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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 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.

opennotspecifiedDec 2022View details →

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.

opennotspecifiedDec 2022View details →

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)."

opencc-zeroFeb 2023View details →

Genetic differentiation of a critically endangered population of the limpet Patella candei candei d'Orbigny, 1840, in the Canary Islands

The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d'Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically differentiated from the closely related P. candei crenata for the first time. Moreover, genetic differentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.

opencc-zeroFeb 2023View details →

Data from: Evidence of low within-pair genetic relatedness in a relict population of Thorn-tailed Rayadito despite long-term isolation

Investigating whether mating patterns are biased in relation to kinship in isolated populations can provide a better understanding of the occurrence of inbreeding avoidance mechanisms in wild populations. Here we report on the genetic relatedness (r) among breeding pairs in a relict population of Thorn-tailed Rayadito (Aphrastura spinicauda) in north-central Chile that has experienced a long-term history of isolation. We used simulations based on eight years of data to assess whether mating is random with respect to relatedness. We found that mean and median population values of pair relatedness tended to be lower than randomly generated values, suggesting that mating is not random with respect to kinship. We hypothesize that female-biased dispersal is the main mechanism reducing the likelihood of mating among kin, and that the proportion of related pairs (i.e., r > 0.125) in the study population (25%) would presumably be higher in the absence of sex-biased dispersal. The occurrence of other mechanisms such as extra-pair copulations, delayed breeding and active inbreeding avoidance through kin discrimination cannot be dismissed and require further study.

opencc-zeroApr 2023View details →

Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10 - 11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and 8 microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining of the Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

opencc-by-4.0May 2023View details →

Data for Selfing species has greater genetic diversity and less structure than related outcrossing species due to seed dispersal and population history in Roscoea (Zingiberaceae)

Data matrix of two species with nexus format.

opencc-zeroMay 2023View details →

Origin and genetic variability of populations of the invasive plant Rumex alpinus L. in the Giant (Krkonoše) Mountains

Monk's rhubarb, Rumex alpinus L. (R. alpinus), is a perennial plant native to the mountains of Central and Southern Europe. Currently, the distribution of R. alpinus has been partly affected by its utilization as a vegetable and a medicinal herb. In the mountains of the Czech Republic, it is considered an invasive plant, probably introduced into the Krkonoše Mountains by colonists from the Alps. This study's main aim was to verify whether R. alpinus was introduced into the Krkonoše Mountains by alpine colonists or whether it was anthropogenically introduced from the Carpathians. Furthermore, the genetic structure of native and introduced populations of R. alpinus was determined. For the evaluation of genetic structure, 417 samples of R. alpinus were collected from the Alps, Carpathians, Balkan, Pyrenees, and Czech Mountains. In total, 12 simple sequence repeat (SSR) markers were applied. The results of AMOVA showed a high 60% variation within populations, 27% variation among groups, and 13% among the population within groups. The overall unbiased gene diversity was high (ĥ = 0.55). The higher level of genetic differentiation among populations (FST = 0.35; p < 0.01) indicated restricted gene flow between populations. Compared to native populations, limited genetic variability was observed in the nonnative populations. It was concluded that local adaptation, low gene exchange, and genetic drift affected the genetic diversity of nonnative R. alpinus. The results support a genetic link between Alpine and Czech genotypes of R. alpinus, while the Carpathians genotypes corresponded to the Balkan genotype.

opencc-zeroJun 2023View details →

Simulation code for: Effects of population size change on the genetics of adaptation following an abrupt change in environment

Since the rediscovery of Mendelian genetics over a century ago, there has been much debate about the evolutionary importance of mutations with large phenotypic effects. While population genetic models predict that large-effect mutations will typically contribute to adaptation following an abrupt change in environment, the prediction applies to populations of stable size and overlooks effects of population size change on adaptation (e.g., population decline following habitat loss; growth during range expansion). We evaluate the phenotypic and fitness effects of mutations contributing to adaptation immediately following an abrupt environmental shift that alters both selection and population size dynamics. We show that large-effect mutations are likely to contribute to adaptation in populations declining to a new carrying capacity, somewhat smaller-effect mutations contribute to evolutionary rescue, and small-effect mutations predominate in growing populations. We also show that the relative contributions of positively selected and overdominant mutations to adaptation depend on interactions between the phenotypic effect size distribution for new mutations and the specific form of population size change during adaptation (i.e., growth, decline, or evolutionary rescue). Our results illustrate how population size dynamics can shape the genetic basis of adaptation, which should motivate empirical comparisons of populations adapting in different demographic contexts.

opencc-zeroJun 2023View details →

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

The Carpathian Mountains were always inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2,300 to 2,700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.

opennotspecifiedJun 2021View details →

Fig. 4 in An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations

Fig. 4. (A) A map of Iran showing the relative geographic location of each habitat, (B) Representative of DNA fragments generated by the UBC807 primer in the nine juniper populations. The left-most (L) column corresponds to the biological ruler (Ladder) and the right-most column () is a negative control., (C) Dendrogram obtained from five ISSR primers using UPGMA method by Dice similarity coefficient for 27 juniper genotypes (D) Principal Component Analysis based on Dice matrix for 27 juniper genotypes.