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An introduction to the ecology and evolution of biodiversity

Lucie Zinger Institut de Biologie de l'École Normale Supérieure, 46 rue d’Ulm, 75005, Paris. [email protected]

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

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What is “biodiversity”? The degree of variation of all life forms Biosphere

• Encompasses all levels of biological organization Genes and genomes Ecosystems

Cells Individuals Populations

Communities

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What is “biodiversity”? The degree of variation of all life forms • Levels of individuals and populations: • Molecular diversity (e.g. neutral vs. adaptive) • Phenotypic diversity (e.g. genes mutation vs. regulation) Harmonia axyridis (>200 color patterns)

1mm

Gautier, M., et al. (2018). The genomic basis of color pattern polymorphism in the harlequin ladybird. Current Biology.

What is “biodiversity”? The degree of variation of all life forms

• Level of the biocenosis (groups of populations): • Taxonomic diversity (often species diversity)

Postcard by François Crozat, edited by the Rhône-Alpes federation of associations for nature protection (FRAPNA)

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What is “biodiversity”?

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The degree of variation of all life forms • Levels of ecosystems (biocenoses and their abiotic conditions): • ecological/ecosystem diversity Landscape scale

Valley of Cocora near Salento, Colombia (Nicolas De Corte / Alamy)

Global scale

Olson, D. et al. (2001). Terrestrial Ecoregions of the World: A New Map of Life on EarthA new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. BioScience, 51(11), 933-938.

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A recent concept in biology • Early naturalists

Aristotle

C. von Linné

A. von Humboldt

C. Darwin

• “biological diversity” : first reference by R. F. Dassmann in A different kind of country (1968). Later popularised by T. Lovejoy in his textbook Conservation biology (1980)

• “biodiversity” : first contraction by W.G. Rosen (1986), then popularised by E.O. Wilson in his textbook Biodiversity (1988) E.O. Wilson

Increasing awareness of biodiversity

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10000 5000 0 1960

"Biodiversity"

15000

1980

Rio Summit

20000

"Biological diversity"

# scientific publications about biodiversity

• Strategy for “sustainable development” • signed by 168 countries • 3 components: • the conservation of biological diversity • the sustainable use of its elements • the fair share of all advantages derived from genetic resources.

2000

2020

Publication year Source “Web of Science”, keyword “biodiversity”

Biodiversity is ... • “… the variability among living organisms from all sources, including terrestrial, marine, and other aquatic ecosystems, and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems“ (United Nations Convention on Biological Diversity, 1992)

• “… the term given to the variety of life on Earth. It is the variety within and between all species of plants, animals and micro-organisms and the ecosystems within which they live and interact. Biodiversity comprises all the millions of different species that live on our planet, as well as the genetic differences within species. It also refers to the multitude of different ecosystems in which species form unique communities, interacting with one another and the air, water and soil” (Swingland, 2011 in Encyclopedia of Biodiversity)

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Biodiversity does… • “… underlies all ecosystem processes. Ecological processes interacting with the atmosphere, geosphere, and hydrosphere determine the environment on which organisms, including people, depend. Direct benefits such as food crops, clean water, clean air, and aesthetic pleasures all depend on biodiversity, as does the persistence, stability, and productivity of natural systems.” (Millenium Ecosystem Assessment, 2005)

• “… is the foundation of life on Earth. It is crucial for the functioning of ecosystems which provide us with products and services without which we couldn’t live. Oxygen, food, fresh water, fertile soil, medicines, shelter, protection from storms and floods, stable climate and recreation - all have their source in nature and healthy ecosystems. But biodiversity gives us much more than this. We depend on it for our security and health; it strongly affects our social relations and gives us freedom and choice.” (IUCN, 2014)

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The dual definition of biodiversity A quantifiable property

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Ecosystem services: the benefits that ecosystems provide to humanity

(today’s course)

A valuable resource for ecosystems functioning and humans welfare (next courses) Adapted from Global Biodiversity Outlook 2. CBD Secretariat 2006, Fig. 1.1

Biodiversity is valuable

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➡ Intrinsic value of life ➡ Antropocentric valuing Ex: Genetic diversity in crops and livestocks increases the resistance to pathogens Ex: Fish stocks Ex: Diversity of food webs or of the gut microbiota increases communities/host resilience to change Ex: Diversity of landscapes promote ecosystems large scale resilience or restoration Millennium Ecosystem Assessment (2005). Ecosystems and Human Well-being: Biodiversity Synthesis. World Resources Institute, Washington, DC.

