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.

Heterospecific pollination by an invasive congener threatens the native American bittersweet, Celastrus scandens.

Invasive plants have the potential to interfere with native species' reproductive success through a number of mechanisms, including heterospecific pollination and hybridization. This study investigated reproductive interactions between a native North American woody vine (American bittersweet, Celastrus scandens) and an introduced congener (oriental bittersweet, C. orbiculatus). The decline of C. scandens in the eastern portion of its range is coincident with the introduction and spread of C. orbiculatus, and the two species are known to hybridize. The relationship between proximity and floral production of conspecific and heterospecific males on fertilization and hybridization rates was measured at a field site in northwestern Indiana, USA where both species occur and reproduce. We found that the invasive vine had an extreme advantage in both male and female floral production, producing nearly 200 times more flowers per staminate plant and 65 times more flowers per pistillate plant than the native. Using nuclear microsatellite DNA markers we found that hybridization rates were asymmetric; 39% of the C. scandens seeds tested were hybrids, compared to only 1.6% of C. orbiculatus seeds. The asymmetric hybridization rates were likely not solely due to greater abundance of C. orbiculatus pollen because experimental hand crosses revealed that C. scandens had a higher rate (41%) of heterospecific fertilization than C. orbiculatus (2.4%). We previously reported that few hybrids were observed in the wild, and hybrids had greatly reduced fecundity. Thus, in our system, the threat posed by heterospecific pollen is not replacement by hybrids or introgression, but rather asymmetric reproductive interference. Reproductive interference extended to distances as great as 100 meters, thus, efforts to conserve the native species must reduce its exposure to C. orbiculatus over a relatively large spatial scale.

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.

Reproductive trade-offs maintain bract color polymorphism in Scarlet Indian paintbrush (Castilleja coccinea).

Populations of scarlet Indian paintbrush (Castilleja coccinea) in the Midwestern United States exhibit a bract color polymorphism, with each population having predominantly yellow or scarlet bracts. We investigated a possible mechanism for this maintenance of bract color polymorphism in C. coccinea by conducting hand-pollination experiments in two nearby populations, one predominantly yellow and one predominantly scarlet. The hand-pollination treatments were either self-pollination or cross pollination using pollen from within and between populations. Both color morphs were used as pollen donors for the within and between crosses. We found that both color morphs of C. coccinea were self-compatible. When the scarlet morph was the maternal plant it had higher seed set. When pollinators were excluded, the yellow morph outperformed the scarlet morph in fruit set and seed set. The apparent trade-offs between a higher reproductive output in the scarlet morph and a reproductive assurance advantage in the yellow morph may explain the maintenance of the polymorphism in C. coccinea. While many previous studies have provided evidence for pollinator preference playing a role in floral color polymorphism, the results of the current study indicate that reproductive assurance, which would be important for fluctuations in pollinator abundance or colonizing new areas, may act as a selective agent to maintain such polymorphisms.

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.

Sex in the City: Breeding Behavior of Urban Peregrine Falcons in the Midwestern US.

Peregrine falcons (Falco peregrinus) were extirpated from most of the continental United States by widespread use of the pesticide DDT in the 1960s. Populations have rebounded with banning of the pesticide and successful implementation of captive breeding and hacking programs. An essentially new population of Midwestern peregrines now exists that is comprised almost entirely of urban-nesting birds. The new population is considered to be of mixed ancestry, occurs at relatively high densities, and has nest sites in close proximity, factors that could influence breeding behaviors including mate fidelity, nest-site fidelity, extra-pair paternity, and natal dispersal. We investigated these behaviors using a combination of field observations and DNA microsatellite genotyping. Data for eleven microsatellite DNA markers, including eight newly developed for the species, were analyzed from a total of 350 birds from nine Midwestern cities, representing 149 broods collected at 20 nest sites. To document breeding behavior, parentage was inferred by likelihood techniques when both parents were sampled and by parental genotype reconstruction when only one parent was sampled. In cases where neither parent was sampled, a sibship reconstruction approach was used. We found high mate fidelity and nest-site fidelity in urban peregrines; in 122 nesting attempts made by long-term breeders, only 12 (9.8%) mate changes and six (4.9%) nest-site changes occurred. Only one brood (of 35 tested) revealed extra-pair paternity and involved a male tending two offspring of a recently acquired mate. Natal dispersal patterns indicated that female peregrines dispersed on average 226 km, almost twice the distance of males (average 124 km). Despite the novel environment of cities, our results suggest that monogamous breeding, nest fidelity, and female natal dispersal are high in urban peregrines, not unlike other raptors living in non-urban habitats.

Development of microsatellite loci of pod mahogany, Afzelia quanzensis (Fabaceae), by Illumina shotgun sequencing, and cross-amplification in A. africana.

PREMISE OF THE STUDY: Microsatellite loci were developed for Afzelia quanzensis (Fabaceae) as a first step toward investigating genetic diversity and population structure of the species in its native range. METHODS AND RESULTS: Illumina shotgun sequencing was used to generate raw sequence reads, which were searched for potential microsatellite loci. A total of 70 potential microsatellite loci were tested for amplification and polymorphism, and 39 successfully amplified. Of the 39 loci that amplified, 12 were polymorphic while 27 were monomorphic. The 12 polymorphic loci were cross-amplified in A. africana, and eight successfully amplified. CONCLUSIONS: The 12 polymorphic microsatellite loci can be used for genetic studies of A. quanzensis, which can help determine its conservation status. Eight loci can also be used for genotyping in A. africana.

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.

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.

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.

