1. Ancient DNA and UV-B radiation and its ecological and evolutionary impacts
John Birks
Bio 301 Lecture 4

2. Introduction
Explanation of distributional patterns
Palaeobiological data
Genetic data
Integration of palaeobiology and phylogeography
‘First’ and ‘second’ generation studies
‘Third’ and ‘fourth’ generation studies
Ancient DNA (a-DNA)
Human a-DNA
Analytical criteria
‘Spectacular’ a-DNA studies
Ancient plant DNA
Conclusions

3. UV-B radiation – A driver of speciation?
Introduction
Late-Permian extinction event
Species ‘swarms’
Biological responses to changing UV-B over time
UV-B, diversity, and speciation
Why is pollen yellow?
Why are there so many species in the tropical rain forest?
Conclusions

4. INTRODUCTION Explanation of Distributional Patterns
Geographical distribution of a species derives from
Contemporary processes (ecophysiological processes, species interactions, disturbance regimes, dispersal and establishment, etc.)
Historical processes (decadal to centennial-scale legacies of disturbance or dominance in local patches or areas to deeply rooted phylogenetic divergences at continental to global scales)

5. Quaternary environmental changes over the past 2
Quaternary environmental changes over the past 2.6 million yrs of Earth’s history have had dramatic biogeographical and ecological effects but not so dramatic evolutionary impacts.
Signatures of Quaternary history are apparent in the spatial patterns of species distributions and genetic variation across the globe today.

6. Species have adjusted their geographical ranges in response to environmental (mainly climate) change during the Quaternary – strong individualistic responses, migrations and habitat shifts, but few extinctions.
These historical events leave clues of two kinds on the landscape
Physical remains of ancient organisms preserved in a few local geological settings, providing direct fossil evidence of their former existence “the factual basis for phytogeography”
Genetic composition as inferred from phenotypic traits and molecular markers

7. Both types of clues were used since the mid 19th century to infer the biogeographical history of species – Charles Darwin, Charles Lyell, Asa Gray, Alfred Russell Wallace
Keenly gathered information from modern-day distributions and morphological variation and from Quaternary (and Tertiary) fossils to support their arguments and discussions (cf. Lyell and Darwin)

8. The use of these dual sources were greatly refined in the late 19th and 20th centuries
Plant macrofossils – Clement and Eleanor Reid, Alfred Gabriel Nathhorst, Knud Jensen, Frank Mitchell, Harry Godwin, Bill Watts, Hilary Birks, and others
Modern distributional patterns, phenotypic traits, and co-occurrence patterns – Axel Blytt, Eric Hultén, Rolf Nordhagen, Eilif Dahl, Donald Pigott, Max Walters, and others

9. Since 1960s, major developments in both approaches
Quaternary palaeobiology – 14C-dating, synthesis of pollen and macrofossil data into continental- scale data-bases allowing synoptic mapping of distributional patterns through time (e.g. isochrone and isopollen maps to study migration patterns)
Biogeographical evidence – developed from species occurrences to morphological and phenotypic traits to biochemical markers to, most recently, molecular DNA markers.
Despite these developments, surprisingly few attempts to integrate the wealth of genetic and palaeobiological data now available to elucidate biogeographical history.

10. Notable exceptions
Fagus sylvatica Magri et al. (2006) New Phytol. 171: (see Lecture 2)
Quercus robur & Q. petraea Petit et al. (2002) Forest Ecol Management 156: 49-74
Also Pinus and Abies in Europe
See Petit et al. (2008) Science 330:

11. Palaeobiological Data
All historical sciences have to rely on imperfect and fragmentary evidence
Palaeobiological evidence of ecological history restricted to a limited number of depositional situations (lack of oxygen, permanently waterlogged, etc.). Such situations are absent from many regions and are unevenly distributed elsewhere.
Site density decreases and age uncertainties increase with age.
Pollen data provide complex view of past vegetation, distorted by differential pollen production and dispersal and by taxonomic smoothing (nearly all grass pollen is one pollen type). A Fagus (beech) pollen grain in lake sediments may have come from a tree growing on the lake shore or from a population 1, 10, or 100 km away. No way of knowing!
Macrofossil data impart taxonomic and spatial precision but they are idiosyncratic in relation to sampling, occurrence, and representation. Some lakes are ‘good’ for macrofossils, others are ‘very poor’ for no obvious reasons

12. Despite its limitations, the palaeobiological record does tell us something about past species distributions and the mechanisms behind their dynamics.
Pollen and macrofossils can be used together to refine interpretations of each other
Spatial-scale differences between pollen and macrofossils can reveal patterns across a range of scales when data are mapped in geographical networks

13. However, both pollen and macrofossil data are blind to several features of plant migration
Even with dense network of sites, cannot exclude possibility that some isolated population was too small or too far away from the site to be detected. Incomplete picture, particularly of small, isolated populations.
Tells us nothing about dynamics below morphological species level. What were the source populations for colonisation at a particular site? What were the spatial and temporal patterns of range expansion?
1) expanding front, 2) series of jump dispersals with secondary coalescence, 3) set of parallel pathways from multiple sources, 4) pincer movement from two directions, 5) sequence of successive waves representing different genotypes, 6) some combination of these
Palaeobiological data often show patterns corresponding to one or more of these hypotheses (e.g. 1,2,4) but spatial and temporal limitations preclude definitive interpretations.

