Riverscape genetics of the orangethroat darter complex.

Freshwater darters belonging to the orangethroat darter species complex, or Ceasia, are widely distributed in the Central and Southern United States, with ranges that span both glaciated and unglaciated regions. Up to 15 species have been recognized in the complex, with one, Etheostoma spectabile, having a widespread northern distribution and another, Etheostoma pulchellum, having a sizeable southern distribution. The other species in the complex have much more restricted distributions in unglaciated regions of the Central Highlands. We sampled 384 darters from 52 sites covering much of the range of Ceasia and evaluated patterns of genetic diversity, genetic structure, and pre- and post-glacial patterns of range contraction and expansion. We anticipated finding much stronger signals of genetic differentiation and diversification in unglaciated regions, given the higher species diversity and levels of endemism reported there. Surprisingly, microsatellite genotyping revealed two well-differentiated genetic clusters of E. spectabile in samples from glaciated regions, one confined to the Illinois River basin and another found in the Wabash drainage and Great Lakes tributaries. This suggests that there was expansion from two isolated glacial refugia, with little subsequent post-glacial gene flow. Fish collected from throughout the unglaciated region were less genetically differentiated. Fish assigned to Etheostoma burri and Etheostoma uniporum based on collection sites and morphological characters were not genetically differentiated from E. spectabile samples from the region. Hybridization and introgression occurring in the Central Highlands may confound genetic delineation of species in this region of high endemism and diversity.

Dispersal ability correlates with range size in Amazonian habitat-restricted birds.

Understanding how species attain their geographical distributions and identifying traits correlated with range size are important objectives in biogeography, evolutionary biology and biodiversity conservation. Despite much effort, results have been varied and general trends have been slow to emerge. Studying species pools that occupy specific habitats, rather than clades or large groupings of species occupying diverse habitats, may better identify ranges size correlates and be more informative for conservation programmes in a rapidly changing world. We evaluated correlations between a set of organismal traits and range size in bird species from Amazonian white-sand ecosystems. We assessed if results are consistent when using different data sources for phylogenetic and range hypotheses. We found that dispersal ability, as measured by the hand-wing index, was correlated with range size in both white-sand birds and their non-white-sand sister taxa. White-sand birds had smaller ranges on average than their sister taxa. The results were similar and robust to the different data sources. Our results suggest that the patchiness of white-sand ecosystems limits species' ability to reach new habitat islands and establish new populations.

Connecting Amazonian, Cerrado, and Atlantic forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins (Neopelma/Tyranneutes, Aves: Pipridae).

Several biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. Using DNA sequence data, we determined phylogenetic relationships, temporal and geographic patterns of diversification, and recent intraspecific population genetic patterns, relative to the history of these biomes. We found Neopelma to be a paraphyletic genus, as N. chrysolophum is sister to Neopelma + Tyranneutes, with an estimated divergence of approximately 18 Myrs BP, within the oldest estimated divergence times of other Amazonian and Atlantic forest avian taxa. Subsequent divergences in the group occurred from Mid Miocene to Early Pliocene and involved mainly the Amazonian species, with an expansion into and subsequent speciation in the Cerrado gallery forests by N. pallescens. We found additional structure within N. chrysocephalum and N. sulphureiventer. Analysis of recent population dynamics in N. chrysocephalum, N. sulphureiventer, and N. pallescens revealed recent demographic fluctuations and restrictions to gene flow related to environmental changes since the last glacial cycle. No genetic structure was detected across the Amazon River in N. pallescens. The tyrant-manakins represent an old historical connection between the Amazon and Atlantic Forest.

Drivers of synchrony of acorn production in the valley oak (Quercus lobata) at two spatial scales.

We investigated spatial synchrony of acorn production by valley oaks (Quercus lobata) among individual trees at the within-population, local level and at the among-population, statewide level spanning the geographic range of the species. At the local level, the main drivers of spatial synchrony were water availability and flowering phenology of individual trees, while proximity, temperature differences between trees, and genetic similarity failed to explain a significant proportion of variance in spatial synchrony. At the statewide level, annual rainfall was the primary driver, while proximity was significant by itself but not when controlling for rainfall; genetic similarity was again not significant. These results support the hypothesis that environmental factors, the Moran effect, are key drivers of spatial synchrony in acorn production at both small and large geographic scales. The specific environmental factors differed depending on the geographic scale, but were in both cases related to water availability. In addition, flowering phenology, potentially affecting either density-independent pollination failure (the pollination Moran effect) or density-dependent pollination efficiency (pollen coupling), plays a key role in driving spatial synchrony at the local geographic scale.

