Tim P. Birt

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.

Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus

Peregrine falcon populations underwent devastating declines in the mid‐20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re‐introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east–west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east–west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa.

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.

Rangewide Population Genetic Structure of Xantus's Murrelet (Synthliboramphus hypoleucus)

ABSTRACT. Population genetic structure was characterized in Xantuss Murrelet (Synthliboramphus hypoleucus) by analyzing variation in the mitochondrial control region (505 samples) and 12 microsatellite loci (428 samples) in birds captured at all 13 current breeding areas in southern California and northwestern Baja California, Mexico. The two types of molecular markers were consistent in revealing strong genetic differentiation between the two currently recognized subspecies (S. h. hypoleucus and S. h. scrippsi) and little or no differentiation among breeding areas within subspecies. Estimates of gene flow were essentially zero, and no evidence for admixture was found. Gene flow among breeding locations within subspecies, on the other hand, was seemingly high. Given these genetic results, as well as clear morphological differences between the subspecies and the apparent lack of interbreeding at breeding areas where the two forms are sympatric, we suggest that two species be recognized. Both forms are genetically distinct from Craveris Murrelet (S. craveri), a closely related species whose breeding range partially overlaps that of Xantuss Murrelet. Taxonomic subdivision of Xantuss Murrelet introduces new conservation concerns, especially for S. h. hypoleucus, which urgently requires greater study and protective efforts.

Cryptic introgression between murre sister species (Uria spp.) in the Pacific low Arctic: frequency, cause, and implications

As southern species undergo northward range expansions, reports of hybridization between temperate and arctic taxa are increasing, which may have important implications for the evolution, conservation, and management of arctic species. The extent of hybridization between temperate common murres (Uria aalge) and arctic thick-billed murres (U. lomvia), seabirds in the family Alcidae, has been the subject of debate. In a previous survey of variation in mitochondrial DNA (mtDNA) in common and thick-billed murres sampled from throughout the North Pacific and low Arctic, 12 of 327 common murres (~4%) were found to possess DNA sequences characteristic of thick-billed murres. In the present study, we surveyed variation in three nuclear introns in 230 common murres and 56 thick-billed murres and report that these putative hybrids carry various combinations of intron alleles from common and thick-billed murres. Analysis using the program STRUCTURE indicated that nine of these individuals possessed high proportions of thick-billed murre intron alleles, two possessed alleles in F1 and F2 proportions, and one individual possessed predominantly common murre intron alleles. We propose that the asymmetric mtDNA introgression we observed is most likely the result of mate choice at mixed colonies based on differences in male mating behaviours. Our results highlight that hybridization between thick-billed and common murres is more prevalent than previously thought, which may have important implications for the conservation and management of arctic-dwelling thick-billed murres as common murres expand northward.

EVIDENCE OF RECENT POPULATION DIFFERENTIATION IN ORANGE- CROWNED WARBLERS (VERMIVORA CELATA) IN HAIDA GWAII

ABSTRACT. The Haida Gwaii archipelago (formerly the Queen Charlotte Islands) off northern British Columbia hosts many endemic taxa of plants and animals, including 9 endemic subspecies of birds. Genetic studies suggest that some of these taxa originated in a glacial refugium in the area, whereas other taxa apparently arose after the recession of the glaciers. The Orange-crowned Warbler (Vermivora celata) is a Nearctic—Neotropic migrant passerine broadly distributed across North America. To gain insight into the importance of historical fragmentation versus recent differentiation in diversification of the Haida Gwaii avifauna, we analyzed geographic variation in 8 microsatellite loci and the mitochondrial control region among Orange-crowned Warblers from 7 breeding localities, including 2 of the 4 currently recognized subspecies (V.c. celata and V. c. lutescens). We found modest genetic differentiation among populations, with an isolation-by-distance pattern among western populations and significant differentiation between subspecies. Results from several analyses indicate that differences between Haida Gwaii and other western populations arose through restrictions in gene flow after the recession of the glaciers. Thus, patterns of genetic diversity in western Orange-crowned Warbler populations do not provide evidence that the species persisted in a Pleistocene refugium in the area of Haida Gwaii.

The Arctic: Glacial Refugium or Area of Secondary Contact? Inference from the Population Genetic Structure of the Thick-Billed Murre (Uria lomvia), with Implications for Management

Quaternary glaciations affected the distribution of many species. Here, we investigate whether the Arctic represented a glacial refugium during the Last Glacial Maximum or an area of secondary contact following the ice retreat, by analyzing the genetic population structure of the thick-billed murre (Uria lomvia), a seabird that breeds throughout the North Atlantic, North Pacific and Arctic Oceans. The thick-billed murre is a species of socio-economic importance and faces numerous threats including hunting, oil pollution, gill netting, and climate change. We compared variation in the mitochondrial DNA (mtDNA) control region (n = 424), supplemented by 4 microsatellite loci (n = 445), among thick-billed murres sampled throughout their range. MtDNA data indicated that colonies comprise 4 genetically differentiated groups (Φst = 0.11-0.81): 1) Atlantic Ocean plus New Siberian Islands region, 2) Cape Parry, 3) Chukchi Sea, and 4) Pacific Ocean. Microsatellite variation differed between Atlantic and Pacific populations. Otherwise, little substructure was found within either ocean. Atlantic and Pacific populations appear to have been genetically isolated since the last interglacial period and should be considered separate evolutionary significant units for management. The Chukchi Sea and Cape Parry appear to represent areas of secondary contact, rather than arctic refugial populations.

MINIMAL GENETIC STRUCTURE IN THE CERULEAN WARBLER DESPITE EVIDENCE FOR ECOLOGICAL DIFFERENTIATION AMONG POPULATIONS

Abstract. The Cerulean Warbler (Setophaga cerulea) is one of the most rapidly declining warblers in North America. Our previous genetic work suggested that this migratory songbird has no significant population genetic structure in the northern and western parts of its breeding range, and for conservation purposes we assigned all sampled populations to a single genetic management unit. Here, we expand this work to include the entire breeding range of the Cerulean Warbler, given recent evidence for morphological and ecological differentiation between the northern and southern sections of that range. We assayed variation in four microsatellite loci and an 841-base-pair fragment of the mitochondrial control region, finding support for low but significant population-genetic structure in the mitochondrial marker. Estimates of population-genetic structure for pairs of sampling locations did not detect a clear geographic pattern of differentiation, and a hierarchical AMOVA did not reveal significant structure between northern and southern locations. These findings, together with previously published evidence for high rates of contemporary dispersal among breeding locations, may support the hypothesis of a long history of gene flow among ecologically distinct Cerulean Warbler populations or may suggest that more recent anthropogenic dispersal has homogenized the genetic signature of differentiation that may have existed in pre-settlement populations.