Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentuscomplex) across Europe

Abstract Phylogeography examines the spatial genetic structure of species. Environmental niche modelling (or ecological niche modelling; ENM) examines the environmental limits of a species’ ecological niche. These two fields have great potential to be used together. ENM can shed light on how phylogeographical patterns develop and help identify possible drivers of spatial structure that need to be further investigated. Specifically, ENM can be used to test for niche differentiation among clades, identify factors limiting individual clades and identify barriers and contact zones. It can also be used to test hypotheses regarding the effects of historical and future climate change on spatial genetic patterns by projecting niches using palaeoclimate or future climate data. Conversely, phylogeographical information can populate ENM with within-species genetic diversity. Where adaptive variation exists among clades within a species, modelling their niches separately can improve predictions of historical distribution patterns and future responses to climate change. Awareness of patterns of genetic diversity in niche modelling can also alert conservationists to the potential loss of genetically diverse areas in a species’ range. Here, we provide a simplistic overview of both fields, and focus on their potential for integration, encouraging researchers on both sides to take advantage of the opportunities available.

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Comparative Genome-Wide Survey of Single Nucleotide Variation Uncovers the Genetic Diversity and Potential Biomedical Applications among Six Macaca Species

International Journal of Molecular Sciences ◽

10.3390/ijms19103123 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3123 ◽

Cited By ~ 2

Author(s):

Jing Li ◽

Zhenxin Fan ◽

Tianlin Sun ◽

Changjun Peng ◽

Bisong Yue ◽

...

Keyword(s):

Genetic Diversity ◽

Biomedical Applications ◽

Biomedical Application ◽

Distribution Patterns ◽

Protein Digestion ◽

Disease Category ◽

Single Nucleotide ◽

Bioinformatic Tools ◽

Genome Wide ◽

Outlier Tests

Macaca is of great importance in evolutionary and biomedical research. Aiming at elucidating genetic diversity patterns and potential biomedical applications of macaques, we characterized single nucleotide variations (SNVs) of six Macaca species based on the reference genome of Macaca mulatta. Using eight whole-genome sequences, representing the most comprehensive genomic SNV study in Macaca to date, we focused on discovery and comparison of nonsynonymous SNVs (nsSNVs) with bioinformatic tools. We observed that SNV distribution patterns were generally congruent among the eight individuals. Outlier tests of nsSNV distribution patterns detected 319 bins with significantly distinct genetic divergence among macaques, including differences in genes associated with taste transduction, homologous recombination, and fat and protein digestion. Genes with specific nsSNVs in various macaques were differentially enriched for metabolism pathways, such as glycolysis, protein digestion and absorption. On average, 24.95% and 11.67% specific nsSNVs were putatively deleterious according to PolyPhen2 and SIFT4G, respectively, among which the shared deleterious SNVs were located in 564–1981 genes. These genes displayed enrichment signals in the ‘obesity-related traits’ disease category for all surveyed macaques, confirming that they were suitable models for obesity related studies. Additional enriched disease categories were observed in some macaques, exhibiting promising potential for biomedical application. Positively selected genes identified by PAML in most tested Macaca species played roles in immune and nervous system, growth and development, and fat metabolism. We propose that metabolism and body size play important roles in the evolutionary adaptation of macaques.

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Back to the future of a rare plant species of the Chihuahuan desert: tracing distribution patterns across time and genetic diversity as a basis for conservation actions

Biodiversity and Conservation ◽

10.1007/s10531-020-01962-2 ◽

2020 ◽

Vol 29 (6) ◽

pp. 1821-1840

Author(s):

Ana Gabriela Zacarías-Correa ◽

Andrés Lira-Noriega ◽

Emmanuel Pérez-Calix ◽

Marie-Stéphanie Samain ◽

Andrea D. Wolfe

Keyword(s):

Genetic Diversity ◽

Plant Species ◽

Chihuahuan Desert ◽

Distribution Patterns ◽

Rare Plant ◽

Rare Plant Species ◽

The Future ◽

Conservation Actions

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Genetic Diversity in Marine Planktonic Ciliates (Alveolata, Ciliophora) Suggests Distinct Geographical Patterns – Data From Chinese and European Coastal Waters

Frontiers in Marine Science ◽

10.3389/fmars.2021.643822 ◽

2021 ◽

Vol 8 ◽

Author(s):

Maximilian H. Ganser ◽

Dominik Forster ◽

Weiwei Liu ◽

Xiaofeng Lin ◽

Thorsten Stoeck ◽

...

