Concerted evolution of duplicated mitochondrial control regions in three related seabird species

<p>Abstract</p> <p>Background</p> <p>Many population genetic and phylogenetic analyses of mitochondrial DNA (mtDNA) assume that mitochondrial genomes do not undergo recombination. Recently, concerted evolution of duplicated mitochondrial control regions has been documented in a range of taxa. Although the molecular mechanism that facilitates concerted evolution is unknown, all proposed mechanisms involve mtDNA recombination.</p> <p>Results</p> <p>Here, we document a duplication of a large region (cytochrome <it>b</it>, tRNA^Thr, tRNA^Pro, ND6, tRNA^Gluand the control region) in the mitochondrial genome of three related seabird species. To investigate the evolution of duplicate control regions, we sequenced both control region copies (CR1 and CR2) from 21 brown (<it>Sula leucogaster</it>), 21 red-footed (<it>S. sula</it>) and 21 blue-footed boobies (<it>S. nebouxii</it>). Phylogenetic analysis suggested that the duplicated control regions are predominantly evolving in concert; however, approximately 51 base pairs at the 5' end of CR1 and CR2 exhibited a discordant phylogenetic signal and appeared to be evolving independently.</p> <p>Conclusions</p> <p>Both the structure of the duplicated region and the conflicting phylogenetic signals are remarkably similar to a pattern found in <it>Thalassarche </it>albatrosses, which are united with boobies in a large clade that includes all procellariiform and most pelecaniform seabirds. Therefore we suggest that concerted evolution of duplicated control regions either is taxonomically widespread within seabirds, or that it has evolved many times.</p

Cryptic species and independent origins of allochronic populations within a seabird species complex (Hydrobates spp.)

Humans are inherently biased towards naming species based on morphological differences, which can lead to reproductively isolated species being mistakenly classified as one if they are morphologically similar. Recognising cryptic diversity is needed to understand drivers of speciation fully, and for accurate estimates of global biodiversity and assessments for conservation. We investigated cryptic species across the range of band-rumped storm-petrels (Hydrobates spp.): highly pelagic, nocturnal seabirds that breed on tropical and sub-tropical islands in the Atlantic and Pacific Oceans. In many breeding colonies, band-rumped storm-petrels have sympatric but temporally isolated (allochronic) populations; we sampled all breeding locations and allochronic populations. Using mitochondrial control region sequences from 754 birds, cytochrome b sequences from 69 birds, and reduced representation sequencing of the nuclear genomes of 133 birds, we uncovered high levels of genetic structuring. Population genomic analyses revealed up to seven unique clusters, and phylogenomic reconstruction showed that these represent seven monophyletic groups. We uncovered up to six independent breeding season switches across the phylogeny, spanning the continuum from genetically undifferentiated temporal populations to full allochronic species. Thus, band-rumped storm-petrels encompass multiple cryptic species, with non-geographic barriers potentially comprising strong barriers to gene flow

Future directions in conservation research on petrels and shearwaters

Shearwaters and petrels (hereafter petrels) are highly adapted seabirds that occur across all the world's oceans. Petrels are a threatened seabird group comprising 124 species. They have bet-hedging life histories typified by extended chick rearing periods, low fecundity, high adult survival, strong philopatry, monogamy and long-term mate fidelity and are thus vulnerable to change. Anthropogenic alterations on land and at sea have led to a poor conservation status of many petrels with 52 (42%) threatened species based on IUCN criteria and 65 (52%) suffering population declines. Some species are well-studied, even being used as bioindicators of ocean health, yet for others there are major knowledge gaps regarding their breeding grounds, migratory areas or other key aspects of their biology and ecology. We assembled 38 petrel conservation researchers to summarize information regarding the most important threats according to the IUCN Red List of threatened species to identify knowledge gaps that must be filled to improve conservation and management of petrels. We highlight research advances on the main threats for petrels (invasive species at breeding grounds, bycatch, overfishing, light pollution, climate change, and pollution). We propose an ambitious goal to reverse at least some of these six main threats, through active efforts such as restoring island habitats (e.g., invasive species removal, control and prevention), improving policies and regulations at global and regional levels, and engaging local communities in conservation efforts

Relative Alignment between the Magnetic Field and Molecular Gas Structure in the Vela C Giant Molecular Cloud Using Low- and High-density Tracers

We compare the magnetic field orientation for the young giant molecular cloud Vela C inferred from 500 μm polarization maps made with the BLASTPol balloon-borne polarimeter to the orientation of structures in the integrated line emission maps from Mopra observations. Averaging over the entire cloud we find that elongated structures in integrated line-intensity or zeroth-moment maps, for low-density tracers such as 12CO and 13CO J → 1 – 0, are statistically more likely to align parallel to the magnetic field, while intermediate- or high-density tracers show (on average) a tendency for alignment perpendicular to the magnetic field. This observation agrees with previous studies of the change in relative orientation with column density in Vela C, and supports a model where the magnetic field is strong enough to have influenced the formation of dense gas structures within Vela C. The transition from parallel to no preferred/perpendicular orientation appears to occur between the densities traced by 13CO and by C18O J → 1 – 0. Using RADEX radiative transfer models to estimate the characteristic number density traced by each molecular line, we find that the transition occurs at a molecular hydrogen number density of approximately 103 cm−3. We also see that the Centre Ridge (the highest column density and most active star-forming region within Vela C) appears to have a transition at a lower number density, suggesting that this may depend on the evolutionary state of the cloud

