially temperature.

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11

Pertile, Giorgia, Jacek Panek, Karolina Oszust, Anna Siczek, and Magdalena Frąc. "Intraspecific functional and genetic diversity ofPetriella setifera." PeerJ 6 (February 28, 2018): e4420. http://dx.doi.org/10.7717/peerj.4420.

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The aim of the study was an analysis of the intraspecific genetic and functional diversity of the new isolated fungal strains ofP. setifera. This is the first report concerning the genetic and metabolic diversity ofPetriella setiferastrains isolated from industrial compost and the first description of a protocol for AFLP fingerprinting analysis optimised for these fungal species. The results showed a significant degree of variability among the isolates, which was demonstrated by the clearly subdivision of all the isolates into two clusters with 51% and 62% similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clearly different patterns of carbon substrates utilization between the isolates resulting in a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These results suggest that genetic diversity does not always match the level of functional diversity, which may be useful in discovering the importance of this fungus to ecosystem functioning. The results indicated thatP. setiferastrains were able to degrade substrates produced in the degradation of hemicellulose (D-Arabinose, L-Arabinose, D-Glucuronic Acid, Xylitol, γ-Amino-Butyric Acid, D-Mannose, D-Xylose and L-Rhamnose), cellulose (α-D-Glucose and D-Cellobiose) and the synthesis of lignin (Quinic Acid) at a high level, showing their importance in ecosystem services as a decomposer of carbon compounds and as organisms, which make a significant contribution to carbon cycling in the ecosystem.The results showed for the first time that the use of molecular biology techniques (such as AFLP and BIOLOG analyses) may allow for the identification of intraspecific diversity of as yet poorly investigated fungal species with favourable consequences for our understanding their ecosystem function.

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12

Jiang, Y., C. K. M. Tsui, S. A. Ahmed, F. Hagen, Z. Shang, A. H. G. Gerrits van den Ende, P. E. Verweij, H. Lu, and G. S. de Hoog. "Intraspecific Diversity and Taxonomy of Emmonsia crescens." Mycopathologia 185, no. 4 (July 24, 2020): 613–27. http://dx.doi.org/10.1007/s11046-020-00475-4.

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13

Zeng, J. S., K. Fukushima, K. Takizawa, Y. C. Zheng, K. Nishimura, Y. Gräser, G. S. De Hoog, et al. "Intraspecific diversity of species of thePseudallescheria boydiicomplex." Medical Mycology 45, no. 6 (January 2007): 547–58. http://dx.doi.org/10.1080/13693780701435341.

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14

Wilkinson, Anna, Martin Solan, Andrew F. S. Taylor, Ian J. Alexander, and David Johnson. "Intraspecific Diversity Regulates Fungal Productivity and Respiration." PLoS ONE 5, no. 9 (September 7, 2010): e12604. http://dx.doi.org/10.1371/journal.pone.0012604.

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15

Paz-Vinas, Ivan, Géraldine Loot, Virgilio Hermoso, Charlotte Veyssière, Nicolas Poulet, Gaël Grenouillet, and Simon Blanchet. "Systematic conservation planning for intraspecific genetic diversity." Proceedings of the Royal Society B: Biological Sciences 285, no. 1877 (April 25, 2018): 20172746. http://dx.doi.org/10.1098/rspb.2017.2746.

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Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus,Phoxinus phoxinus, Barbatula barbatula,Gobio occitaniae,Leuciscus burdigalensisandParachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.

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16

Moy, G. W., S. A. Springer, S. L. Adams, W. J. Swanson, and V. D. Vacquier. "Extraordinary intraspecific diversity in oyster sperm bindin." Proceedings of the National Academy of Sciences 105, no. 6 (February 11, 2008): 1993–98. http://dx.doi.org/10.1073/pnas.0711862105.

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17

Mathieu, Stephanie, Loïc Cusant, Christophe Roux, and Nicolas Corradi. "Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes." New Phytologist 220, no. 4 (June 27, 2018): 1129–34. http://dx.doi.org/10.1111/nph.15275.

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18

Tao, Yu-Tian, Fang Suo, Sergio Tusso, Yan-Kai Wang, Song Huang, Jochen B. W. Wolf, and Li-Lin Du. "Intraspecific Diversity of Fission Yeast Mitochondrial Genomes." Genome Biology and Evolution 11, no. 8 (July 25, 2019): 2312–29. http://dx.doi.org/10.1093/gbe/evz165.

