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

Using the unique spectral signature of guano to identify unknown seabird colonies

Despite the threats faced by seabirds in both terrestrial and marine habitats, even basic knowledge of the locations of colonies, population sizes and trends is lacking for many remote areas of the world. Recent studies have shown that the guano of Adélie penguins can be identified from Landsat Enhanced Thematic Mapper (ETM) imagery and used to map colonies on coasts around continental Antarctica. Our study highlights a new technique based on the unique spectral signature of guano that can be used to discriminate seabird colonies from background geology and vegetation in a wider range of natural environments, including the vegetated and zoologically-diverse region of the Antarctic Peninsula; moreover, the method was effective for all densely colonial, surface-nesting seabirds. Using Landsat ETM imagery, we correctly identified all known seabird colonies of over 50 pairs in the area of Marguerite Bay. Almost all other areas with a similar spectral signature that were outside known breeding areas were single pixels that were readily distinguishable from genuine colonies. If these were excluded, only 4.1% of pixels appeared to represent unknown breeding or roosting sites, and warrant further investigation. The spatial extent of the guano provided a general guide to the number of individuals present, but further work would be required to determine the accuracy of this method for estimating population size. Spectral profiles of guano collected by satellite and hand-held spectrometers were compared with available data in spectral libraries and did not match with any known geological profile. There may also be potential for discriminating colonies of different species that differ in phenology and show seasonal changes in diet by the carefully-timed acquisition of suitable satellite imagery. We conclude that the remotely-sensed guano signature is a good indicator of the location of seabird breeding or roosting sites, with potentially wide application to other areas of the world

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

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

Abstract: 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

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 Darwin Initiative funded much of the RSPB’s work on Henderson Island and therefore sample collection and analysis, the latter also supported by the Sir Peter Scott Commemorative Expedition to the Pitcairn Islands

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

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

Assessment of genotype imputation methods

Several methods have been proposed to impute genotypes at untyped markers using observed genotypes and genetic data from a reference panel. We used the Genetic Analysis Workshop 16 rheumatoid arthritis case-control dataset to compare the performance of four of these imputation methods: IMPUTE, MACH, PLINK, and fastPHASE. We compared the methods' imputation error rates and performance of association tests using the imputed data, in the context of imputing completely untyped markers as well as imputing missing genotypes to combine two datasets genotyped at different sets of markers. As expected, all methods performed better for single-nucleotide polymorphisms (SNPs) in high linkage disequilibrium with genotyped SNPs. However, MACH and IMPUTE generated lower imputation error rates than fastPHASE and PLINK. Association tests based on allele "dosage" from MACH and tests based on the posterior probabilities from IMPUTE provided results closest to those based on complete data. However, in both situations, none of the imputation-based tests provide the same level of evidence of association as the complete data at SNPs strongly associated with disease

Research engagement of health sciences librarians: a survey of research-related activities and attitudes

Introduction: The extent to which health sciences librarians are engaged in research is a little-studied question. This study assesses the research activities and attitudes of Medical Library Association (MLA) members, including the influence of work affiliation. Methods: An online survey was designed using a combination of multiple-choice and open-ended questions and distributed to MLA members. Responses were analyzed using descriptive statistics, content analysis, and significance testing. The authors used statistical tools and categorized openended question topics by the constant comparative method, also applying the broad subject categories used in a prior study. Pearson’s chi-square analysis was performed on responses to determine significant differences among respondents employed in three different institutional environments. Results: Analysis showed that 79% of respondents read research articles at least once a month; 58% applied published research studies to practice; 44% had conducted research; 62% reported acting on research had enhanced their libraries; 38% had presented findings; and 34% had authored research articles. Hospital librarians were significantly less likely than academic librarians to have participated in research activities. Highly ranked research benefits, barriers, and competencies of health sciences librarians are described. Conclusions: Findings indicate that health sciences librarians are actively engaged in research activities. Practice implications for practitioners, publishers, and stakeholders are discussed. Results suggest that practitioners can use published research results and results from their own research to affect practice decisions and improve services. Future studies are needed to confirm and extend these findings, including the need for intervention studies to increase research and writing productivity

The Spitzer c2d Survey of Weak-line T Tauri Stars II: New Constraints on the Timescale for Planet Building

One of the central goals of the Spitzer Legacy Project ``From Molecular Cores to Planet-forming Disks'' (c2d) is to determine the frequency of remnant circumstellar disks around weak-line T Tauri stars (wTTs) and to study the properties and evolutionary status of these disks. Here we present a census of disks for a sample of over 230 spectroscopically identified wTTs located in the c2d IRAC (3.6, 4.5, 4.8, and 8.0 um) and MIPS (24 um) maps of the Ophiuchus, Lupus, and Perseus Molecular Clouds. We find that ~20% of the wTTs in a magnitude limited subsample have noticeable IR-excesses at IRAC wavelengths indicating the presence of a circumstellar disk. The disk frequencies we find in these 3 regions are ~3-6 times larger than that recently found for a sample of 83 relatively isolated wTTs located, for the most part, outside the highest extinction regions covered by the c2d IRAC and MIPS maps. The disk fractions we find are more consistent with those obtained in recent Spitzer studies of wTTs in young clusters such as IC 348 and Tr 37. From their location in the H-R diagram, we find that, in our sample, the wTTs with excesses are among the younger part of the age distribution. Still, up to ~50% of the apparently youngest stars in the sample show no evidence of IR excess, suggesting that the circumstellar disks of a sizable fraction of pre-main-sequence stars dissipate in a timescale of ~1 Myr. We also find that none of the stars in our sample apparently older than ~10 Myrs have detectable circumstellar disks at wavelengths < 24 um. Also, we find that the wTTs disks in our sample exhibit a wide range of properties (SED morphology, inner radius, L_DISK/L*, etc) which bridge the gaps observed between the cTTs and the debris disk regimes.Comment: 54 pages, 13 figures, Accepted by Ap