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

Biodiversity is a “state of nature” • The variation in the diversity of life in a given area and at a given time period is represented by: • the variety: the number of different types • the quality and quantity: which and how much of each type • the distribution: location of an attribute of biodiversity ~10,000 bird species known on earth

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Several aspects of biodiversity for the hierarchical structure of life

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Variety

Quality/ Quantity

Distribution

Adapted from Noss, R. F. (1990). Indicators for monitoring biodiversity: a hierarchical approach. Conservation biology, 4(4), 355-364.

Species-centred definition of biodiversity • The number of species in a given community and the number of individuals belonging to each species • BUT: what is an individual?

Andrews, J. H. (1998). Bacteria as modular organisms. Annual Reviews in Microbiology, 52(1), 105-126.

Unitary organisms

Modular organisms

➡ number of individuals, cover, biomass, cell density

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Species-centred definition of biodiversity

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• The number of species in a given community and the relative abundance belonging to each species • BUT: what is a species?

See Mayden, R. L. (1997). A hierarchy of species concepts: the denouement in the saga of the species problem. Chicago De Queiroz, K. (2007). Species concepts and species delimitation. Systematic biology, 56(6), 879-886.

Species-centred definition of biodiversity • Other cons: • only one level of biodiversity is investigated • does not account for variation in species functions

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Species-centred definition of biodiversity

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• Pros: massive amount of data ➡ Can inform on species turnover (extinction-immigration) and ecology-evolution

GBIF | Global Biodiversity Information Facility: > 500 years of observations > 109 occurrence records > 106 verified species

https://www.gbif.org/

Measuring biodiversity • The number of species in a given community and the relative abundance belonging to each species • Usually one particular clade or a group of organisms (e.g. macro invertebrates in a river, or trees in a forest). Which one is more diverse? A

B

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Measuring biodiversity • The number of species in a given community and the relative abundance belonging to each species • Usually one particular clade or a group of organisms (e.g. macro invertebrates in a river, or trees in a forest). Which one is more diverse? A

B

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Richness and evenness

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• Any attempt to measure biodiversity quickly runs into the problem that it is a fundamentally multidimensional concept ➡ “A community’s diversity index is merely a single descriptive statistic, only one of the many needed to summarize its char- acteristics, and by itself, not very informative.” (Pielou,1975) • 3 types of biodiversity measures: • Species richness: the number of different species in the community • Species evenness: the equality of numerical abundance of species in the community • Species diversity: a composite measure of species richness and evenness

Biodiversity metrics

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• Species richness

S = total number of species, with pi the relative abundance of species i • Common species diversity indices

H=− λ=

S

S

∑ i=1

pi2 ∑ i=1

pi ln(pi)

Shannon-Weaver diversity index a measure of uncertainty in predicting the identity of individuals

Simpson diversity index (1949) a measure of the probability of equivalence between two entities taken at random

• BUT: • H and λ are not a number of species • Non linearity For more details, see Jost, L. (2006). Entropy and diversity. Oikos, 113(2), 363-375.

Biodiversity metrics

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• A unified framework: the number of equally-common species (“Hill numbers”): inverse of the weighted average of species proportional abundance S

( piq)1/(1−q) ∑ i=1

q

D=

=

1 q−1

S ∑i=1 piq

0

D=S

q→1

S

∑ i=1

D=

a weighting coefficient that gives more weigh to abundant species

q=0 : Species richness

lim qD = exp( 2

q : the “order” of diversity

1

S

∑i=1 pi2

pi ln(pi))

q→1 : exponential of the ShannonWeaver index q=2 : inverse of the Simpson index For more details, see Jost, L. (2006). Entropy and diversity. Oikos, 113(2), 363-375.

Biodiversity metrics

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• A unified framework: the number of equally-common species (“Hill numbers”): inverse of the weighted average of species proportional abundance Diversity qD

Simulated communities: S = 50, N=500, varying evenness

Order q Chao, A., Chiu, C. H., & Jost, L. (2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annual Review of Ecology, Evolution, and Systematics, 45, 297-324.