14. Genetic Data
Genetic data contain information below the species level that can help to address these and related questions (e.g. Fagus sylvatica study of Magri et al. 2006).
But the genetic evidence has its own limitations.
Can only obtain evidence where extant native populations occur today
Such populations and their associated genetic patterns, represent the culmination of a long and presumably complex history with erasures, overlays, and other distortions in their DNA
The spatial genetic patterns themselves make little sense except in the context of the history of the populations. Interpretation governed by i) density of sampling, ii) number and quality of genetic markers, and iii) accuracy and sophistication of the palaeobiological data and insights into the genetic data

15. Integration of Palaeobiology and Phylogeography
Both palaeobiological and genetic data are needed together to understand distributional patterns
Have tended to develop along separate pathways with, until recently, an important asymmetry
Palaeobiologists have, with few exceptions, relied exclusively on fossil records as their source of inference and have ignored (or even questioned) the relevance of genetic evidence.
Phylogeographers have recognised from the outset that interpretation of genetic patterns requires independent knowledge of history, and have used (not always correctly!) geological, palaeoclimatic, and palaeoecological literature to generate and test hypotheses to explain observed genetic patterns

16. First- and Second-Generation Studies
With few exceptions, phylogeographers did not enlist the help of palaeobiologists with the result that many first- generation phylogeographic interpretations were based on overly simplistic views of Quaternary biogeography and climatic history. They miss the richness and complexity of Quaternary climate and vegetation dynamics revealed by recent detailed palaeoecological studies at a range of spatial and temporal scales completed in the last two decades.
When DNA-based phylogeography was getting underway, understanding of Quaternary dynamics was undergoing rapid change and thus phylogeographers were using Quaternary literature and data-bases that were fast becoming obsolete. No excuse for repeating the mistakes of years later in 2012!

17. Recommend reading
Magri et al. (2006) New Phytologist 171: (Fagus)
Petit et al. (2002) Forest Ecology and Management 156: (Quercus)
Both exemplary studies involve DNA studies of large numbers of extant populations throughout the geographical range of the tree, make full use of palaeobiological data, and careful data analysis where ‘the data are allowed to speak for themselves’
These represent state-of-the-art second-generation studies integrating Quaternary palaeobiology and phylogeography
What about future third or even fourth generation studies?

18. Third- and Fourth-Generation Studies
Third generation – not only incorporate sampling of new genetic data and use all palaeobiological data, but also include targetted palaeobiological sampling to obtain new and/or better palaeobiological records. Productive strategy can develop in which genetic studies tell palaeobiologists where data are critically needed and palaeobiological studies can identify targets for intensive genetic sampling. Need continuous dialogue between phylogeographers and palaeobiologists.

19. Fourth generation – integrated palaeobiological and phylogeographical studies may lead to the fourth-generation fusion of physical and genetic evidence via ancient DNA (a-DNA) studies.
Development of spatial arrays of a-DNA records integrated with modern phylogeography, standard but detailed palaeobiological studies, and independent palaeoclimatic records (e.g. stable isotopes, chironomid-inferred temperatures) could, in theory, revolutionise our understanding of what actually happens to species and populations in changing environments.
What is the status of a-DNA studies?

20. ANCIENT DNA (a-DNA)
Ancient DNA – any DNA recovered from biological samples can provide a direct approach to reconstructing history of life
Bones and scales
Preserved seeds and resting eggs
Permafrost and ice samples
Fossil animals
Fossil plant material (seeds, pollen)
Sediments
a-DNA may provide insights into extant and extinct populations and species and inform us about biological change through time

21. In theory, could provide ‘evolutionary time travel’ to explore empirically how biota and species, including Homo sapiens, have responded to environmental change. Results are of importance to biologists, ecologists, phylogeographers, anthropologists, medical scientists, geneticists, climatologists, and archaeologists and economists interested in the economies of past civilisations.
a-DNA was, in 2010, considered one of the top ten ‘big ideas’ of the decade, leading to
draft nuclear sequence of Neanderthals
discovery of a new hominid from Denisova Cave in Siberia

22. Human a-DNA
Gibbons (2010)
Calloway (2011)

23. Gibbons (2011)

24. a-DNA suggests two episodes of limited gene flow
modern genomes 
Neanderthal remains 
Denisova Cave  third group with distinct ancient genome
Arrows show commonly accepted migration routes of modern humans out of Africa
African populations genetically highly diverse
Bustamante & Henn (2010)
a-DNA suggests two episodes of limited gene flow
genetic mixing from Neanderthals to modern humans shortly after exit from Africa
subsequent mixing with the Denisovan population. Only affected ancestors of present-day Melenasians who colonised Papua New Guinea ~45,000 years ago.

