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Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous "losses" of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.

There have been numerous declines and extinctions of native fauna in Aotearoa New Zealand since human settlement. Against this background of loss there have been remarkable advances in conservation management, including the use of conservation translocations to reduce extinction risk and restore depauperate ecosystems. Here we review conservation translocations in Aotearoa New Zealand. Our review assembles knowledge from Aotearoa New Zealand's rich history of faunal translocations and describes six key considerations for successfully establishing translocated populations: (1) What values will be met by a translocation? (2) What is the natural and conservation history of the translocation candidate? (3) Does the release site habitat match that of the proposed source population, and if not, why is the release site considered appropriate and can management ameliorate differences? (4) Will dispersal be a problem? (5) Will genetic management be required and how realistic is it that this management will be implemented? (6) What do future developments mean for the management of translocated populations? We discourage a focus on any single element of translocation planning but rather encourage all people involved in translocations, particularly decision makers, to explicitly recognise that successful translocations typically have multiple, values-based objectives. We also support recommendations that the principles of good translocation decision-making are embedded in government policy. [ABSTRACT FROM AUTHOR]

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities. [ABSTRACT FROM AUTHOR]

Summary: Cook's Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand's North and South Islands. We found significant population genetic structure between the two extant Cook's Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook's Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook's Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only. [ABSTRACT FROM AUTHOR]

The Masked Booby is a highly vagile, pantropical seabird of which up to six subspecies have been recognised: S. d. dactylatra, S. d. californica, S. d. personata, S. d. melanops, S. d. bedouti and S. d. tasmani. The genetic distinction of several S. dactylatra colonies has been previously investigated, but this has not yet been conducted for the Bedout Island population in Western Australia, which has been considered by some to be part of a distinct subspecies. Suspected population decline on Bedout Island has renewed interest in determining the extent to which genetic novelty might be threatened. To answer this question, morphological and mitochondrial control region sequence variation were used to determine the distinction of the Bedout Island population. Whereas the morphological measures were equivocal, six haplotypes were identified from 31 individuals, none of which were shared by individuals previously sampled from the Indo-Pacific. The Bedout Island haplotypes were most closely related to other haplotypes found in a distinct Indian Ocean haplogroup, but haplotype frequencies at Bedout Island differed significantly from all other. This indicates that the Bedout Island population rarely exchanges mitochondrial genes with any of the other Masked Booby colonies presently studied, which may reflect dependence on local recruitment for its persistence. [ABSTRACT FROM AUTHOR]

We evaluate evidence that reducing mammalian predators benefits threatened and declining grasshoppers in the Mackenzie Basin, New Zealand. Long-term population trends of Sigaus minutus are investigated under three control regimes: high intensity, indirect control through prey reduction and no control. We then test whether predator control benefits conservation management of Brachaspis robustus by translocating wild-caught individuals to areas of moderate versus no predator control. A significant positive trend in S. minutus counts occurred under high intensity and indirect control, suggesting that mammalian predator control is beneficial. Differences in the decline of translocated B. robustus were observed between moderate and no predator control release sites but could not be unequivocally attributed to predator densities. We recommend replicated predator control studies be undertaken to develop a predator management strategy which will enable grasshopper recovery, and investigate the potential for meso-predator release and prey-switching under regimes that target specific mammals. [ABSTRACT FROM AUTHOR]