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opencc-zeroApr 2022View details →

Data from: Tracking population genetic signatures of local extinction with herbarium specimens

Background and Aims Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. Methods We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex-situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. Key Results Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as powerful predictor of functional connectivity which may promote decision making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. Conclusions Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex-situ population and a germination trial underscores the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

opencc-zeroJun 2022View details →

Data from: Climate matching and anthropogenic factors contribute to the colonisation and extinction of local populations during avian invasions

Concern about the impacts of biological invasions has generated a great deal of interest in understanding factors that determine invasion success. Most of our current knowledge comes from static approaches that use spatial patterns as a proxy of temporal processes. These approaches assume that species are present in areas where environmental conditions are the most favourable. However, this assumption is problematic when applied to dynamic processes such as species expansions when equilibrium has not been reached. In our work, we analyse the roles played by human activities, climatic matching, and spatial connectivity on the two main underlying processes shaping the spread of invasive species (i.e., colonisation and extinction) using a dynamic modelling approach. For this, we used a large dataset that has recorded the occurrence of two invasive bird species -the ring-necked and the monk parakeets- in the Iberian Peninsula from 1991 to 2016.

opencc-zeroJun 2022View details →

Data from: Gradual warming prior to the end-Permian mass extinction

The biggest known mass extinction in the history of animal life occurred at the Permian-Triassic boundary and has often been linked to global warming. Previous studies suggested that a geologically rapid (less than 40 kyr) temperature increase of more than 10°C occurred simultaneously with the main extinction pulse. This hypothesis is challenged by geochemical and palaeontological data indicating profound environmental perturbations and a temperature rise prior to the main extinction. Using Secondary Ion Mass Spectrometry (SIMS), we measured oxygen isotope ratios from Changhsingian (Late Permian) ostracods of northwestern Iran. Our data show that ambient seawater temperature began to rise at least 300 kyr prior to the main extinction event. Gradual warming by approximately 12°C was probably responsible for initial environmental degradation that eventually culminated in the global end-Permian mass extinction.

opencc-by-4.0Aug 2022View details →

Data for Han et al., 2022, PNAS, "Low dinosaur biodiversity in central China 2 million years prior to the end-Cretaceous mass extinction"

This zip file contains data presented in the PNAS paper “Low dinosaur biodiversity in central China 2 million years prior to the end-Cretaceous mass extinction” by Han et al., 2022.  Folder “Thermal Demag RawData” contains four subfolders that contain all the thermal demagnetization data used in this paper. Magnetic remanence measurements of the natural remanent magnetization (NRM) and the remanences after thermal demagnetization were performed by a three-axis cryogenic magnetometer (2G 760) in a magnetically shielded room (residual field < 300 nT).

opencc-zeroAug 2022View details →

Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations

Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting in local extinction and recolonization through evolving dispersal, facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favour increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.

opencc-by-4.0Sep 2022View details →

Variations of the urban PM2.5 chemical components and corresponding light extinction for three heating seasons in the Guanzhong Plain, China

The basic data of the thesis “Variations of the urban PM2.5 chemical components and corresponding light extinction for three heating seasons in the Guanzhong Plain, China”.

opencc-by-4.0Dec 1860View details →

1—7. Thespesius occidentalis. 8-17 in Extinct vertebrata from the Judith River and Great Lignite formations of Nebraska.

1—7. Thespesius occidentalis. 8-17 Ischyrotherium antiquum.

opencc-zeroApr 2024View details →

Extant and extinct bilby genomes combined with indigenous knowledge improve conservation of a unique Australian marsupial

The Ninu (Greater bilby, Macrotis lagotis) is a desert-dwelling, culturally and ecologically important marsupial. In collaboration with Indigenous rangers and conservation managers, we generated the first Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (Lesser bilby, Macrotis leucura). We developed and tested a scat SNP panel, based on our genomic datasets, to inform current and future conservation actions, to undertake future ecological assessments, and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of targeted conservation actions, like translocations, in the contemporary metapopulation (N=363 Ninu). Resequenced genomes (temperate Ninu=6; semi-arid Ninu=6; Yallara=4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathway adaptations to aridity. Despite their 45-year long captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life-history. We also investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus; an XY1Y2 sex chromosome system generated by fusion of the X with a large telocentric autosome; and expansions in olfactory receptor genes. Together, we demonstrate the holistic value of genomics in improving key conservation management actions, understanding unique biological traits, and developing tools for Indigenous rangers to monitor remote wild populations.