25. a-DNA is a major research field in archaeology
2001
2005

26. Such great enthusiasm for a-DNA was not always the case
a-DNA molecules from recent material are characteristically degraded into short pieces and present only in trace amounts
contamination and the synthesis of spurious DNA sequences via PCR (polymerase chain reaction) are major risks
early claims in 1980s of 80 million year old dinosaur DNA turned out to be human DNA
frequent bacterial or human contamination of proposed a-DNA samples has resulted in many flawed studies

27. Analytical Quality Criteria
a-DNA labs now have nine criteria for authenticity as standardised criteria. Still not always possible to follow them all. In practice, many a-DNA studies incorporate only a subset of the nine criteria even now.

28. Criteria (Cooper & Poinar 2000)
Physically isolated work area
Control amplifications – multiple extractions and PCR controls
Appropriate molecular behaviour – amplification strength carefully selected
Reproducibility
Cloning – verify PCR sequences by cloning amplified products
Independent replication by different labs
Biochemical preservation – evidence for quality of preservation
Quantitation – competitive PCR
Associated remains – examine associated material

29. Ancient DNA:
‘Do it right or not at all’ – Cooper & Poinar (2000)
See papers available from the Student Portal by
de Bruyn et al. (2011)
Gilbert et al. (2005)
Hebsgaard et al. (2005)
on assessing a-DNA studies

30. Other spectacular a-DNA studies that pass at least 6 of the 9 criteria (Papers on Portal – discussion in Class 6)
Woolly mammoths
Debruyne et al. (2008)
Gibbons (2005, 2010)
Pennisi (2005)
Poinar et al. (2006)
Miller et al. (2008)
Cave bears
Knapp et al. (2009)
Noonan et al. (2005)
Palaeo-Eskimo
Dalton (2010)
Curry (2007)
Rasmussen et al. (2008)
Lambert & Huynen (2010)
Reindeer hunting/ husbandry
Bjørnstad et al. (2012)
Ice-core study
Willerslev et al. (2007)

31. Ancient Plant DNA
a-DNA from plants extracted from permafrost soils, dry cave earths, lake sediments, fossil pollen, fossil seeds, fossil wood in archaeological sites, peat, rodent middens
Also bacterial and fungal DNA from lake sediments and permafrost soils
a-DNA preserved in varying amounts and with varying preservation in a range of sedimentary environments – not necessarily of great age
Wood remains yrs Liepelt et al. (2006)
Peat yrs Suyama et al. (2008)
Bacteria yrs Madeja et al. (2009)
Leaves million yrs Kim et al. (2004)

32. a-DNA from permafrost soils in Siberia
NE Siberia, cores 2-30 m deep, extracted chloroplast DNA and animal DNA 30,000-40,000 years old.
Found at least 19 vascular plant taxa - Cyperaceae, Poaceae, Liliaceae, Ericaceae, Salicaceae, Fabaceae, Rosaceae, Polygonaceae, Caryophyllaceae, Asteraceae, Papaveraceae, Campanulaceae, etc., plus 3 more families.
Also mammoth, musk ox, horse, lemming, hare, and bison DNA.
Willerslev et al. (2003) Science 300: ; 407

33. Change in plant composition and diversity through time in permafrost core samples. (A) For each time period, the proportion of shrubs, herbs, and mosses observed is indicated, along with the proportion of all taxa that are detected or not detected in samples from the previous time point. Clone sequences 96% identical are assumed to represent one taxon. (B) Changes in taxonomic diversity through time, as measured by the number of sequence groups (clone sequences with <96% similarity) divided by the total number of clone sequences obtained for that sample. To standardise the number of clones sequenced, sequence diversity was measured in each sample with 1000 data sets of 32 randomly chosen clones. Black dots represent permafrost samples; white dots represent New Zealand cave samples.

34. Being used as a ‘fossil’ to identify fossils and to estimate biodiversity. Not being used as a palaeogenetic tool.
Permafrost soil contains not only plant a-DNA but also megafaunal a-DNA (mammoth, bison, horse, etc.), and a-DNA from fungi, yeasts, lichen mycobionts, plant-parasitic fungi, even tree- associated macrofungi (?in LGM tundra?). Megafaunal a-DNA could be from faeces, hair, skin, and nails.
Large and unknown source area.

35. Sønstebø et al. (2010) Molecular Ecology Resources 10: 1009-1018
Looked at a-DNA with the P6 loop using ‘next- generation sequencing’ in two permafrost soils from Siberia (15,810 and 22,960 14C yrs BP)
Identified 47 taxa in 22,960 yr BP sample and 17 in 15,810 yr BP sample. Data-base of 842 arctic species
Results make good sense ecologically, data are semi-quantitative (%), and agree with detailed plant macrofossil data. a-DNA used as a palaeobiological tool not a palaeogenetic tool.

