| 1. |
- Grasse, P., et al.
(författare)
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GEOTRACES Intercalibration of the Stable Silicon Isotope Composition of Dissolved Silicic Acid in Seawater
- 2017
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Ingår i: Journal of Analytical Atomic Spectrometry. - London. - 0267-9477. ; 32, s. 562-578
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Tidskriftsartikel (refereegranskat)abstract
- The first inter-calibration study of the stable silicon isotope composition of dissolved silicic acid in seawater, d30Si(OH)4, is presented as a contribution to the international GEOTRACES program. Eleven laboratories from seven countries analyzed two seawater samples from the North Pacific subtropical gyre (Station ALOHA) collected at 300 m and at 1000 m water depth. Sampling depths were chosen to obtain samples with a relatively low (9 mmol L-1, 300 m) and a relatively high (113 mmol L-1, 1000 m) silicic acid concentration as sample preparation differs for low- and high concentration samples. Data for the 1000 m water sample were not normally distributed so the median is used to represent the central tendency for the two samples. Median d30Si(OH)4 values of +1.66‰ for the low-concentration sample and +1.25‰ for the high-concentration sample were obtained. Agreement among laboratories is overall considered very good; however, small but statistically significant differences among the mean isotope values obtained by different laboratories were detected, likely reflecting inter-laboratory differences in chemical preparation including preconcentration and purification methods together with different volumes of seawater analyzed, andthe use of different mass spectrometers including the Neptune MC-ICP-MS (Thermo Fisher™, Germany), the Nu Plasma MC-ICP-MS (Nu Instruments™, Wrexham, UK), and the Finnigan™ (now Thermo Fisher™, Germany) MAT 252 IRMS. Future studies analyzing d30Si(OH)4 in seawater should also analyze and report values for these same two reference waters in order to facilitate comparison of data generated among and within laboratories over time.
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| 2. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 3. |
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| 4. |
- Radchuk, Viktoriia, et al.
(författare)
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Adaptive responses of animals to climate change are most likely insufficient
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
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| 5. |
- Bouchal, Johannes M., 1979-
(författare)
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Reconciling the stratigraphy and depositional history of the Lycian orogen-top basins, SW Anatolia
- 2019
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Ingår i: Palaeobiodiversity and Palaeoenvironments. - Heidelberg : Springer Science and Business Media LLC. - 1867-1594 .- 1867-1608. ; 99, s. 551-570
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Tidskriftsartikel (refereegranskat)abstract
- Terrestrial fossil records from the SW Anatolian basins are crucial both for regional correlations and palaeoenvironmental reconstructions. By reassessing biostratigraphic constraints and incorporating new fossil data, we calibrated and reconstructed the late Neogene and Quaternary palaeoenvironments within a regional palaeogeographical framework. The culmination of the Taurides in SW Anatolia was followed by a regional crustal extension from the late Tortonian onwards that created a broad array of NE-trending orogen-top basins with synchronic associations of alluvial fan, fluvial and lacustrine deposits. The terrestrial basins are superimposed on the upper Burdigalian marine units with a c. 7 myr of hiatus that corresponds to a shift from regional shortening to extension. The initial infill of these basins is documented by a transition from marginal alluvial fans and axial fluvial systems into central shallow-perennial lakes coinciding with a climatic shift from warm/humid to arid conditions. The basal alluvial fan deposits abound in fossil macro-mammals of an early Turolian (MN11–12; late Tortonian) age. The Pliocene epoch in the region was punctuated by subhumid/humid conditions resulting in a rise of local base levels and expansion of lakes as evidenced by marsh-swamp deposits containing diverse fossilmammal assemblages indicating late Ruscinian (lateMN15; late Zanclean) age. A second pulse of extension, accompanied by regional climatic changes, prompted subsequent deepening of the lakes as manifested by thick and laterally extensive carbonate successions. These lakes, which prevailed c. 1 myr, later shrank due to renewed progradation of alluvial fans and eventually filled up and dried out, reflected by marsh-swamp deposits at the top of a complete lacustrine succession that contains diverse micro-mammal assemblages indicating a latest Villanyian (MN17; Gelasian) age. A third pulse of tectonic reorganisation and associated extension dissected the basins into their present-day configuration from the early Pleistocene onwards under warm/humid climatic conditions. The new age data provide means to correlate deposits across various basins in the region that help to place the basin development into a regional tectonic framework, which can be attributed to the consequence of the well-articulated regional phenomena of slab-tear/detachmentinduced uplift followed by crustal extension and basin formation (late Tortonian), the outward extension of the Aegean arc (early Pliocene) and eventually accompanied by westward extrusion of the Anatolian Plate (early Pleistocene).
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| 6. |
- Fielding, Christopher R., et al.
