ORCID Profile
0000-0002-2882-7996
Current Organisation
NIWA - The National Institute of Water and Atmospheric Research Ltd.
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Publisher: Wiley
Date: 07-11-2022
DOI: 10.1111/JBI.14516
Abstract: 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 s le design through data filtering to the sharing of data, which should particularly assist new users. All taxa. Worldwide. 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. 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 s ling 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. GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow—across s ling, library preparation and sequencing, identifying and filtering s les 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.
Publisher: The Royal Society
Date: 05-2023
Abstract: Detached buoyant kelp can disperse thousands of kilometres at sea and can colonize newly available shores in the wake of disturbances that wipe out competitors. Localized earthquake uplift can cause extirpation of intertidal kelp populations followed by recolonization. Sources of recolonizing kelp can be detectable in genomic structure of contemporary populations. Our field observations combined with LiDAR mapping identified a previously unrecognized zone of uplifted rocky coastline in a region that is slowly subsiding. Intertidal kelp ( Durvillaea antarctica ) on the uplifted section of coast is genetically distinctive from nearby populations, with genomic signatures most similar to that of kelp 300 km to the south. Genetic ergence between these locations suggests reproductive isolation for thousands of years. Combined geological and genetic data suggest that this uplift event occurred during one of four major earthquakes between 6000 and 2000 years ago, with one of the younger events most likely. Extirpation of the pre-existing kelp required sudden uplift of approximately 2 metres, precluding several small incremental uplift events. Our results show the power of integrating biological (genomic) analyses with geological data to understand ancient geological processes and their ecological impacts.
Publisher: Wiley
Date: 21-06-2022
DOI: 10.1111/MEC.16535
Abstract: Large‐scale disturbance events have the potential to drastically reshape bio ersity patterns. Notably, newly vacant habitat space cleared by disturbance can be colonized by multiple lineages, which can lead to the evolution of distinct spatial “sectors” of genetic ersity within a species. We test for disturbance‐driven sectoring of genetic ersity in intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot, following the high‐magnitude 1855 Wairarapa earthquake in New Zealand. Specifically, we use genotyping‐by‐sequencing (GBS) to analyse fine‐scale population structure across the uplift zone and apply machine learning to assess the fit of alternative recolonizaton models. Our analysis reveals that specimens from the uplift zone carry distinctive genomic signatures potentially linked to post‐earthquake recolonization processes. Specifically, our analysis identifies two parapatric spatial‐genomic sectors of D. antarctica at Turakirae Head, which experienced the most dramatic uplift. Based on phylogeographical modelling, we infer that bull kelp in the Wellington region was probably a source for recolonization of the heavily uplifted Turakirae Head coastline, via two parallel, eastward recolonization events. By identifying multiple parapatric genotypic sectors within a recently recolonized coastal region, the current study provides support for the hypothesis that competing lineage expansions can generate striking spatial structuring of genetic ersity, even in highly dispersive taxa.
Publisher: Wiley
Date: 26-05-2021
DOI: 10.1111/JPY.13179
Abstract: Understanding the forces that shape species distributions is increasingly important in a fast‐changing world. Although major disturbance events can adversely affect natural populations, they can also present new opportunities, for ex le by opening up habitat for colonization by other lineages. Following extensive geographic s ling, we use genomic data to infer a range extension following disturbance for an ecologically important intertidal macroalgal species. Specifically, we genotyped 288 southern bull kelp ( Durvillaea ) plants from 28 localities across central New Zealand. All specimens from the North Island were expected to be D. antarctica , but unexpectedly 10 s les from four sites were identified as D. poha . Extensive s ling from the northern South Island (105 s les at five locations) confirmed the absence of D. poha north of the Kaikōura Peninsula. The North Island specimens of D. poha therefore reveal a biogeographic disjunction, some 150 km northeast of the nearest (South Island) population of this species. Based on strong geographic correspondence between these North Island s les and historic disturbance, we infer that tectonic upheaval, particularly earthquake‐generated landslides, likely extirpated local D. antarctica and created an opportunity for a northward range expansion event by D. poha . Close phylogenomic relationships between this new North Island population and South Island s les support a geologically recent northward expansion, rather than a deeper evolutionary origin. These findings indicate the potential of large‐scale disturbances to facilitate sudden biogeographic range expansions, and they emphasize the ability of genomic analyses with fine‐scale s ling to reveal long‐lasting signatures of past disturbance, dispersal, and colonization.
Location: New Zealand
Location: United Kingdom of Great Britain and Northern Ireland
Location: United States of America
No related grants have been discovered for Felix Vaux.