The Authors

Many seabirds exhibit high natal philopatry despite their extreme dispersal ability and delayed reproduction, and some exhibit phenotypic clustering in colonies and fostering or adoption of neighbouring chicks. Previous investigations of kinship in a small thick-billed murre colony Uria lomvia (Alcidae) in Norway revealed high relatedness among breeders on cliff ledges. To investigate the presence of kin groups and within-colony genetic sub-structuring elsewhere, we investigated kinship within a larger murre colony on Coats Island, Nunavut, Canada. Morphological (five characters) and genetic data (five microsatellite loci and a fragment of the mitochondrial cytochrome b gene) were analysed. Strong morphological differentiation was found among ledges. Genetic structuring was overall weak but significant at the coarse scale for males among ledges and on the east vs. the west side of the colony. Global spatial autocorrelation analyses did not detect consistent, widespread spatial patterns, although local 2D analyses provided some evidence of a tendency for larger neighbourhood sizes for females and a broad range of small to large neighbourhoods for males. Average withinledge relatedness was low overall, but ranged widely from slightly unrelated to greater than the level of cousins in both sexes. Kin-level relationships occurred on ledges more frequently for same-sex groups than expected by chance, suggesting that recruiting breeders (especially females) avoid or are unable to settle directly adjacent to relatives particularly of the opposite sex. Behavioural studies of natal dispersal of murres at Coats I. indicating that both sexes are highly philopatric, but that up to one-fifth of females may disperse, are concordant with this study. Overall, structuring was weaker than in Norway, and may be explained in part by genetic marker and sampling artifacts, and by the lack of genetic equilibrium suspected in the much larger Canadian Arctic colony. Natal philopatry may be an important factor driving the diversification of seabirds and kin groups in other colonies and species and may be more widespread than is currently acknowledged. Natal site fidelity (natal philopatry) can strongly impact the genetic structure of populations. Philopatry over many generations can promote genetic structure both among-and within-populations, and the formation of kin groups. Within small groups evolution can proceed at a faster rate due to non-random mating (Kingston an

Data from: Mechanisms of global diversification in the brown booby (Sula leucogaster) revealed by uniting statistical phylogeographic and multilocus phylogenetic methods

Recent theoretical and empirical research suggests that statistical models based on coalescent theory can improve both phylogeographic and phylogenetic inference. An approach that involves elements of both statistical phylogeography (e.g., Isolation with Migration analyses) and multilocus phylogenetic inference (e.g., *BEAST) may be particularly useful when applied to populations with relatively old divergence times. Here we use such an approach in the globally distributed brown booby (Sula leucogaster). We sampled 215 individuals from all major breeding areas and genotyped them at eight microsatellite and three nuclear intron loci. We found that brown booby populations were highly differentiated and that colonies can be grouped into four major genetic populations (Caribbean Sea, Central Atlantic Ocean, Indo-Central Pacific, and Eastern Pacific). These populations apparently diverged in the absence of gene flow and, with one exception, currently exchange few to no migrants. The Eastern Pacific population diverged from all other populations approximately one million years ago [90% highest posterior density: 330 000 – 2 000 000 years ago] and exhibits a distinct male plumage, relative to other populations. However, recent gene flow from the Indo-Central Pacific into the Eastern Pacific appears to have occurred, suggesting that approximately one million years of genetic isolation and divergence in male plumage colour are not sufficient to prevent interbreeding. Gene flow following secondary contact of the Indo-Central Pacific and Eastern Pacific populations was not detected in previous mitochondrial DNA (mtDNA) studies, and the contrast between the mtDNA results and our current results highlights the advantage of a multilocus phylogeographic approach

The magnitude of selection on growth varies among years and increases under warming conditions in a subarctic seabird

Abstract Because of ongoing rapid climate change, many ecosystems are becoming both warmer and more variable, and these changes are likely to alter the magnitude and variability of natural selection acting on wild populations. Critically, changes and fluctuations in selection can impact both population demography and evolutionary change. Therefore, predicting the impacts of climate change depends on understanding the magnitude and variation in selection on traits across different life stages and environments. Long-term experiments in wild settings are a great opportunity to determine the impact of environmental conditions on selection. Here we examined variability in the strength of selection on size traits of nestling black-legged kittiwakes (Rissa tridactyla) in a 25-year study including a food supplementation experiment on Middleton Island in the Gulf of Alaska. Using mixed effect models, we examined the annual variability of stage-specific and resource-specific selection gradients across 25 years. We found that (a) larger and heavier hatchlings were the most likely to survive during early ontogeny, (b) non-food supplemented younger nestlings in a brood experienced the strongest selection, and (c) warmer conditions increased the magnitude of selection on nestling mass and affected non-food supplemented and second-hatched nestlings the most. Our results suggested that variable resource dynamics likely caused some of the changes in selection from year to year and that warming conditions increased the strength of selection on subarctic seabird growth. However, our experimental manipulation revealed that local environmental heterogeneity could buffer the selection expected from broader climatic changes. Consequently, understanding the interactive effects of local conditions and general changes in climate seems likely to improve our ability to predict future selection gradients

Leigh_et.al.data_used_in_synthesis

Genetic diversity estimates per study included in the synthesis. References for the original studies used are included in the spreadsheet

Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes

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 pop- ulation 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