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Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.

Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully (Gobiomorphus cotidianus), from 5 to 90 m depth in four South Island lakes to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna. Les gradients de profondeur dans les lacs sont souvent des facteurs cles de divergence des populations et de speciation chez les poissons. La Nouvelle-Zelande compte de nombreux lacs profonds, mais aucun poisson specialiste des profondeurs, ni cas de speciation intralacustre. Nous avons echantillonne un poisson benthique indigene, Gobiomorphus cotidianus, a des profondeurs allant de 5 a 90 m dans quatre lacs de l'lle du Sud, afin de verifier s'il presentait une differenciation morphologique, ecologique ou genetique associee a la profondeur. Les poissons preleves a de plus grandes profondeurs etaient uniformement caracterises par des corps plus etroits, alors que d'autres caracteres morphologiques presentaient des relations variables avec la profondeur. Les valeurs d'isotopes stables de carbone et d'azote des poissons augmentaient avec la profondeur, suivant generalement les tendances isotopiques en fonction de la profondeur de proies invertebrees benthiques. Le genotypage par sequenqage a fait ressortir une certaine differenciation a l'echelle du genome entre deux des lacs, mais aucun indice de structuration genetique a l'interieur d'un meme lac le long de gradients de profondeur. Ces resultats indiquent que des G. cotidianus sont tour a tour associes a des habitats de faible profondeur et de plus grande profondeur au cours de leur vie, mais aucun indice d'une progression vers une divergence genetique a l'interieur d'un meme n'a ete releve. L'apparente absence de divergence genetique intralacustre chez des poissons neo-zelandais pourrait s'expliquer par une combinaison de facteurs environnementaux et de contraintes intrinseques a la faune de poissons d'eau douce derives de poissons marins de Nouvelle-Zelande. [Traduit par la Redaction], Introduction Environmental gradients are important regulators of biodiversity, contributing to community turnover, population structure, and long-term evolutionary diversification (Doebeli and Dieckmann 2003; Seehausen et al. 2008). Water depth is a [...]

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time‐calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts. [ABSTRACT FROM AUTHOR]

Fertility‐targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression and results from mouse knockout models. This framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non‐drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. In addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives. [ABSTRACT FROM AUTHOR]

Recent genomic evidence suggest that kea (Nestor notabilis) have a non-functional RH2 opsin gene potentially leading to impaired vision in the green region of the electromagnetic spectrum. In New Zealand, it is standard procedure to add green dye to aerial poison baits used in mammalian predator control operations to deter native birds from eating toxic bait. A visual deficiency could impact how kea perceive and interact with green-dyed baits and thus have unforeseen consequences for kea conservation. Here, we sequenced the partial RH2 gene of seven wild kea and re-analysed the kea genome raw sequencing data of the RH2 locus. We demonstrate that the reported premature stop codon is most likely an assembly artefact. An extended analysis of the published genomes of all three extant New Zealand parrots of the superfamily Strigopoidea confirms that the RH2 gene is functional in this entire group. [ABSTRACT FROM AUTHOR]

Aim: Genotyping‐by‐sequencing (GBS) and similar reduced‐representation sequencing methods, such as restriction site‐associated DNA sequencing (RADseq), have been revolutionary for genetic analyses in biogeography. However, navigating the many different methodological and analytical approaches and numerous sources of potential error can be overwhelming. We provide an overview of key considerations for biogeographical research using GBS, from sample design through data filtering to the sharing of data, which should particularly assist new users. Taxon: All taxa. Location: Worldwide. Methods: We review recent advances for GBS and compare differences among GBS methods and analytical approaches. We highlight the concerns most relevant for biogeographical research, and emphasise practical limitations for studies on non‐model organisms. Results: GBS methods vary substantially and recent literature demonstrates the need for careful study design and data filtering relevant to the study organism and hypothesis under investigation. Biogeographical research using non‐model organisms or long‐term sampling are likely to face some practical limitations compared to ideal GBS study designs. The methodological information recorded in published manuscripts often varies. We outline a general framework for planning and undertaking biogeographical research using GBS. Main conclusions GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow—across sampling, library preparation and sequencing, identifying and filtering samples and loci, biogeographical analyses, and sharing data—is crucial for improving scientific reproducibility and compatibility among GBS datasets. This review outlines ways to improve and simplify GBS research, thereby enhancing our capacity to use genomic data to address broad‐scale biogeographical questions. [ABSTRACT FROM AUTHOR]