Diana F. Tomback

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clarks Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as

The evolution of bird-dispersed pines*

10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

The Need to Quantify Ecosystem Services Provided By Birds

SummaryTwenty of approximately 100 species of pines (Pinus spp.) have wingless seeds, and 19 of these are in the subgenusStrobus. Eight of the wingless-seedStrobus pines are known to be dispersed by seed-storing corvids, particularly the nutcrackers (Nucifraga spp.), and the other 11 are presumed to be. The principal consequences of these nearly obligate bird-pine mutualisms include tree clustering and a population structure that differs from that of wind-dispersed pines. The wingless-seedStrobus pines in general are typified by ranges that include xeric conditions and/or high elevations, and large seeds, which are considered to be adaptive under either xeric or competitive conditions. The proposed evolutionary scenario for bird dependency begins with the distribution of ancestralStrobus pines into high elevation or semi-desert environments, sympatric with one or more seed-storing corvid forms, and an increase in seed size. We propose that dependency on birds for seed dispersal has occurred primarily in subgenusStrobus, becauseStrobus pines tend more towards winglessness and increased seed size in stressful environments than doPinus pines. Seed winglessness and other bird-pine traits probably arose from a combination of genetic drift in small populations and selection by corvids.

Alpine treeline of western North America; linking organism-to-landscape dynamics

— 1 — The Auk, Vol. 128, Number 1, pages 1−14. ISSN 0004-8038, electronic ISSN 1938-4254.  2011 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2011.10248 8Present address: Loras College, 1450 Alta Vista, Dubuque, Iowa 52004, USA. E-mail: harrier2@mchsi.com 9Present address: Department of Biology, University of Utah, 257 South 1400 East, Room 201, Salt Lake City, Utah 84112, USA. The Auk 128(1):1–14, 2011  The American Ornithologists’ Union, 2011. Printed in USA. The Auk An International Journal of Ornithology

DELAYED SEED GERMINATION IN WHITEBARK PINE AND REGENERATION PATTERNS FOLLOWING THE YELLOWSTONE FIRES

Although the ecological dynamics of the alpine treeline ecotone are influenced by climate, it is an imperfect indicator of climate change. Mechanistic processes that shape the ecotone—seed rain, seed germination, seedling establishment and subsequent tree growth form, or, conversely tree dieback—depend on microsite patterns. Growth forms affect wind and snow, and so develop positive and negative feedback loops that create these microsites. As a result, complex landscape patterns are generated at multiple spatial scales. Although these mechanistic processes are fundamentally the same for all forest-tundra ecotones across western North America, factors such as prior climate, underlying geology and geomorphology, and genetic constraints of dominant tree species lead to geographic differences in the responses of particular ecotones to climate change.

Invasive pathogen threatens bird–pine mutualism: implications for sustaining a high-elevation ecosystem

Whitebark pine (Pinus albicaulis) seeds are dispersed by Clarks Nutcracker (Nucifraga columbiana), a bird that makes caches under 2-3 cm of soil. Cached seeds may delay germination for one or more years in part because of underdeveloped embryos at the time of seed dispersal. Consequently, whitebark pine may show a soil seed bank strategy

ALLOZYME FREQUENCIES IN A LINEAR SERIES OF SONG DIALECT POPULATIONS

Human-caused disruptions to seed-dispersal mutualisms increase the extinction risk for both plant and animal species. Large-seeded plants can be particularly vulnerable due to highly specialized dispersal systems and no compensatory regeneration mechanisms. Whitebark pine (Pinus albicaulis), a keystone subalpine species, obligately depends upon the Clarks Nutcracker (Nucifraga columbiana) for dispersal of its large, wingless seeds. Clarks Nutcracker, a facultative mutualist with whitebark pine, is sensitive to rates of energy gain, and emigrates from subalpine forests during periods of cone shortages. The invasive fungal pathogen Cronartium ribicola, which causes white pine blister rust, reduces whitebark pine cone production by killing cone-bearing branches and trees. Mortality from blister rust reaches 90% or higher in some whitebark pine forests in the Northern Rocky Mountains, USA, and the rust now occurs nearly rangewide in whitebark pine. Our objectives were to identify the minimum level of cone production necessary to elicit seed dispersal by nutcrackers and to determine how cone production is influenced by forest structure and health. We quantified forest conditions and ecological interactions between nutcrackers and whitebark pine in three Rocky Mountain ecosystems that differ in levels of rust infection and mortality. Both the frequency of nutcracker occurrence and probability of seed dispersal were strongly related to annual whitebark pine cone production, which had a positive linear association with live whitebark pine basal area, and negative linear association with whitebark pine tree mortality and rust infection. From our data, we estimated that a threshold level of approximately 1000 cones/ha is needed for a high likelihood of seed dispersal by nutcrackers (probability > or = 0.7), and that this level of cone production can be met by forests with live whitebark pine basal area > 5.0 m2/ha. The risk of mutualism disruption is greatest in northern most Montana (USA), where three-year mean cone production and live basal area fell below predicted threshold levels. There, nutcracker occurrence, seed dispersal, and whitebark pine regeneration were the lowest of the three ecosystems. Managers can use these threshold values to differentiate between restoration sites requiring planting of rust-resistant seedlings and sites where nutcracker seed dispersal can be expected.