(författare)
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A multidisciplinary approach to resolving the end-Guadalupian extinction
- 2023
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Ingår i: Evolving Earth. - : Elsevier. - 2950-1172. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- The transition from the middle to late Permian (Guadalupian–Lopingian) is claimed to record one or more extinction events that rival the ‘Big Five’ in terms of depletion of biological diversity and reorganization of ecosystem structure. Yet many questions remain as to whether the events recorded in separate regions were synchronous, causally related, or were of a magnitude rivaling other major crises in Earth’s history. In this paper, we survey some major unresolved issues related to the Guadalupian–Lopingian transition and offer a multidisciplinary approach to advance understanding of this under-appreciated biotic crisis by utilizing records in Southern Hemisphere high-palaeolatitude settings. We focus on the Bowen-Gunnedah-Sydney Basin System (BGSBS) as a prime site for analyses of biotic and physical environmental change at high palaeolatitudes in the middle and terminal Capitanian. Preliminary data suggest the likely position of the mid-Capitanian event is recorded in regressive deposits at the base of the Tomago Coal Measures (northern Sydney Basin) and around the contact between the Broughton Formation and the disconformably overlying Pheasants Nest Formation (southern Sydney Basin). Initial data suggest that the end-Capitanian event roughly correlates to the transgressive “Kulnura Marine Tongue” in the middle of the Tomago Coal Measures (northern Sydney Basin) and strata bearing dispersed, ice-rafted gravel in the Erins Vale Formation (southern Sydney Basin). Preliminary observations suggest that few plant genera or species disappeared in the transition from the Guadalupian to Lopingian, and the latter interval saw an increase in floristic diversity.
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| 7. |
- Frank, T.D., et al.
(författare)
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Pace, magnitude, and nature of terrestrial climate change through the end-Permian extinction in southeastern Gondwana
- 2021
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Ingår i: Geology. - : Geological Society of America. - 0091-7613 .- 1943-2682. ; 49:9, s. 1089-1095
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Tidskriftsartikel (refereegranskat)abstract
- Rapid climate change was a major contributor to the end-Permian extinction (EPE). Although well constrained for the marine realm, relatively few records document the pace, nature, and magnitude of climate change across the EPE in terrestrial environments. We generated proxy records for chemical weathering and land surface temperature from continental margin deposits of the high-latitude southeastern margin of Gondwana. Regional climate simulations provide additional context. Results show that Glossopteris forest-mire ecosystems collapsed during a pulse of intense chemical weathering and peak warmth, which capped ∼1 m.y. of gradual warming and intensification of seasonality. Erosion resulting from loss of vegetation was short lived in the low-relief landscape. Earliest Triassic climate was∼10–14 °C warmer than the late Lopingian and landscapes were no longer persistently wet. Aridification, commonly linked to the EPE, developed gradually, facilitating the persistence of refugia for moisture-loving terrestrial groups.
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| 8. |
- Hailer, Frank, et al.
(författare)
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Phylogeography of the white-tailed eagle, a generalist with large dispersal capacity
- 2007
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 34:7, s. 1193-1206
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Tidskriftsartikel (refereegranskat)abstract
- Aim Late Pleistocene glacial changes had a major impact on many boreal and temperate taxa, and this impact can still be detected in the present-day phylogeographic structure of these taxa. However, only minor effects are expected in species with generalist habitat requirements and high dispersal capability. One such species is the white-tailed eagle, Haliaeetus albicilla, and we therefore tested for the expected weak population structure at a continental level in this species. This also allowed us to describe phylogeographic patterns, and to deduce Ice Age refugia and patterns of postglacial recolonization of Eurasia. Location Breeding populations from the easternmost Nearctic (Greenland) and across the Palaearctic (Iceland, continental Europe, central and eastern Asia, and Japan). Methods Sequencing of a 500 base-pair fragment of the mitochondrial DNA control region in 237 samples from throughout the distribution range. Results Our analysis revealed pronounced phylogeographic structure. Overall, low genetic variability was observed across the entire range. Haplotypes clustered in two distinct haplogroups with a predominantly eastern or western distribution, and extensive overlap in Europe. These two major lineages diverged during the late Pleistocene. The eastern haplogroup showed a pattern of rapid population expansion and colonization of Eurasia around the end of the Pleistocene. The western haplogroup had lower diversity and was absent from the populations in eastern Asia. These results suggest survival during the last glaciation in two refugia, probably located in central and western Eurasia, followed by postglacial population expansion and admixture. Relatively high genetic diversity was observed in northern regions that were ice-covered during the last glacial maximum. This, and phylogenetic relationships between haplotypes encountered in the north, indicates substantial population expansion at high latitudes. Areas of glacial meltwater runoff and proglacial lakes could have provided suitable habitats for such population growth. Main conclusions This study shows that glacial climate fluctuations had a substantial impact on white-tailed eagles, both in terms of distribution and demography. These results suggest that even species with large dispersal capabilities and relatively broad habitat requirements were strongly affected by the Pleistocene climatic shifts.
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| 9. |
- Hempel, Elisabeth, et al.
(författare)
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Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:2100
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Tidskriftsartikel (refereegranskat)abstract
- Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the ‘museum population’, possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.
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| 10. |
- Tan, David J.X., et al.
(författare)
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Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis
- 2018
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Ingår i: Scientific Reports. - 2045-2322.
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Tidskriftsartikel (refereegranskat)abstract
- Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.
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