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opencc-zeroDec 2015View details →

Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. Results: A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. Conclusions: Our results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period's cyclical climatic fluctuations.

opencc-zeroDec 2011View details →

Data from: Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands

Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and inter-population gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely-related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multi-locus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, E. formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the south-east Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.

Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S-DIVA algorithm using ultrametric COI tree calculated in BEAST 2.4 software. Numbers at the tips of the trees correspond to the sampling locations on the map (designated as in Fig. 1). Letters represent most likely ancestral range. Sectors in circles indicate the percent of total range probability. Biogeographical regions in the map as in Piepenburg et al. (2011), Ekimova et al. (2019), Laakkonen et al. (2021).

Fig. 2 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 2. Morphology of Arctic Priapulus caudatus. A. Individual WS19002 from the intertidal of the White Sea, showing the body division into introvert (in), trunk (tr) and caudal appendage (ca). B. Frontal scanning electron microscopical (SEM) image of individual WS19002 from the White Sea showing the longitudinal rows of scalids (sc) and the pentagons of pharyngeal teeth (the first five pentagons are labelled with numbers. C. Individual XZ4889 from the Barents Sea, for abbreviations see A. D, E. Frontal view on individual XZ5288 from the Laptev Sea with light microscopy (D) and SEM (E). F. Lateral view on everted pharyngeal teeth in individual XZ5496 from the East-Siberia Sea. Pharyngeal teeth of pentagons 1 to 6 are labelled. G, H. Individual XZ5374 from the Laptev Sea, for abbreviations in G see figure A. H is a magnification showing the ring papillae (rp), posterior warts (pw) and the vesicles (ves) of the caudal appendage.

Fig. 1 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 1. Sampling locations: 1 – Northwest Atlantic (Cobscook Bay), 2 – North Sea (Scotland), 3 – North Sea (Bergen), 4 – Skagerrak (Kristineberg), 5 – Baltic Sea (Oresund), 6 – Norwegian Sea (Tromsø), 7 – Barents Sea (Dalnie Zelentsy), 8 – White Sea, 9 – Barents Sea (Russkaya Gavan), 10 – Kara Sea (Abrosimov Bay), 11 – Gulf of Ob, 12 – Laptev Sea (Severnaya Zemlya), 13 – Laptev Sea (Vilkitsky Strait), 14 – shelf of the Laptev Sea, 15 – Laptev Sea (Buor- Haya), 16 – shallow of the East Siberian Sea, 17 – East Siberian Sea (Chaunskaya Bay), 18 – Chuckchi Sea (Gerold Island), 19 – Sea of Okhotsk (Magadan), 20 – North Pacific (Kamchatka), 21 – North Pacific (Alaska). Green circles indicate individuals from GenBank, yellow circles indicate our samples. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 6. Single-gene Bayesian trees for 16S and FoxQ2 markers. Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 60 are shown.

Fig. 9 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 9. Divergence time estimates from BEAST analysis for major Priapulus caudatus clades with different calibration scenarios (CS). Dates are in millions of years. Green dots indicate the main divergence nodes, orange dots show Okhotsk clade divergence node. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 7. Haplotype TCS network from COI for Priapulus caudatus (including available sequences from GenBank). Frames indicate the main haplogroups, tick marks between haplotypes indicate number of substitutions, relative size of the circles reflects the number of individuals in the haplotype. Colors indicate sample location. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 4. Distribution of five main COI clades around the studied area (including available sequences from GenBank).

Fig. 5 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 5. Right: Bayesian phylogenetic tree of Priapulus caudatus based on COI dataset (without sequences from GenBank). Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 60 are shown. Blue and yellow boxes show 28S + 18S genotypes. Individuals in yellow boxes belong to the intertidal genotype, individuals in blue boxes belong to the subtidal genotype; individuals in half-yellow-half-blue boxes are heterozygotes. Asterisks mark individuals collected in the intertidal (0 m), the rest are from the subtidal (5–500 m). Left: intertidal (yellow worms) and subtidal (blue worms) populations of Priapulus caudatus. Some larvae from intertidal populations pass to the subtidal with the tide. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 3. Single-gene Bayesian trees for COI marker (including all available sequences from GenBank). Numbers above nodes indicate bootstrap values from Bayesian Interference (BI), black numbers below—posterior probabilities from Maximum Likelihood (ML), only bootstrap values> 50 are shown.

Fig. 8 in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816

Fig. 8. Ultrametric COI tree calculated in BEAST 2.4 software under the Birth-Death model in 107 MCMC generations (including available sequences from GenBank). Black numbers above branches indicate millions of years (Mya); white numbers below indicate posterior probabilities. On the left side: classic subdivision of the Pliocene-Pleistocene according to Horikawa et al. (2015), M¨oller et al. (2019), and Astakhov and Semionova (2021). Grey boxes indicate glacial periods.

publicMar 2010View details →

Data from: Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia

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publicJun 2012View details →

Data from: Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands

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publicSep 2011View details →

Data from: Pleistocene speciation in the genus Populus (Salicaceae)

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publicJun 2019View details →

Data from: Speciation and subsequent secondary contact in two edaphic endemic primroses driven by Pleistocene climatic oscillation

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publicOct 2025View details →

Data from: Pleistocene speciation and glacial refugia in a temperate freshwater biodiversity hotspot

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publicAug 2013View details →

Data from: Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

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