Invasive Pathogens At Alpine Treeline: Consequences for Treeline Dynamics

Evaluating the biological consequences of avian song dialects is important in at least two ways. First, where appropriate experimental evidence is available, we know that dialect markers in song are learned (Marler, 1970; Marler and Mundinger, 1971). Dialect systems thus offer an opportunity to determine if and how culturally transmitted vocal signals, a fundamental feature of many songbird societies, influence patterns of gene flow. Second, despite much fine descriptive work, few attempts have been made to connect the field of behavioral research on song dialects to that of evolutionary genetics. The central issue is whether or not population specific vocal signals (dialects) cause mating to take place primarily among members of the same dialect population. This question does not specify any particular behavioral mechanism that might be hypothesized nor should it suggest that gene migration is an all-or-none phenomenon. Gene flow between adjacent dialects may vary in amount or direction depending upon such possible influences as dialect discrimination affecting mate selection, recency of contact of the populations (Remington, 1968), availability of unoccupied breeding habitat, or major environmental disturbances. If song dialects reduce gene migration among dialect populations, however, then it is reasonable to predict that neighboring dialect populations may exhibit genetic differences (Templeton, 1980a). The divergence may occur because of founder effect, genetic drift, or because of selective differences in occupied habitats as when, for example, dialects occur along an environmental gradient (Endler, 1977). differential coadaptation of genomes may also be involved. Possible outcomes of the interaction of gene flow, environmental gradients, magnitude of selection pressures, and population size have only recently begun to yield to theoretical analysis (Endler, 1977; Slatkin, 1978; Lande, 1980) and we hope that our studies may be of some use in this regard. Our field data, while not constituting a test of this developing theory, may serve to underscore the significance of gene flow in population differentiation. The four song dialect populations of Whitecrowned Sparrows treated here extend over a total of only 35 km distance in an environment of apparent homogeneity in climate and vegetation. In view of the potentially high vagility of these birds, the possible consequences of discontinuities in gene flow caused by social structure may be more easily discovered. In this report we provide allozyme frequency data from four dialect populations occurring in a linear sequence along the central California coast. From these data we describe the nature and extent of genetic differentiation within and among the four song dialect populations to test the hypothesis of genetic differentiation of dialects.

Modelling stand dynamics in whitebark pine (Pinus albicaulis) forests

The potential impact of invasive forest pathogens on alpine treeline dynamics has not previously been considered. Whitebark pine (Pinus albicaulis), a foundation and keystone species of subalpine forests and major component of alpine treeline in the northern Rocky Mountains of the United States and southern Canada, is infected nearly range-wide by the exotic pathogen Cronartium ribicola, which causes white pine blister rust. A major component of treeline in the northern Rocky Mountains, whitebark pine initiates tree islands on the eastern slope in northwestern Montana more than any other conifer species. Blister rust infects whitebark pine throughout the region, and both infection and mortality are already evident at treeline. We discuss the cascading ecological effects of the loss of treeline whitebark pine and expected changes in landscape vegetation patterns. Potential implications of the loss of whitebark pine for northwestern Montana treelines are examined in the context of climate change within a conceptual model. We speculate that exotic pathogens could potentially confound predictions of treeline responses to global warming in many geographic regions.

Blister Rust Prevalence in Krummholz Whitebark Pine: Implications for Treeline Dynamics, Northern Rocky Mountains, Montana, U.S.A

Abstract The ecological process model firesum (a fire su ccession mo del) has been adapted to whitebark pine ( Pinus albicaulis ) forests of the inland Northwest and Rocky Mountains, U.S.A. firesum simulates tree establishment, growth, and mortality on a 400-m 2 plot. Also modelled are live and dead fuel accumulations, fire behavior, fuel reduction, and insect and disease mortality. The following influences on tree establishment and growth are simulated in the model: temperature, water stress, site quality, and light conditions. An additional submodel in firesum simulates the mutualistic relationship between the Clarks nutcracker ( Nucifraga columbiana ) and the whitebark pine. Seed caches made by the Clarks nutcracker are evidently responsible for most whitebark pine regeneration. Whitebark pine seeds are also an important food for red squirrels ( Tamiasciurus hudsonicus ), black bear ( Ursus americana ), and especially grizzly bears ( Ursus arctos horribilis ). Infestations of white pine blister rust ( Cronartium ribicola ) and mountain pine beetle ( Dendroctonus ponderosae ), and successional replacement by shade-tolerant conifers can reduce whitebark pine populations, which can adversely impact dependent wildlife species. The model firesum was used to investigate the effects of fire, insects, and disease on whitebark pine regeneration and growth. Model predictions of basal area by tree species are presented for contrasting disturbance scenarios. Simulation predictions indicate severe reduction in some whitebark pine populations if current trends are not altered. Model predictions from a test were compared with inventory data from actual postfire stands.