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opencc-by-4.0Dec 2019View details →

Influence of Paleolithic Range Contraction, Admixture and Long-Distance Dispersal on Genetic Gradients of Modern Humans in Asia

Each folder is identified according to the scenario, and contains another folder with the input files (files *.txt, *.par, *.sam, *.asc) to simulate it, the corresponding simulated genetic data (files *.arp) and the derived PC maps (files *.png). A file with the locations of the samples is also included (coord.txt). * Pure Paleolithic expansion *  The folder “Paleo” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion, ignoring the range contraction induced by the LGM and LDD events. * Pure Paleolithic expansion considering the range contraction induced by the LGM *  The folder “Paleo_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion suffering the range contraction induced by the LGM.  * Pure Paleolithic expansion considering long-distance dispersal (LDD) events *  The folder “Paleo_LDD” contains the input files (INFILES), the genetic data  and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion considering LDD events.  * Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and East Asia considering the range contraction induced by the LGM *  The folder “Paleo2NeoIR0_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and later from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and East Asia considering LDD events *  The folder “Paleo2NeoIR0_LDD” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by two Neolithic expansions from Middle East and later from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from Middle East considering the range contraction induced by the LGM *  The folder “Paleo_MiddleEastNeoIR0_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0) from Middle East suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering the range contraction induced by the LGM *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES) and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from Middle East considering LDD events *  The folder “Paleo_MiddleEastNeoIR0_REC” contains the input files  (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0) from Middle East considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering LDD events *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES) the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from Middle East considering the range contraction induced by the LGM *  The folder “Paleo_MiddleEastNeoIR004_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering the range contraction induced by the LGM *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES), the genetic data  and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0.04) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from Middle East considering LDD events *  The folder “Paleo_MiddleEastNeoIR004_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering LDD events *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files  (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0.04) from East Asia considering LDD events.

opencc-zeroNov 2023View details →

Synergistic polyploidization and long-distance dispersal enable the global diversification of yellowcresses (Rorippa, Brassicaceae)

<div> Aim: Long-distance dispersal (LDD) plays an important role in shaping the distribution of global biodiversity. Polyploidy could favor invasion and thereby facilitate LDD. However, how and to what extent polyploidy interacts with LDD is unclear. Here, we test the putative role of polyploidy in the global dispersal of Rorippa species.</div> <div> </div> <div> Location: Global.</div> <div> </div> <div> Time period: Late Miocene to present.</div> <div> </div> <div> Major taxa studied: Rorippa.</div> <div> </div> <div> Methods: We traced the biogeographic and speciation history for 17 diploids and 41 polyploids of Rorippa using variation from plastid genomes and multiple nuclear loci. The ploidy role in dispersal rate difference was demonstrated using trait-dependent biogeographic modeling.</div> <div> </div> <div> Results: LDD shaped the amphitropical disjunction of Rorippa, during which polyploids showed higher dispersal rates than those of diploids, with 5.6× increase under the best-fitted model. Five diploids and 21 polyploids were identified as products of transoceanic speciation events. Polyploidy-involved LDD was more common in terms of polyploidization following LDD than those preceding LDD.</div> <div> </div> <div> Main conclusions: We demonstrate that polyploidy would be not only a driver but also a responder of LDD in Rorippa, highlighting a synergistic relationship between them. Our results provide a framework to uncover the biogeographic consequences of polyploidization and the joint roles of polyploidy and LDD in shaping the distribution of biodiversity.</div>

opencc-zeroFeb 2024View details →

Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa

Characterising patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries, and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7,510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into: Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterised by an isolation by distance pattern (IBD) (r2 = 0.78, p<0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events which act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa, and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

opencc-by-4.0Jul 2022View details →

Supplementary material for: Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift

