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Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common—not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X . cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X . birchmanni × X . malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X . birchmanni and X . cortezi .

Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.

Aim: We test whether populations of the Mesoamerican azure-crowned hummingbird, Amazilia cyanocephala (Trochilidae), located east and west of the Isthmus of Tehuantepec are genetically, morphologically and environmentally differentiated and examine the relative role of drift and selection in driving diversification. Location: Mexico. Methods: We sequenced the mitochondrial ATPase-6 and ATPase-8 genes and the control region of 130 individuals collected throughout the range of the species in Mexico. Population genetic methods and coalescent tests were used to reconstruct the phylogeography of the species. Morphological and niche variation between genetic groups of A. cyanocephala were assessed. Results: The data revealed two genetic groups separated by the Isthmus of Tehuantepec in the late Pleistocene (49,300—75,800 years ago), with the split occurring in the presence of gene flow. Deviations from demographic equilibrium were detected for the two genetic groups, indicating more recent population expansions. Amazilia cyanocephala individuals from populations on either side of the Isthmus of Tehuantepec differed in morphology and were distributed in unique environmental space. A coalescent-based test indicated that selection is driving the observed morphological differentiation. Main conclusions: Our findings implicate the Isthmus of Tehuantepec as a permeable barrier driving recent diversification of A. cyanocephala in the presence of gene flow. The two A. cyanocephala mitochondrial DNA (mtDNA) groups corresponding with morphological and environmental niche differences, in concert with the results of a coalescent-based test, suggest that selection has been strong enough to counteract the effects of gene flow.

Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis , a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens , and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec ( c . 1.4 Ma), and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the Isthmus of Tehuantepec and more recent Pleistocene climatic events in driving isolation and population divergence. Coalescent analyses of the evolution of phenotypic traits suggest that selection is driving song evolution in wedge-tailed sabrewings but drift could not be rejected as a possibility for morphological divergence.

ContextFunctional connectivity of semiaquatic species is poorly studied despite that freshwater ecosystems are amongst the most threatened worldwide due to habitat deterioration. The Neotropical otter, Lontra longicaudis, is a threatened species that represents a good model to evaluate the effect of landscape-riverscape features on genetic structure and gene flow of freshwater species.ObjectivesWe aimed to assess the spatial genetic structure of L. longicaudis and to evaluate the landscape-riverscape attributes that shape its genetic structure and gene flow at local sites (habitat patches) and between sites (landscape matrix).MethodsWe conducted the study in three basins located in Veracruz, Mexico, which have a high degree of ecosystem deterioration. We used a non-invasive genetic sampling and a landscape genetics individual-based approach to test the effect stream hierarchical structure, isolation-by-distance, and isolation-by-resistance on genetic structure and gene flow.ResultsWe found genetic structure that corresponded to the latitudinal and altitudinal heterogeneity of the landscape and riverscape, as well as to the hierarchical structure of the streams. Open areas and steep slopes were the variables affecting genetic structure at local sites, whereas areas with suitable habitat conditions, higher ecosystem integrity and larger streams enhanced gene flow between sites.ConclusionsThe landscape-riverscape characteristics that maintain functional connectivity of L. longicaudis differed between the upper, middle, and lower basins. Our results have important implications for the conservation of the species, including the maintenance of larger suitable areas in Actopan and the necessity to improve connectivity in Jamapa, through the establishment of biological corridors.

We assessed geographic patterns of genetic variation and connectivity in the widely distributed coral-reef fish Abudefduf saxatilis at different temporal scales. We sequenced two mitochondrial regions (cytochrome b and control region) and genotyped 12 microsatellite loci in a total of 296 individuals collected from 14 reefs in two biogeographic provinces in the tropical western Atlantic Ocean and from three provinces within the Caribbean Sea. We used phylogeography, population genetics and coalescent methods to assess the potential effects of climatic oscillations in the Pleistocene and contemporary oceanographic barriers on the population genetic structure and connectivity of the species. Sequence analyses indicated high genetic diversity and a lack of genetic differentiation throughout the Caribbean and between the two biogeographic provinces. Different lines of evidence depicted demographic expansions of A. saxatilis populations dated to the Pleistocene. The microsatellites exhibited high genetic diversity, and no genetic differentiation was detected within the Caribbean; however, these markers identified a genetic discontinuity between the two western Atlantic biogeographic provinces. Migration estimates revealed gene flow across the Amazon–Orinoco Plume, suggesting that genetic divergence may be promoted by differential environmental conditions on either side of the barrier. The climatic oscillations of the Pleistocene, together with oceanographic barriers and the dispersal potential of the species, constitute important factors determining the geographic patterns of genetic variation in A. saxatilis .