Keyword(s):

Genetic Diversity ◽

Coastal Waters ◽

Phylogenetic Analyses ◽

Distribution Patterns ◽

Geographical Patterns ◽

Network Analyses ◽

Planktonic Ciliates ◽

Geographic Patterns ◽

Abundant Otus ◽

Fine Resolution

Unraveling geographic distribution patterns of planktonic protists is a central goal in marine microbial ecology. Using a novel combination of recently developed phylogenetic and network analyses on a V4 18S rDNA metabarcoding dataset, we here analyzed the genetic diversity of marine planktonic ciliate communities in Chinese and European coastal waters. Thereby, our approach provided an unprecedented perspective on geographic patterns inferred from ciliate genetic diversity and accomplished a very fine resolution down to single nucleotides within operational taxonomic units (OTUs). While most OTUs (87%) exclusively contained sequences of either Chinese or European origin, those OTUs detected in both regions comprised the vast majority of reads (84%). Phylogenetic analyses of OTUs belonging to the same taxon revealed genetically distinct clades that were geographically restricted to either Chinese or European coastal waters. The detection of signature nucleotides emphasized this genetic distinction of Chinese and European clades. Second-level clustering of OTUs and reference sequences in two selected taxa (the oligotrichid Spirotontonia and the tintinnid Tintinnidium) revealed the presence of several potentially new species or ones lacking genetic reference data. Geographic patterns were also discovered by network analyses within 700 widespread and abundant OTUs; in 77 of these OTUs, European and Chinese sequences formed significantly assortative groups. These assortative groupings indicated a higher genetic similarity among sequences from the same region than between sequences from different regions. Our results demonstrate that detailed analyses of metabarcoding data down to single nucleotide differences expand our perception of geographical distribution patterns and provide insights into historic and ongoing effective dispersal in protists. The congruent discovery of geographic patterns at different levels of resolution (between and within OTUs) suggests that cosmopolitan distribution in marine planktonic ciliates is less common than previously postulated.

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Genetic Diversity and the Conservation of Eucalyptus crucis Maiden

Australian Journal of Botany ◽

10.1071/bt9880447 ◽

1988 ◽

Vol 36 (4) ◽

pp. 447 ◽

Cited By ~ 41

Author(s):

JF Sampson ◽

SD Hopper ◽

SH James

Keyword(s):

Genetic Diversity ◽

Tree Species ◽

Distribution Patterns ◽

Similar Distribution ◽

Allozyme Data ◽

Isolated Populations ◽

Low Frequencies ◽

Granite Outcrops ◽

The Mean ◽

Allozyme Loci

E. crucis Maiden occurs as small, isolated populations confined to granite outcrops in south-western Australia. The level and distribution of genetic diversity at 11 allozyme loci in 10 populations were estimated. Ten loci were polymorphic. However, many alleles were fixed in populations and occurred at low frequencies in others. The mean expected panmictic heterozygosity for populations was low when compared with tree species in general but similar to other tree species occurring in small, isolated populations. The level of population differentiation was high, as expected for small, isolated populations undergoing genetic fixation through genetic drift. The majority of the differentiation was attributable to between-population rather than between-subspecies differentiation. Analyses of allozyme data suggest that the mating system of E. crucis may be adapted to maintain diversity within populations by selection favouring heterozygous, presumably outcrossed progeny. The optimal strategy for the conservation of the genetic resources of E. crucis and other eucalypts with similar distribution patterns is considered in the light of this and previous studies.

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Genetic diversity in rosewood saplings (Aniba rosaeodora ducke, Lauraceae): an ecological approach

Acta Amazonica ◽

10.1590/s0044-59672008000400014 ◽

2008 ◽

Vol 38 (4) ◽

pp. 707-714 ◽

Cited By ~ 3

Author(s):

Ronaldo Pereira Santos ◽

Wilson Roberto Spironello ◽

Paulo de Tarso Barbosa Sampaio

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Distribution Patterns ◽

Ecological Approach ◽

Adult Trees ◽

High Incidence ◽

Adult Tree ◽

High Gene ◽

Disturbed Forest ◽

High Level

This article takes an ecological approach to the genetic diversity of Rosewood (Aniba rosaeodora Ducke) in a central Amazonian terra firme forest north of Manaus. Planted Rosewood setting, under partial shaded canopy, were assessed in terms of fruiting production, frugivory, and seed dispersal. Using RAPD molecular analysis procedures, the influence of the spatial distribution of adult trees on the genetic diversity (polymorphism) of saplings was assessed with genetic samples from 34 reproductive trees and 60 saplings. The density and distribution patterns the reproductive trees did not modify the sapling"s diversity (1.86%, AMOVA). Two types of adult tree dispersion were identified; i) clumped and ii) more widely dispersed. Polymorphism (77.5%) and gene flow were high between these. Although more sapling genetic variability in areas with a higher density of mature plants was not as high as expected, density did not affect the genetic diversity of samplings, indicating a high incidence of gene flow amongst trees. In planted Rosewood population (surrounded by low disturbed forest), fruiting trees experienced a high level of removal of seeds by toucans (Rhamphastidae), about of 50%. The high gene flow found among native trees suggested that toucans, promoting seed rain at short and long distances from maternal trees, actively contribute to the maintenance of genetic diversity within wild rosewood populations.

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