Contrasting stripes are a widespread feature of group living in birds, mammals and fishes.

Grouping is a widespread form of predator defence, with individuals in groups often performing evasive collective movements in response to attack by predators. Individuals in these groups use behavioural rules to coordinate their movements, with visual cues about neighbours' positions and orientations often informing movement decisions. Although the exact visual cues individuals use to coordinate their movements with neighbours have not yet been decoded, some studies have suggested that stripes, lines, or other body patterns may act as conspicuous conveyors of movement information that could promote coordinated group movement, or promote dazzle camouflage, thereby confusing predators. We used phylogenetic logistic regressions to test whether the contrasting achromatic stripes present in four different taxa vulnerable to predation, including species within two orders of birds (Anseriformes and Charadriiformes), a suborder of Artiodactyla (the ruminants), and several orders of marine fishes (predominantly Perciformes) were associated with group living. Contrasting patterns were significantly more prevalent in social species, and tended to be absent in solitary species or species less vulnerable to predation. We suggest that stripes taking the form of light-coloured lines on dark backgrounds, or vice versa, provide a widespread mechanism across taxa that either serves to inform conspecifics of neighbours' movements, or to confuse predators, when moving in groups. Because detection and processing of patterns and of motion in the visual channel is essentially colour-blind, diverse animal taxa with widely different vision systems (including mono-, di-, tri-, and tetrachromats) appear to have converged on a similar use of achromatic patterns, as would be expected given signal-detection theory. This hypothesis would explain the convergent evolution of conspicuous achromatic patterns as an antipredator mechanism in numerous vertebrate species.

Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark.

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice.

Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km2 islet of Raso, Cape Verde, since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2-8 linked MHC-I loci. Within-locus homozygosity is high, contributing to low population-wide diversity. Conversely, each individual had comparably many alleles, 6-16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species' adaptive potential.

Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes.

Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that selection for recombination suppression has acted repeatedly and independently on certain genetic backgrounds. Here, we perform comparative genomics of a bird clade (larks and their sister lineage; Alaudidae and Panuridae) where multiple autosome-sex chromosome fusions appear to have formed expanded sex chromosomes. We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between parts of four avian chromosomes: Z, 3, 4A and 5. Within these four chromosomes, we found evidence of five evolutionary strata where recombination had been suppressed at different time points, and show that stratum age explained the divergence rate of Z-W gametologs. Next, we analysed chromosome content and found that chromosome 3 was significantly enriched for genes with predicted sex-related functions. Finally, we demonstrate extensive homology to sex chromosomes in other vertebrate lineages: chromosomes Z, 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5). Our results provide insights into and support for repeated evolution of sex chromosomes in vertebrates.

When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine.

The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.

Global assessment of marine plastic exposure risk for oceanic birds.

Plastic pollution is distributed patchily around the world's oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.

Widespread translocation from autosomes to sex chromosomes preserves genetic variability in an endangered lark.

Species that pass repeatedly through narrow population bottlenecks (<100 individuals) are likely to have lost a large proportion of their genetic variation. Having genotyped 92 Raso larks Alauda razae, a Critically Endangered single-island endemic whose world population in the Cape Verdes over the last 100 years has fluctuated between about 15 and 130 pairs, we found variation at 7 of 21 microsatellite loci that successfully amplified, the remaining loci being monomorphic. At 6 of the polymorphic loci variation was sex-linked, despite the fact that these microsatellites were not sex-linked in the other passerine birds where they were developed. Comparative analysis strongly suggests that material from several different autosomes has been recently transferred to the sex chromosomes in larks. Sex-linkage might plausibly allow some level of heterozygosity to be maintained, even in the face of persistently small population sizes.

Survival of a long-lived single island endemic, the Raso lark Alauda razae, in relation to age, fluctuating population and rainfall.

Estimating and understanding variation in survival rates is crucial for the management of threatened species, especially those with limited population sizes and/or restricted ranges. Using a capture-resighting dataset covering 2004-2017, we estimate adult survival in the Raso lark Alauda razae, a Critically Endangered single-island Cape Verdean endemic, whose population varied 25-fold during the study. Average annual adult survival was similar for males (0.813 ± 0.011) and females (0.826 ± 0.011) over the period. These values are high for a temperate passerine but not unusual for an insular tropical species like the lark. The oldest bird was recorded 13 years after first ringing. There was strong evidence that survival varied among years (between 0.57 and 0.95), being generally higher in wetter years. Survival, especially of males, was lower when the population was large, but only in drier years. Survival declined with age but there was no evidence that this decline was other than linear. High survival, even in the face of dry conditions, at least when the population is depressed, has probably contributed to the persistence of the species on its 7 km2 island home over several centuries.

Divergent foraging strategies during incubation of an unusually wide-ranging seabird, the Murphy's petrel.

Divergent foraging strategies may emerge within a population due to a combination of physiological and environmental factors; yet to persist, neither strategy should offer a consistent selective advantage over the alternative in the long term. Murphy's petrels Pterodroma ultima from Henderson Island (24°20'S, 128°20'W) in the South Pacific Ocean are highly vagile, and exhibit two distinct foraging trip types during incubation; similar proportions of birds undertake either looping trips around the South Pacific Gyre to waters off Peru (hereafter "East") or trips south-west of the colony towards the Subtropical Front ("South") (mean maximum ranges of c. 3800 or 2000 km from the colony, respectively). However, the relative benefits of the distinct trip types remain unclear. Through tracking birds with GPS and salt-water immersion loggers in 2015, the fine-scale foraging behaviour was examined for East (trip durations: 14.1-19.8 days, maximum ranges 2387-4823 km) and South trips (12.9-25.8 days, 1565-1991 km). Data on behaviour classified from GPS tracks, the number of wet bouts per hour (a proxy for landing rates) and wind speeds, were used to distinguish two distinct foraging modes: birds on East trips spent more time in directed movement, whereas those on South trips spent a greater proportion of time in area-restricted search (ARS) behaviour. East trips were associated with higher overall mass gain, and wet bouts occurred in equal proportions during directed movement and ARS behaviour. This suggests that in unproductive marine environments, it may be more profitable to maximise area covered to increase the chances of encountering prey. Analysis of lower-resolution geolocator data (collected from 2011 to 2014) indicated that individuals were largely consistent in trip type between years. Since birds that conducted East trips were 19% lighter on departure from the colony and experienced more frequent tailwinds on foraging trips, we speculate that these birds may benefit from reduced movement costs, whilst also experiencing reduced competition for foraging opportunities.

Globally important islands where eradicating invasive mammals will benefit highly threatened vertebrates.

Invasive alien species are a major threat to native insular species. Eradicating invasive mammals from islands is a feasible and proven approach to prevent biodiversity loss. We developed a conceptual framework to identify globally important islands for invasive mammal eradications to prevent imminent extinctions of highly threatened species using biogeographic and technical factors, plus a novel approach to consider socio-political feasibility. We applied this framework using a comprehensive dataset describing the distribution of 1,184 highly threatened native vertebrate species (i.e. those listed as Critically Endangered or Endangered on the IUCN Red List) and 184 non-native mammals on 1,279 islands worldwide. Based on extinction risk, irreplaceability, severity of impact from invasive species, and technical feasibility of eradication, we identified and ranked 292 of the most important islands where eradicating invasive mammals would benefit highly threatened vertebrates. When socio-political feasibility was considered, we identified 169 of these islands where eradication planning or operation could be initiated by 2020 or 2030 and would improve the survival prospects of 9.4% of the Earth's most highly threatened terrestrial insular vertebrates (111 of 1,184 species). Of these, 107 islands were in 34 countries and territories and could have eradication projects initiated by 2020. Concentrating efforts to eradicate invasive mammals on these 107 islands would benefit 151 populations of 80 highly threatened vertebrates and make a major contribution towards achieving global conservation targets adopted by the world's nations.

Rates of movement of threatened bird species between IUCN red list categories and toward extinction.

In recent centuries bird species have been deteriorating in status and becoming extinct at a rate that may be 2-3 orders of magnitude higher than in prehuman times. We examined extinction rates of bird species designated critically endangered in 1994 and the rate at which species have moved through the IUCN (World Conservation Union) Red List categories of extinction risk globally for the period 1988-2004 and regionally in Australia from 1750 to 2000. For Australia we drew on historical accounts of the extent and condition of species habitats, spread of invasive species, and changes in sighting frequencies. These data sets permitted comparison of observed rates of movement through the IUCN Red List categories with novel predictions based on the IUCN Red List criterion E, which relates to explicit extinction probabilities determined, for example, by population viability analysis. The comparison also tested whether species listed on the basis of other criteria face a similar probability of moving to a higher threat category as those listed under criterion E. For the rate at which species moved from vulnerable to endangered, there was a good match between observations and predictions, both worldwide and in Australia. Nevertheless, species have become extinct at a rate that, although historically high, is 2 (Australia) to 10 (globally) times lower than predicted. Although the extinction probability associated with the critically endangered category may be too high, the shortfall in realized extinctions can also be attributed to the beneficial impact of conservation intervention. These efforts may have reduced the number of global extinctions from 19 to 3 and substantially slowed the extinction trajectory of 33 additional critically endangered species. Our results suggest that current conservation action benefits species on the brink of extinction, but is less targeted at or has less effect on moderately threatened species.

Rat eradication comes within a whisker! A case study of a failed project from the South Pacific.

To enhance their conservation value, several hundred islands worldwide have been cleared of invasive alien rats, Rattus spp. One of the largest projects yet undertaken was on 43 km(2) Henderson Island in the Pitcairn group, South Pacific, in August 2011. Following massive immediate mortality, a single R. exulans was observed in March 2012 and, subsequently, rat numbers have recovered. The survivors show no sign of resistance to the toxicant used, brodifacoum. Using pre- and post-operation rat tissue samples from Henderson, plus samples from around the Pacific, we exclude re-introduction as the source of continued rat presence. Microsatellite analysis of 18 loci enabled comparison of genetic diversity of Henderson rats before and after the bait drop. The fall in diversity measured by allele frequency change indicated that the bottleneck (N e) through which the breeding population passed was probably around 50 individuals, representing a census population of about 60-80 animals. This is the first failed project that has estimated how close it was to success.

The food consumption of the world's seabirds.

Improving knowledge of the population sizes of all the world's seabirds allows this provisional estimate of their annual food consumption. Knowing the body mass and energy density of prey it is possible to employ standard metabolic equations to estimate daily and hence annual consumption of a seabird. Using this approach, and assuming that, at the least, there are three individuals alive for every recorded breeding pair, the annual food consumption of all the world's seabirds is 70 million tonnes (Mt: 95% CI 55.9-83.7 Mt). The total obviously increases if more liberal assumptions are made about the number of individuals alive per breeding pair. The principal consumers are mostly high-latitude, often pelagic species-penguins, petrels and auks. The total is similar to the global fisheries landings, currently ca. 80 Mt.

Unravelling dispersal patterns in an expanding population of a highly mobile seabird, the northern fulmar (Fulmarus glacialis).

The northern fulmar (Fulmarus glacialis) is an abundant seabird whose Northeast Atlantic population has expanded dramatically over the past 100 years. Archaeological evidence suggests that Iceland and St Kilda were the ancestral populations from which essentially all other colonies in the region were derived. We collected samples from seven breeding colonies around the North Atlantic and used mitochondrial DNA analysis to ask whether population structure was present and, if so, where there was evidence about which colony was the dominant source population. Our data reveal a pattern consistent with isolation by distance, suggesting that, even though capable of flying great distances, most birds return to breed either at their own or neighbouring colonies. Interestingly, although most colonizers appear to have come originally from Iceland, our analysis also identifies St Kilda as a possible source. However, this secondary pattern appears to be largely an artefact, and can be attributed to the low haplotype diversity on St Kilda which yields a much clearer isolation by distance signal than that generated by birds dispersing from Iceland, where haplotype diversity is extremely high. Consequently, we urge caution when interpreting patterns in which populations vary greatly in the genetic diversity they harbour.

Cytochrome b divergence between avian sister species is linked to generation length and body mass.

It is increasingly realised that the molecular clock does not tick at a constant rate. Rather, mitochondrial mutation rates are influenced by factors such as generation length and body mass. This has implications for the use of genetic data in species delimitation. It could be that speciation, as recognised by avian taxonomists, is associated with a certain minimum genetic distance between sister taxa, in which case we would predict no difference in the cytochrome b divergence of sister taxa according to the species' body size or generation time. Alternatively, if what taxonomists recognise as speciation has tended to be associated with the passage of a minimum amount of time since divergence, then there might be less genetic divergence between sister taxa with slower mutation rates, namely those that are heavier and/or with longer generation times. After excluding non-flying species, we analysed a database of over 600 avian sister species pairs, and found that species pairs with longer generation lengths (which tend to be the larger species) showed less cytochrome b divergence. This finding cautions against using any simple unitary criterion of genetic divergence to delimit species.

Vertical transmission of feather lice between adult blackbirds Turdus merula and their nestlings: a lousy perspective.

There is limited information about the natural history of the transmission of feather lice (Phthiraptera) from parent birds to their young. This article therefore examines the transmission of 4 species of feather lice from parent blackbirds to their nestlings in an English population, and addresses questions formulated from the perspective of the lice. The lice that disperse onto the several young in the nest were mostly found on the larger chicks, those with higher survival prospects. The lice dispersing to chicks were overwhelmingly nymphs, which cannot be sexed morphologically, and so the prediction that the adult lice dispersing would be disproportionately female, potential founders of a new population, was only supported for the most numerous species, Brueelia merulensis. There was no evidence that louse dispersal to chicks was density dependent and more likely when the parents were more heavily infested. Finally, I predicted that lice might aggregate on female blackbirds, which undertake more brooding, to increase their chance of transmission to nestlings. For 1 louse species, B. merulensis, prevalence, but not louse intensity, was higher on female than male blackbirds. For 2 other louse species, Philopterus turdi and Menacanthus eurysternus, no differences between male and female blackbirds were detected.

The eye of a procellariiform seabird, the Manx shearwater, Puffinus puffinus: visual fields and optical structure.

The Manx shearwater, Puffinus puffinus, is a pelagic sea bird which feeds from the surface of the sea and by shallow surface and plunge dives. Visits to breeding colonies are made at night. The mononuclear retinal field of the Manx shearwater eye is 148 degrees wide and is asymmetric with respect to the optic axis. The nasal and temporal hemi-fields equal 65 and 83 degrees, respectively. The binocular field is long and narrow, and the central placement of the bill suggests that vision is used to guide the bill position during foraging. A schematic model of the shearwater eye's optical system is presented, together with reanalysed data on the optical structure in the eye of the pigeon, Columba livia. The eyes of these two species are nearly identical in axial length and overall shape, but they are of quite different optical design. The shearwater eye has a shorter focal length and higher maximum image brightness, and the ratio of corneal:lens refractive power equals 0.4 and 1.6 in pigeon and shearwater eyes, respectively. In Manx shearwater eyes, the ratio of focal length:axial length and the ratio of lens refractive power:corneal refractive power may be correlated with a nocturnal life style. It is not clear whether the relatively low refractive power of the cornea is best regarded as a feature correlated with an amphibious life style or whether it is a consequence of adaptations for nocturnal activity.

Novel area serving binocular vision in the retinae of procellariiform seabirds.

Procellariiforms are pelagic seabirds which fly close to the sea surface and feed either by taking items from the surface or by shallow diving. The retinal ganglion cells in five species (Manx shearwater, Puffinus puffinus, Kerguelen petrel, Pterodroma brevirostris, great shearwater, Puffinus gravis, broad-billed prion, Pachyptila vittata, and common diving petrel, Pelecanoides urinatrix) were examined by Nissl staining and also by silver staining in the case of the common diving petrel. In all five species, a well-defined region in the dorsotemporal retina, close to the ora, was identified. This region is characterized by the presence of ganglion cells which are both regularly arrayed and larger than those found in the rest of the retina. These cells also have a large dendritic field of sparsely branched dendrites with much dendritic overlap between cells, thick axons, and dendrites confined to the proximal inner plexiform layer. Morphologically, they appear similar to the alpha cells of the retina in cats. It is suggested that the region containing these cells should be regarded as a retinal area, and the name area giganto cellularis is proposed. In the Manx shearwater, it is found that this novel area projects visually into the binocular field below the bill. Unlike previously described areas in avian retinae, it seems that this novel area is not concerned with high spatial resolution. It may function in the detection of objects on the sea surface and/or be concerned with the detection of the actual sea surface as a bird flies low over it.