36. Is a-DNA leaching and movement a factor in soil DNA studies?
Haile et al. (2007) Molecular Biology & Evolution 24:
Two cave sites on North Island, New Zealand. Sheep are an introduced animal so its DNA is a marker of contamination by modern DNA.
Found sheep DNA in strata that contained moa DNA (an extinct flightless bird). DNA had migrated downwards.
Amount of sheep DNA decreased as age of sediments increased.
Sedimentary a-DNA unlikely to be wind-borne and physical remains of organisms or their excreta must be incorporated in the sediments for their DNA to be detected.

37. Biogeographical shifts inferred from a-DNA
Kuch et al. (2002) Molecular Ecology 11:
11,700 yr rodent midden from Atacama Desert, Chile
a-DNA 5 families, 3 orders
Macrofossils 13 families
More diverse flora than today – more Poaceae, Solanaceae, and Fabaceae. All found today at higher elevations and in more humid areas.
a-DNA used to identify the rodent that formed the midden as Phyllotis limatus, only found km north of the site today.

38. Biogeographical shifts inferred from a-DNA
Poinar et al. (1998) Science 281:
Molecular coproscopy of dung of extinct ground sloth in Gypsum Cave, Nevada
Plants present occur today at elevations 800 m higher than the cave.
Major ecological shifts.

39. Ancient DNA and pollen
So far, the organisms that produced the a-DNA are not all known and a-DNA is being used as a means of identification.
Alternative approach is to extract a-DNA from identified fossils to reconstruct past lineages.
Pollen contains haploid DNA and is the means of dispersal to haploid DNA of ovules. Consists of 2-3 haploid cells (large vegetative cells including several plastids and mitochondria). Organelle DNA is thus present in pollen.

40. Pollen from species with paternal inheritance of plastid DNA (e. g
Pollen from species with paternal inheritance of plastid DNA (e.g. 6 of the 7 families of conifers) is rich in plastid DNA at maturation, and the existence of these multiple copies makes this source of DNA the best prospect for a-DNA studies using pollen.
Nuclear DNA, in contrast, present only as a single copy (and is subject to recombination that complicates its use in phylogeography).
Plant mitochondrial DNA evolves too slowly, whereas plastid DNA appears to be ideal for phylogeographical reconstruction.

41. As a source of a-DNA, pollen has a disadvantage in that from each grain there is only one change for extracting DNA of each type (nuclear, plastid, mitochondrial) in contrast to bone, tissue, or wood. Replicability comes from the ready access to a large number of pollen grains (e.g ), giving the possibility of a statistical population of genotypes, rather than a strong dependence on the successful extraction from a few (or even one) genotypes.
Methods: Bennett & Parducci (2006) The Holocene 16:

42. Applications Parducci et al. (2005)
Chloroplast DNA from Pinus pollen in central Sweden 100 and 10,000 yrs old. Identical – no change
Suyama et al. (1996)
Chloroplast DNA from Abies pollen >100,000 yrs old in Japan
Paffetti et al. (2007)
Chloroplast DNA from Fagus orientalis pollen (angiosperm) 45,000 yrs old
Magyari et al. (2011)
Chloroplast DNA from Picea pollen and cones from South Carpathians. Showed a-DNA from early Holocene similar to today but earlier forms had a greater level of genetic variation. Loss of ancient allele types probably due to repeated bottlenecks during the Holocene. Major discovery – loss of genetic diversity during Holocene.

43. Magyari et al. (2011)

44. Pollen a-DNA future directions
Pollen is probably the most abundant late- Quaternary fossil. Potentially ideal in a-DNA studies
Investigate population-level dynamics in time and space
Trace ancestry of populations and develop phylogenetic trees that include extinct taxa
Develop technique over the last glacial-interglacial cycle, and investigate the extent to which evolutionary changes are influenced by climatic changes of a glacial-interglacial oscillation.
Much to be done. Very demanding work. Results so far not particularly exciting but things may hot up soon!

45. a-DNA from macrofossils in lake sediments
Anderson-Carpenter et al. (2011) BMC Evolutionary Biology 11: 30
Looked at a-DNA in bulk sediment and in macrofossils from 4 tree species in 7 small lakes in Upper Michigan and Wisconsin
Could only extract DNA from sediments younger than 4600 yrs old. Regional-scale feature, possibly due to drop in lake-levels before 4000 yrs ago, leading to better oxygenated conditions and decay
sen = senescent material

46. a-DNA and genetic responses to environmental change
Surprisingly few such studies!
Epp et al. (2010) J. Paleolimnol. 43:
Alkaline-saline crater lake in Kenya. Examined a-DNA of Brachionus rotifers
Dominated by B (red), then a change to A (blue) after deposition of volcanic ash, changing back to B but with a new haplotype D (green) while lake levels were falling. Subtle genetic shifts.

47. Hadly et al. (2004) PLoS Biology 2: e290
Two small mammal species Microtus montanus and Thomomys talpoides in Lamar Cave, Wyoming during late- Holocene climatic change. Used a-DNA to compare two independent estimates of population size (ecological and genetic).
Showed that population size decreased when climate changed and one species showed declining genetic diversity, as predicted from simple population genetic models. Consistent with selection hypothesis, but independent evidence suggests differences in gene flow which depends on the life-history strategy of the species.

