Mitochondrial DNA sequence evolution and phylogeny of the Atlantic Alcidae, including the extinct great auk (Pinguinus impennis).

-Common Murres (Uria aalge) exhibit an unusual molt sequence. Primary molt begins at a focus between P4 and P7 and progresses in two rapid concurrent waves, proximally to P1, and distally to P10. The only other birds known to have a similar molt sequence are caracaras and falcons (Falconidae), parrots (Psittaciformes), and Pied Kingfishers (Ceryle rudis). Great Auks (Pinguinus impennis) also appear to have followed the same primary-molt sequence. Phylogenies for the Alcidae indicate that Great Auks, Common Murres, Thickbilled Murres (Uria lomvia), Razorbills (Alca torda), and Dovekies (Alle alle) share a common ancestor and are more closely related to one another than to other alcids. This suggests that the unusual sequence of primary molt in Common Murres is a shared-derived character that occurs in the other four species in their clade but has been overlooked. Adult male Common Murres have significantly shorter secondaries and longer primaries, on average, than do adult females, resulting in a slightly higher aspect ratio in males. Secondary molt begins when primary molt is more than one-third completed. Secondaries are replaced rapidly but sequentially (not synchronously or simultaneously); molt appears to proceed from two foci, proximally from S1 to S4, and both proximally and distally from S8, but more data are needed to clarify this point. Rectrix molt begins when primary molt is two-thirds completed. Rectrix loss and replacement occur rapidly, possibly synchronously, and in no apparent order. Adults molt about two weeks later than nonbreeding subadults. We found no differences in the timing of molt between the sexes in adults or subadults. Duration of flight-feather molt can vary from less than 25 days to more than 80 days, possibly reflecting interyear variation in prey abundance. Received 12 February 1997, accepted 9 December 1997. RELATIVE TO MOST OTHER TOPICS in ornithology, virtually all aspects of the molting process are poorly documented and understood (Pyle et al. 1987, Jenni and Winkler 1994). This is especially true in seabirds because most species, including all species that become flightless during molt, undergo molt at sea during the nonbreeding season (Palmer 1962, Glutz von Blotzheim and Bauer 1982, Cramp 1977, 1983, Warham 1996). Among alcids, molt has been better studied in Common Murres (Uria aalge) than in many other species (Verwey 1922, 1924, Salomonsen 1944, Stresemann and Stresemann 1966, Birkhead and Taylor 1977), but many aspects of their molt remain poorly known (contra Harris and Wanless 1990). As an extension of studies on seabird entanglement in gill nets in Puget Sound (Thompson et al. 1998), we studied molt in Common 4E-mail: thompcwt@dfw.wa.gov Murres. The phenology of breeding in Common Murres differs by two months or more among geographic areas. Thus, flight-feather molt scores in postbreeding adults might be useful for identifying breeding location (e.g. Oregon vs. Washington); this is important for determining the demographic effect of mortality caused by gill nets or other anthropogenic activities on different breeding populations of Common Murres. MATERIALS AND METHODS In 1993, commercial gill net fisheries occurred for summer sockeye salmon (Onchorhynchus nerka) in northern Puget Sound and for fall chum salmon (0. keta) in Hood Canal and central Puget Sound, Washington (Pierce et al. 1994). To evaluate various modified gill net designs, test fisheries were done in 1993 by Washington Sea Grant, and in 1993 and 1996 by Washington Sea Grant and Washington Department of Fish and Wildlife. Entangled seabirds were collected: (1) from commercial fisheries in 1993 from 1

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.

At the Gannet Islands, Labrador, the proportion of Thick-billed Murres (Uria lomvia) that successfully reared a chick that left the colony was significantly lower (mean = 63%) than that of Common Murres (Uria aalge; 82%) in each of 3 years of study. The physical and social features of the breeding site were the only factors known to influence breeding success. For both murre species, breeding success increased with ledge width, and whereas most Common Murres bred on the widest ledges, relatively few Thick-billed Murres did so. The success of each species did not differ significantly on ledges of the same width. We suggest that Common and Thick-billed murres competed for breeding sites and that Common Murres obtained a disproportionate share of the "best" sites. This occurred because Common Murres outnumbered Thick-billed Murres by about 40:1 and because cliff habitat was in short supply. Whereas Thick-billed Murres bred only on cliffs, Common Murres were able to breed on cliffs and flat ground nearer sea level. Additional circumstantial evidence supports the idea that Common and Thick-billed murres at the Gannet Islands compete for breeding sites.