The Neotropical otter, Lontra longicaudis , is an ecologically important species for freshwater ecosystems that is threatened due to habitat destruction and hunting. However, there is limited information regarding the population sizes, genetic diversity, genetic structure and gene flow of the species, which is crucial for the elaboration of conservation plans. The aim of this study was to isolate and characterize microsatellites for L. longicaudis , using Illumina paired-end-sequencing. Initial amplification tests were performed in 48 loci, out of which, 13 yielded high-quality PCR products and thus were further evaluated. Genetic diversity and discrimination power of the 13 microsatellite loci was assessed using 19 non-invasive samples collected in the Jamapa basin in Veracruz, Mexico and blood samples from six captive individuals. All loci were polymorphic, the number of alleles per locus ranged from 4 to 10, the observed heterozygosity from 0.21 to 0.69, and the expected heterozygosity from 0.55 to 0.82. The combined set of 13 microsatellites showed a high power for discriminating among individuals (probability of identity P ID  = 1.551 × 10 −16 ) and among siblings (probability of identity of siblings P IDSIB  = 3.349 × 10 −06 ). A combination of nine loci are sufficient to discriminate among siblings with high confidence (P IDSIB  < 0.0001). The new set of microsatellites for the Neotropical otter reported here will provide a useful genetic tool to assess population genetic patterns and ecological parameters of the species.

Habitat deterioration and fragmentation increase the risk of wildlife extirpation as they have strong impacts on population size, genetic diversity and gene flow. Small populations are more susceptible to these factors because the loss of genetic diversity by drift and inbreeding occurs at faster rates. Therefore, estimates of genetic diversity and population sizes of threatened and small wildlife populations in deteriorated landscapes are critical for managing and conservation. Here, we used a non-invasive sampling approach in combination with eleven microsatellite loci to evaluate genetic diversity, genetic structure, and demographic parameters of the Neotropical otter (Lontra longicaudis) in three river basins (Actopan, La Antigua and Jamapa), which are priority conservation areas for Veracruz, Mexico. Our results revealed moderate genetic diversity and genetic structure among river basins. However, we detected first-generation migrants among basins, suggesting current gene flow. Effective population size for each basin was considerably lower than the value (Ne < 100) suggested to maintain genetic variation of populations in the short-term. Similarly, census population size was lower than estimates reported for L. longicaudis in a conserved region in Mexico. We did not find evidence of recent genetic bottlenecks for any basin. Our genetic and demographic results suggest that L. longicaudis in the three river basins could be experiencing genetic isolation and erosion, with La Antigua being the most vulnerable basin. Natural fragmentation and habitat deterioration seem to be shaping the observed patterns of genetic variation in the Neotropical otter.

Genetic and morphological variation within species are determined by intrinsic and extrinsic factors, which jointly or separately can promote population divergence. In freshwater systems, the structure of the basins, geographic distance, climatic fluctuations of the Pleistocene as well as extant environmental variation are important drivers of population divergence. Xiphophorus hellerii is a fish widely distributed in basins of the Gulf of Mexico slope. We used mitochondrial DNA sequences, geometric morphometrics and ecological niche modeling to investigate the roles of geographic and environmental factors in population divergence of X. hellerii. We found strong genetic structure conforming to the Stream Hierarchy and isolation by distance models. Demographic tests and ecological niche modeling suggested that the niche and populations of the species underwent contractions and expansions during the Pleistocene. Body shape of X. hellerii varied among basins and hydrological regions. Temperature seems to affect body shape, as individuals with shallow bodies were found in basins with low temperature and high altitudes. We found significant relationships between genetics, morphology, geography and the environment. Our study suggests that X. hellerii from different basins and hydrological regions have followed independent evolutionary routes and that environmental and geographical factors have played an important role in population divergence.

• Premise of the study: Eighteen microsatellite loci of distylous Palicourea padifolia were isolated and characterized for population genetics studies. • Methods and Results: Following a microsatellite enrichment protocol, 18 primer pairs amplified successfully, and the polymorphism of the loci was initially evaluated in 15 individuals from three populations in Mexico. Seven loci were polymorphic, and their variability was further assessed in 60 individuals from three populations. The total number of alleles per locus, combining samples from all populations, ranged from 7 to 12. Nei's genetic diversity average across loci was 0.681, 0.714, and 0.703 for El Riscal, Montebello, and Ruiz Cortínez, respectively. Palicourea padifolia individuals had one to four alleles, confirming the polyploidy of this species. • Conclusions: These markers will facilitate genetic diversity studies of P. padifolia across its distribution range and facilitate investigations on the evolution of its breeding system.