48. Hofreiter et al. (2012) Quat. Sci. Rev. 33: 1-13
DNA recovery through time for coprolites (human, sloth) and sediments (permafrost, temperate, marine, and freshwater). Extends to 500,000 yrs, mainly last 10,000 yrs

49. Conclusions a-DNA studies are, with considerable care, possible
Need very great care in sampling, laboratory techniques, and analytical techniques
Need to follow the 9 criteria of Cooper & Poinar (2000) – not always done
In Quaternary palaeobiology, a-DNA has been primarily used as a means of identifying fossil taxa. Very little done on genetic variability, adaptation, or environmental impacts
Great contributions in archaeology
Botanical applications perhaps a touch of ‘much ado about nothing’. Will no doubt change in the future

50. UV-B RADIATION – A DRIVER OF SPECIATION?
Influences stratosphere and troposphere and hence solar radiation, atmospheric circulation, precipitation, and temperature near Earth’s surface.
Can, in conjunction with solar wind and solar cosmic rays, cause small variations in solar activity that can be amplified to causes significant climatic changes.
UV-B radiation ( nm) currently 1.5% of incoming solar radiation. Amount changes over time

51. Why should UV-B be potentially important in speciation?
Willis et al. (2009) J. Biogeography 36:
Wavelength: nm
Common effects of 20% elevated UV-B are
reduced plant height
decreased shoot mass
reduced leaf area
increased UV-B absorbing pigments
increased genetic mutations
Elevated UV-B levels have been shown to change the rate of mutation and hence genetic change and speciation rates.

52. Much work has been done on effects of elevated UV-B on organisms and ecosystems, including human health
Individuals
Reduction in plant height and above-ground biomass
Decreased shoot mass
Reduction in leaf area
Increase in UV-B absorbing pigments in cuticles, pollen and spores, wood, and seed coats
Genetic mutations
Decrease in overall fitness
2001
Ecosystems
Changes in nutrient cycling
Decreased shoot mass
Increased rates of N fixation
Increased litter decomposition
2009

53. UV-B radiation currently 1.5% of incoming solar radiation
Major changes have occurred in recent times and in Deep-Time
In some time intervals, areas have received % more UV-B than today
Possible mechanisms
Changes in thickness of stratospheric ozone layer
Solar activity
Milankovitch orbital fluctuations
Volcanic events
Variations in cloud cover

54. Late Permian Mass Extinction Event (250 Myr ago)
Most devastating ecological event of all time, made worse by two earlier events at 260 and 270 Myr.
Ecosystems were destroyed worldwide
50% of all families of marine and terrestrial animals went extinct
80-96% species loss
Probably only 4-20% species survived
Total extinction of blastoid echinoderms, tabulate and rugose corals, graptolites, and trilobites. Two thirds of tetrapod families went extinct

55. Biologically a few taxa appeared in almost all areas and there seems to have been a quick taxonomic recovery.
When examined in fine stratigraphical detail, diversity never recovered to pre-extinction levels.
Sahney & Benton (2008)

56. What may have caused this massive mass extinction?
No evidence for asteroid impact.
Current hypothesis centres on the Siberian Traps, 2 million km3 of basalt lava covering 1.6 million km2 of Eastern Russia at depths of m.
Massive eruption in less than 1 Myr right at the end of the Permian.
Major changes in oxygen isotopes at end of Permian suggesting a global temperature rise of 6°C. This could reduce ocean circulation and cause a lack of oxygen (anoxia) on sea-floor.
But carbon isotopes show a sharp negative change from 2-4 parts per thousand to -2 parts per thousand. This implies a dramatic increase in the light 12C isotope. But what caused this?

57. Gas hydrates – formed from remains of marine plankton that sink to sea-bed and become buried. Over millions of years, huge amounts of carbon are transported to deep oceans and are trapped as methane in a frozen ice lattice.
If gas hydrates are disturbed by an earthquake or sea-water warms, gas hydrates may be dislodged and methane is released and rushes to surface. Gas hydrates are at depth and under high pressure. In rush to surface, gas hydrates expand as much as 160 times. Contain carbon as the light 12C isotope.

58. Terrestrial extinctions
Current idea – largely driven by the rise of atmospheric CO2 and global warming
Siberian Trap volcanism
 CO2
 CO2
 SO4- and NO3-
 CH4
Melting of gas hydrates
Global warming
 ocean circulation
 upwelling
Acid rain
Marine anoxia
 productivity
Terrestrial extinctions
Marine extinctions

59. What effects did mass extinction events have on plants?
Originally thought that there was little or no evidence for mass extinction in the plant fossil record.
Is this likely?
If you go to a zoo and shoot all the animals, you have the end of the zoo.
If you go to a plant nature reserve and burn all the plants, within 2-10 years, a large number of species reappear.
Also in Gould’s scheme of evolutionary processes, without mass extinctions, dinosaurs would still dominate the vertebrate world. If there are no mass extinctions in the plant world, modern vegetation would be dominated by lycopods, Bennettitales, or early gymnosperms like cycads.
Do we need an upper layer in Gould’s scheme for plant evolution – one driven by competition and selection of lineages? A return to Darwinian principles of natural selection but at the level of species rather than individuals as in natural selection.