We compared the shape and eggshell thickness of Great Auk Pinguinus impennis eggs with those of its closest relatives, the Razorbill Alca torda, Common Guillemot Uria aalge and Brünnich's Guillemot Uria lomvia, in order to gain additional insights into the breeding biology of the extinct Great Auk. The egg of the Great Auk was most similar in shape to that of Brünnich's Guillemot. The absolute thickness of the Great Auk eggshell was greater than that of the Common Guillemot and Razorbill egg, which is as expected given its greater size, but the relative shell thickness at the equator and pointed end (compared with the blunt end) was more similar to that of the Common Guillemot. On the basis of these and other results we suggest that Great Auk incubated in an upright posture in open habitat with little or no nest, where its pyriform egg shape provided stability and allowed safe manoeuvrability during incubation. On the basis of a recent phylogeny of the Alcidae, we speculate that a single brood patch, a pyriform egg and upright incubation posture, as in the Great Auk and the two Uria guillemots, is the ancestral state, and that the Razorbill – the Great Auk's closest relative – secondarily evolved two brood patches and an elliptical egg as adaptations for horizontal incubation, which provides flexibility in incubation site selection, allowing breeding in enclosed spaces such as crevices, burrows or under boulders, as well as on open ledges.

Sympatric nesting seabird species are often found to differ in one or more aspects of their foraging ecology. This is usually interpreted as resource partitioning, potentially due to current or past competition, but other explanations have been proposed. Three closely related species of alcids breeding together in subarctic southwest Greenland differed in several aspects of their foraging ecology during chick rearing. Thick-billed Murres (Uria lomvia) and Common Murres (U. aalge) did not differ in their diving behavior but both species differed markedly with Razorbills (Alca torda). Thick-billed Murres foraged mainly close to the colony, whereas Common Murres and Razorbills also made foraging trips to the mainland coast. Common Murres made significantly more bouts (series of dives) per trip than Thick-billed Murres, but significantly fewer dives per bout than Razorbills. Median dive depth of Thick-billed and Common murres was twice that of Razorbills. Thick-billed Murres nested on open ledges and spent most of their non-foraging time on the ledge attending the chick. Common Murres and Razorbills nested under boulders and in crevices and often left their chicks alone (particularly at night) and rested on the water. One interpretation of this pattern is that the risk of predation from Glaucous Gulls (Larus hyperboreus) was much higher on open ledges, and that Thick-billed Murres therefore had to guard their chicks at all times.

Since the late 1600s it has been assumed that the Great AukPinguinus impenniswas similar to the Common GuillemotUria aalgeand Brünnich's GuillemotUria lomviain having a single, central brood patch. Through the examination of eight mounted museum specimens, we show that this is incorrect and that, like its closest relative the RazorbillAlca torda, the Great Auk had two lateral brood patches. We discuss how such misinformation persisted for so long. We also review the relationship between the number of brood patches and clutch size in the Alcidae. One implication of two brood patches is that the Great Auk would have incubated in a horizontal posture like the Razorbill, rather than in a semi‐upright posture like theUriaguillemots. Assuming that the Great Auk incubated like the Razorbill, it would probably have done so horizontally with its single egg pressed against one of the two lateral brood patches, positioned against the inside of one tarsus (and partially on the web of one foot), and with the wing on that side drooped to provide additional protection for the egg. Incubating in this way may have meant that the Great Auk's pyriform egg would have enabled it to use both level and sloping terrain, as in theUriaguillemots (but unlike the Razorbill). A horizontal incubation also has implications for estimates of their breeding density, which we estimate to have been around four pairs per square metre and, hence numbers on its largest known colony, Funk Island, Newfoundland (maximum 250 000 pairs).