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Abstract The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.

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19

CLAUSI, MIRELLA, DIEGO LEONE, and SERGEI E. SPIRIDONOV. "HAPLOTYPE DIVERSITY OF STEINERNEMA FELTIAE (NEMATODA: STEINERNEMATIDAE) IN EURASIA." Redia 103 (December 1, 2020): 133–36. http://dx.doi.org/10.19263/redia-103.20.21.

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Phylogenetic analysis of ITS rDNA sequences of the entomopathogenic nematode Steinernema feltiae Filipjev, 1934 (Wouts, Mráček, Gerdin and Bedding, 1982) was used to infer intraspecific genetic variability of this rhabditid nematode. Nucleotide intraspecific differences among S. feltiae isolates reached the level of 19 base pairs per ITS rDNA region, i.e. up to 2.9%. Several weakly or moderately supported intraspecific clades were detected. Sicilian and Swiss isolates of S. feltiae were found clustering together. Swiss strain ‘St. Bernard’ has been isolated on the St. Bernardino mountain pass in Switzerland in 2000. Phylogenetic relationships among S. feltiae isolates were inferred by using three different methods (maximum parsimony, neighbor joining and maximum likelihood). The topologies of the phylogenetic trees were identical and thus only ML tree is presented. ML tree revealed that S. feltiae isolates from Israel and Armenia grouped at the basal position of the tree, while in the spanning network obtained with POPART software, Iranian and Ukrainian isolates were the closest to the outgroup. In all methods of analyses, the European and Siberian strains of S. feltiae occupied terminal positions. Thus, further studies on the intraspecific genetic variability of entomopathogenic nematodes is needed.

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20

Hupało, Kamil. "Revisiting the past − novel insight into intraspecific molecular diversity and phylogeny of widespread Echinogammarus berilloni." Knowledge & Management of Aquatic Ecosystems, no. 421 (2020): 46. http://dx.doi.org/10.1051/kmae/2020038.

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Echinogammarus berilloni (Catta, 1878) is a widespread and euryecious species, inhabiting large parts of Southwestern Europe. Additionally, it is recognized as one of the non-native and invasive species, increasing its range to Central Europe. Even though it is widely used as a model organism in a variety of ecological and ecotoxicological studies, its intraspecific molecular diversity has been overlooked. In this study, the publicly available genetic data reveal high level of intraspecific diversity, supporting presence of up to four phylogenetically distinct genetic lineages. Furthermore, the results indicate that the taxon is not monophyletic. The importance of considering its intraspecific diversity is discussed, highlighting the potential implications for future studies as well as the need for further detailed taxonomic studies.

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21

Yang, Mi Yeon, and Myung Sook Kim. "Phylogeography of the economic seaweeds <italic>Chondrus</italic> (Gigartinales, Rhodophyta) in the northwest Pacific based on <italic>rbc</italic>L and COI-5P genes." Algae 37, no. 2 (June 15, 2022): 135–47. http://dx.doi.org/10.4490/algae.2022.37.5.29.

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The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI- 5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.

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Schöb, Christian, Sarah Kerle, Alison J. Karley, Luna Morcillo, Robin J. Pakeman, Adrian C. Newton, and Rob W. Brooker. "Intraspecific genetic diversity and composition modify species-level diversity-productivity relationships." New Phytologist 205, no. 2 (September 24, 2014): 720–30. http://dx.doi.org/10.1111/nph.13043.

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23

Zichello, Julia M., Karen L. Baab, Kieran P. McNulty, Christopher J. Raxworthy, and Michael E. Steiper. "Hominoid intraspecific cranial variation mirrors neutral genetic diversity." Proceedings of the National Academy of Sciences 115, no. 45 (October 22, 2018): 11501–6. http://dx.doi.org/10.1073/pnas.1802651115.

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Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique toHomo sapiensbut is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest that neutral evolutionary processes such as mutation, gene flow, and genetic drift have played an important role in generating cranial variation within species. These findings are consistent with previous work on human cranial morphology and improve our understanding of the evolutionary processes that generate intraspecific cranial shape diversity within hominoids. This work has implications for the analysis of selective and developmental pressures on the cranium and for interpreting shape variation in fossil hominin crania.

