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opennotspecifiedDec 2016View details →

FIGURE 1 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation

FIGURE 1. Distribution of the species of the Hemiphyllodactylus harterti group in Peninsular Malaysia.

opennotspecifiedDec 2016View details →

FIGURE 2 in Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation

FIGURE 2. Maximum-likelihood phylogram of the Hemiphyllodactylus harterti group with Bayesian posterior probabilities followed by maximum likelihood bootstrap values.

FIGURE 3 in Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

FIGURE 3 Results of demographic modelling (δaδi; Gutenkunst et al., 2009) and demographic parameter estimation (G-PHOCS; Gronau et al., 2011) analyses. (a) Stylized representation of the best supported model from δaδi with parameters superimposed from G-PHOCS. (b) The fit between the best-supported model and the data is shown using the two-dimensional site frequency spectrum (2D-SFS) and plots of the residuals

FIGURE 2 in Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

FIGURE 2 Results of the HIEST version 2.0 (Fitzpatrick, 2012) analysis. (a) Joint maximum likelihood estimates of ancestry (S value) and interclass heterozygosity (H value) for Schistometopum thomense (S. thomense) and Schistometopum ephele (S. ephele) for 41 diagnostic single nucleotide polymorphisms (SNPs). Individuals are coloured by morphology (yellow, unflecked = yellow; brown, flecked = grey) indicating that most admixed individuals (intermediate S and H values) are flecked. (b) H values plotted against latitude show that admixed individuals are restricted to the centre of the island at the contact zone. Individuals are coloured according to S values (≥0.9 or ≤0.1)

FIGURE 1 in Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

FIGURE 1 Schistometopum sampling on São Tomé Island. (a) Map shows distribution of genomic samples with the size of circles proportional to the number of individuals at that site. Individuals with at least 90% ancestry assigned to Schistometopum thomense (S. thomense) are shown in purple, 90% ancestry assigned to Schistometopum ephele (S. ephele) in green, and admixed individuals in orange. Site abbreviations are as follows: AA, Anselmo Andrade; BO, Bombaim; BS, Bom Sucesso; CN, Contador Valley North; CS, Contador Valley South; CV, Canavial; JA, Java + Abade; LB, Lemba River; ML, Rio Maria Luisa; ON, Obo National Park; PA, Porto Alegre; QI, Quisinda; RD, Rio d'Ouro; SF, Santa Fe; SL, Santa Luzia. The type locality of S. ephele (Água Izé, 400–700 m) is probably between the coastal community of Água Izé (indicated by black star) and Java. (b) Plot of ancestry coefficients estimated with ADMIXTURE version 1.3.0 (Alexander et al. (2009) for K = 2. Circles above the plot show the haplotype of each individual from the mitochondrial ND4 locus, and morphological assignment (yellow, unflecked = yellow; brown, flecked = grey). (c) ND4 haplotype network for new samples and previously published data (Stoelting et al., 2014) estimated in PopART (Leigh & Bryant, 2015). Twenty-six mutations separate the haplotype groups. (d) Principal component analysis (PCA) of single nucleotide polymorphism (SNP) data with individuals coloured according to their ancestry assignment from (b). Photo credits: A. Stanbridge

FIGURE 4 in Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

FIGURE 4 Summary of environmental space occupancy analyses. (a) Photos of habitat in representative dry (top) and wet (bottom) regions of São Tomé Island. (b) Violin plot of precipitation values at sites for pure and admixed caecilians (top), bar plots of land cover (middle), and bar plots of soil types and ages (bottom). (c) Annual precipitation (mm) across the island, with drier habitat in the north and wetter habitat in the south (top), land cover across the island, adapted from Soares (2017; middle), and soil types and ages across the island, adapted from Caldeira and Munhá (2002) and Stoelting et al. (2014; bottom). Photo credits: J. Shevock, A. Stanbridge

opencc-zeroApr 2022View details →

Data from: Hidden island endemic species, and their implications for cryptic speciation within soil arthropods

Aim: Specialisation to the soil environment is expected to constrain the spatial scale of diversification within animal lineages. In this context, the existence of flightless arthropod lineages, adapted to soil environments, but with broad geographic ranges, represent something of an anomaly. Here we investigate the diversification process within one such 'anomalous' soil specialist: Geomitopsis franzi Coiffait, 1978, an eyeless and flightless beetle species strongly adapted to the endogean environment but distributed across several oceanic islands. Location: Canary Islands Taxon: Geomitopsis (Coleoptera, Staphylinidae) Methods: We performed an integrative study, including molecular phylogenetics, population genomics, and morphometry. Four DNA regions (two mitochondrial and two nuclear) were amplified and sequenced for 159 specimens from 58 localities sampled across five islands for phylogenetic analyses, and a dated phylogenetic tree was obtained using a mitogenome dataset. ddRAD-seq data was generated to evaluate mtDNA lineages in sympatry against the biological species concept. Results: We found high levels of genetic differentiation (>8% COI gene divergence) among populations from different islands and among geographically coherent lineages within single islands. Lineages within Tenerife presented significant patterns of isolation by distance, with ddRAD-seq providing evidence that lineages represent biological species. Morphometric analyses revealed limited variation, with most lineages lacking diagnostic characters. Main conclusions: Geomitopsis franzi is comprised of at least seven lineages that merit consideration as biological species, and is best considered as a complex of cryptic species. The limited morphological variation across these lineages is consistent with adaptation to the endogean environment placing strong constraints on morphological change. The evolution of cryptic species should be favoured when such constraints are coupled with limited dispersal ability, which characterises G. franzi, and is a trait that broadly characterises the soil mesofauna. We suggest that cryptic species diversity is likely to be a recurrent feature across soil adapted arthropod species with range sizes that appear inconsistent whith a low potential for dispersal.