The ability to recognize mates, kin, offspring and neighbors by their individually distinctive traits-individual recognition (IR)-is widespread in animals. Much work has investigated IR from the perspective of the recognizer, but less is known about the extent to which signals have evolved to facilitate IR. To explore this, one approach is to compare putative identity signals among species that differ in life history and extent of IR. In Common Murres (Uria aalge), a colonially breeding seabird, the eggs of individual females are remarkably variable in terms of color and pattern (maculation). Common Murres also appear to recognize their own eggs, leading to the hypothesis that variable egg phenotypes evolved to promote recognizability. However, we lack a quantitative assessment of the egg pattern information in Common Murres and their close relatives. Here, we analyzed images of eggs laid by four alcid species: Common Murres, Thick-billed Murres (Uria lomvia), Razorbills (Alca torda) and Dovekies (Alle alle). We extracted pattern measures believed to be relevant to bird vision and calculated Beecher's information statistic (Hs ), which allowed us to compare the amount of identity information contained in each species' egg patterns. Murres, which nest in dense colonies and can recognize their own eggs, have egg patterns with a relatively large amount of identity information compared to Razorbills and Dovekies. Egg recognition has not been demonstrated in Razorbills and Dovekies, whose colonies are less dense. Our results are consistent with the hypothesis that complex patterns of Murre eggs may have evolved to increase individual recognizability.

BackgroundThe monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP).MethodsThe mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens.ResultsThe AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species.ConclusionsPhylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.

Like many seabirds, auks spend most of the year in offshore areas. Information on which oceanic areas they rely on throughout the winter is therefore important in understanding their population dynamics and establishing appropriate conservation measures. The breeding populations of Thick-billed Murres (Uria lomvia), Common Murres (Uria aalge) and Razorbills (Alca torda) in Iceland have been reported declining for the last 30 years. Thick-billed Murres have shown the most alarming rate of decrease, while Razorbills have declined the least. To help understand these changes, we collected information about the non-breeding distribution of these three species by using light-based geolocation. Geolocators were deployed on breeding adults in three different colonies in Iceland in 2013 and 2014. Data showed that the three species’ wintering areas differed substantially. Thick-billed Murres wintered off the west coast of Greenland and East Greenland/Northern Iceland, Common Murres favoured areas around Iceland/East Greenland and to the southwest along the Mid-Atlantic Ridge, and Razorbills were mostly distributed around Iceland. Although some intraspecific variation was evident, we conclude that the population development of Thick-billed Murres in Iceland is likely to be largely influenced by environmental conditions in west Greenland, while Common Murres and Razorbills are more dependent on the oceanic area around Iceland. The results may therefore prove to be an important platform for understanding the population dynamics of these three species in Iceland and informing conservation actions.

One new mitochondrial genome of Indonemoura auriformis from the family Nemouridae (Insecta: Plecoptera) was sequenced in the study. The mitochondrial genome has the length of 15,718 bp, encoding 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The whole nucleotide composition biased adenine and thymine with A + T accounting for 69.9%. Nine PCGs and 14 tRNA genes are encoded in the J chain, the other four PCGs, eight tRNAs, and two rRNA genes are encoded in the chain of N. The mitochondrial genome includes 13 gene overlaps and 12 intergenic spacers. Most PCGs strictly use the ATN as start codon, and terminate with traditional stop codon (TAA and TAG). Except the tRNASer(AGN) seems to lack dihydrogen glycine arm, all tRNA genes of the mitochondrial genome are the typical clover secondary structure. The phylogenetic tree of PCGs dataset based on bayesian inference (BI) and maximum likelihood (ML) analysis show the same tree topology. Both ML and BI analysis support the sister-group relationship between Amphinemuria and Nemoura. Meanwhile, Capniidae is closely related to Taeniopterygidae.

Several aspects of the breeding biology of Common Murres (Uria aalge) and Thick-billed Murres (Uria lomvia) in 1981–1983, at the Gannet Islands, Labrador, are described. At this colony there were ca. 60 000 pairs of Common Murres, and 1400 pairs of Thick-billed Murres. Common Murres were slightly heavier and had significantly shorter wings, and longer, narrower bills than Thick-billed Murres. The timing of egg laying varied between years (late breeding in one year was associated with late ice breakup), but the median laying date of Common Murres was consistently earlier (by up to 10 days) than that of Thick-billed Murres. For both species median laying dates fell between mid and late June each year. Common Murre eggs were larger and relatively longer than Thick-billed Murre eggs, but in both species fresh egg weight was about 11% of adult body weight. Incubation periods were similar in each species (33 days), but chick-rearing periods were longer in Common Murres (24 days) than in Thick-billed Murres (21 days) in all years. Seasonal patterns of colony attendance were broadly similar in the two species each year, except that Common Murres showed a consistent increase in numbers between laying and chick departure, and tended to remain at the colony for less time after chicks had departed compared with Thick-billed Murres. All birds of both species left the colony by mid-September each year.