Raw data and input files for phylogenetic and biogeographic analysis of the article "Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift". Supplementary material S1. Matrix of phenotypic characters in .ss format. Supplementary material S2. Alignment of COI sequences in fasta format.. Supplementary material S3. Alignment of H3 sequences in fasta format. Supplementary material S4. Alignment of 16S sequences in fasta format before trimming with gblocks. Supplementary material S5. Alignment of 28S sequences in fasta format before trimming with gblocks. Supplementary material S6. Input for running parsimony analysis using TNT (phenotypic data only). Supplementary material S7. Input for running Bayesian inference using MrBayes (phenotypic data only). Supplementary material S8. Input for running parsimony analysis using TNT (sequence data only). Supplementary material S9. Input for running Bayesian inference using MrBayes (sequence data only). Supplementary material S10. Input for running parsimony analysis using TNT (total evidence). Supplementary material S11. Input for running Bayesian inference using MrBayes (total evidence). Supplementary material S12. Input for running parsimony analysis using TNT (total evidence, dataset with reduced number of terminals). Supplementary material S13. Input for running Bayesian inference using MrBayes (total evidence, dataset with reduced number of terminals). Supplementary material S14. Input for running Bayesian inference using MrBayes (total evidence) and estimating node ages using tip-dating. Supplementary material S15. Input for running Bayesian inference using Beast (sequence data only) and estimating node ages using node-dating. Supplementary material S16. Raw geographic distances among areas in each time slice and dispersal probability matrices for each biogeographic model. Supplementary material S17. Inputs for estimating ancestral ranges and performing biogeographic stochastic maps for our dataset. Supplementary material S18. Consensus tree found with parsimony analysis using TNT (phenotypic data only). Supplementary material S19. Consensus tree found with Bayesian inference using MrBayes (phenotypic data only). Supplementary material S20. Consensus tree found with parsimony analysis using TNT (sequence data only). Supplementary material S21. Consensus tree found with Bayesian inference using MrBayes (sequence data only). Supplementary material S22. Consensus tree found with parsimony analysis using TNT (total evidence). Supplementary material S23. Consensus tree found with Bayesian inference using MrBayes (total evidence). Supplementary material S24. Consensus tree found with parsimony analysis using TNT (total evidence, dataset with reduced number of terminals). Supplementary material S25. Consensus tree found with Bayesian inference using MrBayes (total evidence, dataset with reduced number of terminals). Supplementary material S26. Consensus tree found with Bayesian inference using MrBayes (total evidence) and with node ages estimated using tip-dating. Supplementary material S27. Maximum clade credibility tree found with Bayesian inference using Beast (sequence data only) and with node ages estimated using node-dating.

opencc-zeroApr 2022View details →

Path-finding algorithm as a dispersal assessment method for invasive species with human-vectored long-distance dispersal event

Aim: An assessment method that can precisely represent human-vectored long-distance dispersals (HVLDD) is currently in need for effective management of invasive species. Here, we focused on HVLDD happening along roads and proposed a path-finding algorithm as a more precise dispersal assessment tool than the most widely used Euclidean distance method by using pine wilt disease (PWD) as a case study. Location: Busan Metropolitan City, Republic of Korea Methods: A path-finding algorithm, which calculates distances by considering spatial distribution of road networks, was tested for its effectiveness in estimating dispersal distances of HVLDD events. To this end, annual HVLDD cases were classified from entire PWD occurrence data from 2016 to 2019 and their dispersal distances were calculated using the path-finding algorithm and the Euclidean distance method. We constructed potential dispersal ranges based on the occurrence points in 2016, 2017, and 2018 using the respective year's mean dispersal distance for both methods, and their performances in accounting for each subsequent year's HVLDD cases were compared to determine which method calculated more precise distances. The information on which road class contributed more to dispersal occurrences and distances was analysed as well using the proposed algorithm. Results: The potential dispersal ranges of the path-finding algorithm accounted for more future anthropogenic infection cases than the ones that used the Euclidean distance method, validating its higher functionality. It also revealed that most HVLDDs started and ended on small roads, and large roads constituted the majority of the total dispersal length. Main Conclusions: The path-finding algorithm has proven to be a more effective dispersal assessment method for HVLDD events. It can help design effective control strategies. Thus, we encourage using the path-finding algorithm for dispersal assessment of invasive species that move along road networks, as well as for the development of more powerful HVLDD prediction models.a

opencc-by-4.0Mar 2022View details →

Data for: "Dynamic species distribution modeling reveals the pivotal role of human-mediated long-distance dispersal in plant invasion"

