Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Groenen, M. ; Lohse, H. - \ 2014
Molecular Ecology 23 (2014)22. - ISSN 0962-1083 - p. 5566 - 5574.
last glacial period - pig genomes - quaternary - evolution - reveals - domestication - demography - inference - sundaland - history
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling
Wielstra, B.M. ; Crnobrnja-Isailovic, J. ; Litvinchuk, S.N. ; Reijnen, B.T. ; Skidmore, A.K. ; Sotiropoulos, K. ; Toxopeus, A.G. ; Tzankov, N. ; Vukov, T. ; Arntzen, J.W. - \ 2013
Frontiers in Zoology 10 (2013)1. - ISSN 1742-9994 - 14 p.
crested newt - niche conservatism - climate-change - hybrid zone - gene flow - time - space - introgression - quaternary - evolution
Introduction The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial. Results We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps. Conclusions The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the ‘southern richness and northern purity’ paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an ‘extra-Mediterranean’ refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges
The paleobotanical record of Colombia: Implications for biogeography and biodiversity
Hooghiemstra, H. ; Wijninga, V.M. ; Cleef, A.M. - \ 2006
Annals of the Missouri Botanical Garden 93 (2006)2. - ISSN 0026-6493 - p. 297 - 324.
high-andean biota - south-america - tropical mountains - eastern-cordillera - northern andes - pollen record - rain-forest - pliocene - quaternary - montane
Plant microfossil and macrofossil associations obtained from six dated sections from the area of the basin of Bogota¿ (2550 m, Eastern Cordillera, Colombia) show the evolution of the late Neogene Andean montane forest, triggered by the Andean orogeny. Progressive adaptation of warm tropical taxa to cool montane conditions, evolution of new neotropical montane taxa, and immigration of temperate Laurasian, Holarctic, and Austral-Antarctic elements gave shape to the present-day montane forest. Vegetational characteristics inferred from fossil plant associations reveal the altitude at the time of deposition. Neogene forests are floristically compared with contemporary forests at comparable altitudinal intervals in the surroundings of the Bogota¿ basin; however, the absence of taxa that had not yet arrived, or evolved, is most salient and shows that non-analogue plant communities are common. The main phases of montane forest development are: (1) pre-uplift phase of the late Miocene with abundant lowland taxa with tropical or neotropical affinities (Mauritia Kunth, Amanoa Aubl., Ceiba Miller, and representatives of Humiriaceae); montane forest rich in Podocarpaceae (potentially including Nageia Gaertn., Podocarpus L'He¿r., Prumnopitys Phil., and Retrophyllum C. N. Page) covered other previously uplifted areas in the region; (2) toward the early Pliocene the area was uplifted to ca. 1000 m; the relative proportion of temperate taxa of North American and southern South American stock increased and occupied the slopes of the low mountains; and (3) by the middle Pliocene uplift had proceeded to ca. 2000-2200 m and tropical lowland taxa, which are now restricted to altitudes below 1000 m, are no longer recorded in the fossil plant associations; the increase in the number of newly appearing montane taxa (Myrica L., Turpinia Vent., Gunnera L., Bocconia L., Gaiadendron G. Don f., Daphnopsis C. Martius, and Monnina Ruiz & Pav.) suggests a significant increase of diversity. Until the late Pliocene there is little to no evidence for the existence of the pa¿ramo; taxa such as Xyris L., Hypericum L., Carex L., Montia L., and Ranunculus L. might have formed swamp or bog vegetation only. It is believed that these taxa colonized mountaintops with half-open vegetation; these areas extended when the mountains reached above upper forest line elevations. The distribution areas of the endemic genera of the Espeletiinae largely coincide with the youngest parts (<5 Ma) of the northern Andes. Changing climatic conditions forced individual plant species to migrate vertically. Composition of plant communities changed continuously and vegetation belts frequently were altitudinally squeezed or offered possibilities for expansion. This long process stimulated speciation and provoked sequential non-analogue vegetation types. Thus, the biodiversity hotspot of the northern Andes has a dynamic history
Late-Holocene evolution of the Mahakam delta, East Kalimantan, Indonesia
Storms, J.E.A. ; Hoogendoorn, R.M. ; Dam, R.A.C. ; Hoitink, A.J.F. ; Kroonenberg, S.B. - \ 2005
Sedimentary Geology 180 (2005)3-4. - ISSN 0037-0738 - p. 149 - 166.
