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opencc-zeroAug 2021View details →

Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

Of two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular setting. As a single flowering cherry occurring on Ulleung Island in East Sea, Prunus takesimensis Nakai has been presumed as derived through anagenetic speciation on the Island. Based on morphological similarities, P. sargentii distributed in adjacent continental areas and islands has been suggested as its purported continental progenitor. However, the overall genetic complexity and resultant non-monophylies of closely related flowering cherries have hindered determining their phylogenetic relationships as well as establishing concrete continental progenitor and insular derivative relationship. Based on extensive sampling of wild flowering cherries including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, this study inferred the origin and evolution of P. takesimensis using multiple different molecular markers. As the result of phylogeny and population genetic structure analyses based on SNPs detected by MIG-Seq and complementary cpDNA haplotypes, we could provide the extensive and convincing evidence for (1) the monophyly of P. takesimensis, (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor), (3) the geographic origin of P. takesimensis via single introduction from source population of P. sargentii in Korean Peninsula, (4) no significant genetic reduction in anagenetically derived insular species P. takesimsnsis compared to continental progenitor P. sargentii, (5) no strong population genetic structuring or geographical patters in the insular derived species, and (6) Mig-seq method as an effective tool to unravel complex evolutionary history of plant groups.

opencc-zeroSep 2023View details →

Supplementary material for: Intermittent migration can induce pulses of speciation in a two-island system

Geographic barriers can come and go depending on natural conditions. These fluctuations cause population cycles of expansion and contraction, introducing intermittent migrations that may not hinder speciation but rather promote diversification. Here, we study a neutral two-island speciation model with intermittent migration driven by sea-level fluctuations. Seabed depth modulates isolation and connection periods between the islands, with migration occurring during connection periods with a certain probability. Mating is restricted to genetically compatible individuals on the same island, and offspring inherit genomes from both parents through recombination. We observe speciation pulses that would not occur under strict isolation or continuous migration, with infrequent, instantaneous increases in species richness happening at different times depending on the combination of geographic settings and migration probability. The resulting dynamic patterns of richness exhibit contrasting behavior between connected and isolated scenarios, often including species that do not persist. Prolonged isolation can reduce richness to one species per island, resembling patterns commonly associated with archipelagos under sea-level fluctuations. Together with other studies, our results in out-of-equilibrium populations support the relevance of investigating the impact of variable migration on diversification, particularly in regions of high diversity.

publicNov 2023View details →

Supplementary material for: Intermittent migration can induce pulses of speciation in a two-island system

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publicApr 2025View details →

Data from: Speciation with gene flow in an island endemic hummingbird

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publicAug 2021View details →

Genome-wide SNP analysis elucidates the evolution of Prunus takesimensis in Ulleung Island: Genetic consequences of anagenetic speciation

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opencc-zeroJul 2020View details →

Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.

opencc-zeroDec 2014View details →

Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Harnessing the power of genomic scans, we test the debated 'species pump' hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically inter-connected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75–130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification.

opencc-zeroDec 2015View details →

Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate 'genomic island of speciation'

Speciation with gene flow may be aided by reduced recombination helping to build linkage between genes involved in the early stages of reproductive isolation. Reduced recombination on chromosome X has been implicated in speciation within the Anopheles gambiae complex, species of which represent the major Afrotropical malaria vectors. The most recently diverged, morphologically indistinguishable, species pair, A. gambiae and Anopheles coluzzii, ubiquitously displays a 'genomic island of divergence' spanning over 4 Mb from chromosome X centromere, which represents a particularly promising candidate region for reproductive isolation genes, in addition to containing the diagnostic markers used to distinguish the species. Very low recombination makes the island intractable for experimental recombination studies, but an extreme hybrid zone in Guinea Bissau offers the opportunity for natural investigation of X-island recombination. SNP analysis of chromosome X hemizygous males revealed: (i) strong divergence in the X-island despite a lack of autosomal divergence; (ii) individuals with multiple-recombinant genotypes, including likely double crossovers and localized gene conversion; (iii) recombination-driven discontinuity both within and between the molecular species markers, suggesting that the utility of the diagnostics is undermined under high hybridization. The largely, but incompletely protected nature of the X centromeric genomic island is consistent with a primary candidate area for accumulation of adaptive variants driving speciation with gene flow, while permitting some selective shuffling and removal of genetic variation.

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.

opencc-zeroDec 2014View details →

Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.

opencc-zeroDec 2014View details →

Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

FIGURES 18–23 in Gone with the wind: westward dispersal across the Indian Ocean and island speciation in Hemicordulia dragonflies (Odonata: Corduliidae)

FIGURES 18–23. Distribution of discussed genera. The courses of storms from May to November in the northern hemisphere and November to May in the southern hemisphere are indicated by arrows (after Times Books 1997). (18) Hemicordulia and Procordulia dragonflies, pale shading: main range in Australasia and Pacific; dark shading: H. africana n. sp.; crosses and pale shading: H. similis; square: H. virens; circle: H. atrovirens n. sp.; (19) Teinobasis damselflies, pale shading: main range in Australasia and Pacific; dark shading: T. alluaudi; (20) Collocalia swiftlets; (21) Copsychus magpie robins; (22) Hypsipetes bulbuls; (23) Pteropus flying foxes.

FIGURES 2–11. 2–6 in Gone with the wind: westward dispersal across the Indian Ocean and island speciation in Hemicordulia dragonflies (Odonata: Corduliidae)

FIGURES 2–11. 2–6, Male appendages of Hemicordulia species in dorsal view. (2) H. asiatica; (3) H. virens; (4) H. atrovirens n. sp.; (5) H. similis; (6) H. africana n. sp.; 7–11, Male appendages of Hemicordulia species in lateral view. (7) H. asiatica; (8) H. virens; (9) H. atrovirens n. sp.; (10) H. similis; (11) H. africana n. sp.

FIGURES 12–17. Vulvar scale and S9 in Gone with the wind: westward dispersal across the Indian Ocean and island speciation in Hemicordulia dragonflies (Odonata: Corduliidae)

FIGURES 12–17. Vulvar scale and S9 of Hemicordulia species in ventral view. (12) H. asiatica; (13) H. virens; (14) H. atrovirens n. sp.; (15) aberrant H. similis (cf. Fraser 1949); (16) typical H. similis; (17) H. africana n. sp.

FIGURES 24–25 in Gone with the wind: westward dispersal across the Indian Ocean and island speciation in Hemicordulia dragonflies (Odonata: Corduliidae)

FIGURES 24–25. Geographic (24) and altitudinal (25) distribution of H. africana n. sp. relative to large water bodies. Filled circles are known records (present paper), open circles forested localities near large waterbodies that have recently been intensively surveyed by V. Clausnitzer (pers. comm.), except Mbala by Pinhey (1984). Many sites in the region away from large water bodies have also been researched. A line connects each site to the altitude of the nearest large water body.

opennotspecifiedDec 2016View details →

FIGURE 5 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 5. Upper: adult male Hemiphyllodactylus titiwangsaensis (LSUDPC 6708) from the type locality of Cameron Highlands, Pahang. Middle: adult male H. cf. titiwangsaensis (LSUDPC 2868) from Fraser's Hill, Pahang. Lower: adult male H. cf. titiwangsaensis (LSUDPC 6444) from Genting Highlands, Pahang.