All the data needed to reproduce the results and Figures of our article: Botella, C., Bonnet, P., Hui, C., Joly, A., & Richardson, D. M. (2022). Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion. Biology, 11(9), 1293. <a href="https://doi.org/10.3390/biology11091293">https://doi.org/10.3390/biology11091293</a> Please, find the R scripts and guidelines to reproduce our results on the article's Github repository : <a href="https://github.com/ChrisBotella/plectranthus_barbatus/tree/main">https://github.com/ChrisBotella/plectranthus_barbatus/tree/main</a>

Fig. 8 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 8. Scanning electron microscopy. Polymerurus insularis sp. nov. A–B, D. Paratype (ZUEC GCH 59). C, E. Paratype (ZUEC GCH 60). A–B. Posterior dorsal view. C. Detail of the furca base in posterior dorsolateral view. D–E. Details of the furcal rami. Abbreviations: fb = furca base; fr = furcal rami; sc-4 = Type 4 scales; sc-5 = Type 5 scales. Scale bars = 10 µm.

Fig. 4 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 4. Light microscopy – DIC. Polymerurus insularis sp. nov. Posterior region of the body. A. Paratype (ZUEC GCH 56). B, D. Holotype (ZUEC GCH 55). C. Paratype (ZUEC GCH 57). A–B. Posterior dorsal view. C. Posterior dorsolateral view. D. Posterior ventral view. Abbreviations: fr = furcal rami; sc-1 = Type 1 scales; sc-2 = Type 2 scale; sc-3 = Type 3 scales; sc-4 = Type 4 scales. Scale bars = 40 µm.

Fig. 5 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 5. Close-up of the different types of scales described forPolymerurus insularis sp. nov.A–C. Paratype (ZUEC GCH 59). D, F. Holotype (ZUEC GCH 55). E. Paratype (ZUEC GCH 56). A–C. Scanning electron microscopy. D–F. Light microscopy – DIC. A. Detail of a section of the dorsal middle trunk, showing the most common type of scale, Type 1, with emphasis on its characteristic shape. B. Detail of a section of the dorsal posterior trunk, showing Type 2 and Type 3 scales. C–E. Detail of the transition between the dorsal posterior trunk and the dorsal furca base, showing the particular scale covering of this region. F. Detail of the transition between the ventral posterior trunk and the ventral furca base, showing the particular scale covering this region. Abbreviations: sc-1 = Type 1 scales; sc-2 = Type 2 scale; sc-3 = Type 3 scales; sc-4 = Type 4 scales; sc-5 = Type 5 scales; sc-6 = Type 6 scales; sc-7 = Type 7 scales; sc-8 = Type 8 scales; svs = small ventral pair of spines. Scale bars: A–C = 5 µm; D = 10 µm; E = 15 µm; F = 10 µm.

Fig. 3 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 3. Light microscopy – DIC. Polymerurus insularis sp. nov., holotype (ZUEC GCH 55). A–C. Correspond to the most anterior third of the specimen. A. Anterior dorsal region. B. Anterior internal region. C. anterior ventral region. D–F. Correspond to the trunk. D. Dorsal trunk. E. Internal trunk. F. Ventral trunk. G–I. Correspond to the posterior third of the specimen. G. Dorsal posterior third. H. Internal posterior third. I. Ventral posterior third. Abbreviations: ce = cephalion; ct = cephalic bristles; eg = egg; hy = hypostomium; i = intestine; is = interciliary spines; lc = locomotory cilia; lce = lateral cephalic expansions; mo = mouth; ne = nephridia; pl = pleurae; ph = pharynx; PhIJ = pharyngealintestinal junction; sc-1 = Type 1 scales; sc-2 = Type 2 scale; sc-3 = Type 3 scales; sc-4 = Type 4 scales; vs = Type 1 ventral scale. Scale bars = 20 µm.

Fig. 1 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 1. Sampling location, at the state of Pernambuco, Fernando de Noronha archipelago, Brazil A. Brazil. B. Fernando de Noronha Archipelago. C. Xaréu açude. Images provided by Google Earth (A–B) and Prof Dr Felipe Toledo, University of Campinas (C).