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24

Veech, Joseph A., Thomas O. Crist, and Keith S. Summerville. "INTRASPECIFIC AGGREGATION DECREASES LOCAL SPECIES DIVERSITY OF ARTHROPODS." Ecology 84, no. 12 (December 2003): 3376–83. http://dx.doi.org/10.1890/02-3127.

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25

Zhivotovsky, L. A., and G. O. Osmanova. "Ecogeographic Units and the Protection of Intraspecific Diversity." Biology Bulletin 47, no. 2 (March 2020): 123–34. http://dx.doi.org/10.1134/s1062359020020144.

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26

El-Dougdou, K. A., A. R. Sofy, G. A. Hameed, and R. A. Dawood. "Intraspecific Diversity of Cucumber mosaic Cucumoviridae in Egypt." International Journal of Virology 10, no. 2 (March 15, 2014): 94–102. http://dx.doi.org/10.3923/ijv.2014.94.102.

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27

Hamer, Jorin, Birte Matthiessen, Silvia Pulina, and Giannina S. I. Hattich. "Maintenance of Intraspecific Diversity in Response to Species Competition and Nutrient Fluctuations." Microorganisms 10, no. 1 (January 6, 2022): 113. http://dx.doi.org/10.3390/microorganisms10010113.

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Intraspecific diversity is a substantial part of biodiversity, yet little is known about its maintenance. Understanding mechanisms of intraspecific diversity shifts provides realistic detail about how phytoplankton communities evolve to new environmental conditions, a process especially important in times of climate change. Here, we aimed to identify factors that maintain genotype diversity and link the observed diversity change to measured phytoplankton morpho-functional traits Vmax and cell size of the species and genotypes. In an experimental setup, the two phytoplankton species Emiliania huxleyi and Chaetoceros affinis, each consisting of nine genotypes, were cultivated separately and together under different fluctuation and nutrient regimes. Their genotype composition was assessed after 49 and 91 days, and Shannon’s diversity index was calculated on the genotype level. We found that a higher intraspecific diversity can be maintained in the presence of a competitor, provided it has a substantial proportion to total biovolume. Both fluctuation and nutrient regime showed species-specific effects and especially structured genotype sorting of C. affinis. While we could relate species sorting with the measured traits, genotype diversity shifts could only be partly explained. The observed context dependency of genotype maintenance suggests that the evolutionary potential could be better understood, if studied in more natural settings including fluctuations and competition.

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Foxx, Alicia J. "Species variability in the relative strength of intraspecific and interspecific interactions." Folia Oecologica 49, no. 2 (July 1, 2022): 168–74. http://dx.doi.org/10.2478/foecol-2022-0019.

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Abstract Understanding cases in restoration and in agriculture in which species diversity improves productivity and ecosystem functioning is crucial due the need to restore degraded habitat and improve crop productivity for a growing human population. Reaching these diversity benefits is likely influenced by the dynamic of less negative interspecific than intraspecific interactions that promote diversity. But further testing is needed to understand the relationship of intraspecific-relative to interspecific interactions. Here I used seedlings from three native and one introduced species used in restoration in the western United States in pairwise interaction combinations and found that the study species varied in shoot biomass in response to interaction treatments of the control, intraspecific, and interspecific interactions (R 2 = 0.7, p < 0.001), and that intraspecific interactions were more negative than interspecific interactions for four of five of the pairings. Overall, as shoot mass size differences increased between interspecific neighbors, interactions became more positive (R 2 = 0.6, p < 0.001). These findings point to variability in species responses in whether the focal species compete more intensely with conspecific or heterospecific neighbors and indicates the need for more careful selection of interacting species for meeting both agricultural and restoration goals.

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Kami, James A., and Paul Gepts. "Phaseolin nucleotide sequence diversity in Phaseolus. I. Intraspecific diversity in Phaseolus vulgaris." Genome 37, no. 5 (October 1, 1994): 751–57. http://dx.doi.org/10.1139/g94-107.

