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Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus)Avila-Cervantes, JoseArias, CarlosVenegas-Anaya, MiryamVargas, MartaLarsson, Hans C. E.McMillan, W. OwenDOI: info:10.1111/evo.14139v. 75No. 2245–259
Avila-Cervantes, Jose, Arias, Carlos, Venegas-Anaya, Miryam, Vargas, Marta, Larsson, Hans C. E., and McMillan, W. Owen. 2021. "Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus)." Evolution 75 (2):245– 259. https://doi.org/10.1111/evo.14139
ID: 157996
Type: article
Authors: Avila-Cervantes, Jose; Arias, Carlos; Venegas-Anaya, Miryam; Vargas, Marta; Larsson, Hans C. E.; McMillan, W. Owen
Abstract: The final formation of the Central American Isthmus (CAI) about 3.5 million years ago altered global ocean circulation, connected North and South America terrestrial biotas, and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile (Crocodylus acutus) to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history, and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: (1) Caribbean and the Panama Canal, (2) Pacific coast, and (3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20,000 years ago, which is younger than the formation of the CAI, coinciding with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.
Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing PatternsConcha, CarolinaWallbank, Richard W. R.Hanly, Joseph J.Fenner, JenniferLivraghi, LucaRivera, Edgardo SantiagoPaulo, Daniel F.Arias, CarlosVargas, MartaSanjeev, ManuMorrison, ColinTian, DavidAguirre, PaolaFerrara, SabrinaFoley, JessicaPardo-Diaz, CarolinaSalazar, CamiloLinares, MauricioMassardo, DarliCounterman, Brian A.Scott, Maxwell J.Jiggins, Chris D.Papa, RiccardoMartin, ArnaudMcMillan, W. O.DOI: info:10.1016/j.cub.2019.10.0101–19
Concha, Carolina, Wallbank, Richard W. R., Hanly, Joseph J., Fenner, Jennifer, Livraghi, Luca, Rivera, Edgardo Santiago, Paulo, Daniel F., Arias, Carlos, Vargas, Marta, Sanjeev, Manu, Morrison, Colin, Tian, David, Aguirre, Paola, Ferrara, Sabrina, Foley, Jessica, Pardo-Diaz, Carolina, Salazar, Camilo, Linares, Mauricio, Massardo, Darli, Counterman, Brian A., Scott, Maxwell J., Jiggins, Chris D., Papa, Riccardo, Martin, Arnaud, and McMillan, W. O. 2019. "Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing Patterns." Current Biology 1– 19. https://doi.org/10.1016/j.cub.2019.10.010
ID: 153256
Type: article
Authors: Concha, Carolina; Wallbank, Richard W. R.; Hanly, Joseph J.; Fenner, Jennifer; Livraghi, Luca; Rivera, Edgardo Santiago; Paulo, Daniel F.; Arias, Carlos; Vargas, Marta; Sanjeev, Manu; Morrison, Colin; Tian, David; Aguirre, Paola; Ferrara, Sabrina; Foley, Jessica; Pardo-Diaz, Carolina; Salazar, Camilo; Linares, Mauricio; Massardo, Darli; Counterman, Brian A.; Scott, Maxwell J.; Jiggins, Chris D.; Papa, Riccardo; Martin, Arnaud; McMillan, W. O.
Abstract: To what extent can we predict how evolution occurs? Do genetic architectures and developmental processes canalize the evolution of similar outcomes in a predictable manner? Or do historical contingencies impose alternative pathways to answer the same challenge? Examples of Müllerian mimicry between distantly related butterfly species provide natural replicates of evolution, allowing us to test whether identical wing patterns followed parallel or novel trajectories. Here, we explore the role that the signaling ligand WntA plays in generating mimetic wing patterns in Heliconius butterflies, a group with extraordinary mimicry-related wing pattern diversity. The radiation is relatively young, and numerous cases of wing pattern mimicry have evolved within the last 2.5–4.5 Ma. WntA is an important target of natural selection and is one of four major effect loci that underlie much of the pattern variation in the group. We used CRISPR/Cas9 targeted mutagenesis to generate WntA-deficient wings in 12 species and a further 10 intraspecific variants, including three co-mimetic pairs. In all tested butterflies, WntA knockouts affect pattern broadly and cause a shift among every possible scale cell type. Interestingly, the co-mimics lacking WntA were very different, suggesting that the gene networks that pattern a wing have diverged considerably among different lineages. Thus, although natural selection channeled phenotypic convergence, divergent developmental contexts between the two major Heliconius lineages opened different developmental routes to evolve resemblance. Consequently, even under very deterministic evolutionary scenarios, our results underscore a surprising unpredictability in the developmental paths underlying convergence in a recent radiation.
