Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
Browse
38 results
Search Results
Item Metadata preservation and stewardship for genomic data is possible, but must happen now(2022-09-15) Crandall ED; Toczydlowski RH; Liggins L; Holmes AE; Ghoojaei M; Gaither MR; Wham BE; Pritt AL; Noble C; Anderson TJ; Barton RL; Berg JT; Beskid SG; Delgado A; Farrell E; Himmelsbach N; Queeno SR; Trinh T; Weyand C; Bentley A; Deck J; Riginos C; Bradburd GS; Toonen RJItem Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific(Elsevier Inc, 2022-11) Samayoa AP; Struthers CD; Trnski T; Roberts CD; Liggins LRemote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.Item Importance of timely metadata curation to the global surveillance of genetic diversity(Wiley Periodicals LLC on behalf of Society for Conservation Biology, 2023-08) Crandall ED; Toczydlowski RH; Liggins L; Holmes AE; Ghoojaei M; Gaither MR; Wham BE; Pritt AL; Noble C; Anderson TJ; Barton RL; Berg JT; Beskid SG; Delgado A; Farrell E; Himmelsbach N; Queeno SR; Trinh T; Weyand C; Bentley A; Deck J; Riginos C; Bradburd GS; Toonen RJGenetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. Importancia de la curación oportuna de metadatos para la vigilancia mundial de ladiversidad genéticaResumen:La diversidad genética intraespecífica representa un nivel fundamental, pero ala vez subvalorado de la biodiversidad. La diversidad genética puede indicar la resilienciade una especie ante el clima cambiante, por lo que su medición es relevante para muchosobjetivos de la política de conservación mundial y nacional. Muchos estudios producenuna gran cantidad de datos sobre la diversidad a nivel genético de las poblaciones silvestres,aunque la mayoría (87%) no incluye los metadatos espaciales y temporales asociados paraque sean reutilizados en los programas de monitoreo o para reconocer la soberanía de lasnaciones o los pueblos indígenas. Realizamos un “datatón” distribuido para cuantificar ladisponibilidad de estos metadatos faltantes y para probar la hipótesis que supone que estadisponibilidad se deteriora con el tiempo. También trabajamos para reparar los metadatosfaltantes al extraerlos de los artículos asociados publicados, los repositorios en línea yla comunicación directa con los autores. Iniciamos con 838 candidatos de conjuntos dedatos genómicos (representación reducida y genoma completo) tomados de la colabo-ración internacional para la base de datos de secuencias de nucleótidos y determinamosque 561 incluían en su mayoría muestras tomadas de poblaciones silvestres. Restauramoscon éxito los metadatos espaciotemporales en el 78% de estos 561 conjuntos de datos (n=440 conjuntos de datos con información sobre 45,105 individuos de 762 especies en 17filos). El análisis de los artículos y los repositorios virtuales fue mucho más productivo quecontactar a los 351 autores, quienes tuvieron un 45% de respuesta a nuestros correos. Engeneral, el 23% de nuestras consultas descubrieron metadatos útiles. La probabilidad derecuperar metadatos espaciotemporales declinó de manera significativa conforme incre-mentó la antigüedad del conjunto de datos. Hubo una disminución anual del 13.5% enlos metadatos asociados con los artículos publicados y los repositorios virtuales y hastauna disminución anual del 22% en los metadatos que sólo estaban disponibles mediante lacomunicación con los autores. Este rápido deterioro en la disponibilidad de los metadatos,duplicado en estudios de otros tipos de datos biológicos, debería motivar la pronta actual-ización de las políticas del intercambio de datos y las prácticas de los investigadores paraasegurar que en las ciencias de la conservación no se pierda para siempre el contexto valiosoproporcionado por los metadatos.Item Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD(Springer Nature BV, 2021-08) Laikre L; Hohenlohe PA; Allendorf FW; Bertola LD; Breed MF; Bruford MW; Funk WC; Gajardo G; González-Rodríguez A; Grueber CE; Hedrick PW; Heuertz M; Hunter ME; Johannesson K; Liggins L; MacDonald AJ; Mergeay J; Moharrek F; O’Brien D; Ogden R; Orozco-terWengel P; Palma-Silva C; Pierson J; Paz-Vinas I; Russo I-RM; Ryman N; Segelbacher G; Sjögren-Gulve P; Waits LP; Vernesi C; Hoban SItem Comparative phylogeography in the genomic age: Opportunities and challenges(John Wiley and Sons Ltd, 2022-12) McGaughran A; Liggins L; Marske KA; Dawson MN; Schiebelhut LM; Lavery SD; Knowles LL; Moritz C; Riginos C; Byrne MAim: We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory; and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. Location: World-wide. Taxon: All. Methods: We review the literature to discuss the future of CP - particularly examining CP insights enabled by genomics that may not be possible for single species and/or few molecular markers. We focus on how geography and species' natural histories interact to yield congruent and incongruent patterns of neutral and adaptive processes in the context of both historical and recent rapid evolution. We also consider how CP genomic data are being stored, accessed, and shared. Results: With the widespread availability of genomic data, the shift from a single- to a multi-locus perspective is resulting in detailed historical inferences and an improved statistical rigour in phylogeography. However, the time and effort required for collecting co-distributed species and accruing species-specific ecological knowledge continue to be limiting factors. Bioinformatic skills and user-friendly analytical tools, alongside the computational infrastructure required for big data, can also be limiting. Main conclusions: Over the last ~35 years, there has been much progress in understanding how intraspecific genetic variation is geographically distributed. The next major steps in CP will be to incorporate evolutionary processes and community perspectives to account for patterns and responses among co-distributed species and across temporal scales, including those related to anthropogenic change. However, the full potential of CP will only be realised if we employ robust study designs within a sound comparative framework. We advocate that phylogeographers adopt such consistent approaches to enhance future comparisons to present-day findings.Item The future of molecular ecology in Aotearoa New Zealand: an early career perspective(Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2022-07-14) Liggins L; Arranz V; Braid HE; Carmelet-Rescan D; Elleouet J; Egorova E; Gemmell MR; Hills SFK; Holland LP; Koot EM; Lischka A; Maxwell KH; McCartney LJ; Nguyen HTT; Noble C; Olmedo Rojas P; Parvizi E; Pearman WS; Sweatman JAN; Kaihoro TR; Walton K; Aguirre JD; Stewart LC; Moss SThe skills, insights, and genetic data gathered by molecular ecologists are pivotal to addressing many contemporary biodiversity, environmental, cultural, and societal challenges. Concurrently, the field of molecular ecology is being revolutionised by rapid technological development and diversification in the scope of its applications. Hence, it is timely to review the future opportunities of molecular ecological research in Aotearoa New Zealand, and to reconcile them with philosophies of open science and the implications for Indigenous data sovereignty and benefit sharing. Future molecular ecologists need to be interdisciplinary, equipped to embrace innovation, and informed about the broader societal relevance of their research, as well as advocates of best practice. Here, we present an ideal future for molecular ecology in Aotearoa, based on the perspectives of 23 early career researchers from tertiary institutions, Crown Research Institutes, research consultancies, and government agencies. Our article provides: a guide for molecular ecologists embarking on genetic research in Aotearoa, and a primer for individuals in a position to support early career molecular ecologists in Aotearoa. We outline our goals and highlight specific considerations–for molecular ecology and the scientific community in Aotearoa–based on our own experience and aspirations, and invite other researchers to join this dialogue.Item Regional patterns of mtDNA diversity in Styela plicata, an invasive ascidian, from Australian and New Zealand marinas(CSIRO PUBLISHING, 7/03/2013) Torkkola J; Riginos C; Liggins LThe ascidian Styela plicata is abundant in harbours and marinas worldwide and has likely reached this distribution via human-mediated dispersal. Previous worldwide surveys based on mitochondrial cytochrome oxidase one (COI) sequences have described two divergent clades, showing overlapping distributions and geographically widespread haplotypes. These patterns are consistent with recent mixing among genetically differentiated groups arising from multiple introductions from historically distinct sources. In contrast, a study of Australian S. plicata using nuclear markers found that population differentiation along the eastern coast related to geographic distance and no evidence for admixture between previously isolated genetic groups. We re-examined the genetic patterns of Australian S. plicata populations using mtDNA (CO1) to place their genetic patterns within a global context, and we examined New Zealand populations for the first time. We found that the haplotypic compositions of Australian and New Zealand populations are largely representative of other worldwide populations. The New Zealand populations, however, exhibited reduced diversity, being potentially indicative of a severely bottlenecked colonisation event. In contrast to results from nuclear markers, population differentiation of mtDNA among Australian S. plicata was unrelated to geographic distance. The discrepancy between markers is likely to be a consequence of non-equilibrium population genetic processes that typify non-indigenous species. © 2013 CSIRO.Item Evaluating edge-of-range genetic patterns for tropical echinoderms, Acanthaster planci and Tripneustes gratilla, of the Kermadec Islands, southwest