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Most information about the molecular biology of phaseolin, the major seed storage protein in Phaseolus vulgaris, has been obtained from the T-type phaseolin, which is characteristic of the Andean gene pool of the species. In the work reported here, two cDNA clones for the S-type phaseolin representing the other major, Middle American gene pool were isolated and sequenced. Analysis of the DNA sequences revealed the presence of two subtypes of S phaseolin, α and β, depending on the presence or absence, respectively, of a 27-bp direct repeat. These are similar to the α- and β-phaseolin subtypes found in the Andean, T phaseolin; however, the additional 15-bp direct repeat also found in the T α-phaseolin gene type was apparently absent from the S α-phaseolin genes. The overall sequence identity was greater between the α or β subtypes of different gene pools than between the a or p subtypes within gene pools. This implies that the gene subtypes were formed prior to the formation of the two major gene pools of P. vulgaris. Analysis of the putative amino acid sequence revealed that both the 'Sanilac' phaseolin subtypes contained an additional methionine, however, not at the same site. This opens the possibility of increasing the nutritionally limiting methionine level in phaseolin either through protein engineering or by screening accessions for recombinant phaseolin sequences that combine both substitutions.Key words: seed storage protein, multigene family, direct repeat.

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30

Bischof, Eva Alexandra, Nils Schlüter, and Jens Lehmann. "Geometric morphometric analysis of morphologic disparity, intraspecific variation and ontogenetic allometry of beyrichitine ammonoids." PLOS ONE 17, no. 2 (February 10, 2022): e0263524. http://dx.doi.org/10.1371/journal.pone.0263524.

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Beyrichitine ammonoids of NV Nevada reveal a high taxonomic diversity of Anisian (Middle Triassic). This diversity is, however, in contrast to their relatively low morphologic disparity. Depending on the exact definition, morphologic disparity of a data set is a direct consequence of the sum of all ontogenetic changes. In the past, however, the interplay of both morphological processes has only rarely been addressed. Using geometric morphometric methods, this study aims at a quantification of allometric processes and the morphologic disparity of beyrichitine ammonoids. The multivariate statistical analysis revealed that morphologic disparity, intraspecific variation respectively, within and between the studied species seems to be the result of deviations in the ontogenetic allometric growth pattern (i.e. heterochrony). During deposition of the studied stratigraphic sequence, a general progressive pedomorphism (juvenilization) was observed. The intraspecific variability pattern coincides with the total morphologic disparity of the analyzed species, which suggests that intraspecific variability facilitated morphologic disparity. The comparison of ontogenetic allometric patterns and changes in intraspecific variation and morphologic disparity are likely to refine our understanding of the intrinsic factors influencing the speciation of this group.

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Dukes, Caroline D., Frans Janssens, Ernesto Recuero, and Michael S. Caterino. "Specific and Intraspecific Diversity of Symphypleona and Neelipleona (Hexapoda: Collembola) in Southern High Appalachia (USA)." Diversity 14, no. 10 (October 7, 2022): 847. http://dx.doi.org/10.3390/d14100847.

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Collembola, commonly known as springtails, are important detritivores, abundant in leaf litter and soil globally. Springtails are wingless hexapods with many North American species having wide distributions ranging from as far as Alaska to Mexico. Here, we analyze the occurrence and intraspecific diversity of springtails with a globular body shape (Symphypleona and Neelipleona), in southern high Appalachia, a significant biodiversity hotspot. The peaks of high Appalachia represent ‘sky islands’ due to their physical isolation, and they host numerous endemic species in other taxa. We surveyed globular Collembola through COI metabarcoding, assessing geographic and genetic diversity across localities and species. Intraspecific diversity in globular Collembola was extremely high, suggesting that considerable cryptic speciation has occurred. While we were able to associate morphospecies with described species in most of the major families in the region (Dicyrtomidae, Katiannidae, Sminthuridae, and Sminthurididae), other families (Neelidae, and Arrhopalitidae) are in more pressing need of taxonomic revision before species identities can be confirmed. Due to poor representation in databases, and high intraspecific variability, no identifications were accomplished through comparison with available DNA barcodes.

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32

Dentovskaya, S. V., L. A. Kadnikova, A. A. Kislichkina, A. G. Bogun, and A. P. Anisimov. "INTRASPECIFIC DIVERSITY OF YERSINIA PESTIS CHAPERONE/USHER SECRETION APPARATUSES." Russian Journal of Infection and Immunity 8, no. 4 (January 16, 2019): 555. http://dx.doi.org/10.15789/2220-7619-2018-4-5.4.

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33

Elbrecht, Vasco, Ecaterina Edith Vamos, Dirk Steinke, and Florian Leese. "Estimating intraspecific genetic diversity from community DNA metabarcoding data." PeerJ 6 (April 9, 2018): e4644. http://dx.doi.org/10.7717/peerj.4644.

