http://hdl.handle.net/2027.42/58366 2017-07-10T01:22:58Z 2017-07-10T01:22:58Z Nazareno, Alison G Dick, Christopher W Lohmann, Lúcia G http://hdl.handle.net/2027.42/136763 2017-05-12T07:29:33Z 2017-05-01T00:00:00Z

Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species Nazareno, Alison G; Dick, Christopher W; Lohmann, Lúcia G Wallace’s riverine barrier hypothesis postulates that large rivers, such as the Amazon and its tributaries, reduce or prevent gene flow between populations on opposite banks, leading to allopatry and areas of species endemism occupying interfluvial regions. Several studies have shown that two major tributaries, Rio Branco and RioNegro, are important barriers to gene flow for birds, amphibians and primates. No botanical studies have considered the potential role of the Rio Branco as a barrier,while a single botanical study has evaluated the Rio Negro as a barrier. We studied an Amazon shrub, Amphirrhox longifolia (A. St.-Hil.) Spreng (Violaceae), as a model totest the riverine barrier hypothesis. Twenty-six populations of A. longifolia were sampled on both banks of the Rio Branco and Rio Negro in the core Amazon Basin.Double-digest RADseq was used to identify 8,010 unlinked SNP markers from thenuclear genome of 156 individuals. Data relating to population structure support the hypothesis that the Rio Negro acted as a significant genetic barrier for A. longi-folia. On the other hand, no genetic differentiation was detected among populations spanning the narrower Rio Branco, which is a tributary of the Rio Negro. This study shows that the strength of riverine barriers for Amazon plants is dependent on the width of the river separating populations and species-specific dispersal traits. Future studies of plants with contrasting life history traits will further improve our under-standing of the landscape genetics and allopatric speciation history of Amazon plant diversity. Fundação de Ampara Pesquisa do Estado de São Paulo (FAPESP), Grant/AwardNumber: 2013/12633-8; 2015/07141-4,2012/50260-6; Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq), Grant/Award Number: 307781/2013-5; National Science Foundation,Grant/Award Number: FESD 1338694, DEB1240869

2017-05-01T00:00:00Z Nazareno, Alison Bemmels, Jordan B. Dick, Christopher W Lohmann, Lúcia G http://hdl.handle.net/2027.42/136081 2017-02-12T08:28:26Z 2017-01-01T00:00:00Z

Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species Nazareno, Alison; Bemmels, Jordan B.; Dick, Christopher W; Lohmann, Lúcia G High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.

2017-01-01T00:00:00Z Thomson, A. M. Dick, C. W. Pascoini, A. L. Dayananda, S. http://hdl.handle.net/2027.42/117500 2016-03-17T19:46:49Z 2015-09-18T00:00:00Z

Despite introgressive hybridization, North American birches (Betula spp.) maintain strong differentiation at nuclear microsatellite loci Thomson, A. M.; Dick, C. W.; Pascoini, A. L.; Dayananda, S. Extensive chloroplast introgression has been documented in polyploid Betula species of eastern North America. However, the extent to which the nuclear genomes of these species are differentiated is unknown. Therefore, we evaluated genetic differentiation among largely sympatric Betula papyrifera, B. alleghaniensis, and B. lenta using nuclear microsatellite markers. Principal components analysis (PCA) and analysis of molecular variation (AMOVA) were used to evaluate genetic differentiation. Bayesian model-based clustering was used to identify putatively admixed individuals. Despite a high incidence of allele sharing, all of the species were significantly differentiated even within zones of sympatry. A number of individuals were identified as possibly admixed between B. papyrifera and B. alleghaniensis and between B. alleghaniensis and B. lenta. Admixture estimates between B. alleghaniensis and B. papyrifera increased significantly moving northward into the sympatric zone, suggesting the occurrence of hybridization in previously glaciated habitats. In contrast, admixture proportions of B. papyrifera and B. alleghaniensis did not show a significant geographic trend, which points to recent ancestry as the likely cause of allele sharing between these two species. We suggest that allele sharing of B. papyrifera and B. alleghaniensis results from a combination of ongoing gene flow and historic introgression via pollen swamping during northward colonization into post-glacial environments.

2015-09-18T00:00:00Z Juarez, Bryan http://hdl.handle.net/2027.42/112032 2015-07-15T07:27:51Z 2015-01-01T00:00:00Z

Ecomorphological change in lobe-finned fishes (Sarcopterygii): disparity and rates Juarez, Bryan Patterns of vertebrate cranial/post-cranial trait diversification are not well-understood. Two ecological hypotheses, the ‘head-first’ model and the ‘stages’ model, predict the ordered decoupling of cranial/post-cranial ecomorphological diversification. Rate (tempo) analyses and macroevolutionary model-fitting (mode) analyses are often used to test whether cranial traits or post-cranial traits diversify earlier in vertebrates. Here we reconstructed the tempo and mode of cranial/post-cranial trait evolution in lobe-finned fishes (Sarcopterygii), a group containing coelacanths, lungfishes, and tetrapodomorph fishes, to test for differences in the timing of vertebrate cranial/post-cranial trait diversification. We collected full-skeletal geometric morphometric coordinate and PC-reduced data for 57 species of aquatic and semi-aquatic lobe- fins since the Paleozoic. We performed rate, raw disparity through time, phylogenetic signal and model-fitting (multivariate BM, EB and OU) analyses using both coordinate data and PC- reduced data but did not model-fit the coordinate data due to computational constraints. The BM (best fit model) rate parameter is highest for post-cranial traits but cranial trait disparity is highest throughout the majority of lobe-fin evolution, supporting the ‘head-first’ model, with peaks in the Middle to Upper Devonian and Jurassic. We also find that PCA reduction increases trait variance, creating bias in favor of early post-cranial trait diversification. We conclude that cranial ‘head-first’ ecomorphological diversification drove the early Paleozoic radiation of aquatic and semi-aquatic lobe-fins, but more research may be needed to understand conflicting patterns in the Mesozoic when taxonomic diversity was substantially lower among “living fossils”. vii Ecomorphological change in lobe-finned fishes (Sarcopterygii): disparity and rates By: Bryan H. Juarez1 and Lauren C. Sallan2 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor; bryanhjuarez@gmail.com Earth and Environmental Science & Evolution Cluster, University of Pennsylvania; lsallan@sas.upenn.edu Keywords: Lobe fin, geometric morphometrics, PCA, Brownian Motion, Early Burst

2015-01-01T00:00:00Z