Ancient plant DNA in lake sediments Parducci, Laura; Bennett, Keith D.; Ficetola, Gentile Francesco ...
The New phytologist,
20/May , Letnik:
214, Številka:
3
Journal Article
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Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of ...palaeofloras.Hitherto, ancient frozen soils have proved excellent in preservingDNAmolecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a fewmetres fromthe sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNAfromlake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here,we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progressmade up to the present.Weargue that aDNAanalyses add newand additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to ...overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.
Post-settlement faunal extinction rates are widely cited statistics and help to understand the magnitude of recent biodiversity loss driven by human activity. However, extinction rate estimates can ...vary greatly depending on factors such as the geographic boundaries of the region being considered, how the faunal group is defined, completeness of fossil records, and taxonomic frameworks. Here, I combine recently described extinct bird species with the latest taxonomic revisions and well-defined geographic regions to provide an updated estimate of post-settlement extinction rates for the New Zealand avifauna. The results show that extinction rates varied regionally from 50% species extinction on the North Island to just 14.5% on offshore islands. As a whole, the New Zealand mainland and its offshore islands lost 30.9% of bird species, although this rate increases to 32.8% with the inclusion of the distinct Chatham Islands/Rēkohu avifauna.
Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. ...We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6-8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Large herbivores facilitate a range of important ecological processes yet globally have experienced high rates of decline and extinction over the past 50,000 years. To some extent this lost function ...may be replaced through the introduction of ecological surrogate taxa, either by active management or via historic introductions. However, comparing the ecological effects of herbivores that existed in the same location, but at different times, can be a challenging proposition. Here we provide an example from New Zealand that demonstrates an approach for making such comparisons. In New Zealand it has been suggested that post-19th Century mammal introductions (e.g. deer and hare) may have filled ecological niches left vacant after the 15th Century AD extinction of large avian herbivores (moa). We quantified pollen assemblages from fecal samples deposited by these two asynchronous herbivore communities to see whether they were comparable. The fecal samples were collected at the same location, and in a native-dominated vegetation community that has experience little anthropogenic disturbance and their contents reflect both the local habitat and diet preferences of the depositing herbivore. The results reveal that the current forest understory is relatively sparse and species depauperate compared to the prehistoric state, indicating that deer and moa had quite different impacts on the local vegetation community. The study provides an example of how combining coprolite and fecal analyses of prehistoric and modern herbivores may clarify the degree of ecological overlap between asynchronous herbivore communities and provide insights into the extent of ecological surrogacy provided by introduced taxa.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Contributes to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. ...Identifies at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). Source: National Library of New Zealand Te Puna Matauranga o Aotearoa, licensed by the Department of Internal Affairs for re-use under the Creative Commons Attribution 3.0 New Zealand Licence.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Human-caused forest transitions are documented worldwide, especially during periods when land use by dense agriculturally-based populations intensified. However, the rate at which prehistoric human ...activities led to permanent deforestation is poorly resolved. In the South Island, New Zealand, the arrival of Polynesians c. 750 years ago resulted in dramatic forest loss and conversion of nearly half of native forests to open vegetation. This transformation, termed the Initial Burning Period, is documented in pollen and charcoal records, but its speed has been poorly constrained. High-resolution chronologies developed with a series of AMS radiocarbon dates from two lake sediment cores suggest the shift from forest to shrubland occurred within decades rather than centuries at drier sites. We examine two sites representing extreme examples of the magnitude of human impacts: a drier site that was inherently more vulnerable to human-set fires and a wetter, less burnable site. The astonishing rate of deforestation at the hands of small transient populations resulted from the intrinsic vulnerability of the native flora to fire and from positive feedbacks in post-fire vegetation recovery that increased landscape flammability. Spatially targeting burning in highly-flammable seral vegetation in forests rarely experiencing fire was sufficient to create an alternate fire-prone stable state. The New Zealand example illustrates how seemingly stable forest ecosystems can experience rapid and permanent conversions. Forest loss in New Zealand is among the fastest ecological transitions documented in the Holocene; yet equally rapid transitions can be expected in present-day regions wherever positive feedbacks support alternate fire-inhibiting, fire-prone stable states.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in children. NAFLD has become increasingly recognized in pediatric populations with type 1 diabetes (T1D) .... Also, NAFLD is emerging as an independent risk factor for cardiovascular disease (CVD) . Arterial stiffness is an index of subclinical atherosclerosis and can predict cardiovascular events and mortality.
Objectives: The aim of this pilot study was to estimate the prevalence of NAFLD in children with T1D and to examine the relationship between NAFLD and arterial stiffness.
Subjects and Methods: A cross-sectional pilot study of 18 children (age 7-20 years) with a diagnosis of T1D for at least 5 years without secondary causes of chronic liver disease. The main study measures included: 1. Detection of fatty liver in children with T1D measured by controlled attenuation parameter (CAP) using FibroScan and 2. Measurement of arterial stiffness by pulse wave velocity (PWV) using SphygmoCor. We also aimed to measure hepatic fibrosis by FibroScan and insulin sensitivity (IS) by using a validated surrogate marker.
Results: The prevalence of NAFLD was approximately 19% of study participants. We found positive correlations between CAP and PWV values, which suggests higher arterial stiffness with higher degree of fatty liver. Median PWV was higher in participants with steatosis compared to those without steatosis, 6.vs. 6.5 m/s. We also found negative correlations between IS and both arterial stiffness and steatosis (R=-0.56, p=0.038) , (R=-0.56, p=0.063) , respectively.
Conclusions: Our findings suggest that NAFLD is common in participants with T1D and in this study was associated with higher arterial stiffness. Our study is consistent with previously reported associations between decreased IS and presence of microvascular complications. Larger randomized controlled trials are required to evaluate whether NAFLD predicts the incidence of CVD events in T1D.
Disclosure
R.Zeiad: None. M.Crespo: None. J.R.Wood: Research Support; AstraZeneca, Boehringer Ingelheim International GmbH, Insulet Corporation, MannKind Corporation. R.M.Farrell: Stock/Shareholder; Dexcom, Inc., Tandem Diabetes Care, Inc.
Funding
18117-FRAP 2020-21
Type 1 diabetes is a chronic autoimmune disorder that results in destruction of insulin-producing cells in the pancreas. The autoimmune process is thought to be waxing and waning resulting in ...variable endogenous insulin secretion ability. An example of this is the honeymoon phase or partial remission phase of type 1 diabetes, during which optimal control of blood glucoses can be maintained with significantly reduced exogenous insulin, and occasionally exogenous insulin can be temporarily discontinued altogether. Understanding this phase is important because even fairly small amounts of endogenous insulin secretion is associated with reduced risk of severe hypoglycemia and microvascular complications.
Extinctions have altered island ecosystems throughout the late Quaternary. Here, we review the main historic drivers of extinctions on islands, patterns in extinction chronologies between islands, ...and the potential for restoring ecosystems through reintroducing extirpated species. While some extinctions have been caused by climatic and environmental change, most have been caused by anthropogenic impacts. We propose a general model to describe patterns in these anthropogenic island extinctions. Hunting, habitat loss and the introduction of invasive predators accompanied prehistoric settlement and caused declines of endemic island species. Later settlement by European colonists brought further land development, a different suite of predators and new drivers, leading to more extinctions. Extinctions alter ecological networks, causing ripple effects for islands through the loss of ecosystem processes, functions and interactions between species. Reintroduction of extirpated species can help restore ecosystem function and processes, and can be guided by palaeoecology. However, reintroduction projects must also consider the cultural, social and economic needs of humans now inhabiting the islands and ensure resilience against future environmental and climate change.
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