To study the influence of inter- and intra-specific interactions on patterns of ecological segregation in nonbreeding habitat, we used geolocators to track year-round movements of congeneric and partially sympatric Thick-billed Murres (Uria lomvia (L., 1758)) and Common Murres (Uria aalge (Pontoppidan, 1763)) from seven Canadian colonies during 2007–2011. Locations from 142 individuals were (i) examined for species- and colony-specific spatiotemporal patterns, (ii) mapped with environmental data, and (iii) used to delineate core wintering areas. Compared with Common Murres, Thick-billed Murres dispersed across a wider range of latitudes and environments, had larger winter ranges, and showed greater variation in seasonal timing of movements. These interspecific differences were consistent at two scales: among colonies spanning a wide latitudinal range and at a sympatric colony. Intraspecifically, nonbreeding ecological segregation was more pronounced among colonies of Thick-billed Murres than of Common Murres: colonies of Thick-billed Murres tended to follow distinct movement patterns and segregate by latitude, whereas colonies of Common Murres segregated very little; moreover, the extent of segregation was more variable among Thick-billed Murres than Common Murres. For Thick-billed Murres, rather than complete divergence of winter ecological niche from Common Murres, we found a “widening” of an overlapping niche. This strategy of increased movement flexibility may enable Thick-billed Murres to mitigate competition both intra- and inter-specifically; we propose this movement strategy may have played a role in species divergence.

The land snail Cernuellavirgata (da Costa, 1778) is widely considered as a pest to be quarantined in most countries. In this study, the complete mitochondrial genome of Cernuellavirgata is published. The mitochondrial genome has a length of 14,147 bp a DNA base composition of 29.07% A, 36.88% T, 15.59% C and 18.46% G, encoding 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The complete nucleotide composition was biased toward adenine and thymine, A+T accounting for 69.80%. Nine PCGs and 14 tRNA genes are encoded on the J strand, and the other four PCGs and eight tRNA genes are encoded on the N strand. The genome also includes 16 intergenic spacers. All PCGs start strictly with ATN, and have conventional stop codons (TAA and TAG). All tRNAs fold into the classic cloverleaf structure, except tRNAArg, tRNASer(UCN), tRNASer(AGN) and tRNAPro. The first three lack the dihydrouridine arm while the last lacks the TψC arm. There are 502 bp long noncoding regions and 418bp long gene overlaps in the whole mitochondrial genome, accounting for 3.54% and 2.95% of the total length respectively. Phylogenetic analyses based on the sequences of the protein coding genes revealed a sister group relationship between the Hygromiidae and the Helicidae.

The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes

We used proteomic profiling to taxonomically classify extinct, alongside extant bird species using mass spectrometry on ancient bone-derived collagen chains COL1A1 and COL1A2. Proteins of Holocene and Late Pleistocene-aged bones from dodo (Raphus cucullatus) and great auk (Pinguinus impennis), as well as bones from chicken (Gallus gallus), rock dove (Columba livia), zebra finch (Taeniopygia guttata) and peregrine falcon (Falco peregrinus), of various ages ranging from the present to 1455 years old were analysed. HCl and guandine-HCL-based protein extractions from fresh bone materials yielded up to 60% coverage of collagens COL1A1 and COL1A2, and extractions from ancient materials yielded up to 46% coverage of collagens COL1A1 and COL1A2. Data were retrieved from multiple peptide sequences obtained from different specimens and multiple extractions. Upon alignment, and in line with the latest evolutionary insights, protein data obtained from great auk grouped with data from a recently sequenced razorbill (Alca torda) genome. Similarly, protein data obtained from bones of dodo and modern rock dove grouped in a single clade. Lastly, protein data obtained from chicken bones, both from ancient and fresh materials, grouped as a separate, basal clade. Our proteomic analyses enabled taxonomic classification of all ancient bones, thereby complementing phylogenetics based on DNA.