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Papers by Mary Ashley

International Journal of Plant Sciences, Jun 1, 2019

International Journal of Plant Sciences, 2019

International Journal of Plant Sciences, Feb 1, 2018

Premise of research. Quercus tomentella is a tree species endemic to the California Channel Islan... more Premise of research. Quercus tomentella is a tree species endemic to the California Channel Islands and Isla Guadalupe. Given its distribution across six widely separated islands, significant genetic structure would be expected, despite the propensity of oaks for long-distance pollen dispersal. In comparison, its close mainland relative, Quercus chrysolepis, has a more continuous range and fewer barriers to gene flow. Methodology. We sampled Q. tomentella from all the islands in its range (N p 345) and Q. chrysolepis from five mainland sites and on the islands where it occurs (N p 100) and genotyped the trees using eight polymorphic microsatellite loci. Genetic differentiation within and between species was examined using genetic distances, analysis of molecular variance, Bayesian clustering (both spatial and nonspatial approaches), a neighbor-joining tree, and genetic discontinuities indicative of barriers to gene flow. We also looked for evidence of population bottlenecks. Pivotal results. A high level of clonality was found in Q. tomentella on Santa Catalina Island and Santa Rosa Island, but genetic variability was high in both species and at all sites, including the tiny surviving population on Isla Guadalupe. Genetic distance measures were significant between most populations of both species. The most surprising result is that the two species were not clearly differentiated, and genetic clusters identified through both spatial and nonspatial analyses were shared between species. Conclusions. The island endemic Q. tomentella and the widespread Q. chrysolepis are not well-differentiated species. Further work is needed to clarify the relationships within and among these species. Insular populations of Q. tomentella are genetically diverse and distinct; the remaining population found on Isla Guadalupe warrants protection and management to support recruitment.

American Journal of Botany, 2016

Premise of the study: Understanding historical patterns of colonization and subsequent gene flow ... more 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. Muller, 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 was 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.

International Journal of Plant Sciences, 2016

Premise of research. Hybridization among oaks is well documented and is of special concern in con... more Premise of research. Hybridization among oaks is well documented and is of special concern in conservation efforts directed toward threatened or endangered Quercus, species such as Quercus hinckleyi. Methodology. This study uses DNA microsatellite analysis to characterize hybridization between the threatened oak Q. hinckleyi C.H. Muller and two putative hybridizing species, Quercus pungens Liebmann and Quercus vaseyana Buckley. The two potential hybridizers were sampled at Guadalupe Mountains National Park (GUMO), approximately 320 km from the current range of Q. hinckleyi. Quercus pungens and two possible hybrids located in near proximity to the relict populations of Q. hinckleyi were also sampled. Pivotal results. Genetic variability was high in all three species, with mean number of alleles per locus ranging from 12.625 to 17.875, mean observed heterozygosity from 0.734 to 0.807, and mean expected heterozygosity from 0.851 to 0.869. Quercus hinckleyi is genetically differentiated from the putative hybridizers and has two distinct genetic clusters within its metapopulation. The two hybridizer species from GUMO, where they are sympatric, are not differentiated. The population identified as Q. pungens found near Q. hinckleyi is genetically distinct from the GUMO samples and has five of eight genets with greater than 90% Q. hinckleyi introgression. Two of the 14 identified Q. hinckleyi in close proximity to this population had Q. pungens introgression. Bayesian clustering analysis showed that 5% of the samples identified as Q. hinckleyi in the field were hybrids, and one putative hybrid was confirmed genetically. Conclusions. While there is some hybridization in the Q. hinckleyi population, we found no evidence of genetic swamping. This may be explained by the spatial isolation of the Q. hinckleyi remnants relative to other oak species and by its common asexual (cloning) method of reproduction.

Critical Reviews in Plant Sciences, 2010

DNA microsatellites provide plant ecologists with molecular markers precise enough to assign pare... more DNA microsatellites provide plant ecologists with molecular markers precise enough to assign parentage to seeds and seedlings. This allows the exact distance and trajectory of successful pollen to be traced to characterize pollination patterns. Parentage assignment of established seedlings also allows researchers to accurately determine how far new recruits have traveled from their seed parent. This paper reviews the history and development of molecular parentage assignment in studies of native plants, as well as the limitations and constraints to this approach. This paper also reviews 53 articles published in the past 15 years that use parentage assignment to study pollination and seed dispersal in native plants. These parentage studies have overturned many common assumptions regarding pollen and seed dispersal patterns. They show that long-distance dispersal of pollen is common in both wind and animal dispersed systems, with average pollination distances commonly being hundreds of meters. The pollination neighborhood is often extremely large, and simple dispersal functions based on distance alone fail to make accurate predictions of pollination. Rather than hindering gene flow, fragmentation and isolation sometimes, and perhaps even commonly, results in increased pollination distances. Studies of seed dispersal using parentage assignment have also yielded some surprises. We now know that it may be erroneous to assume that seeds growing under the crown of a conspecific adult are growing beneath their mother, or that seed dispersal distances are more limited than pollen dispersal distances. Taken together, the studies to date demonstrate that both seed and pollen dispersal are quite complex phenomenon influenced by many ecological processes.