Species abundance distribution

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• Barro Colorado Island 50ha plot: 225 tree species, 21457 individuals (dbh > 10 cm). ➡ Asymmetric, log-normal distribution

Most species are rare

Few are abundant

See more on SADs in Magurran, A. E., & McGill, B. J. (Eds.). (2011). Biological diversity: frontiers in measurement and assessment. Oxford University Press.

Species abundance distribution

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• Estimating diversity and size of communities at large scales ATDN plots n=1170 S=4962 sp N=639,639 ind.

Extrapolation Observed data

100 billions tree individuals

16,000 tree species

Ter Steege, et al. (2013). Hyperdominance in the Amazonian tree flora. Science, 342(6156), 1243092.

Species abundance distribution

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Ecological succession

Old abandonment: • high diversity • higher evenness Recent abandonment: • low richness • hyperdominance • Structuration

Bazzaz, F. A. (1975). Plant species diversity in old-field successional ecosystems in southern Illinois. Ecology, 56(2), 485-488.

Biodiversity in a spatial context Rank abundance curve 500

Richness

50

Evenness

1

5

1 set of species 0

50

100

150

200

Species rank

S Species abundance distribution

D=(

∑ i=1

15

25

q

piq)1/(1−q)

5

Diversity based on “Hill numbers”: number of equally-common species for a given q order 0

site 1

# Species

(e.g. a plot, a patch, a site)

Species abundance

α diversity : local scale

0.0

1.0

2.0

log10 # Individuals

3.0

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Biodiversity in a spatial context β diversity : differences between localities site 5

site 3 site 2

site 4 site 1

2 | site1 ∩ site2 | | site1 | + | site2 | ds = 1 − s

s=

q=0

Sorensen distance Presence/absence. Complementarity to the intersect of communities divided by their sum. S

SMH =

2 ∑i=1 pi1 pi2

2 2 ( ∑i=1 pi1 + ∑i=1 pi2) S

S

q=2

dSMH = 1 − SMH Morisita-Horn distance Abundances. Probabilities that individuals taken at random belong to the same species in each or any of both communities See more on SADs in Magurran, A. E., & McGill, B. J. (Eds.). (2011). Biological diversity: frontiers in measurement and assessment. Oxford University Press. Chao, A., Chiu, C. H., & Jost, L. (2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. Annual Review of Ecology, Evolution, and Systematics, 45, 297-324.

Biodiversity in a spatial context γ diversity : regional diversity

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➡ Total diversity in a region is composed of α and β diversity

Multiplicative definition (Whittaker 1960, 1972) :

γ = α¯ × β Hill numbers (effective number of species)

Additive definition (Lande, 1996):

γ = α¯ + β entropy measures

See Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88(10), 2427-2439.

Biodiversity: indices vs. indicators • Presence or abundance of one or set of species that summarize the biocenosis or ecosystem status. • Conservation, assessments and communication purposes: Must have a clear proximate basis, be robust and easy to understand and use Indicator species

Keystone species

Limnephilus politus

Canis lupus

Flagship species Ailuropoda melanoleuca

Umbrella species Panthera tigris

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Keystone species and conservation

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Top predators and trophic cascades

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• Direct effects: predation on elks and coyotes • Indirect effects: • Predation release on pronghorn and small mammals • Herbivore release on woody plants • Changes in habitat and stream morphology beneficial for birds, beavers, plants and bears

Ripple, et al. (2014). Trophic cascades from wolves to grizzly bears in Yellowstone. Journal of Animal Ecology, 83(1), 223-233. See also the romantic version here : https://www.youtube.com/watch?v=rSzQ9w5TCqc

Biodiversity indicators based on species conservation status (IUCN) Extinct in the Wild

Near threatened

• Classification of species into threat categories • Scoring system based on ≠ criteria: population size, geographic range, trends, and extinction probability • Working groups of experts specialised on taxonomic groups and regions • Constantly updated

IUCN Red list

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

How to sample biodiversity? • Different sampling methods: • Observational • Traps • Video/audio records • environmental DNA • Need to be representative • Observed area extent? • Observation frequency? • Need to be standardized

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Accumulation/rarefaction curves to deal with sampling effort differences

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• Species accumulation with sample size : allows to compare samples independently from sampling effort

FIT

• Count of arthropod species in different habitats during 38 days with ≠ sampling trapping methods

Missa, O., et al. (2009). Monitoring arthropods in a tropical landscape: relative effects of sampling methods and habitat types on trap catches. Journal of Insect conservation, 13(1), 103.