60. McElwain & Punyasena (2007) TREE 22: 548-557
Plants and mass extinction events
Event
Fauna family (%)
Flora family (%)
Terrestrial
Marine
Global
Regional
Late Ordovician ? 24
Late Devonian 44 28
<5
30-40
Late Permian 62 50 19
Late Triassic 22 23 17
Late Cretaceous 6 15
18-30
Floral extinctions much less than animal extinctions at global scale, but more extensive at the regional scale.
Now appears that although plants persisted across mass extinction boundaries, there may have been major changes in their abundance.

61. Consider Late Permian mass extinction event –
C isotope shift
–3-5%
CO2 (ppmv)
>2000 
Asteroid impact
(+)
Volcanism
++ (Siberian Traps)
Global temp change (°C)
>8

62. Change in plant community structure and d13C isotope shifts (red line)
Change in plant community structure and d13C isotope shifts (red line). Major animal extinction times shown in grey.
McElwain & Punyasena (2007)
Late Permian – many malformed lycopod spores, possibly a result of increased UV-B radiation.
See plant community instability soon after mass extinctions, rather than global plant extinctions. Plant community changes may have had effects on terrestrial ecosystem functioning such as biogeochemical cycles.

63. Severe disruption of stratosphere ozone balance (80% thinning) during massive Siberian Trap volcanic eruptions – may have increased UV radiation and caused widespread mutation.
Abundant mutant deformed Lycopodium spores and pollen grains at this time on several continents.
Foster & Afonin (2005)

64. Visscher et al. (2004)
Altered plant genomes and their proper functioning, and caused dieback of vegetation, especially woody plants.
“Mutation caused by cosmic radiation could account for not only extinction, but also for accelerated origination of clades” Schindewolf (1954)

65. Common patterns of plant changes at mass extinction events
Permanent or temporary loss of ecological dominants at regional scales over thousands to millions of years.
Recoveries over millions of years.
Prolonged instability at Late Triassic and Late Permian events.
Although few plant families were lost, extinction at species level was highly selective. High loss of insect-pollinated taxa at Late Cretaceous event and of insect-pollinated cycads at the Late Triassic event.
Most post extinction-event survivors had low abundances before the event. Probably poor competitors in pre-event time, but competitive balances changed after extinction event.

66. Likelihood of extinction changed
Likelihood of extinction changed. Rarities as defined as having low relative abundances in last quartile (25%) of rank distributions went extinct more at Late Triassic event but not at the other events.
Plant families show incredible resilience across the mass extinction events. Do not show mass extinctions but show major ecological changes with impacts on ecosystem function – primary productivity and run-off rates and biogeochemical cycles (e.g. increased particulate and nutrient flux from land into oceans at Late Permian and Late Devonian).
No primary role in the overall patterns of plant evolution, in contrast to animals.

67. Plant groups show amazing taxonomic resilience across faunal mass extinction events, possibly to the great breadth of morphological, anatomical, and physiological traits that plants have. Great survivors!
Can we learn anything from the mass extinction events concerning the present sixth mass extinction in Earth’s history?
reproductively specialised groups suffered disproportionately in previous mass extinctions, providing Deep-Time support for predictions from metapopulation dynamics
need to consider assemblages as a whole rather than individual species in modelling future responses

68. Not a complete picture – ignores Milankovitch cycles
Three levels of processes controlling evolutionary patterns as seen in the geological record – Gould (1985)
Level
Period
Cause
Evolutionary processes
First -
Microevolutionary change through natural selection in more-or-less stable assemblages
Second
Geographic isolation (continental drift, creation of islands, etc)
Macroevolutionary change through speciation in conditions of geographical isolation (allopatric speciation)
Third
Ca. 26 Myr
Mass extinctions
Loss of species and higher taxa
Not a complete picture – ignores Milankovitch cycles

69. Species-rich ‘Swarms’ or ‘hotspots’ within the Himalaya
Huge diversity of one genus (up to 300 species) in an area. Many ‘neo-endemics’. Himalaya has more such species ‘swarms’ than any other mountain area in the world.
Pedicularis Primula Cremanthodium
Meconopsis Saussurea Saxifraga
Rhododendron Ligularia Gentiana
Corydalis

70. Pedicularis
Pedicularis oederi, Norway
Pedicularis tricolor, Sichuan

71. Pedicularis przewalskii, Qinghai Pedicularis siphonantha, Bhutan

72. Pedicularis bella, Bhutan Pedicularis decorissima, Sichuan
Photo: Mike Grant
Pedicularis bella, Bhutan
Pedicularis decorissima, Sichuan

