Bradley C. Congdon

Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms.

Combination of the targeted amplification of nuclear introns and the analysis of single‐stranded conformational polymorphisms has the potential to provide an inexpensive, rapid, versatile and sensitive genetic assay for evolutionary studies and conservation. We are developing primers and protocols to analyse nuclear introns in vertebrates, and are testing them in a population genetic study of marbled murrelets Brachyramphus marmoratus. Here we present protocols and results for introns for aldolase B, α‐enolase, glyceraldehyde‐3‐phosphate dehydrogenase and lamin A. Results suggest that this approach presents a potentially powerful method for detecting genetic variation within and among local populations and species of animals: (i) a variety of genes can be surveyed, including genes of special interest such as those involved in disease resistance; (ii) assays are rapid and relatively inexpensive; (iii) large numbers of genes can be assayed, enabling accurate estimation of variation in the total genome; (iv) almost any mutation can be detected in the genes amplified; (v) the exact nature of variation can be investigated by sequence analysis if desired; (vi) statistical methods previously developed for proteins and/or sequence data can be used; (vii) protocols can be easily transferred to other species and other laboratories; and (viii) assays can be performed on old or degraded samples, blood or museum skins, so that animals need not be killed. Results of analyses for murrelets support earlier evidence that North American and Asiatic subspecies represent reproductively isolated species, and that genetic differences exist among murrelets from different sites within North America.

Polymerase chain reaction (PCR) primers for the amplification of five nuclear introns in vertebrates

[Extract] Advancements in evolutionary genetics, as well as the conservation of biodiversity, increasingly require direct analyses of sequence variation in nuclear DNA. Recent studies indicate that nuclear introns have variabilities useful for both phylogenetics and population genetics (reviewed in Friesen 2000); however, use of introns is currently limited by the paucity of polymerase chain reaction (PCR) primers that have been demonstrated to have broad taxonomic utility (although several primers with less general or uncertain utilities have been published; reviewed in Friesen 2000). We have designed 30 general PCR primers for nuclear introns for vertebrates.

MECHANISMS OF POPULATION DIFFERENTIATION IN MARBLED MURRELETS: HISTORICAL VERSUS CONTEMPORARY PROCESSES

Abstract.— Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum‐likelihood analysis of allele frequencies suggested that murrelets from “mainland” sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation‐by‐distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early–mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands.

Observed and predicted effects of climate on Australian seabirds

Abstract Although there is growing evidence of climate warming, for many regions the broader effects of climate variation on marine top predators remains unknown owing to the difficulty in obtaining, for synthesis, long-term and short-term datasets on multiple species. In the Australian region, climatic and oceanographic variability and change have been shown to affect marine species, often with profound consequences. Many seabirds are apex predators for which changes in climatic and oceanic dynamics have driven range movements poleward, reduced breeding success and altered breeding timing for some species. Here we review the literature to assess and determine the vulnerability of Australian seabirds to variation and change in climate and identify which species and ecosystems may be more resilient to future climate warming. It is clear from this synthesis that not all Australian seabirds are affected similarly, with responses varying by species and location. In addition, the paucity of information on the distribution and biology of seabird prey, foraging patterns and movements of seabirds, and the ability of seabirds to switch between prey species or adjust timing of life-cycles make generalisations about potential effects of future climate change and adaptive capacity in seabirds difficult. This applies both within Australia and elsewhere, where data are similarly sparse.