Accumulation/rarefaction curves to deal with sampling effort differences

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• Species accumulation with sample size : allows to compare samples independently from sampling effort

• Forested • Open FIT

Missa, O., et al. (2009). Monitoring arthropods in a tropical landscape: relative effects of sampling methods and habitat types on trap catches. Journal of Insect conservation, 13(1), 103.

Species distribution survey • Plot scale observations of tree species presence

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ATDN plots n=1170 S=4962 sp N=639,639 ind.

• Statistical interpolation of species based on punctual occurrences Example with two hyperdominant tree species

Ter Steege, et al. (2013). Hyperdominance in the Amazonian tree flora. Science, 342(6156), 1243092.

Acoustic survey of biodiversity

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• Acoustic records in two African forests (mainly birds, amphibians and insects) Simulated communities Simulated chorus of 5 birds , 5 amphibians and 5 insects

Sueur, J., et al. (2008). Rapid acoustic survey for biodiversity appraisal. PloS one, 3(12), e4065.

DNA-based mesures of diversity

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• Human Microbiome project • Alpha diversity (within a person) = substantial variation among individuals and heterogeneity among habitats (high diversity in mouth and low in vagina) Skin

Oral

Gut Urogenital

α diversity (1/Simpson, log2 transformed)

Nasal

Huttenhower, et al. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207.

DNA-based mesures of diversity

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• Human Microbiome project • Beta diversity= more/less variable within habitat but steep variations across habitat and body location

Huttenhower, et al. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207. Bouslimani, A., et al. (2015). Molecular cartography of the human skin surface in 3D. PNAS, 112(17), E2120-E2129.

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

Biodiversity is not equally distributed in space • Measures of species richness and biodiversity taken as a whole are misleading because species and other descriptors of biodiversity such as population and genetic diversity are not equally distributed in space – this distribution is scale and level (e.g., taxonomy, gene) dependent. • Understanding why some species, genes or populations are more abundant at one place rather than another has been one major research question in ecology. Distribution patterns may be explained by assembly rules, that depend on several factors: • abiotic constraints: climate conditions, soil types, etc • biotic interactions: competition, trophic/mutualistic interactions. • dispersal: movement of individuals across space • neutral processes: demographic processes • evolutionary history including speciation, adaptive radiations

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Biogeography and ecology

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Biogeography: Explanation of irregular and regular distribution patterns at large spatial/temporal scales. E.g.: definitions of biotas, geographic barriers to dispersal, history and geography of clade diversification MACROECOLOGY

Ecology: Explanation of irregular and regular distribution patterns at small spatial/temporal scales. E.g. : processes of extinction and colonization, maintenance of diversity, interaction networks See Jenkins, D. G., & Ricklefs, R. E. (2011). Biogeography and ecology: two views of one world.

Biogeography and ecology Biogeography Dispersal and vicariance

Ecology Niche exclusion and coexistence

https://evolution.berkeley.edu/evolibrary/news/091001_madagascar

Begon et al. Ecology (11th edition)

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Biogeography and ecology

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• “Ecologists must broaden their concepts of community processes and incorporate data from systematics, biogeography, and paleontology into analyses of ecological patterns and tests of community theory.” (Ricklefs, 1987) Jenkins, D. G., & Ricklefs, R. E. (2011). Biogeography and ecology: two views of one world.

• “Until we synthesize the ecology and evolution of species formation, habitat shift, and establishment of secondary coexistence, it is unlikely that we will be able to interpret patterns of biodiversity in terms of the processes that produce them. I am very much in favor of injecting genetics and evolution into ecology, and vice versa…” (Ricklefs, 2000).

Examples of broad scale spatial patterns Species-area relationship

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Latitudinal gradient of diversity

Precipitation-diversity relationship

Gaston, K. J. (2000). Global patterns in biodiversity. Nature, 405(6783), 220.

Species-area relationships (SAR) • Species richness from a same group (e.g., reptiles, predators) increases with the habitat area

• Arrhenius power function (1921), supported by Preston (1960,1962) Begon et al. Ecology (11th edition)

S = cA z log(S) = log(c) + z log(A)

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Species-area relationships (SAR)

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• Possible explanations: • More individuals ➡ sampling artefact • More habitat heterogeneity ➡ ecological niche • More biogeographical provinces ➡ evolution and origination Pure area effects found from manipulations of island sizes

Species-area curves for ants on New Guinea (a mainland) and the isolated islands nearby. The island curve is steeper (a higher z) than the New Guinea curve.

