Jeff A. Johnson

Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens.

Greater prairie‐chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie‐chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range‐wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range‐wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie‐chickens that have female‐biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie‐chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long‐term persistence of prairie‐chicken populations.

Temporal changes in allele frequencies and low effective population size in greater prairie‐chickens

The number of greater prairie‐chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo‐likelihood approach that accounted for migration, estimates of Ne (15–32 prairie‐chickens within each management area) were 10 times lower than census numbers from booming‐ground counts. These low estimates of Ne are consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reduced Ne, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie‐chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.

Beyond the beneficial effects of translocations as an effective tool for the genetic restoration of isolated populations

Translocations are becoming increasingly popular as appropriate management strategies for the genetic restoration of endangered species and populations. Although a few studies have shown that the introduction of novel alleles has reversed the detrimental effects of inbreeding over the short-term (i.e., genetic rescue), it is not clear how effective such translocations are for both maintaining neutral variation that may be adaptive in the future (i.e., genetic restoration) and increasing population viability over the long-term. In addition, scientists have expressed concerns regarding the potential genetic swamping of locally adapted populations, which may eliminate significant components of genetic diversity through the replacement of the target population by the source individuals used for translocations. Here we show that bird translocations into a wild population of greater prairie-chickens (Tympanuchus cupido pinnatus) in southeastern Illinois were effective in both removing detrimental variation associated with inbreeding depression as well as restoring neutral genetic variation to historical levels. Furthermore, we found that although translocations resulted in immediate increases in fitness, the demographic recovery and long-term viability of the population appears to be limited by the availability of suitable habitat. Our results demonstrate that although translocations can be effective management tools for the genetic restoration of wild populations on the verge of extinction, their long-term viability may not be guaranteed unless the initial conditions that led to most species declines (e.g., habitat loss) are reversed.

Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation.

Population bottlenecks may reduce genetic variation and potentially increase the risk of extinction. Here, we present the first study to use historic samples to analyse loss of variation at the major histocompatibility complex (MHC), which plays a central role in vertebrate disease resistance. Balancing selection acts on the MHC and could moderate the loss of variation expected from drift; however, in a Wisconsin population of greater prairie‐chickens (Tympanuchus cupido), the number of MHC class II B alleles per individual declined by 44% following a population bottleneck, compared to a loss of only 8% at microsatellites. Simulations indicate that drift likely reduced MHC variation at the population level, as well as within individuals by reducing the number of gene copies per individual or by fixing the same alleles across multiple loci. These multiple effects of genetic drift on MHC variation could have important implications for immunity and fitness.

Effects of recent population bottlenecks on reconstructing the demographic history of prairie‐chickens

Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie‐chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajimas D, mismatch distribution, and mdiv). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajimas D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (θ), population divergence time (t), and time to the most recent common ancestor (TMRCA) from mdiv were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.

Vulture restaurants and their role in reducing diclofenac exposure in Asian vultures

Summary The provision of supplementary food at vulture restaurants is a well-established tool in the conservation of vulture species. Among their many applications, vulture restaurants are used to provide a safe food source in areas where carcasses are commonly baited with poisons. Rapid and extensive declines of vultures in the Indian subcontinent have been attributed to the toxic effects of diclofenac, a pharmaceutical used in the treatment of livestock, to which vultures are exposed while feeding on the carcasses of treated animals. A vulture restaurant was established at the Oriental White-backed Vulture Gyps bengalensis colony at Toawala, in Punjab province Pakistan, to test the effectiveness of the technique in modifying ranging behaviour and mortality at the colony. Six male vultures were fitted with satellite transmitters to describe variation in movement and home-range during periods when safe food was alternately available and withheld at the vulture restaurant. There was considerable variation in individual home-range size (minimum convex polygons, MCP, of 1,824 km 2 to 68,930 km 2 ), with birds occupying smaller home-ranges centred closer to the restaurant being more successful in locating the reliable source of food. Fixes showed that 3 of the tagged vultures fed at the vulture restaurant and the home-range of each bird declined following their initial visit, with a 23–59% reduction in MCP. Mean daily mortality during provisioning was 0.072 birds per day (8 birds in 111 days), compared with 0.387 birds per day (41 birds in 106 days) during non-provisioning control periods. Vultures tended to occupy greater home-ranges, cover greater distances each day and spend proportionately more time in the air during the late brooding and post-breeding seasons. Attendance at the vulture restaurant also declined during this period with fewer birds visiting less often and no tagged vultures visiting the vulture restaurant at all. These findings indicate that vulture restaurants can reduce, but not eliminate, vulture mortality through diclofenac exposure and represent a valuable interim measure in slowing vulture population decline locally until diclofenac can be withdrawn from veterinary use.

Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle

The critically endangered Madagascar fish‐eagle (Haliaeetus vociferoides) is considered to be one of the rarest birds of prey globally and at significant risk of extinction. In the most recent census, only 222 adult individuals were recorded with an estimated total breeding population of no more than 100–120 pairs. Here, levels of Madagascar fish‐eagle population genetic diversity based on 47 microsatellite loci were compared with its sister species, the African fish‐eagle (Haliaeetus vocifer), and 16 of these loci were also characterized in the white‐tailed eagle (Haliaeetus albicilla) and the bald eagle (Haliaeetus leucocephalus). Overall, extremely low genetic diversity was observed in the Madagascar fish‐eagle compared to other surveyed Haliaeetus species. Determining whether this low diversity is the result of a recent bottleneck or a more historic event has important implications for their conservation. Using a Bayesian coalescent‐based method, we show that Madagascar fish‐eagles have maintained a small effective population size for hundreds to thousands of years and that its low level of neutral genetic diversity is not the result of a recent bottleneck. Therefore, efforts made to prevent Madagascar fish‐eagle extinction should place high priority on maintenance of habitat requirements and reducing direct and indirect human persecution. Given the current rate of deforestation in Madagascar, we further recommend that the population be expanded to occupy a larger geographical distribution. This will help the population persist when exposed to stochastic factors (e.g. climate and disease) that may threaten a species consisting of only 200 adult individuals while inhabiting a rapidly changing landscape.

Genetic structure among continental and island populations of gyrfalcons

Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub‐Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (FST). With the microsatellite results, significant population structure (FST, principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1–16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial‐age refugium to their current circumpolar distribution. Additional sampling of gyrfalcons from Fennoscandia and Russia throughout Siberia is necessary to test putative gene flow between Norway and Alaska and Canada as suggested by this study.

Prioritizing species conservation: does the Cape Verde kite exist?

The Cape Verde kite (Milvus milvus fasciicauda) is considered to be one of the rarest birds of prey in the world and at significant risk of extinction. For this reason there is great interest in both the taxonomic and the population status of this group. To help resolve its taxonomic status, we provide phylogenetic analyses based on three mitochondrial genes for a sampling of kites in the genus Milvus, including a broad geographical sampling of black kites (Milvus migrans), red kites (Milvus milvus), Cape Verde kite museum specimens collected between 1897 and 1924, and five kites trapped on the Cape Verde Islands during August 2002. We found that the historical Cape Verde kites, including the type specimen, were non-monophyletic and scattered within a larger red kite clade. The recently trapped kites from the Cape Verde Islands were all phylogenetically diagnosed as black kites. Our findings suggest that the traditional Cape Verde kite is not a distinctive evolutionary unit, and the case for species status, as recently suggested by others, is not supported. We do find support for recognition of at least one clade of yellow-billed kites, traditionally considered as a black kite subspecies, as a distinctive phylogenetic species.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene.

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed eight independent loci for 1-7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate.