| 1. |
- Polme, S., et al.
(author)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Journal article (peer-reviewed)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 2. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Steinthorsdottir, Margret, et al.
(author)
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The Miocene: The Future of the Past
- 2021
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In: Paleoceanography and Paleoclimatology. - : American Geophysical Union (AGU). - 2572-4517 .- 2572-4525. ; 36:4
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Journal article (peer-reviewed)abstract
- The Miocene epoch (23.03–5.33 Ma) was a time interval of global warmth, relative to today. Continental configurations and mountain topography transitioned toward modern conditions, and many flora and fauna evolved into the same taxa that exist today. Miocene climate was dynamic: long periods of early and late glaciation bracketed a ∼2 Myr greenhouse interval—the Miocene Climatic Optimum (MCO). Floras, faunas, ice sheets, precipitation, pCO2, and ocean and atmospheric circulation mostly (but not ubiquitously) covaried with these large changes in climate. With higher temperatures and moderately higher pCO2 (∼400–600 ppm), the MCO has been suggested as a particularly appropriate analog for future climate scenarios, and for assessing the predictive accuracy of numerical climate models—the same models that are used to simulate future climate. Yet, Miocene conditions have proved difficult to reconcile with models. This implies either missing positive feedbacks in the models, a lack of knowledge of past climate forcings, or the need for re-interpretation of proxies, which might mitigate the model-data discrepancy. Our understanding of Miocene climatic, biogeochemical, and oceanic changes on broad spatial and temporal scales is still developing. New records documenting the physical, chemical, and biotic aspects of the Earth system are emerging, and together provide a more comprehensive understanding of this important time interval. Here, we review the state-of-the-art in Miocene climate, ocean circulation, biogeochemical cycling, ice sheet dynamics, and biotic adaptation research as inferred through proxy observations and modeling studies.
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| 4. |
- Sánchez-Barreiro, Fátima, et al.
(author)
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Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
- 2023
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In: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 40:9
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Journal article (peer-reviewed)abstract
- The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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| 5. |
- Sánchez‐Barreiro, Fátima, et al.
(author)
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Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )
- 2021
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:23, s. 6355-6369
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Journal article (peer-reviewed)abstract
- Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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| 6. |
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| 7. |
- Barnett, Ross, et al.
(author)
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Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
- 2020
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In: Current Biology. - 0960-9822 .- 1879-0445.
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Journal article (peer-reviewed)abstract
- Summary Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
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| 8. |
- Claybourn, Thomas M., 1989-, et al.
(author)
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BRACHIOPODS FROM THE BYRD GROUP (CAMBRIAN SERIES 2, STAGE 4) CENTRAL TRANSANTARCTIC MOUNTAINS, EAST ANTARCTICA: BIOSTRATIGRAPHY, PHYLOGENY AND SYSTEMATICS
- 2020
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In: Papers in Palaeontology. - : Wiley. - 2056-2799 .- 2056-2802. ; 6:3, s. 349-383
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Journal article (peer-reviewed)abstract
- Brachiopods from Cambrian Series 2, Stage 4 carbonate strata of the Byrd Group in the Central Transantarctic Mountains, East Antarctica, are described for the first time. These include six lingulate, one paterinate, and one rhynchonelliform taxa, including the new lingulate brachiopod Plicarmus wildi gen. et sp. nov. The biostratigraphy correlates closely to the brachiopods recently reported from the Xinji Formation (Shuiyu section) in North China, as well as brachiopods recovered from the Dailyatia odyssei Zone across the Arrowie Basin of South Australia. These findings also support the previously identified close palaeobiogeography of these regions. The first unambiguous example of the acrotretid brachiopod Eohadrotreta zhenbaensis Li and Holmer outside South China is also identified in the context of its ontogenetic stages. Well preserved specimens of the acrotheloid Schizopholis yorkensis (Holmer and Ushatinskaya in Gravestock et al.) facilitates a new reconstruction of its musculature and visceral region. This data is synthesised into a new cladistic analysis that resolves Acrotheloidea as a well-supported monophyletic clade and supports previous hypotheses of a morphocline in acrotheloid evolution.
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| 9. |
- Denk, Thomas, et al.
(author)
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The Pleistocene flora of Bezhan, southeast Albania: early appearance of extant tree species
- 2021
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In: Historical Biology. - : Taylor & Francis. - 0891-2963 .- 1029-2381. ; 33, s. 283-305
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Journal article (peer-reviewed)abstract
- The piggyback basin of Bezhan, southeastern Albania, was formed during the late Neogene and contains Pliocene/Pleistocene deposits. These continental deposits consist of marls, siltstones and clays separated by a thin series of lignite-seams alternating with clays (Bezhan formation). We investigated leaf fossils and dispersed pollen from marls of the upper portion of this formation. Fifty-two plant taxa comprising algae, gymnosperms, and angiosperms were recovered. Of these, at least 19% belong to extant species and less than 16% belong to taxa today extinct in western Eurasia. Tsuga is represented by three pollen taxa with affinities to modern Chinese, Japanese, and North American species. Herbaceous taxa indicative of steppe (Artemisia, Amaranthaceae) occur in low quantities (≤1%)suggesting an interglacial setting. Four vegetation units are recognised: Wet riparian and aquatic vegetation, mesic oak forest, dry sub-Mediterranean woodland, and montane conifer forest. A comparison of the Bezhan flora with well-dated Pliocene and Pleistocene floras of Italy suggests a Calabrian (late early Pleistocene) age for the upper unit. This estimate is based on the abundance of extant taxa, the absence of subtropical taxa, and threshold values of particular taxa (Tsuga, Carya). The findings are in agreement with age estimates for extant tree species from molecular studies.
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| 10. |
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