Journal of Mammalogy, 1996

In this paper, we consider approximability issues of the following four problems: triangle packin... more In this paper, we consider approximability issues of the following four problems: triangle packing, full sibling reconstruction, maximum profit coverage and 2-coverage. All of them are generalized or specialized versions of set-cover and have applications in biology ranging from fullsibling reconstructions in wild populations to biomolecular clusterings; however, as this paper shows, their approximability properties differ considerably. Our inapproximability constant for the triangle packing problem improves upon the previous results in [16, 19]; this is done by directly transforming the inapproximability gap of Håstad for the problem of maximizing the number of satisfied equations for a set of equations over GF(2) [26] and is interesting in its own right. Our approximability results on the full siblings reconstruction problems answers questions originally posed by Berger-Wolf et al. [6, 7] and our results on the maximum profit coverage problem provides almost matching upper and lower bounds on the approximation ratio, answering a question posed by Hassin and Or [25].

Molecular Biology and Evolution, 1993

Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have ... more Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have been subject to considerable debate. One confounding factor may be the lack of data on intraspecific variation. To test this hypothesis, we examined the effect of intraspecific mtDNA diversity on the phylogenetic reconstruction of another Plio-Pleistocene radiation of higher primates, thefascicularis group of macaque (Macaca) monkey species. Fifteen endonucleases were used to identify 10 haplotypes of 40-47 restriction sites in A4. mulatta, which were compared with similar data for the other members of this species group. Interpopulational, intraspecific mtDNA diversity was large (0.5%-4.5%), and estimates of divergence time and branching order incorporating this variation were substantially different from those based on single representatives of each species. We conclude that intraspecific mtDNA diversity is substantial in at least some primate species. Consequently, without prior information on the extent of genetic diversity within a particular species, intraspecific variation must be assessed and accounted for when reconstructing primate phylogenies. Further, we question the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates.

Journal of Molecular Evolution, 2000

Two mitochondrial genes, the proteincoding cytochrome c oxidase subunit II (COII) gene and a port... more Two mitochondrial genes, the proteincoding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points. Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find significant rate differences among taxa. A likelihoodratio test, however, rejected a molecular clock for both genes. Neither calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict for tapir relationships.

Applications in plant sciences, 2016

Microsatellite loci were developed for Afzelia quanzensis (Fabaceae) as a first step toward inves... more 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. 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. 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.

Contemporary Issues in Genetics and Evolution, 2001

We perform a meta-analysis on morphological data from four island rodent populations exhibiting m... more We perform a meta-analysis on morphological data from four island rodent populations exhibiting microevolution (<≈ 100 years). Data consisting of incidences of skeletal variants, cranial, and external measurements are from house mice (Mus musculus) on one Welsh and one Scottish island, black rats (Rattus rattus) on two Galapagos islands, and deer mice (Peromyscus maniculatus) on three California Channel islands. We report extremely high rates of microevolution for many traits; 60% of all mensural traits measured changed at a rate of 600 d or greater (max. 2682 d). The proportion of all mensural traits evolving at 600-800 d (23%) was idiosyncratic and departed from an expected negative exponential distribution. We argue that selection, rather than founder events, is largely responsible for the substantial shifts in morphology seen among insular rodents. Examining individual traits, there is a trend towards the nose becoming longer and wider, while the skull becomes shallower, shown by both rats and mice on five different islands. We found a significant correlation between island size and degree of skeletal variant evolution and between island distance from the mainland (or nearest island) and degree of cranial and external character evolution. Thus, microevolution of rodents is greater on smaller and more remote islands.