73. Meconopsis discigera, Bhutan

74. Meconopsis horridula ssp. racemosa, Sichuan
Meconopsis horridula ssp. horridula, Tibet

75. Meconopsis integrifolia Sichuan Meconopsis pseudointegrifolia Yunnan

76. Meconopsis simplicifolia Tibet Meconopsis punicea Sichuan

77. Meconopsis lancifolia Sichuan Meconopsis delavayi Yunnan

78. Meconopsis aculeata NW India Meconopsis speciosa Yunnan

79. Meconopsis pseudovenusta, Yunnan Meconopsis quintuplinervia, Sichuan

80. Meconopsis tibetica, Tibet
Rediscovered in 2005 and described in 2006

81. Many of these highly localised species-rich swarms are in high mountain areas, often of relatively recent (Tertiary) age.
Commonest interpretation is that these ‘swarms’ are caused by rapid habitat isolation resulting from isolation as the land is uplifted. Combined with locally changing conditions, result is allopatric speciation in a small area.
Alternative hypothesis: these speciation patterns occurred, in part at least, as a result of changing UV-radiation experienced by the plants as the landmass was uplifted. Provides a sympatric speciation mechanism, or at least a mechanism that does not require total geographical isolation. Such isolation does not exist in places like Tibetan Plateau – very uniform landscape and topography.

82. Ratio of Himalayan endemics to total species richness steadily increases with altitude.
Isolation effect more and more important at high altitudes above 5000 m. Also high UV-B radiation.
0.6
0.4
Ratio of endemics
0.2
0.0
1000
2000
3000
4000
5000
6000
Altitude
Saussurea bhutkesh
Rheum nobile

83. UV-B has varied in the past, related to Milankovitch orbital mechanisms, as well as varying spatially.
More variation at high latitudes due to lower sun angles and lower radiation values.
Over last 250 thousand years, UV-B is calculated to have varied from -26% less to +32% more than today.
March equinox 60°N
-10% to +12% variation
Willis et al. (2009)

84. What are the biological responses to changing UV-B over time?
UV-B changes with altitude and the formation of ‘dwarf forest’ at the upper limit of tropical mountain cloud forest may be related to UV-B
Stunted tree growth
Small thick leaves
Extra pigments
But no evidence for dwarf forest in last glacial period
Photos: Bill Baker

85. (TMCF = tropical montane cloud forest)
If temperatures decreased but UV-B stayed the same, climate too cold for trees to be in the UV-B zone, hence no dwarf forest.
(TMCF = tropical montane cloud forest)
Flenley (1993)

86. Is there a relation between increased UV-B, diversity, and speciation?
Only one fossil record to indicate UV-B changes through time, but only in Holocene.
Look at effect of increased UV-B related to mountain uplift in Deep-Time.
Amount of UV-B received at a point on Earth is mainly determined by distance from the sun.
Changes in UV-B amount can result from latitudinal/longitudinal tectonic plate movement or altitudinal movement (mountain uplift).
UV-B gets stronger by about 15% per km vertically.

87. Qinghai-Tibet Plateau, 5000 m elevation
Uplifted in last 120 Myr as a result of collision of Indian subcontinental plate with Eruasian plate.
Can calculate UV-B change as Tibetan Plateau uplifted:
increased by approximately 100% - twice as much UV-B at 5000 m than at sea-level 50 Myr ago
Willis et al. (2009)

88. Tibetan Plateau is centre for several swarms of neo-endemic species
Saussurea – over 250 endemic species
Ligularia-Cremanthodium-Parasenecio – 200 endemic species
Nannoglottis – 80 endemic species
Ligularia sagitta
Cremanthodium bruneopilosum
Parasenecio deltophyllus

89. Saussurea 250 endemic spp. bhuktesh superba brunneopilosa tangutica
medusa

90. Saussurea gossipiphora
Saussurea gnaphaloides (6400 m)
Saussurea tridactyla
Photos: Toshio Yoshido

91. Molecular phylogeny of Saussurea in Qinghai shows series of ‘bursts of diversification’ associated in time with stages in uplift of Tibetan Plateau and then explosive species radiation in last 20 Myr.
Similar picture for other Tibetan plants, for Andean mountain plants, and for mountain mosses and liverworts.
Perhaps during intervals of uplift, increased UV-B radiation (up to 100% greater than present) associated with the uplift may have caused significant changes to plant populations through an increase in mutation rates. leading to molecular evolution and ultimately speciation.

92. Linked to this, increased UV-B would influence growth responses, leading to the development of distinctive plant morphological types.
Higher the altitude, the more times populations in the landscape would have undergone these processes.
May explain the increase in the proportion of endemic plant species with altitude in the Himalaya and the Chinese mountains.
Possible that UV-B may have had effects disproportionately large relative to the amount of incoming UV-B radiation, as most incoming radiation is visible or infra-red.

