Title: The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns
AbstractAim
To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test.
Location
The Indo‐Pacific Ocean.
Time period
Pliocene through the Holocene.
Major taxa studied
Fifty‐six marine species.
Methods
We tested eight biogeographic hypotheses for partitioning of the Indo‐Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦSTdistributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦSTwith a distance‐based redundancy analysis (dbRDA).
Results
We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦSTthat was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦSTthat were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance.
Main conclusions
Although there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield ΦSTvalues that range from 0 to nearly 0.5.
Leaché, Adam D.; Portik, Daniel M.; Rivera, Danielle; Rödel, Mark‐Oliver; Penner, Johannes; Gvoždík, Václav; Greenbaum, Eli; Jongsma, Gregory F. M.; Ofori‐Boateng, Caleb; Burger, Marius; et al(
, Journal of Biogeography)
AbstractAim
Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrogChiromantis rufescens.
Location
Guinean and Congolian rain forests, West and Central Africa.
Taxon
Chiromantis rufescens.
Methods
We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples ofC. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial.
Results
Population structure withinC. rufescensresembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene.
Main conclusions
Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history ofC. rufescenswas shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.
Pirani, Renata M.; Werneck, Fernanda P.; Thomaz, Andréa T.; Kenney, Mariah L.; Sturaro, Marcelo J.; Ávila‐Pires, Teresa C. S.; Peloso, Pedro L. V.; Rodrigues, Miguel T.; Knowles, L. Lacey(
, Journal of Biogeography)
AbstractAim
Present Amazonian diversity patterns can result from many different mechanisms and, consequently, the factors contributing to divergence across regions and/or taxa may differ. Nevertheless, the river‐barrier hypothesis is still widely invoked as a causal process in divergence of Amazonian species. Here we use model‐based phylogeographic analyses to test the extent to which major Amazonian rivers act similarly as barriers across time and space in two broadly distributed Amazonian taxa.
Local
Amazon rain forest.
Taxon
The lizardGonatodes humeralis(Sphaerodactylidae) and the tree frogDendropsophus leucophyllatus(Hylidae).
Methods
We obtained RADseq data for samples distributed across main river barriers, representing main Areas of Endemism previously proposed for the region. We conduct model‐based phylogeographic and genetic differentiation analyses across each population pair.
Results
Measures of genetic differentiation (based onFSTcalculated from genomic data) show that all rivers are associated with significant genetic differentiation. Parameters estimated under investigated divergence models showed that divergence times for populations separated by each of the 11 bordering rivers were all fairly recent. The degree of differentiation consistently varied between taxa and among rivers, which is not an artifact of any corresponding difference in the genetic diversities of the respective taxa, or to amounts of migration based on analyses of the site‐frequency spectrum.
Main conclusions
Taken together, our results support a dispersal (rather than vicariance) history, without strong evidence of congruence between these species and rivers. However, once a species crossed a river, populations separated by each and every river have remained isolated—in this sense, rivers act similarly as barriers to any further gene flow. This result suggests differing degrees of persistence and gives rise to the seeming contradiction that the divergence process indeed varies across time, space and species, even though major Amazonian rivers have acted as secondary barriers to gene flow in the focal taxa.
Feng, Ling; Takiya, Daniela M.; Krishnankutty, Sindhu M.; Dietrich, Christopher H.; Zhang, Yalin(
, Systematic Entomology)
Abstract
Sharpshooters (Cicadellinae), a large subfamily of the Cicadellidae, exhibit a global distribution and a broad array of ecological preferences. To explore the phylogenetic relationships and roles of global historical, biotic and biogeographic processes in the diversification of sharpshooters, we analysed DNA sequence data from three mitochondrial and two nuclear genes for 243 taxa representing all Cicadellinae tribes, generic groups, regional faunas and data of geographic distributions of sharpshooter species compiled from online databases and available literature. The maximum likelihood (ML) and Bayesian inference (BI) analyses strongly support the monophyletic clade including Cicadellinae and Phereurininae. Divergence time estimates and biogeographic analyses suggest that sharpshooters originated in the Neotropical region or were more widespread in Gondwana during the Early Cretaceous and diversified through a combination of ancient vicariance and dispersal following the evolution of angiosperm‐dominated habitats. The earliest divergence during the Cretaceous gave rise to Oriental and New World lineages, the latter of which subsequently dispersed into the Old World and gave rise to the diverse endemic fauna of Madagascar. The Oriental lineage shows high diversity and endemism in tropical Asia and the Pacific, with striking distributional discontinuities in Wallacea. These results suggest that a combination of environmental and evolutionary factors including continental‐scale vicariance, long‐distance dispersal and diversification of terrestrial microhabitats and host plants may explain the diversity of the modern sharpshooter fauna.
The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns ofEnhalus acoroidesacross the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based onDAdistance and Bayesian clustering revealed three major clusters ofE. acoroides. Our results indicate that phylogeographic patterns ofE. acoroideshave possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns ofE. acoroides.