Evolutionary history and gene flow of an endemic island oak: Quercus pacifica.

PREMISE OF THE STUDY: Understanding historical patterns of colonization and subsequent gene flow clarifies the evolutionary origins and history of endemic island species. METHODS: Here we use DNA microsatellite markers to characterize the genetic structure of the island endemic species Quercus pacifica K. Nixon & C.H. Mull., found on three of the California Channel Islands, and to examine its relationship to two mainland oaks, Q. berberidifolia and Q. dumosa. KEY RESULTS: We found that Q. pacifica is a genetically cohesive and differentiated evolutionary lineage, diverging from mainland scrub oaks in the Pleistocene with little subsequent introgression. Genetic differentiation of Q. pacifica among islands is small but significant. Both recent and historical gene flow were surprisingly high considering the disjunct distribution of Q. pacifica on islands separated by as much as 125 km of open ocean. Gene flow estimates were highest between the two northern islands and from the northern islands to Santa Catalina. While there is no evidence of recent bottlenecks, historical bottlenecks are indicated on each of the islands. CONCLUSIONS: The genetic cohesiveness of the Q. pacifica species suggests allopatric speciation on the islands with subsequent gene flow that has maintained genetic continuity over great distances.

Landscape genetics and population structure in Valley Oak (Quercus lobata Née).

PREMISE OF THE STUDY: Although long-distance pollen movement is common in wind-pollinated trees, barriers to gene flow may occur in species that have discontinuous ranges or are confined to certain habitat types. We investigated the genetic structure of Quercus lobata Née populations throughout much of their range in California. We assessed the connectivity of populations and determined if barriers to gene flow occurred, and if so, if they corresponded to landscape features. METHODS: We collected leaf samples from 270 trees from 12 stands of Quercus lobata and genotyped these trees using eight polymorphic microsatellite loci. Genetic structure and clustering was evaluated using genetic distance methods, Bayesian clustering approaches, and network analysis of spatial genetic structure. KEY RESULTS: The southernmost population of Quercus lobata sampled from the Santa Monica area comprised a separate genetic cluster from the rest of the species, suggesting that Transverse Ranges such as the San Gabriel Mountains limit gene flow. Population differentiation among the other sites was small but significant. Network analysis reflected higher connectivity among populations along the Central Coast range, with few connections spanning the dry, low Central Valley. CONCLUSIONS: While long distance pollen movement has been shown to be common in oaks, on larger spatial scales, topographic features such as mountain ranges and the large, flat Central Valley of California limit gene flow. Such landscape features explain gene flow patterns much better than geographic distance alone.

Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks.

Sharks are a globally threatened group of marine fishes that often breed in their natal region of origin. There has even been speculation that female sharks return to their exact birthplace to breed ('natal philopatry'), which would have important conservation implications. Genetic profiling of lemon sharks (Negaprion brevirostris) from 20 consecutive cohorts (1993-2012) at Bimini, Bahamas, showed that certain females faithfully gave birth at this site for nearly two decades. At least six females born in the 1993-1997 cohorts returned to give birth 14-17 years later, providing the first direct evidence of natal philopatry in the chondrichthyans. Long-term fidelity to specific nursery sites coupled with natal philopatry highlights the merits of emerging spatial and local conservation efforts for these threatened predators.

Mating between Echinacea angustifolia (Asteraceae) individuals increases with their flowering synchrony and spatial proximity.