opencc-zeroAug 2021View details →

Incipient speciation and the impact on taxonomic decision: a case study using a sky island sister species pair of stag beetle (Lucanus; Lucanidae)

Species delimitation can be difficult when the divergence between focal taxa falls in the incipient stage of speciation, because conflicting results are expected among different data sets and the species limit may differ depending on the applied species concept. We studied the speciation history and investigated the impact on taxonomic decision when using different data types in a Taiwanese endemic sister species pair of stag beetle, Lucanus miwai and L. yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3 %; however, L. miwai may not be monophyletic. Our multispecies coalescent based species delimitation result using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of genealogical divergence index (gdi) corresponded to the species delimitation ambiguous zone. We further showed that post divergence gene flow is unlikely. Our study demonstrates challenges in incipient species delineation, but shows the importance of understanding the speciation history and integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.

opencc-zeroSep 2021View details →

Data from: Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade

Islands have long been recognized as key contributors to biodiversity because islands facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we studied the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands by continental, terrestrial-foraging lineages led to exploitation of a new ecological niche (i.e. arboreal foraging). This transition towards arboreal foraging was associated with evolutionary adaptation towards a new morphological optimum. In addition, arboreal-foraging lineages experienced an increase in speciation rates, which was associated with successful range expansions to other islands as well as back-colonization of continents. Our results provide empirical evidence that diversification on continents can only be fully understood when studying the diversification processes that took place on islands, challenging the view of islands as mere sinks of evolutionary diversity.

Figure 4. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 4. A, geographic distribution of Leptocoma aspasia haplotypes in Wallacea and the Sahul Shelf. Each circle represents an island and the fractions within the circle the haplotypes found on that island, proportioned to represent the frequency of each haplotype. The haplotypes are named according to the species-level divisions suggested by ABGD and coloured to represent the clades supported by our phylogenetic analyses. B, TCS haplotype network of Leptocoma haplotypes. Each circle represents a unique ND2–ND3 haplotype, sized to represent how many birds carried that haplotype. The hatch marks represent mutations between haplotypes, also given as numbers in brackets for the wider divergences. The unfilled, white nodes represent hypothetical ancestral states. C, Bayesian consensus tree of Leptocoma haplotypes. Nodes are labelled with Bayesian probabilities.

Figure 1. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 1. A, map of the Indo-Pacific region with study regions marked inside boxes. The range of the olive-backed sunbird is shaded horizontally in yellow, the range of the black sunbird vertically in purple, both according to BirdLife International. Seas deeper than 200 m are represented by a darker blue. Biogeographic barriers (Wallace, 1863; Lydekker, 1896) are represented with red lines. B, map of south-east Sulawesi and the Wakatobi Islands in Wallacea, with olive-backed sunbird sampling sites marked with yellow downward-pointing triangles, black sunbird sampling sites with purple upward-pointing triangles. C, map of Australia and New Guinea on the Sahul Shelf, with olive-backed sunbird sampling sites marked with yellow downward-pointing triangles, black sunbird sampling sites with purple upward-pointing triangles. D, map of the Bismarck Archipelago with the sampling site of the B10K black sunbird marked with a purple triangle.

Figure 2 in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 2. Simplified version of a combined maximum likelihood (ML) and Bayesian phylogenetic tree of Cinnyris and Leptocoma species sampled in Wallacea and the Sahul Shelf. In this figure, the outgroup is omitted and each major clade in the data is collapsed into a single branch. Tips representing focal populations are marked with coloured circles. Nodes are labelled with Bayesian probability/ ML bootstraps. Full versions of the ML and Bayesian trees, including all outgroup taxa, are provided in the Supporting Information (Figs S7, S8).

Figure 3. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 3. A, geographic distribution of Cinnyris jugularis (sensu Gill et al., 2022) haplotypes in Wallacea and the Sahul Shelf. Each circle represents an island and the fractions within the circle the haplotypes found on that island, proportioned to represent the frequency of each haplotype. The haplotypes are named according to the species-level divisions suggested by ABGD and coloured to represent the clades supported by our phylogenetic analyses. B, TCS haplotype network of Cinnyris haplotypes. Each circle represents a unique ND2–ND3 haplotype, sized to represent how many birds carried that haplotype. The hatch marks represent mutations between haplotypes, also given as numbers in brackets for the wider divergences. The unfilled, white nodes represent hypothetical ancestral states. C, Bayesian consensus tree of Cinnyris haplotypes. Nodes are labelled with Bayesian probabilities.

Figure 5. A in Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)

Figure 5. A, map of the Indo-Pacific with the range of the olive-backed sunbird shaded, as currently recognized by BirdLife International. Sampling sites of the birds included in our 697 bp partial ND2 analysis are marked with different triangles, according to the species they were assigned to by ABGD. Currently recognized subspecies are labelled (Gill et al., 2022). B, mean genetic distance (uncorrected p-distance) between each of the species recognized by ABGD, based on a 697 bp partial ND2 alignment. C, simplified version of a combined maximum likelihood (ML) and Bayesian phylogenetic tree of 697 bp of olive-backed sunbird ND2. In this figure the outgroup is omitted and each of the ABGD species is collapsed into a single branch. Nodes are labelled with Bayesian probability/ ML bootstraps.