brahmaputra river system - ganges-brahmaputra - sediment transport - subaqueous delta - shelf - ocean - quaternary - record
The late-Holocene Mahakam delta, located along the tropical eastern shore of Kalimantan, Indonesia, is considered to be a textbook example of a mixed tide-fluvial dominated delta system. The delta prograded about 60 km during the past 5000 years, which led to the development of a distinct network of distributary and tidal channels. Wave action is low due the limited fetch in the narrow strait of Makassar. Mahakam River discharge is about a quarter of the Mississippi River discharge and is characterized by absence of flood surges. Therefore, natural levees, crevasse splays and avulsions are absent in the delta plain. For the past four decennia, both modern and ancient Mahakam delta deposits have been studied in detail in order to better understand subsurface Miocene and Tertiary Mahakam deposits, which host large volumes of hydrocarbons. This study focuses on the dynamics and stratal patterns of delta plain, delta-front platform deposits and suspended sediments. Due to the predominance of semi-diurnal tides and the associated flow reversals, depositional patterns are highly variable which has resulted in the formation of characteristic sand-mud couplets. The distribution of the sand-mud couplets found in this study differs from previously proposed conceptual models. They are limited to the fluvial domain and form in the distributary channels (lateral channel bar) or at the fluvial dominated delta-front platform, which flanks the mouth bar deposits in offshore direction. The sand-mud couplets which formed as delta-front platform and lateral channel bar deposits are similar and can only be identified based on their 14C age. The sand content decreases significantly towards the tidal dominated areas due to limitation in transport capacity. Turbidity measurements taken in front of the river mouth also show rapid settlement of river plume sediments. Some 22 new AMS 14C dates show that late Holocene sea level history resembles the eustatic sea level curve giving a first approximation of the Late Holocene sea level history for East Kalimantan. The dates suggest that the progradational delta system evolved under conditions of slowly rising sea level, which compares well to the eustatic sea level curve. In addition, calculated averaged deposition rates of the sand-mud couplets indicate that deposition is driven by the spring-neap tide cycles instead of the daily tidal cycle
Quaternary river terrace formation in the Allier basin, France : a reconstruction based on sand bulk geochemistry and 3-D modelling
Veldkamp, A. - \ 1991
Agricultural University. Promotor(en): S.B. Kroonenberg. - S.l. : Veldkamp - 172
geologie - rivieren - sediment - reliëf - waterlopen - geomorfologie - watererosie - geochemie - weer - meteorologische factoren - frankrijk - kwartair - invloeden - geology - rivers - sediment - relief - streams - geomorphology - water erosion - geochemistry - weather - meteorological factors - france - quaternary - influences
The research presented in this thesis is focussed on a quantitative reconstruction of the effects of past environmental dynamics within a fluvial system. The study area is part of the Allier basin (Limagne) in the Auvergne, Massif Central, France.
The research was carried out in several stages. At first field work was carried out to determine the terrace stratigraphy and chronology in more detail. A new age estimate of the Fva (65 m above present river bed) is based on pumice clasts found in the terrace sediments. Younger terraces were dated with14C and Th/U disequilibrium methods. Fx terrace sediments (15 and 10 m above present river bed) were mainly deposited during the Late Weichselian, while the Fwb terrace sediments (25 m above present river bed) have most probably a Late Saalian age. Due to these new age estimates a revision of the existing Allier terrace chronology is necessary. This new chronology shows a large time gap between the deposition of the Fv and Fw terrace sediments.
Next, sands of various terrace units were collected and bulk geochemically measured with XRF. This bulk geochemical research allowed a statistically significant discrimination of different terrace levels. The processes which shape and shaped the actual sand geochemistry were successfully quantified. It was found that grain size has only a very limited effect on bulk geochemical variability while longitudinal sorting processes and weathering have a stronger impact on actual sediment composition. Although the effects of parent material controlled weathering in the Allier sands were successfully modelled, the older terrace sediments are unsuitable for paleoenvironmental reconstructions. Such a reconstruction was done for the Weichselian and Holocene terrace deposits at the Allier/Dore confluence. The sediment mixing behaviour of these rivers is estimated by calculating sediment mixing ratios. This reconstruction started with an investigation of spatial mixing effects of Allier and Dore sediments in time by means of mapping and geostatistics. Results suggest an environmental
Further a large scale and long term model of terrace formation was constructed using finite state modelling. This methodology allows the construction of a general 3-D terrace formation model containing as well quantitative as qualitative knowledge on fluvial systems. Finally, an adapted version for the Allier (LIMTER) is made incorporating all present knowledge on this system. LIMTER allows the formulation and evaluation of long term terrace formation scenarios for the Allier system. Simulation results suggest that terrace stratigraphy in the study area is mainly the result of the internal Allier dynamics and climatic change. Local tectonism caused the development of unpaired terraces while the general regional uplift played a dominant role in terrace formation and preservation in general.