Inter-chromosomal coupling between vision and pigmentation genes during genomic divergenceHench, KosmasVargas, MartaHöppner, Marc P.McMillan, W. O.Puebla, OscarDOI: info:10.1038/s41559-019-0814-5v. 3657–667
Hench, Kosmas, Vargas, Marta, Höppner, Marc P., McMillan, W. O., and Puebla, Oscar. 2019. "Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence." Nature Ecology & Evolution 3:657– 667. https://doi.org/10.1038/s41559-019-0814-5
ID: 151805
Type: article
Authors: Hench, Kosmas; Vargas, Marta; Höppner, Marc P.; McMillan, W. O.; Puebla, Oscar
Abstract: Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets-a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
Multilocus molecular systematics of the circumtropical reef-fish genus Abudefduf (Pomacentridae): history, geography and ecology of speciationCampbell, Matthew A.Robertson, D. RossVargas, Marta I.Allen, Gerald R.McMillan, W. O.DOI: info:10.7717/peerj.5357v. 6
Campbell, Matthew A., Robertson, D. Ross, Vargas, Marta I., Allen, Gerald R., and McMillan, W. O. 2018. "Multilocus molecular systematics of the circumtropical reef-fish genus Abudefduf (Pomacentridae): history, geography and ecology of speciation." PeerJ 6 (e5357):https://doi.org/10.7717/peerj.5357
ID: 148574
Type: article
Authors: Campbell, Matthew A.; Robertson, D. Ross; Vargas, Marta I.; Allen, Gerald R.; McMillan, W. O.
Abstract: We investigated a pantropical sub-family and genus of damselfishes, the sergeant-majors (Pomacentridae: Abudefdufinae: Abudefduf), to identify the tempo and mechanisms of speciation in the lineage. We examined sequence capture data from 500 loci and 20 species, with multiple individuals sampled from across the geographic ranges of widespread species. Utilizing a maximum likelihood framework, as well as a time-calibrated Bayesian phylogeny, the following key questions are addressed: What is the historical tempo of speciation? What are the relative contributions of vicariant, peripatric and parapatric speciation to sergeant-major diversity? How is speciation related to major variation in trophic ecology? The approximately 20 species of sergeant-majors fall into three main lineages. The ancestral condition appears to be benthivory, which is predominant in two lineages comprising six species. The remaining species of sergeant-majors, of which there are at least 15, fall within a clade composed entirely of planktivores. This clade is sister to a benthivore clade that included one species, Abudefduf notatus, in transition to planktivory. Most speciation of sergeant-majors, which appeared ∼24 million years ago, occurred in the last 10 million years. Present distributional patterns indicate vicariant speciation precipitated by the closure of land barriers between both sides of the Atlantic and the Pacific, and the emergence of land between the Indian and Pacific Oceans. Within this backdrop, frequent oscillations in sea level over the last 10 million years also appear to have generated conditions suitable for both peripatric and vicariant speciation, and most speciation within the genus appears linked to these changes in sea level. Diversification within the genus has been concentrated in planktivorous seargeant-majors rather than benthivores. The root cause is unclear, but does not appear to be related to differences in dispersal potential, which is greater in the planktivorous species, due to the ability of their post-larval juveniles to raft with floating debris. This elevated speciation rate in planktivores and their propensity to form local endemics may reflect relaxation of selective pressures (e.g., on crypticity) that limit speciation in benthivorous sergeant-majors. Finally, our data allow us to clarify relationships of geminate sergeant-major species, indicating that there are subdivisions within the Atlantic for both benthivore and planktivore geminate pairs that may have misled previous studies.
Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal communityRodgers, Torrey W.Xu, Charles C. Y.Giacalone, JacalynKapheim, Karen M.Saltonstall, KristinVargas, MartaYu, Douglas W.Somervuo, PanuMcMillan, W. O.Jansen, Patrick A.DOI: info:10.1111/1755-0998.12701v. 17No. 6e133–e145
Rodgers, Torrey W., Xu, Charles C. Y., Giacalone, Jacalyn, Kapheim, Karen M., Saltonstall, Kristin, Vargas, Marta, Yu, Douglas W., Somervuo, Panu, McMillan, W. O., and Jansen, Patrick A. 2017. "Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community." Molecular Ecology Resources 17 (6):e133– e145. https://doi.org/10.1111/1755-0998.12701
ID: 143474
Type: article
Authors: Rodgers, Torrey W.; Xu, Charles C. Y.; Giacalone, Jacalyn; Kapheim, Karen M.; Saltonstall, Kristin; Vargas, Marta; Yu, Douglas W.; Somervuo, Panu; McMillan, W. O.; Jansen, Patrick A.
Abstract: Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared BLAST with the new program PROTAX, and we found that PROTAX improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera-trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by eight years of transect counts and camera-trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys, and has the potential to detect a broader range of species than more commonly used methods. This article is protected by copyright. All rights reserved.