CLOSE GENETIC SIMILARITY BETWEEN TWO SYMPATRIC SPECIES OF TEPHRITID FRUIT FLY REPRODUCTIVELY ISOLATED BY MATING TIME

Abstract.— Two sibling species of tephritid fruit fly, Bactrocera tryoni and B. neohumeralis, occur sympatrically throughout the range of B. neohumeralis in Australia. Isolation between the two species appears to be maintained by a difference in mating time: B. tryoni mates at dusk, whereas B. neohumeralis mates during the middle of the day. A morphological difference in humeral callus color also distinguishes the two species. Despite clear phenotypic evidence that B. tryoni and B. neohumeralis are distinct species, genetic differentiation as measured by four markers–nuclear DNA sequences from the white gene and the ribosomal internal transcribed spacer (ITS2), and mitochondrial DNA sequences from the cytochrome b (cytb) and cytochrome oxidase subunit II (COII) genes–is very small. Minor fixed differences occur in the ITS2 sequence, however, in all other cases the two species exhibit a high level of shared polymorphic variation. The close genetic similarity suggests either that speciation has occurred very rapidly and recently in the absence of any mitochondrial DNA sorting or that the sharing of polymorphisms is due to hybridization or introgression. A third species within the tryoni complex, B. aquilonis, is geographically isolated. Bactrocera aquilonis is also genetically very similar, but in this case there is clear differentiation for the mitochondrial loci. The three species form a group of considerable interest for investigation of speciation mechanisms.

Elevated sea-surface temperature, reduced provisioning and reproductive failure of wedge-tailed shearwaters (Puffinus pacificus) in the southern Great Barrier Reef, Australia

During the 2002 austral summer abnormally high sea-surface temperatures (SST) occurred in the southern Great Barrier Reef (GBR), Australia. This phenomenon was accompanied by reduced provisioning, decreased growth rates and reproductive failure of wedge-tailed shearwaters in the region. In 2002, adults were unable to compensate for changes in either the availability and/or accessibility of forage-fish by increasing food loads or foraging rates. This is one of few studies to explicitly correlate decreases in chick provisioning with above-average annual variation in SST and is the first to do so for a tropical seabird species in the western Pacific. It adds to an increasing number of data sets identifying the potential negative impacts of increasing SST at upper-trophic levels. As SST continue to rise with global climate change, our results predict substantial detrimental effects on seabird populations of the GBR. This finding has important implications for both seabird and coral reef ecosystem management in the region. Our results also suggest that wedge-tailed shearwaters are sensitive indicators to changes in forage-fish availability/accessibility associated with SST variation that can be used to develop models of, and monitor for, these potential impacts.

Sensitivity of tropical seabirds to El Niño precursors

Intense El Niño events severely impact seabird populations, often months in advance of peak temperature anomalies. The trophic mechanisms responsible for these impacts are unknown but are assumed to operate at seasonal scales and to be linked to ocean productivity changes. Precursors to El Niño events include changes in both sea-surface temperature and the depth of the 20 degrees C thermocline. Foraging piscivorous seabirds are known to be sensitive to both thermocline depth and sea-surface temperature change, but the potential influence of these phenomena on breeding dynamics is unknown. Using 18 years of data on three seabirds of the western tropical Pacific, we show that pelagic seabird breeding participation is directly and independently related to changes in both surface chlorophyll concentration and thermocline depth that occur well in advance of El Niño generated sea-surface temperature anomalies. In contrast, breeding in an inshore foraging species is not correlated with any environmental/biological parameters investigated. These findings demonstrate that El Niño related phenomena do not affect seabird prey dynamics solely via productivity shifts at seasonal scales, nor in similar ways across different seabird foraging guilds. Our results also suggest that population declines observed in the western tropical Pacific may be directly related to the frequency and intensity of El Niño anomalies over the study period.

Population genetic structure and conservation of marbled murrelets (Brachyramphus marmoratus)

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ΦST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.

Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae)

Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550–1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies.

Molecular evidence that fireweed (Senecio madagascariensis, Asteraceae) is of South African origin

ITS1 sequence data was obtained for fireweed (Senecio madagascariensis) andS. lautus from Australia,S. madagascariensis andS. inaequidens from South Africa andS. madagascariensis from Madagascar. Despite the low level of variation (0.0–3.4%), these data further resolve the controversy concerning the identity and origin of fireweed. They confirm that fireweed is part of the South AfricanS. madagascariensis/S. inaequidens complex, and indicate that the infestation in Australia originated from South Africa as opposed to Madagascar. This will facilitate a resumption of biological control efforts in Australia and will direct surveys for control agents to South Africa.