Pacific(ROSENSTIEL SCH MAR ATMOS SCI, 1/01/2014) Liggins L; Gleeson L; Riginos CEdge-of-range populations are often typified by patterns of low genetic diversity and high genetic differentiation relative to populations within the core of a species range. The "core-periphery hypothesis," also known as the "central-marginal hypothesis," predicts that these genetic patterns at the edge-of-range are a consequence of reduced population size and connectivity toward a species range periphery. It is unclear, however, how these expectations relate to high dispersal marine species that can conceivably maintain high abundance and high connectivity at their range edge. In the present study, we characterize the genetic patterns of two tropical echinoderm populations in the Kermadec Islands, the edge of their southwest Pacific range, and compare these genetic patterns to those from populations throughout their east Indian and Pacific ranges. We find that the populations of both Acanthaster planci (Linnaeus, 1758) and Tripneustes gratilla (Linnaeus, 1758) are represented by a single haplotype at the Kermadec Islands (based on mitochondrial cytochrome oxidase C subunit I). Such low genetic diversity concurs with the expectations of the "core-periphery hypothesis." Furthermore, the haplotypic composition of both populations suggests they have been founded by a small number of colonists with little subsequent immigration. Thus, local reproduction and self-recruitment appear to maintain these populations despite the ecologically marginal conditions of the Kermadec Islands for these tropical species. Understanding rates of self-recruitment vs reliance on connectivity with populations outside of the Kermadec Islands has implications for the persistence of these populations and range stability of these echinoderm species.© 2014 Rosenstiel School of Marine and Atmospheric Science of the University of Miami.Item The short-lived neon damsel Pomacentrus coelestis: implications for population dynamics.(2017-05) Kingsford MJ; O'Callaghan MD; Liggins L; Gerlach GDaily increments of Pomacentrus coelestis, an abundant and well-studied fish, were validated for the life of the fish and depending on the location, age-maxima were estimated to be 127-160 days on reefs separated by tens to hundreds of kilometres on the Great Barrier Reef. This contrasts with congeners and other damselfishes that live for 5 years or more. Otoliths of P. coelestis were thinner and had different patterns of banding when compared with relatively long-lived congeners. It is suggested that banding patterns in P. coelestis may be related to patterns of maturation and spawning. The consequences of a short life would have a great influence on the population dynamics of this widespread species. Further, the demographics and habitat preferences of this species suggest rapid colonization and establishment of breeding populations that would quickly change the relative abundance of sympatric fishes.Item The population genetic structure of the urchin Centrostephanus rodgersii in New Zealand with links to Australia(1/09/2021) Thomas LJ; Liggins L; Banks SC; Beheregaray LB; Liddy M; McCulloch GA; Waters JM; Carter L; Byrne M; Cumming RA; Lamare MDThe diadematid sea urchin Centrostephanus rodgersii occurs in Australia and New Zealand and has undergone recent southward range extension in Australia as a result of regional warming. Clarifying the population genetic structure of this species across its New Zealand range would allow a better understanding of recent and future mechanisms driving range changes in the species. Here, we use microsatellite DNA data to assess connectivity and genetic structure in 385 individuals from 14 locations across the Australian and New Zealand ranges of the species. We detected substantial genetic differentiation among C. rodgersii populations from Australia and New Zealand. However, the population from Port Stephens (located north of Newcastle), Australia, strongly clustered with New Zealand samples. This suggests that the New Zealand populations recently originated from this area, likely via larval transport in the Tasman Front flow that arises in this region. The weak population genetic structure and relatively low genetic diversity detected in New Zealand (global Fst = 0.0021) relative to Australia (global Fst = 0.0339) is consistent with the former population’s inferred history of recent climate-driven expansion. Population-level inbreeding is low in most populations, but were higher in New Zealand (global Fis = 0.0833) than in Australia (global Fis = 0.0202), suggesting that self-recruitment is playing an increasingly important role in the New Zealand region. Our results suggest that C. rodgersii is likely to spread southwards as ocean temperatures increase; therefore, it is crucial that researchers develop a clearer understanding of how New Zealand ecosystems will be reshaped by this species (and others) under climate change.