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BackgroundDNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal.MethodsThis study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package “JAMP” and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates.ResultsWe detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177–200 OTUs, each containing an average of 2.40–3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stoneflyTaeniopteryx nebulosaand the caddisflyHydropsyche pellucidulashowed a distinct north–south cline with respect to haplotype distribution, while the beetleOulimnius tuberculatusand the isopodAsellus aquaticusdisplayed no clear population pattern but differed in genetic diversity.DiscussionWe developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.

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Eilers, Elisabeth Johanna. "Intra-Individual and Intraspecific Terpenoid Diversity in Erodium cicutarium." Plants 10, no. 8 (July 30, 2021): 1574. http://dx.doi.org/10.3390/plants10081574.

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The chemodiversity between and within individuals of several plant species is remarkable and shaped by the local habitat environment and the genetic background. The forb Erodium cicutarium (Geraniaceae) is globally distributed and partly invasive. This paper hypothesizes a high intra-specific and inter-individual chemical diversity in this species and investigates this by comparing the concentration and diversity of terpenoid compounds in different plant parts, i.e., leaves, blossoms and fruits. Plants were grown from seeds, originating from native range Bavaria (BY), Germany, and invaded range California (CA), USA, populations. In total, 20 different terpenoids were found, which occurred in distinct combinations and the patterns clustered into groups of distinct chemotypes for all plant parts. Several of the chemotypes were specific to plants of one region. The terpenoid compositions of different plant parts within individuals were highly correlated. Chemodiversity was higher in reproductive plant parts compared to the leaves, and higher in plants from BY compared to CA. This study highlights the intra-specific and inter-individual chemodiversity in E. cicutarium, linked to its geographical origin, which may facilitate its invasion success but also calls for further investigation of the role of chemodiversity in invasive plants on interactions with the environment.

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Bleykasten-Grosshans, Claudine, Anne Friedrich, and Joseph Schacherer. "Genome-wide analysis of intraspecific transposon diversity in yeast." BMC Genomics 14, no. 1 (2013): 399. http://dx.doi.org/10.1186/1471-2164-14-399.

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Mechergui, Arij, Wafa Achour, and Assia Ben Hassen. "Intraspecific 16S rRNA gene diversity among clinical isolates ofNeisseriaspecies." APMIS 122, no. 5 (September 11, 2013): 437–42. http://dx.doi.org/10.1111/apm.12164.

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Rowan, R., and N. Knowlton. "Intraspecific diversity and ecological zonation in coral-algal symbiosis." Proceedings of the National Academy of Sciences 92, no. 7 (March 28, 1995): 2850–53. http://dx.doi.org/10.1073/pnas.92.7.2850.

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Clawson, David L. "Harvest Security and Intraspecific Diversity in Traditional Tropical Agriculture." Economic Botany 39, no. 1 (January 1985): 56–67. http://dx.doi.org/10.1007/bf02861175.

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Dimas-Flores, Nohemi, Manuel Serra, and María José Carmona. "Does genetic diversity reduce intraspecific competition in rotifer populations?" Hydrobiologia 705, no. 1 (November 9, 2012): 43–54. http://dx.doi.org/10.1007/s10750-012-1378-4.

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Komarnitsky, I. K., A. M. Samoylov, V. V. Red'ko, V. G. Peretyayko, and Yu Yu Gleba. "Intraspecific diversity of sugar beet (Beta vulgaris) mitochondrial DNA." Theoretical and Applied Genetics 80, no. 2 (August 1990): 253–57. http://dx.doi.org/10.1007/bf00224395.

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De Jonghe, Valerie, An Coorevits, Joachim Vandroemme, Jeroen Heyrman, Lieve Herman, Paul De Vos, and Marc Heyndrickx. "Intraspecific genotypic diversity of Bacillus species from raw milk." International Dairy Journal 18, no. 5 (May 2008): 496–505. http://dx.doi.org/10.1016/j.idairyj.2007.11.007.

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Kleine, Sandra, and Caroline Müller. "Intraspecific plant chemical diversity and its relation to herbivory." Oecologia 166, no. 1 (November 4, 2010): 175–86. http://dx.doi.org/10.1007/s00442-010-1827-6.

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Wood, Connor M., Shawn T. McKinney, and Cynthia S. Loftin. "Intraspecific functional diversity of common species enhances community stability." Ecology and Evolution 7, no. 5 (February 8, 2017): 1553–60. http://dx.doi.org/10.1002/ece3.2721.

