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73 results for “Genetic diversification”
Data from: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)
Background and Aims: Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Methods: Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Key Results: Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). Conclusions: The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and history of islands, with little evidence for ongoing gene exchange between divergent taxa. The present results emphasize the need to investigate further biological and landscape features and contemporary vs. historical processes in driving population divergence and taxon diversification in Aegean plant radiations.
Genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification
<p>184.cp.variations.map.vcf.zip--the chloroplast variation map of 184 samples<br> 184.mt.variations.map.vcf.zip----the mitochondrial variation map of 184 samples<br> aligment1.fa-- the group of grapefruit, sweet orange and sour orange for mitochondrial heteroplasmy analysis<br> aligment2.fa-- the group of lemon for mitochondrial heteroplasmy analysis<br> coverage depth of 184 short reads samples.zip -- the coverage depth of BAMs in mitochondrial variation map in 184 samples<br> Fortunella hindsii mitochondrial genome.gb -- the conservation proteins annotation of kumquat reference mitochondrial genome<br> GWAS-118.samples.input.phenotype.for GWAS.txt -- the inputfiles for GWAS <br> GWAS-LD.linked.input.gwas.vcf.gz -- the LD linked variations for GWAS<br> LD.purning.nuclear.variation.map.vcf.gz -- LD purning nuclear variations for demography analysis<br> normalization.RNA-seqs.txt -- the nomarlization data of expression of mitochondrial genome<br> nuclear.variation.map.vcf.gz -- the nuclaer variation map<br> ORFs annotation based on Augustus.gtf -- the annotation gene structure using Augustus <br> pan-genome and aligned mitochondrial genomes.zip -- the pan-genome(.fa and .gfa) and aligned mitochondrial genomes<br> scaffold-assemblies.zip -- the scaffolds of mitochondrial genomes</p>
Figure 9 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 9. Above: distribution map of Colobopsis samples examined – countries where Colobopsis presence is known from the literature are highlighted in grey. Below: approximate distributions of other Camponotini (Camponotus barbaricus, of C. micans and of C. ruber) which resemble that of CSL Colobopsis.
Figure 10. Colobopsis imitans. A, B, E in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 10. Colobopsis imitans. A, B, E, worker (holotypus); C, D, F, G, soldier (specimen from the type locality). Scale bars: 0.5 mm. Pictures also available on AntWeb.org database, specimen codes: ANTWEB1041481 and ANTWEB1041482.
Figure 5 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 5. Principal component analyses of morphometric data of Colobopsis nest samples according to the two clusters evidenced by NC-PART clustering. Each small dot represents a colony sample. Large dots represent centroids.
Figure 6 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 6. Maximum likelihood phylogenetic tree based on the barcode fragment of the mtCOI gene from the Colobopsis specimens sequenced.
Figure 4 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 4. Dendrogram comparing the results of 'kmeans', and 'hclust' in NC Clustering of Colobopsis morphometric raw data. Two samples (4.5% of the total) are misplaced by both the dendrogram and one of the partitioning analyses, NC-part. kmeans; partially different samples being affected in each of the three analyses. The other partitioning analysis, NC-part. hclust returned the same sample assignment as the LDA did.
Figure 3 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 3. Chromatic ratios calculated from pictures of the Colobopsis CSL and DQL patterns and from pictures of the two putative model species Cr. scutellaris and D. quadripunctatus (N = 2 0 for each species or chromatic form). Boxplots show mean and standard deviation, while whiskers represent minimum and maximum values. Dots correspond to measured individuals. Their dispersal on the X-axis is a randomized graphic effect to avoid overlaps.
Figure 2 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 2. Type material of the described West-Palaearctic Colobopsis, all showing to the 'D. quadripunctatus-like' pattern. A, holotype queen of Colobopsis truncata from Liguria, Italy, preserved at the Turin Natural History Museum (Italy). B, syntype worker of Colobopsis fuscipes from Austria (picture from AntWeb.org, FOCOL2496; photographer: Christiana Klingenberg), preserved at the Museum für Naturkunde der Humboldt-Universität Berlin (Berlin, Germany). Note that the queen's red colour in the anterior heavily sculptured part of the phragmotic head is not relevant to evaluating its chromatic pattern. Scale bars: 0.5 mm.