Fig. 6 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 6. Schematic illustration of dorsal and ventral posterior regions and type scales of Polymerurus insularis sp. nov. A–B. Paratype (ZUEC GCH 56). A. Dorsal view of the posterior end. Some Type 1 scales are faded for a better visualization of Types 2, 3 and 5 scales. B. Ventral view of the posterior end. C. Each type of scale, individually depicted (not to scale). Abbreviations: ff = furcal furrow; fr = furcal rami; lc = locomotory cilia; is = interciliary spines; sc-1 = Type 1 scales; sc-2 = Type 2 scale; sc-3 = Type 3 scales; sc-4 = Type 4 scales; sc-5 = Type 5 scales; sc-6 = Type 6 scales; sc-7 = Type 7 scales; sc-8 = Type 8 scales. Scale bars = 40 µm.

Fig. 9 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 9. Maximum Likelihood tree based on multigene approach with 18S and 28S sequences. Highlighted branches correspond to the Polymerurus Remane, 1927 species sequences. Values on the branches correspond, respectively, to: SH-aLRT support (%) / aBayes support / ultrafast bootstrap support (%).

Fig. 2 in Long distance dispersal and pseudo-cryptic species in Gastrotricha: first description of a new species (Chaetonotida, Chaetonotidae, Polymerurus) from an oceanic island with volcanic rocks

Fig. 2. Light microscopy – DIC. Polymerurus insularis sp. nov., holotype (ZUEC GCH 55). Full body view. A. Dorsal view. B. Internal view. C. Ventral view. Scale bars = 30 µm.

opencc-zeroSep 2023View details →

Urbanization impacts short- but not long-distance natal dispersal in a common orb web spider

Urban environments represent a theatre for life history evolution. Species able to survive in cities can adapt to the local and often divergent environmental conditions compared to rural or (semi-)natural environments. Dispersal determines establishment, gene flow, and thus the potential for local adaptation. Since habitats in urban environments are highly fragmented, and show substantial turnover, contrasting adaptive effects on dispersal are expected. Fragmentation selects against dispersal while patch turn-over is expected to promote the evolution of dispersal. We here show both processes to act in concert when different scales are considered. Dispersal behavior of juvenile, lab-reared garden spiders from three mid-sized European cities were tested under standardized conditions. While long-distance dispersal showed to be overall rare, short-distance dispersal strategies increased with urbanization at small scales, but declined when urbanization was quantified at large scales. We discuss the putative drivers behind these differences in natal dispersal and highlight its importance for urban evolution and ecology.

opencc-zeroMay 2024View details →

The irreplaceable role of surviving megafauna in long-distance seed dispersal: Evidence from an experiment with Neotropical mammals

The downsizing of disperser assemblages by selective defaunation is a worldwide phenomenon thought to have important consequences in animal-dispersed plants. Numerous large-seeded Neotropical plants currently depend on the last megafaunal survivors, the large tapirs Tapirus spp., and medium-sized frugivores. The extent to which medium frugivores are functionally equivalent to tapirs remains unresolved. We combined feeding trials, seed dispersal kernel modeling based on seed retention times and animal movement simulation (Levy walks), and germination experiments in a large-seeded palm to assess the dispersal quality provided by the largest (tapirs) and two medium (foxes and howler monkeys) frugivore species in terms of dispersal distances and gut passage effects on germination. Tapirs retained the seeds in the gut for much longer (mean=221 hours) than howlers (43 h) and foxes (22 h). Median dispersal distance by tapirs (1252 m) was 14 and 40 times larger than that by foxes (88 m) and howlers (31 m), respectively. The seed dispersal kernel of tapirs showed a 5th percentile value (291 m) larger than the 95th percentiles of foxes (285 m) and howlers (108 m). Manually depulped and gut-passed seeds germinated in similar proportions, showing, respectively, 3.5 and 2.5―2.9 times higher values than intact fruits. Germination probability and seed viability decreased with retention time in howlers' and tapirs' gut, with howlers showing a steeper negative relationship. Such detrimental effect implies a trade-off between germination success and dispersal distance. We conclude that tapirs may not play a unique role in germination enhancement but move seeds much further than medium frugivores, thus playing a critical role as long-distance dispersers of many plants. This study provides important insights on palm–frugivore interactions and the potential consequences for large-seeded plants of losing the last megafaunal representatives in the Neotropics.

publicMay 2024View details →

The irreplaceable role of surviving megafauna in long-distance seed dispersal: Evidence from an experiment with Neotropical mammals

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publicApr 2022View details →

Path-finding algorithm as a dispersal assessment method for invasive species with human-vectored long-distance dispersal event

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