Tsang, Susan M.; Wiantoro, Sigit; Veluz, Maria Josefa; Sugita, Norimasa; Nguyen, Y‐Lan; Simmons, Nancy B.; Lohman, David J.(
, Journal of Biogeography)
AbstractAim
Islands provide opportunities for isolation and speciation. Many landmasses in the Indo‐Australian Archipelago (IAA) are oceanic islands, and founder‐event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group.
To infer the biogeographic history ofPteropus, we sequenced up to 6,169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognizedPteropusspecies and subspecies with threeAcerodonoutgroups usingBEASTand subsequently estimated ancestral areas using models implemented inBioGeoBEARS.
Results
Species‐level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor withAcerodon; founder‐event speciation out of Wallacea was a common inference.Pteropusspecies in Micronesia and the western Indian Ocean were also inferred to result from founder‐event speciation.
Main conclusions
Dispersal between regions of the IAA and the islands found therein fostered diversification ofPteropusthroughout the IAA and beyond. Dispersal inPteropusis far higher than in most other volant taxa studied to date, highlighting the importance of inter‐island movement in the biogeographic history of this large clade of large bats.
Crandall, Eric D., Riginos, Cynthia, Bird, Chris E., Liggins, Libby, Treml, Eric, Beger, Maria, Barber, Paul H., Connolly, Sean R., Cowman, Peter F., DiBattista, Joseph D., Eble, Jeff A., Magnuson, Sharon F., Horne, John B., Kochzius, Marc, Lessios, Harilaos A., Liu, Shang Yin Vanson, Ludt, William B., Madduppa, Hawis, Pandolfi, John M., Toonen, Robert J., Contributing Members of the Diversity of the Indo‐Pacific Network, Gaither, Michelle R., and Borregaard, ed., Michael. The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns. Global Ecology and Biogeography 28.7 Web. doi:10.1111/geb.12905.
Crandall, Eric D., Riginos, Cynthia, Bird, Chris E., Liggins, Libby, Treml, Eric, Beger, Maria, Barber, Paul H., Connolly, Sean R., Cowman, Peter F., DiBattista, Joseph D., Eble, Jeff A., Magnuson, Sharon F., Horne, John B., Kochzius, Marc, Lessios, Harilaos A., Liu, Shang Yin Vanson, Ludt, William B., Madduppa, Hawis, Pandolfi, John M., Toonen, Robert J., Contributing Members of the Diversity of the Indo‐Pacific Network, Gaither, Michelle R., & Borregaard, ed., Michael. The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns. Global Ecology and Biogeography, 28 (7). https://doi.org/10.1111/geb.12905
Crandall, Eric D., Riginos, Cynthia, Bird, Chris E., Liggins, Libby, Treml, Eric, Beger, Maria, Barber, Paul H., Connolly, Sean R., Cowman, Peter F., DiBattista, Joseph D., Eble, Jeff A., Magnuson, Sharon F., Horne, John B., Kochzius, Marc, Lessios, Harilaos A., Liu, Shang Yin Vanson, Ludt, William B., Madduppa, Hawis, Pandolfi, John M., Toonen, Robert J., Contributing Members of the Diversity of the Indo‐Pacific Network, Gaither, Michelle R., and Borregaard, ed., Michael.
"The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns". Global Ecology and Biogeography 28 (7). Country unknown/Code not available: Wiley-Blackwell. https://doi.org/10.1111/geb.12905.https://par.nsf.gov/biblio/10461202.
@article{osti_10461202,
place = {Country unknown/Code not available},
title = {The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns},
url = {https://par.nsf.gov/biblio/10461202},
DOI = {10.1111/geb.12905},
abstractNote = {Abstract AimTo test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. LocationThe Indo‐Pacific Ocean. Time periodPliocene through the Holocene. Major taxa studiedFifty‐six marine species. MethodsWe tested eight biogeographic hypotheses for partitioning of the Indo‐Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦSTdistributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦSTwith a distance‐based redundancy analysis (dbRDA). ResultsWe observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦSTthat was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦSTthat were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusionsAlthough there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield ΦSTvalues that range from 0 to nearly 0.5.},
journal = {Global Ecology and Biogeography},
volume = {28},
number = {7},
publisher = {Wiley-Blackwell},
author = {Crandall, Eric D. and Riginos, Cynthia and Bird, Chris E. and Liggins, Libby and Treml, Eric and Beger, Maria and Barber, Paul H. and Connolly, Sean R. and Cowman, Peter F. and DiBattista, Joseph D. and Eble, Jeff A. and Magnuson, Sharon F. and Horne, John B. and Kochzius, Marc and Lessios, Harilaos A. and Liu, Shang Yin Vanson and Ludt, William B. and Madduppa, Hawis and Pandolfi, John M. and Toonen, Robert J. and Contributing Members of the Diversity of the Indo‐Pacific Network and Gaither, Michelle R. and Borregaard, ed., Michael},
}
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