scholarly journals KoT: an automatic implementation of the K/θ method for species delimitation

2021 ◽  
Author(s):  
Yann Spöri ◽  
Fabio Stoch ◽  
Simon Dellicour ◽  
C. William Birky ◽  
Jean-François Flot
Keyword(s):  
Genetic Diversity ◽  
Species Delimitation ◽  
Population Genetic ◽  
Average Distance ◽  
Species Level ◽  
Species Boundaries ◽  
Fasta File ◽  
Genetic Theory ◽  
Putative Species ◽  
The Impact

K/θ is a method to delineate species that rests on the calculation of the ratio between the average distance K separating two putative species-level clades and the genetic diversity θ of these clades. Although this method is explicitly rooted in population genetic theory, it was never benchmarked due to the absence of a program allowing automated analyses. For the same reason, its application by hand was limited to small datasets of a few tens of sequences. We present an automatic implementation of the K/θ method, dubbed KoT (short for "K over Theta"), that takes as input a FASTA file, builds a neighbour-joining tree, and returns putative species boundaries based on a user-specified K/θ threshold. This automatic implementation avoids errors and makes it possible to apply the method to datasets comprising many sequences, as well as to test easily the impact of choosing different K/θ threshold ratios. KoT is implemented in Haxe, with a javascript webserver interface freely available at https://eeg-ebe.github.io/KoT/ .

scholarly journals Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

2017 ◽  
Vol 284 (1854) ◽  
pp. 20162588 ◽  
Author(s):  
Sonal Singhal ◽  
Huateng Huang ◽  
Pascal O. Title ◽  
Stephen C. Donnellan ◽  
Iris Holmes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Species Delimitation ◽  
Population Genetic ◽  
Environmental Heterogeneity ◽  
Genetic Data ◽  
Species Level ◽  
Nominal Species ◽  
Genome Wide ◽  
Census Population Size

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus . To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.

scholarly journals Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

2018 ◽  
Author(s):  
Yanfen Zhao ◽  
Hongxiang Zhang ◽  
Borong Pan ◽  
Mingli Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Divergence Time ◽  
Northwest China ◽  
Northwestern China ◽  
Intraspecific Diversity ◽  
Early Pleistocene ◽  
Helan Mountains ◽  
The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

scholarly journals Weak epistasis may drive adaptation in recombining bacteria

2017 ◽  
Author(s):  
Brian J Arnold ◽  
Michael Gutmann ◽  
Yonatan Grad ◽  
Sam K Sheppard ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Population Genetic ◽  
Cumulative Effects ◽  
Strong Interactions ◽  
Parameter Estimates ◽  
Metapopulation Dynamics ◽  
Genetic Theory ◽  
Multilocus Model ◽  
Heritable Effects ◽  
The Impact

The impact of epistasis on the evolution of multilocus traits depends on recombination. Population genetic theory has been largely developed for eukaryotes, many of which recombine so frequently that epistasis between polymorphisms has not been considered to play a large role in adaptation and has been compared to the fleeting influence of non-heritable effects. Many bacteria also recombine, some to the degree that their populations are described as 'panmictic' or 'freely recombining'. However, whether this recombination is sufficient to limit the ability of selection to act on epistatic contributions to fitness is unknown. We create a sensitive method to quantify homologous recombination in five bacterial pathogens and use these parameter estimates in a multilocus model of bacterial evolution with additive and epistatic effects. We find that even for highly recombining species (e.g. Streptococcus pneumoniae or Helicobacter pylori), selection may act on the cumulative effects of weak (as well as strong) interactions between distant mutations since homologous recombination typically transfers only short segments. Furthermore, whether selection acts more efficiently on physically proximal loci depends on the average recombination tract length. Epistasis may thus play an important role in the adaptive evolution of bacteria and, unlike in eukaryotes, does not need to be strong, involve near loci, or require specific metapopulation dynamics.

Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study

Parasitology ◽  
2016 ◽  
Vol 143 (13) ◽  
pp. 1773-1789 ◽  
Author(s):  
GERARDO PÉREZ-PONCE DE LEÓN ◽  
MARTÍN GARCÍA-VARELA ◽  
CARLOS D. PINACHO-PINACHO ◽  
ANA L. SERENO-URIBE ◽  
ROBERT POULIN
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Species Delimitation ◽  
Nuclear Gene ◽  
Species Tree ◽  
Coi Gene ◽  
Complex Life Cycle ◽  
Species Boundaries ◽  
Intermediate Hosts ◽  
Putative Species

SUMMARYThe recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.

scholarly journals Cryptic molecular diversity in the morphologically variable rotiferan Brachionus quadridentatus (Rotifera: Monogononta)

2019 ◽  
Vol 67 (6) ◽  
Author(s):  
Alma E. Garcia-Morales ◽  
Omar Domínguez-Domínguez
Keyword(s):  
Genetic Diversity ◽  
18S Rdna ◽  
Species Delimitation ◽  
Molecular Diversity ◽  
Rdna Genes ◽  
Coi Mtdna ◽  
Genetic Groups ◽  
Putative Species ◽  
Variable Species ◽  
Morphological Differences