Development and evaluation of microsatellite markers for a native prairie perennial, Echinacea angustifolia (Asteraceae).

PREMISE OF THE STUDY: Microsatellite loci for the native prairie perennial Echinacea angustifolia were developed and evaluated for future use in population structure and paternity studies. • METHODS AND RESULTS: A total of 50 trinucleotide microsatellite regions were identified though an enrichment protocol that prescreens for microsatellite repeats before ligating into a vector. Of these, 11 loci were polymorphic and in Hardy-Weinberg equilibrium in three populations with varying numbers of plants. The loci had between three and 14 alleles and collectively provided high paternity exclusion probabilities. • CONCLUSIONS: These sets of microsatellite primers will provide researchers and land managers with valuable information on the population genetic structure and gene flow between fragmented prairie populations.

Plant genetics for forensic applications.

An emerging application for plant DNA fingerprinting and barcoding involves forensic investigations. Examples of DNA analysis of botanical evidence include crime scene analysis, identifying the source of commercial plant products, and investigation of trade in illicit drugs. Here, we review real and potential applications of DNA-based forensic botany and provide a protocol for microsatellite genotyping of leaf material, a protocol that could be used to link a suspect to a victim or to a crime scene.

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.

Combinatorial reconstruction of half-sibling groups from microsatellite data.

While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for this formulation and develop heuristics. Using biological and synthetic datasets we present experimental results and compare them with the leading alternative software COLONY. We show that our results are competitive and allow half-sibling group reconstruction in the presence of polygamy, which is prevalent in nature.

Pollen-mediated gene flow in isolated and continuous stands of bur oak, Quercus macrocarpa (Fagaceae).

PREMISE OF THE STUDY: Pollination patterns determine the reproductive neighborhood size of plants, the connectivity of populations, and the impacts of habitat fragmentation. We characterized pollination in three populations of Quercus macrocarpa occurring in a highly altered landscape in northeastern Illinois to determine whether isolated remnant stands were reproductively isolated. • METHODS: We used microsatellites to genotype all adults and 787 acorns from two isolated savanna remnants and a stand in an old-growth forest. One isolated remnant occurred in a highly urbanized/industrialized landscape, and one occurred in an agricultural landscape. Parentage assignment was used to assess pollen-mediated gene flow. • KEY RESULTS: Pollen donors from outside the study sites accounted for between 46% and 53% of paternities and did not differ significantly among sites, indicating that similar high levels of gene flow occurred at all three sites. Within stands, the mean pollination distance ranged from 42 to 70 meters, and when accounting for outside pollinations, mean pollination distances were well over 100 meters. Genetic diversity of incoming pollen was extremely high in all three stands. The number of effective pollen donors, N(ep), calculated from paternity assignment was higher than that estimated by an indirect correlated paternity approach. • CONCLUSIONS: Our findings indicate that extremely isolated stands of oaks are unlikely to be genetically and reproductively isolated, and remnant stands may contribute to maintaining genetic connectivity in highly modified landscapes.

High variation in clonal vs. sexual reproduction in populations of the wild strawberry, Fragaria virginiana (Rosaceae).

BACKGROUND AND AIMS: Many plants reproduce both clonally and sexually, and the balance between the two modes of reproduction will vary among populations. Clonal reproduction was characterized in three populations of the wild strawberry, Fragaria virginiana, to determine the extent that reproductive mode varied locally between sites. The study sites were fragmented woodlands in Cook County, Illinois, USA. METHODS: A total of 95 strawberry ramets were sampled from the three sites via transects. Ramets were mapped and genotyped at five variable microsatellite loci. The variability at these five loci was sufficient to assign plants to clones with high confidence, and the spatial pattern of genets was mapped at each site. KEY RESULTS: A total of 27 distinct multilocus genotypes were identified. Of these, 18 genotypes were detected only once, with the remaining nine detected in multiple ramets. The largest clone was identified in 16 ramets. No genets were shared between sites, and each site exhibited markedly different clonal and sexual recruitment patterns, ranging from two non-overlapping and widespread genets to 19 distinct genets. Only one flowering genet was female; the remainder were hermaphrodites. CONCLUSIONS: Local population history or fine-scale ecological differences can result in dramatically different reproductive patterns at small spatial scales. This finding may be fairly widespread among clonal plant species, and studies that aim to characterize reproductive modes in species capable of asexual reproduction need to evaluate reproductive modes in multiple populations and sites.

Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

BACKGROUND: Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 8 polymorphic microsatellites in the whale shark and used these markers to assess genetic variation and population structure in a panel of whale sharks covering a broad geographic region. This is the first record of microsatellite loci in the whale shark, which displayed an average of 9 alleles per locus and mean H(o) = 0.66 and H(e) = 0.69. All but one of the eight loci meet the expectations of Hardy-Weinberg equilibrium. Analysis of these loci in whale sharks representing three major portions of their range, the Pacific (P), Caribbean (C), and Indian (I) Oceans, determined that there is little population differentiation between animals sampled in different geographic regions, indicating historical gene flow between populations. F(ST) values for inter-ocean comparisons were low (PxC = 0.0387, CxI = 0.0296 and PxI = -0.0022), and only CxI approached statistical significance (p = 0.0495). CONCLUSIONS/SIGNIFICANCE: We have shown only low levels of genetic differentiation between geographically distinct whale shark populations. Existing satellite tracking data have revealed both regional and long-range migration of whale sharks throughout their range, which supports the finding of gene flow between populations. Whale sharks traverse geographic and political boundaries during their life history and interbreed with animals from distant populations; conservation efforts must therefore target international protection for this species.