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86 results for “island speciation”
Chemical speciation of copper in a salt marsh estuary near Sapelo Island, Georgia
The concentrations of dissolved copper (Cud), copper-binding ligands, thiourea-type thiols and humic substances (HSCu) were measured in estuarine waters adjacent to Sapelo Island, Georgia, USA, on a monthly basis from April to December 2014. Here we present the seasonal cycle of copper speciation within the estuary and compare it to the development of an annually occurring bloom of ammonia oxidising archaea (AOA) Thaumarchaeota, which require copper for many enzymes. Two types of complexing ligands (L1 and L2) were found to dominate with mean complex stabilities (log K'CuL) of 14.5 and 12.8. Strong complexation resulted in lowering of the free cupric ion (Cu2+) concentration to femtomolar (fM) levels throughout the study and to sub-fM levels during the summer months. A Thaumarchaeota bloom during this period suggests that this organism manages to grow at very low Cu2+ concentrations. Correlation of the concentration of the L1 ligand class with a thiourea-type thiol and the L2 ligand class with HSCu provide convincing evidence for the identity of the ligands. Due to the stronger complex stability, 82 - 99 % of the copper was bound to L1. Thiourea-type thiols form strong Cu(I) species, suggesting that ~90% copper is present as Cu(I) in this region, upsetting the paradigm of its predominance as Cu(II). In view of the very low concentration of free copper (pCu >15 at the onset and during the bloom) and a reputedly high requirement for copper, it is likely that the Thaumarchaeota are able to access the thiol-bound copper directly.
Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
<p><strong>Aim</strong>: The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of 'supertramps', 'great speciators' and relictualization.</p> <p><strong>Location</strong>: The Indo-Pacific, Australia, Asia and Africa.</p> <p><strong>Taxon</strong>: Corvoid passerine birds.</p> <p><strong>Methods</strong>: We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckoo-shrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence.</p> <p><strong>Results</strong>: The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, South-East Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated ('supertramps') or show strong differentiation of local populations ('great speciators'), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in 'great speciators' with intermediate levels of dispersal abilities (as per hand-wing index).</p> <p><strong>Main conclusions</strong>: Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of 'supertramps', 'great speciators' and relictual paleo-endemics within the temporal stages of the taxon cycle.</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
Diversity patterns and speciation processes in a two-island system with continuous migration
<p>Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here we consider a two-island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.</p>
FIGURE 2 in Massif Speciation Events in New Caledonian Lizards: Diversification in the Genus Marmorosphax (Scincidae) Tracks Isolation on the Island's Ultramafic Surfaces
FIGURE 2. Persistent high elevation cloud formation on northwest Massif Katépahié (adjacent to the Massif de Koniambo) during the dry season.
FIGURE 5 in Massif Speciation Events in New Caledonian Lizards: Diversification in the Genus Marmorosphax (Scincidae) Tracks Isolation on the Island's Ultramafic Surfaces
FIGURE 5. Phylogenetic relationships amongst the species and populations of Marmorosphax. Likelihood topology with UFboot and BPP Bayesian posterior probabilities shown respectively. UFboot equal to 100 and BPP equal to 1.0 are represented at nodes with black circles. The numbers in squares represent the four major groups of Marmorosphax and numbers present in circles represent groups for pairwise comparisons. – indicate nodes not recovered by both phylogenetic analyses.
Figure 1 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation
Figure 1. ContinentalFrancewiththedepartmentMayennehighlighted (A) andhabitatmodelforthe Fire salamander indepartment Mayenne (B). Themap representsthe habitat suitability model Ps = (1/ (1 + exp(−0.0303*percent_forest_cover-0.00562*altitude-0.0299*percent_hedgerow_cover + 1.769))) and was visualized with ILWIS 3.6 software58, available at https://52north.org/software/software-projects/ilwis/. Habitat suitability increases from deep blue with a probability of occurrence of zero to deep red with a probability of occurrence at unity (see colour bar). Prime fire salamander habitats are found at higher altitudes and are forested (in black) or with a dense hedgerow cover. Populations genetically investigated are located in and around the largely deciduous forests Forêt de Bourgon (FB) and Bois de Hermet (BH) and listed in Table 1.The outer geographicalcoordinates of the department are 1.239–0.049W and 47.733–48.568N.
Figure 3 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation
Figure 3. (A) Clustering of pairwise Fst-values of Kottenforstfire salamanderpopulations (localities K01-K47) with the UPGMA-method. Numbers K01-K27 represent populations in the western section of the forest and K28-K47 represent populationsin the eastern section of the forest. The basal cluster at Fst <0.04 is composed of two groups (shaded) composed of mostly eastern (14/16 = 88%) or mostlywestern localities (14/15 = 93%). Populations breeding in streams are shown by the letter S. Note that populations that join the dendrogram at higher Fst-values are characterized by mostlysmall effectivepopulation sizes (Ňe ≤ 10, indicated by small open dots; X – Ňe not determined). B top panel - Populationsplotted along the firstand second axis of a principal component analysis. Middle panel - Ellipses represent means ± standarddeviation for sevenstream populations (left ellipse) and 40 non-streampopulations (right ellipse). Lower panel - Ellipsesrepresent means ± standard deviation forthe western (left) and eastern (right) sectionof the Kottenforst, forsmall populations (Ňe ≤ 10) shown by interruptedlines andfor larger populations (Ňe> 10) shown by uninterrupted lines. Notethat for the larger populations the ellipses for western and eastern localities do not overlap.
Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation
Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 analyzed in the framework of allopatric speciation, i.e. a secondary spatial contact of a western pond-breeding lineage and an eastern stream-breeding lineage. The 95% credible cline regions are shown by grey shading. Solid and open round symbolsrepresent larger (Ňe> 10) andsmall populations (Ňe ≤ 10), respectively. Note that the stream-breeding populations that gave the composite genotype its name are all located in the eastern section of the Kottenforst (six data points indicated with a forward slash (/). One 'intermittent stream' in the western section is indicated by a backward slash. Also note the paucity of data at and around the steepest part of the clines. A – loadings on the first PC axis versus geographical distance. The clinecentre is at km 365.3 of the Universal Transverse Mercator (UTM) grid. Cline width is 3952 m. B – frequency of the stream-breeding genotype versus distance (after21). Thecline centre is at UTM km 365.1 and the cline widthis 1108 m. For model details see Supplementary Information VI.
Figure 2 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation
Figure 2. (A) Clustering of pairwise Fst-values of firesalamander populations (Mayenne localities 1–41) with the UPGMA-method. The basal cluster at Fst <0.010 is mostly composed of forest populations (F, 17/21 = 81%) whereas populationsthat jointhe dendrogramat higher Fst-values are mostly fromthe bocage (B, 14/20 = 70%). At Fst> 0.025 the contribution of the bocage populations is eightout of eight. Notethat populations thatjoin the dendrogram at the highest Fst-values are characterizedby mostly small effective population sizes (Ňe ≤ 10, indicated by small open dots). (B) Populations plotted along the first and second axis of a principal component analysis. The 23 forest populations are shown by small solid round symbols and the solid ellipse represents the mean ± standard deviation. Eighteenpopulations from the bocageare shown by large open round symbols, with the mean ± standard deviation shown bythe widerellipse with the interrupted line.
Figure 11 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figure 11. Consensus tree of the three equally parsimonious trees with DELTRAN optimization, all characters of equal weight and unordered. Closed symbols indicate apomorphies, and open symbols indicate probable homoplasy. Numbers above each symbol indicate the character and numbers below the symbol indicate its state. Tree length 66; consistency index 48; retention index 48. A and B indicate the two basal clades of species.
Figure 9 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figure 9. Principal islands of the Galápagos Archipelago (numbers on contour lines indicate elevation in hundreds of metres). Not all satellite islets with Stomion are indicated by name.
Figures 24–29 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figures 24–29. Scanning electron micrographs of the head and pronotum (18 ¥), with inset of pronotal disc (300¥) and the elytral disc (100¥). Figs 24, 25. S. obesum; Figs 26, 27. S. genovesa; Figs 28, 29. S. longulum.
Figures 1–8 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figures 1–8. Habitus figures of eight species of Stomion. Fig. 1. S. galapagoensis. Fig. 2. S. helopoides. Fig. 3. S. cribicollis. Fig. 4. S. longulum. Fig. 5. S. laevigatum. Fig. 6. S. linelli. Fig. 7. S. longicornis. Fig. 8. S. rugosum. From Van Dyke (1953), with permission of California Academy of Sciences. Scale bar = 5 mm.
Figures 12–17 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figures 12–17. Scanning electron micrographs of the head and pronotum (18 ¥) with inset of pronotal disc (300¥) and the elytral disc (100¥). Figs 12, 13. S. longicornis; Figs 14, 15. S. helopoides; Figs 16, 17. S. galapagoensis.
Figures 18–23 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figures 18–23. Scanning electron micrographs of the head and pronotum (18¥), with inset of pronotal disc (300¥) and the elytral disc (100¥). Figs 18, 19. S. punctipennis; Figs 20, 21. S. cribricollis; Figs 22, 23. S. rugosum.
Figures 30–35 in Speciation in Darwin's darklings: taxonomy and evolution of Stomion beetles in the Galápagos Islands, Ecuador (Insecta: Coleoptera: Tenebrionidae)
Figures 30–35. Scanning electron micrographs of the head and pronotum (18¥), with inset of pronotal disc (300¥) and the elytral disc (100¥). Figs 30, 31. S. laevigatum; Figs 32, 33. S. linelli linelli; Figs 34, 35. S. linelli leleupi.
Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
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Diversity patterns and speciation processes in a two-island system with continuous migration
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Data from: Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems
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