Brachionus quadridentatus is a morphologically variable species distributed worldwide. Its taxonomy is confusing due the numerous infrasubspecific variants described in the taxon. Here we explore genetic diversity of certain B. quadridentatus populations, using sequences of COI mtDNA and 18S rDNA genes. With traditional morphology (taxonomic keys), the specimens identified fell into three recognized variants: B. quadridentatus quadridentatus, B. quadridentatus f. brevispinus and B. quadridentatus f. cluniorbicularis. The coalescent species delimitation analysis highly supports the presence of at least three putative species within B. quadridentatus complex in agreement with the phylogenetic result and GMYC analysis with the 18S gene. Nevertheless, the morphological and mitochondrial information show that the variation within each of the three putative species is much more extensive, finding seven monophyletic and highly divergent genetic groups (>10%) that have congruence with the morphotypes found in this study and ABGD analysis, which display clear morphological differences mainly in the diagnostic characters.

scholarly journals Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huaying Wang ◽  
Baiming Yang ◽  
Huan Wang ◽  
Hongxing Xiao
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Population Genetic ◽  
Nuclear Markers ◽  
Genetic Studies ◽  
Population Genetic Diversity ◽  
Polymorphic Microsatellites ◽  
Ssr Primers ◽  
The Impact ◽  
Simple Sequence

AbstractMicrosatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

Genetic diversity and structure of the threatened anti-cancerous plantNothapodytes nimmonianaas revealed by ISSR analysis

2011 ◽  
Vol 9 (4) ◽  
pp. 506-514 ◽  
Author(s):  
V. K. Abdul Kareem ◽  
P. E. Rajasekharan ◽  
S. Mini ◽  
T. Vasantha Kumar
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Gene Diversity ◽  
Species Level ◽  
Conservation Strategy ◽  
Group Method ◽  
Population Genetic Differentiation ◽  
Genetic Diversity And Structure ◽  
Western Ghats Of India

Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations ofNothapodytes nimmonianafrom Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73%), but variance among populations was only 27% and its value, ΦPT = 0.271,P < 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.

Inferring infection processes of a parasitic nematode using population genetics

Parasitology ◽  
2000 ◽  
Vol 120 (2) ◽  
pp. 185-194 ◽  
Author(s):  
S. PATERSON ◽  
M. C. FISHER ◽  
M. E. VINEY
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Parasitic Nematode ◽  
Genetic Theory ◽  
Study Population ◽  
Infection Processes

The distribution of genetic differentiation in a population of the parasitic nematode Strongyloides ratti divided between rat hosts was determined. We applied population genetic theory to these data to determine the source of new infections. We estimate the rate at which a rat acquires a new infection from (a) the existing subpopulation of parasites within that rat (‘self-reinfection’) versus (b) the wider environment (‘immigration’). We find that the observed levels of genetic diversity and differentiation in the study population are consistent with low to moderate rates of self-reinfection and inconsistent with high rates of self-reinfection.

Genetic variation in sand pine (Pinusclausa)

1996 ◽  
Vol 26 (2) ◽  
pp. 244-254 ◽  
Author(s):  
Kathleen C. Parker ◽  
J.L. Hamrick
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Genetic ◽  
Genetic Distances ◽  
Species Level ◽  
Allozyme Diversity ◽  
Present Distribution ◽  
Genetic Bottlenecks ◽  
Florida Panhandle ◽  
Sand Pine

Pinusclausa (Chapm. ex Engelm.) Vasey ex Sarg. is a member of subsection Contortae that is restricted to Florida and the southern tip of Alabama. The present distribution of P. clausa is divided into two purported varieties: var. clausa in peninsular Florida and var. immuginata primarily in the Florida panhandle. We determined allozyme diversity and population genetic structure for 12 populations of var. clausa and 9 populations of var. immuginata. At the species level, 88% of the 26 loci examined were polymorphic. The genetic diversity maintained at both the species (Hes = 0.100) and population (Hep = 0.092) levels was low relative to most other pine species. Genetic differentiation among populations was also relatively low (GST = 0.054). Genetic distances between populations of the same variety (mean D = 0.006) were lower than genetic distances between populations of different varieties (mean D = 0.012). Although allele frequencies at individual loci differed significantly between the two varieties, each variety maintained nearly 99% of the genetic variation apparent at the species level (intervarietal differentiation, Gv = 0.014). The lower levels of genetic diversity in P. clausa may have resulted in part from genetic bottlenecks during periods of range retraction.

scholarly journals Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

2018 ◽  
Author(s):  
Yanfen Zhao ◽  
Hongxiang Zhang ◽  
Borong Pan ◽  
Mingli Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Divergence Time ◽  
Northwest China ◽  
Northwestern China ◽  
Intraspecific Diversity ◽  
Early Pleistocene ◽  
Helan Mountains ◽  
The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

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