Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska

West, Catherine F.; Hofman, Courtney A.; Ebbert, Steve; Martin, John M.; Shirazi, Sabrina; Dunning, Samantha M.; Maldonado, Jesús E.

doi:10.1111/cobi.12865

Cited by 15 publications

(7 citation statements)

References 38 publications

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“…Given their role in energy metabolism, mitochondrial genes contribute to many adaptive and productive traits, and mitochondrial genome (mtGenome, or mitogenome) variation has been associated with phenotype, including hardiness, disease tolerance and resistance, milk production and fertility (Hiendleder et al 2008; see also MITOMAP.org in human). The definition of these specific diagnostic mutations has also improved phylogenetic information and due to their universal application, mitochondrial DNA markers are used for identification of species in food testing and archaeology (Kitpipit et al 2014;Okuma and Hellberg 2015;Kemp et al 2017;Nikitin et al 2017;West et al 2017). The population and evolutionary biology of mitochondrial DNA (mtDNA) sequences have been extensively studied in many species (Robins et al 2007;Tillmar et al 2013;Wani et al 2014;Sharma et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

Mustafa

Schwarzacher

Heslop-Harrison

2018

Mitochondrial DNA Part A

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The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.

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Section: Introductionmentioning

confidence: 99%

Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

Mustafa

Schwarzacher

Heslop-Harrison

2018

Mitochondrial DNA Part A

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“…Our study revealed an unexpected and dynamic pattern of extinction and recolonization for a small-bodied carnivore and illustrates that even federally protected or historically pristine ecosystems have experienced more community turnover than previously appreciated. Given that anthropogenic disturbances have driven the turnover of fauna globally, identifying the biogeographic origins of extant species and documenting historical community composition are critical guideposts to establishing restoration baselines 62 and effectively managing both native and non-native species 18 , 19 . Our work also illustrates the importance of continued regional monitoring, the relevancy of historical surveys, and the need for genetic techniques to establish robust and defensible conservation targets.…”

Section: Discussionmentioning

confidence: 99%

“…Consequently, extensive conservation programs have been established to protect island biodiversity 14 , 15 and to restore departed island communities 16 , 17 . Historical community composition, though, is not always clear, leading to ambiguous restoration baselines and the potential mismanagement of native and invasive species 18 , 19 .…”

Section: Introductionmentioning

confidence: 99%

Dynamic colonization history in a rediscovered Isle Royale carnivore

Manlick

Romanski

Pauli

2018

Sci Rep

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Island ecosystems are globally threatened, and efforts to restore historical communities are widespread. Such conservation efforts should be informed by accurate assessments of historical community composition to establish appropriate restoration targets. Isle Royale National Park is one of the most researched island ecosystems in the world, yet little is actually known about the biogeographic history of most Isle Royale taxa. To address this uncertainty and inform restoration targets, we determined the phylogeographic history of American martens (Martes americana), a species rediscovered on Isle Royale 76 years after presumed extirpation. We characterized the genetic composition of martens throughout the Great Lakes region using nuclear and mitochondrial markers, identified the source of Isle Royale martens using genetic structure analyses, and used demographic bottleneck tests to evaluate (eliminate redundancy of test). 3 competing colonization scenarios. Martens exhibited significant structure regionally, including a distinct Isle Royale cluster, but mitochondrial sequences revealed no monophyletic clades or evolutionarily significant units. Rather, martens were historically extirpated and recolonized Isle Royale from neighbouring Ontario, Canada in the late 20th century. These findings illustrate the underappreciated dynamics of island communities, underscore the importance of historical biogeography for establishing restoration baselines, and provide optimism for extirpated and declining Isle Royale vertebrates whose reintroductions have been widely debated.

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“…The limitations of such associations can lead to potential errors, therefore, failing to achieve valid interpretations, as has been illustrated elsewhere (e.g. Lyman, 2012;Valenzuela & Alcover, 2013a;West et al, 2016). Hence, translocation records need to be connected to tighter radiometric chronologies through direct dating of nonnative animal remains to establish the sequence and timing of introduction events.…”

Section: Introductionmentioning

confidence: 99%

New insights into the historical translocation of the Algerian hedgehog and pine marten throughout the Balearic Islands (Western Mediterranean): refining the radiocarbon‐based chronology

et al. 2021

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In this paper, we refine the colonisation timeframe of pine marten (Martes martes) and Algerian hedgehog (Atelerix algirus) to the Balearic Islands synthesising their occurrence records and providing an accurate chronology through new directly 14 C dated archaeological bone samples. The new dates are significantly earlier than previously reported finds; therefore, both cases currently represent the earliest records for the human-mediated translocation of these species in Europe. These new data not only provide further accurate resolution for previous historical translocation hypothesis but also expand the geographical scope throughout the archipelago. The sequence and timing of introduction events are embedded in different historical timeframes. The time of arrival of the pine marten is now established in the early Roman period, a period that supported a huge wave of introduced alien species into the Balearics. For the Algerian hedgehog, the new records further support the hypothesis that the Almohads were responsible for its introduction to these islands. Both examples illustrate how important it is to connect past translocation records to tighter radiometric chronologies through direct dating on bones of the implicated species.

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Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska

Cited by 15 publications

References 38 publications

Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

Dynamic colonization history in a rediscovered Isle Royale carnivore

New insights into the historical translocation of the Algerian hedgehog and pine marten throughout the Balearic Islands (Western Mediterranean): refining the radiocarbon‐based chronology

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