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Supplementary material 11 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Population structure of Aedes albopictus from the United States and Japan based on 15 microsatellite markers

Supplementary material 10 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Estimates of effective population size based of Connecticut populations obtained with NeEstimator (Do et al. 2014)

Supplementary material 8 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Genetic clusters inferred from all Connecticut collections using discriminant analysis of principal components in the ADEGENET package

Supplementary material 5 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Probability of a recent bottleneck at each Aedes albopictus location, under the infinite allele model (IAM) and the two-phase model (TPM) with variance of 0.36

Figure 5 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 5. Phylogenetic tree (left) and haplotype network (right) based on the analysis of mitochondrial Cytochrome b sequences. Bayesian inference tree is shown; the nodes with the posterior probability support below 0.5 are shown as unresolved. Above the nodes, posterior probabilities are shown, and bootstrap values inferred from ML analysis with RaxML if exceeding 50. The boxes indicate 95% HPD intervals for the estimated split times. Haplotype/ allele networks: size of the pies are proportional to the number of individuals/ alleles.

Figure 1 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 1. Sampling locations of Eunectes spp. Sampling locations of specimens used for genetic analysis pointed, and the individual sample numbers, indicated in supplementary table S1 and figs 4 and 5 shown in frames. Outlines depict ranges of the Eunectes species, after the IUCN Red List website: green – E. murinus, orange – E. deschauenseei, yellow – E. notaeus, red – E. beniensis.

Figure 4 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 4. Assignment of the 20 individuals in the RAPD dataset to genetic groups using STRUCTURE analyses for K = 3 optimal number of clusters (L(K) = -914.64). Each individual is represented by a column, which is partitioned in K coloured segments that represent the genetically based membership to each species cluster. The labels below indicate the species and specimens labels used in the RAPD (and partly sequencing) analysis.

Figure 3 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 3. Dendrogram (between-group average linkage) based on the squared Euclidean distance between population centroids based on the first two discriminant scores.

Figure 2 in Morphological trends and genetic divergence in anacondas, genus Eunectes Wagler, 1830 (Serpentes: Boidae)

Figure 2. Principal Component analyses based on 23 morphological traits, depicting the separation of E. murinus from the other three species of Eunectes along the first two PCA axes.

Figure 7 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)

Figure 7. Summary of genetic diversity indexes, based on 15 microsatellite loci, in three colonies of the Caribbean flamingo. Na = No. of different alleles, Na (Freq ≥ 5%) = No. of different alleles with a frequency ≥ 5%, Ne = No. of effective alleles, I = Shannon's information index, and He = expected heterozygosity. The allelic richness of Galápagos was calculated for 13 rather than 15 loci (FlamHD43 has no data and FlamHD20 has 91.3% of missing data).

Figure 6 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)

Figure 6. Structure results on the clustering of 160 individuals from Phoenicopterus ruber, assuming three populations and using 15 microsatellite loci. The colonies from Cuba and Bonaire showed a signal of structure, even though the most probable number of clusters suggested by the method of Evanno et al. (2005) is two.

Figure 5. The haplotype minimum spanning network using 612 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)

Figure 5. The haplotype minimum spanning network using 612 bp of the cytochrome b gene to compare colonies of Caribbean flamingos from Cuba (N = 49), Bonaire (N = 38) and Galápagos (N = 35).

Figure 4 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)

Figure 4. Genetic structure of Phoenicopteriformes using 17 microsatellite loci. Phoenicoparrus jamesi and Phoeniconaias minor are grouped in the same cluster when K = 5, following Evanno et al. (2005)'s estimation (A), but they separate when K = 6, based on Puechmaille (2016)'s assessment (B).