opencc-zeroMay 2024View details →

Data from: Extinction selectivity obscures patterns of trait-dependent endangerment in Columbiformes

Understanding how extinction has occurred in the recent past is crucial to unravel its main drivers as well as to implement effective conservation practices to minimize global biodiversity loss. It has long been hypothesized that extinction risk is not randomly distributed among traits of species. However, the actual traits making species more prone to extinction may have been overlooked because already extinct species are often not considered in comparative analyses of extinction risk. We characterized the drivers of extinction in a cosmopolitan bird clade, including Holocene and contemporary extinctions potentially related to human impacts, and provided evidence of an 'extinction selectivity' in species traits. We constructed a new phylogenetic hypothesis of the Columbiformes, a cosmopolitan bird clade consisting of 33 recently extinct and 351 extant species. Then, we integrated data on geography, behaviour, and morphology to reveal the drivers of extinction risk. We used phylogenetic generalized least square models to test the effect of geography, behaviour, and morphology on the risk of extinction and identified differences in the drivers of extinction when including vs. excluding recently extinct species. Our analysis revealed that Columbiformes endemic from islands with ground-foraging habits, weak flying abilities, migratory behaviour, and larger body sizes are more vulnerable to extinction. Our results also show that excluding recently extinct species identifies extinction drivers differently from those when including recently extinct species. Only by accurately identifying the traits that increase extinction risk can we develop targeted conservation measures that promote the long-term persistence of threatened species. Extinction selectivity has important implications for the conservation of biological communities and ultimately ecosystem functioning, considering the critical role Columbiformes often play as seed dispersers.

opencc-by-4.0May 2024View details →

UV-Vis absorbance data, molar extinction coefficients and circular dichroism spectra for the two cyanobacterial metabolites anabaenopeptin A and anabaenopeptin B

Data for: "The UV-Vis absorbance spectra, molar extinction coefficients and circular dichroism spectra as well as NMR and mass spectrometry spectra were determined for two prominent secondary metabolites from cyanobacteria, namely anabaenopeptin A and anabaenopeptin B. The compounds were extracted from the cyanobacterium Planktothrix rubescens CBT929 and purified by flash chromatography and HPLC. Exact amounts of isolated compounds were assessed by quantitative 1H-NMR with internal calibrant ethyl 4-(dimethylamino)benzoate in DMSO-d6 at 298 K with a recycle delay (d1) of 120 s. UV-Vis absorbance spectra were recorded in methanol at room temperature. Molar extinction coefficients were determined at 278 nm as 4190 M-1 cm-1 and 2300 M-1 cm-1 in methanol for anabaenopeptin A and anabaenopeptin B, respectively. Circular dichroism spectra and secondary fragmentation mass spectra are also reported."

Fig. 12 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 12. Uncitable molecular survey with random names (cf. Blakemore 2010, 2011, 2012).

Fig. 11 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 11. German South-polar expedition route (not to NZ).

Fig. 10 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 10. Hamburg museum registration card (ditto).

Fig. 9. Hamburg specimen V.8615 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 9. Hamburg specimen V.8615 (non-type) (photo: courtesy curator).

Fig. 8 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 8. Vienna type registration card (ditto).

Fig. 7 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 7. Vienna type specimen as inspected above (photo: courtesy curator).

Fig. 4 in Extinction of Japan's first formally described earthworm (Horst, 1883) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).

Fig. 4. Contemporary view of same landscape showing urbanization (2018 author's image).

Fig. 5 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 5. Distinctive male pores on 18 (ditto).

Fig. 2 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 2. Loaned type as received in Japan in 2016 (author's photo).

Fig. 3 in Redescription of extinct New Zealand earthworm: (Schmarda, 1861) (Annelida, Oligochaeta, Megadrilacea, Megascolecidae)

Fig. 3. Prostomium (author's photo 2016).