Allan J. Baker

The interplay between habitat availability and population differentiation

We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP.

Rapid population decline in red knots: fitness consequences of decreased refuelling rates and late arrival in Delaware Bay

Most populations of migrant shorebirds around the world are in serious decline, suggesting that vital condition–dependent rates such as fecundity and annual survival are being affected globally. A striking example is the red knot (Calidris canutus rufa) population wintering in Tierra del Fuego, which undertakes marathon 30 000 km hemispheric migrations annually. In spring, migrant birds forage voraciously on horseshoe crab eggs in Delaware Bay in the eastern USA before departing to breed in Arctic polar deserts. From 1997 to 2002 an increasing proportion of knots failed to reach threshold departure masses of 180–200 g, possibly because of later arrival in the Bay and food shortage from concurrent over–harvesting of crabs. Reduced nutrient storage, especially in late–arriving birds, possibly combined with reduced sizes of intestine and liver during refuelling, had severe fitness consequences for adult survival and recruitment of young in 2000–2002. From 1997 to 2002 known survivors in Delaware Bay were heavier at initial capture than birds never seen again, annual survival of adults decreased by 37% between May 2000 and May 2001, and the number of second–year birds in wintering flocks declined by 47%. Population size in Tierra del Fuego declined alarmingly from 51 000 to 27 000 in 2000–2002, seriously threatening the viability of this subspecies. Demographic modelling predicts imminent endangerment and an increased risk of extinction of the subspecies without urgent risk–averse management.

CHAPTER 3 – Mitochondrial Control Region Sequences as Tools for Understanding Evolution

The chapter summarizes what is known about the control region of birds in terms of its organization, the location of markers within it, and presents exemplars from laboratory observations illustrating the potential and problems of fast-evolving sequences in elucidating the population structure and molecular systematics of closely related taxa. In addition to transition and transversion substitutions and numerous small indels, length differences accumulate through variation in a number of tandem repeats, and relatively large duplication or deletion of events. Both inter- and intraspecific variations are more common in the two flanking domains than in the conserved central blocks, with tandem repeats occurring primarily in domain III and larger duplications restricted to among-species comparisons. A thorough analysis of intraspecific sequence variation leads inevitably to the consideration of the population genetic processes responsible for major phylogenetic subdivisions in gene trees and to consideration of taxonomic recognition of these discrete clades as subspecies, phylogenetic species, or biological species. A major difficulty illustrated by the knot sequences is that populations are unlikely to be in equilibrium with respect to mutation and genetic drift.

HISTORICAL DEMOGRAPHY AND PRESENT DAY POPULATION STRUCTURE OF THE GREENFINCH, CARDUELIS CHLORIS-AN ANALYSIS OF MTDNA CONTROL-REGION SEQUENCES

Genetic variability within and among 10 geographically distinct populations of Greenfinches (Carduelis chloris) was assayed by directly sequencing a 637 BP part of the mtDNA control region from 194 individuals. Thirteen variable positions defined 18 haplotypes with a maximum sequence divergence of 0.8%. Haplotype (h = 0.28–0.77) and nucleotide (π = 0.058–0.17%) diversities within populations were low, and decreased with increasing latitude (h:rs = –0.81; π: rs = –0.89). The distribution of pairwise nucleotide differences fit better with expectations of a “sudden expansion” than of an “equilibrium” model, and the estimates of long term effective population sizes were considerably lower than current census estimates, especially in northern European samples. Selection is an unlikely cause of observed patterns because the distribution of variability conformed to expectations of neutral infinite alleles model and haplotype diversity across populations was positively correlated with heterozygosity (HE) in nuclear genes (rs = 0.74, P < 0.05). Hence, a recent bottleneck, followed by serial bottlenecking during the process of post‐Pleistocene recolonization of northern Europe, together with recent population expansion provide a plausible explanation for the low genetic diversity in the north. Genetic distances among populations showed a clear pattern of isolation‐by‐distance, and 14% of the haplotypic variation was among populations, the rest being distributed among individuals within populations. In accordance with allozyme and morphological data, a hierarchical analysis of nucleotide diversity recognized southern European populations as distinct from northern European ones. However, the magnitude of divergence in mtDNA, allozymes and morphology were highly dissimilar (morphology > mtDNA > allozymes).

Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds

BackgroundDNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10× mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.ResultsTo test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ) tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution.ConclusionClosely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

Disjunct distribution of highly diverged mitochondrial lineage clade and population subdivision in a marine bivalve with pelagic larval dispersal

Mitochondrial DNA sequence data for 295 individuals of the marine bivalve Macoma balthica (L.) were collected from 10 sites across the European distribution, and from Alaska. The data were used to infer population subdivision history and estimate current levels of gene flow. Inferred historical biogeography was expected to be congruent with colonization of the Atlantic Ocean from the Pacific Ocean after the opening of the Bering Strait 3.5 Ma. In addition, the last glacial maximum, about 18 000 years ago, was expected to have been responsible for most of the present‐day distribution of molecular variation within Europe, because the area must have been recolonized after confinement to France and the south of the British Isles during the last glacial maximum. Current gene flow was hypothesized to be high, because the larvae of M. balthica spend 2–5 weeks drifting in the water column. The geographical distribution of one highly diverged haplotype clade was found to be disjunct and was encountered exclusively in samples from the Baltic Sea and Alaska. A molecular clock calibration for marine bivalve cytochrome‐c‐oxidase I dates this clade as having split off from the other haplotypes 9.8–39 Ma. Multiple colonizations of the Atlantic Ocean from the Pacific by M. balthica may explain the strong differences found between Baltic Sea and other European populations of this species. The sympatric occurrence of the highly diverged mitochondrial lineages in western parts of the Baltic Sea points to secondary admixture. With the use of coalescent analysis, population divergence times for French vs. other non‐Baltic European populations (‘Atlantic population assemblage’) were estimated at a minimum of about 110 000 years ago, well before the last glacial maximum 18 000 years ago. Signatures of population divergence of M. balthica that appear to have originated during the Pleistocene have thus survived the last glacial maximum. Some of the populations within the Atlantic assemblage are currently isolated, while others appear to be connected by gene flow. Apparently, populations of this species can remain highly subdivided in spite of the potential for high gene flow, implying that their population and evolutionary dynamics can be independent.

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control‐region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three‐quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population‐genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.

Rapid genetic differentiation and founder effect in colonizing populations of common mynas (Acridotheres tristis)

Populations of common mynas introduced to Australia, New Zealand, Fiji, Hawaii, and South Africa from India during the last century were compared genetically with the extant native population using isozyme electrophoresis of 39 presumptive loci. Average heterozygosity, mean number of alleles/locus, and the percentage of polymorphic loci are lower in the introduced populations, and the 18% loss of alleles involves only alleles that are rare in the native population. The native population is only weakly subdivided genetically (FST = 0.032) whereas the introduced populations are much more differentiated (FST = 0.123), and the mean genetic distance among them is significantly greater than among native samples.

Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.

RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds.

The Charadriiformes is a large and diverse order of shorebirds currently classified into 19 families, including morphologically aberrant forms that are of uncertain phylogenetic placement within non-passerine birds in general. Recent attempts using morphological characters have failed to recover a well-supported phylogeny depicting higher level relationships within Charadriiformes and the limits to the order, primarily because of inconsistency and homoplasy in these data. Moreover, these trees are incongruent with the relationships presented in the DNA hybridization tapestry of, including the location of the root and the branching order of major clades within the shorebirds. To help clarify this systematic confusion we therefore sequenced the large RAG-1 nuclear exon (2850 bp) from 36 species representing 17 families of shorebirds for which DNA was available. Trees built with maximum parsimony, maximum likelihood or Bayesian methods are topologically identical and fully resolved, with high support at basal nodes. This further attests to the phylogenetic utility of the RAG-1 sequences at higher taxonomic levels within birds. The RAG-1 tree is topologically similar to the DNA hybridization tree in depicting three major subordinal clades of shorebirds, the Charadrii (thick-knees, sheathbills, plovers, oystercatchers, and allies), Scolopaci (sandpipers and jacanas) and the Lari (coursers, pratincoles, gulls, terns, skimmers, and skuas). However, the basal split in the RAG-1 tree is between Charadrii and (Scolopaci+Lari), whereas in the DNA hybridization tree Scolopaci is the sister group to the (Charadrii+Lari). Thus in both of these DNA-based trees the Alcidae (auks, murres, and allies) are not basal among shorebirds as hypothesized in morphological trees, but instead are placed as a tip clade within Lari. The enigmatic buttonquails (Turnicidae), variously hypothesized as being allied to either the Galliformes, Gruiformes, or Charadriiformes, are shown to be a basal lineage in the more conventional Lari clade. Divergence times estimated with rate-smoothing methods and minimum time constraints imposed at nodes with key fossils suggest that Charadriiformes originated in Gondwanaland.