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Luo, Wenbo, Ragan M. Callaway, and Daniel Z. Atwater. "Intraspecific diversity buffers the inhibitory effects of soil biota." Ecology 97, no. 8 (August 2016): 1913–18. http://dx.doi.org/10.1002/ecy.1469.

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Frickel, Jens, Loukas Theodosiou, and Lutz Becks. "Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity." Proceedings of the National Academy of Sciences 114, no. 42 (October 2, 2017): 11193–98. http://dx.doi.org/10.1073/pnas.1701845114.

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Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

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He, Tianhua, Byron B. Lamont, Siegfried L. Krauss, Neal J. Enright, and Ben P. Miller. "Covariation between intraspecific genetic diversity and species diversity within a plant functional group." Journal of Ecology 96, no. 5 (May 14, 2008): 956–61. http://dx.doi.org/10.1111/j.1365-2745.2008.01402.x.

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Maze, Jack, and Roy Turkington. "The influence of pasture age, plant density, and genotype on intraspecific diversity of Trifolium repens (white clover)." Canadian Journal of Botany 74, no. 7 (July 1, 1996): 1189–92. http://dx.doi.org/10.1139/b96-142.

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Morphological variation, as expressed in PCA axis scores, for clovers growing in different aged pastures, was apportioned to pasture age, quadrats within pastures, intraspecific densities within quadrats, and genets within densities. Of those factors that have an effect on variation, genets is the greatest, followed by quadrats, intraspecific density, and age of the pasture. There is also an age-related decline in variation in plants of Trifolium repens as seen in genetic origin, quadrats within a pasture, and intraspecific density. These results indicate a need to determine more accurately the relationship between genetic and phenotypic responses in the decline in among-plant variation over time. Keywords: Trifolium repens, variation.

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Pawlik, Anna, Grzegorz Janusz, Iwona Dębska, Marek Siwulski, Magdalena Frąc, and Jerzy Rogalski. "Genetic and Metabolic Intraspecific Biodiversity ofGanoderma lucidum." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/726149.

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FourteenGanoderma lucidumstrains from different geographic regions were identified using ITS region sequencing. Based on the sequences obtained, the genomic relationship between the analyzed strains was determined. AllG. lucidumstrains were also genetically characterized using the AFLP technique.G. lucidumstrains included in the analysis displayed an AFLP profile similarity level in the range from 9.6 to 33.9%. Biolog FF MicroPlates were applied to obtain data on utilization of 95 carbon sources and mitochondrial activity. The analysis allowed comparison of functional diversity of the fungal strains. The substrate utilization profiles for the isolates tested revealed a broad variability within the analyzedG. lucidumspecies and proved to be a good profiling technology for studying the diversity in fungi. Significant differences have been demonstrated in substrate richness values. Interestingly, the analysis of growth and biomass production also differentiated the strains based on the growth rate on the agar and sawdust substrate. In general, the mycelial growth on the sawdust substrate was more balanced and the fastest fungal growth was observed for GRE3 and FCL192.

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Wu, Jiaqi, Takahiro Yonezawa, and Hirohisa Kishino. "Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection." Genes 13, no. 4 (April 17, 2022): 708. http://dx.doi.org/10.3390/genes13040708.

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It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.

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Minter, Ewan J. A., Phillip C. Watts, Chris D. Lowe, and Michael A. Brockhurst. "Negative frequency-dependent selection is intensified at higher population densities in protist populations." Biology Letters 11, no. 6 (June 2015): 20150192. http://dx.doi.org/10.1098/rsbl.2015.0192.

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Natural populations of free-living protists often exhibit high-levels of intraspecific diversity, yet this is puzzling as classic evolutionary theory predicts dominance by genotypes with high fitness, particularly in large populations where selection is efficient. Here, we test whether negative frequency-dependent selection (NFDS) plays a role in the maintenance of diversity in the marine flagellate Oxyrrhis marina using competition experiments between multiple pairs of strains. We observed strain-specific responses to frequency and density, but an overall signature of NFDS that was intensified at higher population densities. Because our strains were not selected a priori on the basis of particular traits expected to exhibit NFDS, these data represent a relatively unbiased estimate of the role for NFDS in maintaining diversity in protist populations. These findings could help to explain how bloom-forming plankton, which periodically achieve exceptionally high population densities, maintain substantial intraspecific diversity.

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