Optimization Methods and Software, 2007

A new combinatorial approach for modeling and reconstructing sibling relationships in a single ge... more A new combinatorial approach for modeling and reconstructing sibling relationships in a single generation of individuals without parental information is proposed in this paper. Simple genetic constraints on the full-sibling groups, imposed by the Mendelian inheritance rules, are employed to investigate data from codominant DNA markers. To extract the minimum number of biologically consistent sibling groups, the proposed combinatorial approach is employed to formulate this minimization problem as a set covering problem, which is a well-known NP-hard combinatorial optimization problem. We conducted a simulation study of a relaxed version of the proposed algorithm to demonstrate that our combinatorial approach is reasonably accurate and the exact version of the sibling relationship construction algorithm should be pursued. In addition, the results of this study suggest that the proposed algorithm will pave our way to a new approach in computational population genetics as it does not require any a priori knowledge about allele frequency, population size, mating system, or family size distributions to reconstruct sibling relationships.

Oecologia, 1997

The brown-headed cowbird (Molothrus ater) is a generalist obligate brood parasite. Despite intens... more The brown-headed cowbird (Molothrus ater) is a generalist obligate brood parasite. Despite intensive study and growing concern over the negative impact of cowbird parasitism on populations of many hosts, very little is known about the factors in¯uencing communitywide patterns of cowbird parasitism. Using systematic nest searches, nest parasitism was studied over two breeding seasons at a study site in northeastern Illinois encompassing grassland, forest-edge, and forest habitat, supporting a diverse avian community. Parasitism was observed for 18 out of 34 altricial bird species found nesting at the study site. A total of 299 cowbird eggs and nestlings were found in 191 of a total of 593 nests. Analyses revealed several ecological and behavioral factors associated with frequency of parasitism and the resulting distribution of cowbird eggs. Much higher frequencies of parasitism were found in edge and forest habitats than in grassland. Within the edge habitat, open nests were parasitized signi®cantly more often than cavity nests. Among open nests in the edge habitat, the two largest species were never parasitized. Host behavior, particularly egg-ejection behavior, was associated with a reduced observed frequency of parasitism, but at least three species known to eject cowbird eggs were sometimes parasitized. For six common hosts capable of rearing cowbirds, we found no correlation between level of parasitism and host nest-survivorship, suggesting that ®ne-grained assessments of host quality by female cowbirds do not in¯uence patterns of parasitism among acceptable host species, or that dierences in host quality are not great and/or predictable enough for such ®ne-grained assessments. Our results suggest that when a variety of possible nests are available, the level of parasitism on a particular species is a balance between a cowbird's preference for a particular species and the eectiveness of host species' defenses. A conceptual model was developed that incorporates the observed correlation of cowbird eggs or nestlings with habitat, nest-type, host species' body mass, and host behavioral defenses. Additional community-wide studies of cowbird parasitism will test if this model is applicable to other avian communities.

Nucleic Acids Research, 1989

By following the transmission of a heteroplasmic mitochondrial DNA mutation through four generati... more By following the transmission of a heteroplasmic mitochondrial DNA mutation through four generations of Holstein cows, we have documented that substantial shifts in the levels of heteroplasmy can occur between single mammalian generations, that neutral mitochondrial genotypes can segregate in different directions in offspring of the same female, and that a return to homoplasmy may occur in only two or three generations. This apparently rapid rate of mitochondrial DNA segregation in mammals contrasts to the much slower rates observed previously in insects and suggest fundamental differences between taxa regarding the mechanisms of mitochondrial gene transmission.

Molecular Ecology, 2001

The relative success of chimpanzee male mating strategies, the role of male dominance rank and th... more The relative success of chimpanzee male mating strategies, the role of male dominance rank and the success of inbreeding avoidance behaviour can only be assessed when paternities are known. We report the probable paternities of 14 chimpanzees included in a long-term behavioural study of chimpanzees (Pan troglodytes schweinfurthii) at Gombe National Park, Tanzania. DNA samples were collected noninvasively from shed hair and faeces and genotyped using 13-16 microsatellite loci characterized in humans. All 14 offspring could be assigned to fathers within the community. While there is a positive relationship between male rank and reproductive success, we demonstrate that a range of male mating strategies (possessiveness, opportunistic mating and consortships) can lead to paternity across all male ranks. Several adult females were at risk of breeding with close male relatives. Most successfully avoided close inbreeding but in one case a high-ranking male in the community mated with his mother and produced an offspring. In contrast to recent data on chimpanzees (P. t. verus) from the Taï forest, Côte d'Ivoire, no evidence of extra-group paternity was observed in our study. Reanalysis of Taï data using a likelihood approach casts doubt on the occurrence of extra-group paternity in that community as well.

Molecular Ecology, 2005

Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress ex... more Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolationby-distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the non-Arctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.

Molecular Ecology, 2013

E. et al. 2014. Two decades of genetic profiling yields first evidence of natal philopatry and lo... more E. et al. 2014. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Molecular Ecology. 23 (1): pp.

Journal of Computer and System Sciences, 2009