Figure 3 in Phylogeny of the order Phoenicopteriformes and population genetics of the Caribbean flamingo (Phoenicopterus ruber: Aves)

Figure 3. Time-scaled maximum clade credibility tree based on a partial sequence of flamingos cytochrome b (611 bp). The analysis includes the six extant flamingo species; individuals from the Caribbean flamingo (Phoenicopterus ruber) are identified by their colony of origin: CU (Cuba), Bon (Bonaire) and Gal (Galápagos). Blue bars represent the 95% highest posterior density intervals (95% HPD) of the node ages (in millions of years). The crown Phoenicopteridae diversified around 13 (9–18; 95% HPD) Mya followed by the split of the two main extant flamingo clades approximately 7 Mya. The expansion of existing haplotypes of all species occurred in the last two million years. The branch leading to the endemic haplotype from Galápagos, sample 51637, is coloured red.

opencc-zeroDec 2022View details →

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Globularia bisnagarica L. (Plantaginaceae) shows genetic uniformity throughout its disjunctive range

The paper presents the results of studying the morphological and genetic variation in populations of two species from genus Globularia, Globularia bisnagarica L. and Globularia trichosantha Fisch. and May. Both species are relicts and have disjunctive ranges. The analysis involved 25 populations of G. bisnagarica and 4 populations of G. trichosantha growing far apart from the main parts of their ranges. Sequencing of some regions of cpDNA (trnL−trnF, rbcL, and rpS16) and nuclear rDNA (ITS barcoding) revealed an extremely low level of genetic variability in the populations of both studied species. At the same time, G. bisnagarica demonstrates genetic uniformity within the entire disjunctive range. A study of the leaf blade shape variation with the geometric morphometrics approach revealed no clear interpopulation differences for both species; in most cases, the shape varied widely at the intrapopulation level. However, in the case of G. bisnagarica, a subtle trend was found: in populations from habitats with southern locations, the leaves had a narrow, oblong shape, while the populations located to the north, were characterized by wider, spatulate shape of the leaf blade. The assessment of variation in size parameters of plant organs using classical linear morphometrics revealed a more noticeable separation of populations for both G. bisnagarica and G. trichosantha. Modeling with environmental factors, designed to explain the observed patterns of variation, showed that the linear sizes of plant organs were more affected by climatic and topographic factors than the leaf blade shape. The main drivers of morphological variation in morphometric parameters of G. bisnagarica populations were the elevation, mean diurnal range of temperature, and annual precipitation. Variation in morphometric parameters of G. trichosantha populations mostly were driven by the annual mean temperature. Morphological variation observed in populations of G. bisnagarica within the studied fragments of the disjunctive range has exclusively modified nature caused by natural climatic factors and local conditions of population growth.

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FIGURE 2 in Genetic variation among populations of, and evidence of deep divergence within, the Rio Grande Chirping Frog, Eleutherodactylus campi (Anura Eleutherodactylidae)

FIGURE 2. Phylogenetic tree based on Bayesian analysis of mitochondrial 16S rRNA gene sequences. Numbers above nodes are ML Bootstrap (before the slash) and Bayesian Posterior probability (after the slash) values. Numbers below branch nodes correspond to mean divergence date estimates in millions of years. Node bars indicate 95% HPD associated with divergence dates whereas the scale bars indicate time in million years.

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FIGURE 1 in Genetic variation among populations of, and evidence of deep divergence within, the Rio Grande Chirping Frog, Eleutherodactylus campi (Anura Eleutherodactylidae)

FIGURE 1. Eleutherodactylus campi in life, found under a palm log at the edge of a parking lot (Image by Jake M. Scott)."

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Supplementary material 1 from: Leonhardt F, Arranz Aveces C, Müller A, Angin B, Jegu M, Haynes P, Ernst R (2022) Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges. NeoBiota 79: 31-50. https://doi.org/10.3897/neobiota.79.86778

Detailed information on all populations of the three congeneric taxa used in the molecular data sets of this study

opencc-by-4.0Nov 2022View details →

Aberrant phase separation and nucleolar dysfunction can underlie rare genetic diseases

This dataset provides companion data to the paper "Aberrant phase separation and nucleolar dysfunction can underlie rare genetic diseases". It includes raw data, images and computational code to generate the figures in the study.