PREMISE OF THE STUDY: Although spatial distance is considered the primary factor in determining plant mating patterns, flowering time and synchrony are also likely to be important. METHODS: We quantified the relationships of both distance and flowering phenology to the probability of mating between individual plants. In an experimental plot, we followed daily flowering phenology in Echinacea angustifolia, a self-incompatible perennial pollinated by solitary bees. We assigned paternity to 832 of 927 seedlings from 37 maternal plants using 11 microsatellite loci. Potential pollen donors included the experiment plot's 202 flowering plants and a nearby plot's 19 flowering plants. For each maternal plant sampled, we examined the pollen pool by quantifying correlated paternity and the effective number of pollen donors. KEY RESULTS: Significantly more pollinations occurred between neighboring and synchronous plants than expected under random mating, with distance being more important than flowering synchrony. The distance pollen moved varied over the course of the season, with late flowering plants mating with more distant plants compared to early or peak flowering plants. All maternal plants had a diverse set of mates (mean number of effective pollen donors = 23.7), and the composition of the pollen pools overlapped little between maternal plants. CONCLUSION: Both distance and flowering synchrony influenced pollination patterns in E. angustifolia. Our results suggest that pollen movement between incompatible mates and flowering asynchrony could be contributing to the reduced seed set observed in small E. angustifolia remnants. However, we also found that individual plants receive pollen from a diverse group of pollen donors.

Genetic impacts of Anacapa deer mice reintroductions following rat eradication.

The Anacapa deer mouse is an endemic subspecies that inhabits Anacapa Island, part of Channel Islands National Park, California. We used mitochondrial DNA cytochrome c oxidase subunit II gene (COII) and 10 microsatellite loci to evaluate the levels of genetic differentiation and variation in ~1400 Anacapa deer mice sampled before and for 4 years after a black rat (Rattus rattus) eradication campaign that included trapping, captive holding and reintroduction of deer mice. Both mitochondrial and microsatellite analyses indicated significant differentiation between Anacapa deer mice and mainland mice, and genetic variability of mainland mice was significantly higher than Anacapa mice even prior to reintroduction. Bayesian cluster analysis and Principal Coordinates Analysis indicated that East, Middle and West Anacapa mice were genetically differentiated from each other, but translocation of mice among islands resulted in the East population becoming less distinct as a result of management. Levels of heterozygosity were similar before and after management. However, numerous private alleles in the founder populations were not observed after reintroduction and shifts in allele frequencies occurred, indicating that the reintroduced populations experienced substantial genetic drift. Surprisingly, two mitochondrial haplotypes observed in an earlier study of Anacapa deer mice were lost in the 20 years prior to the rat eradication program, leaving only a single haplotype in Anacapa deer mice. This study demonstrates how genetic monitoring can help to understand the re-establishment of endemic species after the eradication of invasive species and to evaluate the effectiveness of the management strategies employed.

Influences of landscape and pollinators on population genetic structure: examples from three Penstemon (Plantaginaceae) species in the Great Basin.

PREMISE OF THE STUDY: Despite rapid growth in the field of landscape genetics, our understanding of how landscape features interact with life history traits to influence population genetic structure in plant species remains limited. Here, we identify population genetic divergence in three species of Penstemon (Plantaginaceae) similarly distributed throughout the Great Basin region of the western United States but with different pollination syndromes (bee and hummingbird). The Great Basin's mountainous landscape provides an ideal setting to compare the interaction of landscape and dispersal ability in isolating populations of different species. METHODS: We used eight highly polymorphic microsatellite loci to identify neutral population genetic structure between populations within and among mountain ranges for eight populations of P. deustus, 10 populations of P. pachyphyllus, and 10 populations of P. rostriflorus. We applied traditional population genetics approaches as well as spatial and landscape genetics approaches to infer genetic structure and discontinuities among populations. KEY RESULTS: All three species had significant genetic structure and exhibited isolation by distance, ranging from high structure and low inferred gene flow in the bee-pollinated species P. deustus (F(ST) = 0.1330, R(ST) = 0.4076, seven genetic clusters identified) and P. pachyphyllus (F(ST) = 0.1896, R(ST) = 0.2531, four genetic clusters identified) to much lower structure and higher inferred gene flow in the hummingbird-pollinated P. rostriflorus (F(ST) = 0.0638, R(ST) = 0.1116, three genetic clusters identified). CONCLUSIONS: These three Penstemon species have significant yet strikingly different patterns of population genetic structure, findings consistent with different interactions between landscape features and the dispersal capabilities of their pollinators.