The terrace research as presented in this thesis shows that it is well possible for any fluvial system to simulate the interaction climate/tectonism and fluvial dynamics. The for the Allier simulated dynamics, net sedimentation during and at the end of a Glacial and net dissection during an Interglacial has no general validity.
Soil formation, microstructure and physical behaviour of Late Weichselian and Holocene Rhine deposits in the Netherlands
Miedema, R. - \ 1987
Agricultural University. Promotor(en): L.J. Pons, co-promotor(en): F.F.R. Koenigs. - S.l. : S.n. - 339
kleimineralen - zware kleigronden - klimaat - overstromingen - geologie - landschap - nederland - pedologie - rivieren - sediment - bodemvorming - bodemmicromorfologie - verwering - glaciale perioden - holoceen - postglaciale perioden - kwartair - rijn - clay minerals - clay soils - climate - floods - geology - landscape - netherlands - pedology - rivers - sediment - soil formation - soil micromorphology - weathering - glacial periods - holocene - postglacial periods - quaternary - river rhine
Dutch Late Weichselian braided river deposits and Holocene meandering river deposits of the Rhine have been studied and compared. Cross sections demonstrate the lateral and vertical variations of the Late Weichselian sediments. Soil mapping of these deposits, even on a very detailed scale, proves very difficult. Best results have been obtained with a legend based on hydrology enabling the distinction of topo-hydrosequences of well drained brown soils, imperfectly drained mottled soils and poorly drained grey soils.
Advanced soil formation and notably the dramatic processes in the Late Weichselian period (decalcification, clay illuviation, pseudogleying, periglacial formation of a highly reoriented, very dense microstructure) have caused clay mineralogical, chemical and physical changes in the Late Weichselian soils.
The well drained and imperfectly drained Late Weichselian soils have an argillic horizon (Alfisols, Luvisols), occasionally with very low base saturation (Ultisols, Acrisols) and with strong subsequent pseudogleying in the imperfectly drained soils. The Holocene soils demonstrate decalcification and biogenic homogenization as well as some gleying according to their drainage position. These soils are classified as Inceptisols (Cambisols), occasionally as Mollisols (Phaeozems).
Less favourable physical characteristics and behaviour (soil strength, structure stability and tillage behaviour) of the Late Weichselian soils and soil material is quantitatively documented. Differences with the Holocene soils and soil material are statistically highly significant and are caused by differences in texture, content, quality and distribution of organic matter and the highly reoriented, very dense microstructure.
Use as permanent grassland or ley in the crop rotation is recommended to increase levels of biological activity. This seems the only remedy for the imperfectly and poorly drained Late Weichselian soils that are compacted by natural soil forming processes not counteracted by biological activity. Very recently improved drainage of large areas of Late Weichselian imperfectly drained soils has increased the saturated hydraulic conductivity to noncritical levels through increased earthworm activity to some metres depth.
Landforms and soils in eastern Surinam (South America)
Boer, M.W.H. de - \ 1972
Landbouwhogeschool Wageningen. Promotor(en): P. Buringh, co-promotor(en): D.J. Doeglas. - Wageningen : Pudoc - ISBN 9789022003824 - 169
geologie - geomorfologie - horizonten - landevaluatie - bodemvorming - bodemgeschiktheid - bodemkarteringen - suriname - verwering - kwartair - geology - geomorphology - horizons - land evaluation - soil formation - soil suitability - soil surveys - suriname - weathering - quaternary
Quaternary geogenesis in eastern Surinam was studied by field methods and sedimentary-petrographic research. The development of the river valleys was explained in terms of changes in sea level, tectonic movements and changes in climate. A preliminary stratigraphy was established.Eight soil profiles were selected for a detailed study of pedogenesis. For this purpose the field data were combined with the results of thin-section analysis and chemical research, including X-ray microprobe analysis. To interpret the mechanical data, a rectangular diagram after Doeglas was used. The chemical data were recalculated into the normative mineralogical composition according to van der Plas & van Schuylenborgh and Burri. Thus bioturbation, clay migration, ferrallization, plinthization, podzolization and the genesis of arable soils were studied.27 soil profiles were classified by the American, the French, and the Brazilian system.