93. Recent attempts at reconstructing changes in UV-B flux through the Holocene
Willis et al. (2011) New Phytologist 192:
Model simulation
Measured para-coumaric acid in Pinus pollen as a proxy for recording UV-B influx through time
Modern
Fossil

94. Now replicated at a site in Scotland
Exciting potentialities if we can reconstruct changes in UV-B flux beyond the Holocene (Magri 2011) in terms of understanding variations in ozone, of environmental impacts, and of evolution
Climate
Environment
Evolution

95. Climate – UV-B reconstructions may help infer variations of ozone in the stratosphere and their effects on climate
Increased solar activity  increased UV-C radiation  photochemical formation of ozone and hence adsorption of UV-B radiation
Past solar variability reconstructed using cosmogenic solar radionuclides such as 10Be and various biological climate proxy data
Using both solar and climate proxies, possible connections between solar activity and climate can be found. UV-B reconstructions make these connections possible at yrs, including the possible role of human activity on climate

96. 2. Environment – UV-B changes have many different direct and indirect effects on terrestrial and aquatic ecosystems
Tendency to reduce biomass accumulation. May have impacts on community composition and biological turnover

97. 3. Evolution – Changes in UV-B may induce mutations and can be expected to influence all aspects of plant genetics up to and including speciation rates and hence the mode and tempo of evolution
Permian mass extinction
Increased speciation rates in Eocene and Miocene may be association with high UV-B values
No means of currently testing them
Need fossil pine pollen covering yrs to test these ideas

98. Why is Pollen Yellow? Flenley (2011) J. Biogeography 36: 809-816
Pine pollen floating at shore of lake in April-May – why is it yellow?
Yellow colour results from flavonoids including anthocyanins
consist of three linked carbon atom rings (one heterocyclic)
can all absorb UV-B radiation
pollen contains DNA for transmission to next generation
Flavonoids could protect the DNA in pollen against UV-B induced mutagenesis.

99. Why are there so Many Species in the Tropical Rain Forest?
Flenley (2011)
A ‘big’ question in ecology and biogeography
Tropical mountain vegetation experiences highest UV-B radiation of any vegetation type in the world. UV-B enhanced by volcanic eruptions releasing aerosols.
Seen that there was strong volcanicity and mutation in late Permian

100. Palynological richness (& biodiversity) shows rapid increase in Palaeocene-Eocene and early Miocene, both times of peak temperatures
DNA phylogenies show increasing diversity at these times
Milankovitch cycles would have caused vertical migrations of tree taxa over about 800 m
These migrations could have led to isolation of mountain peaks, allowing allopatric speciation, especially in the montane elevated UV-B environment
Process when repeated many times could lead to a ‘species pump’ and thus to high biodiversity. Explains genera with so many species, e.g. Rhododendron, Espeletia, and Cymbidium

101. New Tertiary montane volcanic UV-B hypothesis for tropical mountain biodiversity
Pollen needs protection from UV-B radiation
UV-B radiation is mutagenic
UV-B radiation increases with altitude
Tropical mountains experience highest UV-B radiation of any world vegetation type
Several tropical montane genera show isolated species occurrences in isolated mountains (endemic species)
Erupting volcanoes release SO2 and other aerosols that destroy ozone and thus increase UV-B radiation

102. The aerosols are active near their source and spread widely
Tropical regions have many volcanoes
In the Permian, evidence for strong volcanism associated with mutagenesis, presumably by UV-B
Volcanicity is associated with orogeny
Last great orogeny was the Alpine which started in Eocene and was also active in early Miocene
Palynological richness shows rapid increases in Palaeocene-Eocene and early Miocene
Branching of DNA trees of tropical families occurs especially in the Palaeocene-Eocene and early Miocene
Milankovitch cycles would have produced vertical migrations of tropical taxa with a magnitude ~800m

103. Wonderful example of creative lateral thinking across disciplines
Eocene warm phase of Milankovitch cycle
Eocene cool phase of Milankovitch cycle
Flenley (2011)
Wonderful example of creative lateral thinking across disciplines

104. CONCLUSIONS
Quaternary palaeobiological data source of information not only about past flora, vegetation, and environment, but also populations, past distributions, and biodiversity.
Plants respond to environmental change in different ways – persistence, adaptation, migration, extinction.
Migration is the dominant plant response to Quaternary climate changes.
Stasis, surprisingly, is the dominant evolutionary pattern in the Quaternary.

105. Both macro- and micro- (cryptic) refugia are essential in both cold and temperate phases for trees and arctic-alpine plants.
Speciations and extinctions surprisingly rare in the Quaternary, other than extinctions due to human activity.
Much remains to be done before ancient DNA can be used to help test ideas about the evolutionary legacies of the Ice Ages.
UV-B radiation is likely to be a major driver of speciation but much to be learnt about how UV-B has changed over time.

106. Quaternary palaeobiology, phylogeography, Deep-Time palaeobiology, and biogeography have much to contribute to our understanding basic questions of biodiversity changes in space and time and to assessing the evolutionary legacies of the Ice Ages.
Given the complexity of biological responses to climatic changes such as the Ice Ages seen in the fossil record, which range from single-taxon responses to multi-taxon responses, not surprising we are a long way from understanding the evolutionary legacies of the Ice Ages.

107. Single-taxon and multi-taxon responses to climatic changes as seen in the mammal fossil record. Arrows represent processes that link different responses (e.g. range shift  immigration  biotic turnover)
Blois & Hadly (2009)