Figure 11. Colobopsis imitans. A, B, E, F in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 11. Colobopsis imitans. A, B, E, F, queen; C, D, G, male. Specimens from the type locality. Scale bars: 0.5 mm. Pictures also available on AntWeb.org database, specimen codes: ANTWEB1041483 and ANTWEB1041484.
Figure 8 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 8. Trail-following behaviour on Crematogaster scutellaris trails by other ants (indicated with arrows). On the left (A, C, E) CSL Colobopsis; on the right (B, D, F) Camponotus lateralis observed in the same locality performing the same behaviour (photos taken in Palermo (Sicily) during field surveys).
Figure 12 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 12. Male genitalia of Colobopsis imitans in ventral and dorsal view, specimen from the type locality. Scale bars = 0.25 mm.
Figure 1 in Is mimicry a diversification-driver in ants? Biogeography, ecology, ethology, genetics and morphology define a second West-Palaearctic Colobopsis species (Hymenoptera: Formicidae)
Figure 1. The model species and the two detected chromatic model patterns of Colobopsis: A, Crematogaster scutellaris; B, CSL Colobopsis from Sicily; C, Dolichoderus quadripunctatus from Tuscany; D, DQL Colobopsis from Tuscany.
Dispersal ability and its consequences for population genetic differentiation and diversification
<p><span>Dispersal ability is known to influence geographic structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary time scales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.</span></p>
Data from: Post-fire response and genetic diversity in Erica coccinea: connecting population dynamics and diversification in a biodiversity hotspot
Understanding the proceses of biological diversification is a central topic in evolutionary biology. The South African Cape fynbos, one of the major plant biodiversity hotspots out of the tropics, has prompted several hypotheses about the causes of generation and maintenance of biodiversity. Fire has been traditionally invoked as a key element to explain high levels of biodiversity in highly speciose fynbos taxa, such as the genus Erica. In this study, we have implemented a microevolutionary approach to elucidate how plant-response to fire may contribute to explain high levels of diversification in Erica. By using microsatellite markers, we investigated the genetic background of seeder (fire-sensitive) and resprouter (fire-resistant) populations of the fynbos species Erica coccinea. We found higher within-population genetic diversity and higher among-population differentiation in seeder populations and interpreted these higher levels of genetic diversification as a consequence of the comparatively shorter generation times and faster population turnover in the seeder form of this species. Considering that genetic divergence among populations may be seen as the initial step to speciation, the parallelism between these results and the pattern of biodiversity at the genus level offers stimulating insights into understanding causes of speciation of the genus Erica in the Cape fynbos.
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
<p class="MsoNormal"><span class="Fuentedeprrafopredeter1"><span>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. T</span></span><span class="Fuentedeprrafopredeter1"><span>oday, there is only one permanent connection between the Orinoco and Negro </span></span><span class="Fuentedeprrafopredeter1"><span>(Amazon) </span></span><span class="Fuentedeprrafopredeter1"><span>basins, known as the Casiquiare Canal</span></span><span class="Fuentedeprrafopredeter1"><span>. </span></span><span class="Fuentedeprrafopredeter1"><span>However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (<em>Paracheirodon axelrodi),</em> the most important fish in the ornamental world market, is distributed in both basins. Here we investigated </span></span><span class="Fuentedeprrafopredeter1"><em><span>P. axelrodi </span></em></span><span class="Fuentedeprrafopredeter1"><span>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. </span></span><span class="Fuentedeprrafopredeter1"><span>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 </span></span><span class="Fuentedeprrafopredeter1"><span>São</span></span><span class="Fuentedeprrafopredeter1"><span> Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. </span></span><span class="Fuentedeprrafopredeter1"><span>Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. </span></span><span class="Fuentedeprrafopredeter1"><span>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. </span></span><span class="Fuentedeprrafopredeter1"><span>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.</span></span></p>
Data from: Social interactions predict genetic diversification: an experimental manipulation in shorebirds
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Data from: Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus
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Data from: Post-fire response and genetic diversity in Erica coccinea: connecting population dynamics and diversification in a biodiversity hotspot
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Data from: Morphological and genetic discrepancies in populations of Oreocarya paradoxa and O. revealii: the impact of edaphic selection on recent diversification in the Colorado Plateau
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