|Bijdrage tot de kwartair - geologie van Westelijk Noordbrabant
Oosten, M.F. van - \ 1967
(Bennekom) : [s.n.] - 16
geologie - nederland - aardwetenschappen - noord-brabant - kwartair - geology - netherlands - earth sciences - noord-brabant - quaternary
De alluviale gronden van de Maas, de Roer en de Geul in Limburg
Broek, J.M.M. van den; Marel, H.W. van der - \ 1964
Wageningen : Centrum voor Landbouwpublikaties en Landbouwdocumentatie (Verslagen van landbouwkundige onderzoekingen der rijkslandbouwproefstations 645) - 83
bodemclassificatie - bodemtaxonomie - bodemtypen - kwartair - midden-limburg - zuid-limburg - soil classification - soil taxonomy - soil types - quaternary - midden-limburg - zuid-limburg
De alluviale gronden van de Maas, de Roer en de Geul in Limburg
Broek, J.M.M. van den; Marel, H.W. van der - \ 1964
Wageningen : STIBOKA (Mededelingen / Stichting voor Bodemkartering ) - 83
bodemclassificatie - bodemtaxonomie - bodemtypen - nederland - kwartair - midden-limburg - zuid-limburg - soil classification - soil taxonomy - soil types - netherlands - quaternary - midden-limburg - zuid-limburg
In deze publicatie zijn resultaten weergegeven van het fysisch-chemisch onderzoek in de recente alluviale gronden van Maas, Geul en Roer.
Een palynologisch onderzoek van in dekzand ontwikkelde bodemprofielen
Havinga, A.J. - \ 1962
Wageningen University. Promotor(en): C.H. Edelman. - Wageningen : Veenman - 166
bodemkarteringen - landevaluatie - horizonten - bodemgeschiktheid - bodemvorming - paleontologie - palynologie - onderzoek - stuifmeel - Nederland - bodemkunde - kwartair - soil surveys - land evaluation - horizons - soil suitability - soil formation - palaeontology - palynology - research - pollen - Netherlands - soil science - quaternary
The relation was studied between vegetational development and soil formation in the Pleistocene cover sands in the Netherlands, particularly whether forests, rather than heaths, were early involved in the formation of podsolic soils. The pollen content of profiles of various podsols and some gleys were examined, all lying below layers of drift sand and peat of various ages. Beyerinck's palynological method had to be extended with a study of the significance of sand diagrams. In an undisturbed podsol pollen decreased in concentration roughly geometrically from the sand surface downward.
A relation could be observed between the length of the vertical distribution of pollen (pollen profile) and the depth above, in which the original stratification of the Eolian cover sand had entirely disappeared.
It was concluded that most of the pollen permeated before podsolisation, during the biologically very active stage of the homogeneous forest profile. The lowest part of the pollen profile, already fixed, constantly 'grew' on the top through addition of continually younger spectra; in later degradation stages illuviation of pollen could also become significant. A paucity of tree pollen in the whole spectrum could occur after various types of vegetation and after certain conditions of soil moisture.
During the Boreal, Atlantic and Fagus-Carpinus period both homogeneous forest profiles and podsolic profiles occurred under diverse vegetation. During each of these periods homogeneous forest profiles were degraded to new podsolic profiles.
Düne und Moor bei Vogelenzang : Beitrag zur Frage der quartären Niveauveränderungen an der holländischen Nordseeküste
Baren, J. van; Hofker, J. - \ 1927
Wageningen : Veenman (Mitteilungen des Geologischen Instituts der Landbouw hoogeschool, Wageningen no. 11) - 39
duinen - formatie - regressie - transgressie - geologie - moerassen - zwampen - nederland - kwartair - zeespiegelschommelingen - noord-holland - dunes - formation - regression - transgression - geology - marshes - swamps - netherlands - quaternary - sea level fluctuations - noord-holland