From Simberloff, D. (1976). Experimental zoogeography of islands: effects of island size. Ecology, 57(4), 629-648.

SAR and the theory of island biogeography

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• Number of species on an island is determined by a dynamic balance between immigration and extinction rates.

MacArthur & Wilson (1967) The Theory of Island Biogeography From Begon et al. Ecology (11th edition)

Latitudinal gradient of species diversity (LGD)

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• Species diversity increases from the poles to the equator and are maximal in the tropics “The nearer we approach the tropics, the greater the increase in the variety of structure, grace of form, and mixture of colors, as also in perpetual youth and vigor of organic life.”

Humboldt, A. von (1808). Ansichten der Natur mit wissenschaftlichen Erläuterungen, Tübingen. (New edition Eichborn, Frankfurt a. M. 2004)

Latitudinal gradient of species diversity (LGD)

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• A very general pattern Foliar fungal endophytes

Arnold, A. E., & Lutzoni, F. (2007). Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?. Ecology, 88(3), 541-549.

Begon et al. Ecology (11th edition)

Latitudinal gradient of species diversity (LGD)

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Tittensor, D. P., et al. (2010). Global patterns and predictors of marine biodiversity across taxa. Nature, 466(7310), 1098.

Marine species richness (fishes, mammals, invertebrates, etc..), interpolated from ~ 6•106 records, for > 11,000 species

Plant species richness, interpolated from ~ 18,000 plots

Kreft, H., & Jetz, W. (2007). Global patterns and determinants of vascular plant diversity. PNAS, 104(14), 5925-5930.

A multitude of explanations Class of explanations

Examples of scenarios

Artefactual

Species richness increase with geographic area and geographic (continental) areas are lower near the poles

Environmental constraints on ecological processes Evolutionary dynamics

High productivity and energy availability at low latitudes High local climate stability and low climate harshness at low latitudes

Species interactions

More intense species interactions at low latitudes

Expansion from refuge towards high latitudes (“out of the tropics” hypothesis) High evolutionary speeds at low latitudes (“cradles” hypothesis) Longer evolutionary history in the tropics (“museums” hypothesis)

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A multitude of explanations Scenarios

Empirical support

Geographic area

Not a systematic effect in all species tested so far and little evidence that habitat or biome area alone explains the whole pattern

Productivity

Supported by some studies, can be a bimodal relationship between productivity and diversity

Climate stability

Supported by some studies but several exceptions to the rule, can be a bimodal relationship between stability and diversity

Evolutionary dynamics

Recent studies have documented latitudinal clines in extinction-origination and non-equilibrium immigration patterns

Species interactions

Not well supported

“There is no necessary reason why latitudinal gradients exhibited by taxa as distinct as protozoa and mammals, and in environments as structurally different as the deep sea and tropical forests, need be generated in the same way, whatever the attractions of Occam’s razor. Increasingly it seems that patterns in biodiversity are likely to be generated by several contributory mechanisms. The strongest and most general may be those where all the different mechanisms pull in the same direction.” Kevin Gaston, Nature, 2000.

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The kinetic energy hypothesis • The kinetic energy or temperature hypothesis posits: • that at higher temperatures increase metabolic rates, which may promote higher rates of speciation • that range limits are set by thermal tolerance, with more species tolerant of warm conditions

Tittensor, D. P., et al. (2010). Global patterns and predictors of marine biodiversity across taxa. Nature, 466(7310), 1098.

Brown, J. H. (2014). Why are there so many species in the tropics?. Journal of biogeography, 41(1), 8-22.

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Tropics as a cradle, a museum or both? • Cline evolutions scenarios

Arita and Vazquez-Dominguez 2008 Ecology Letters Jablonski et al. 2006 Science

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Estimation of extinction, speciation and migration in mammals

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• Analysis of phylogenetic and distribution patterns in mammals (over 170 My of evolutionary history) supports on average the out-of-the tropic model

Rolland, J., et al. (2014). Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biology, 12(1), e1001775.

Extinction and speciation rates vary across mammals orders

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Higher net diversification rate in the tropics

Higher and lower tropical speciation and extinction rates Higher tropical speciation and extinction rates Lower tropical extinction rates

Higher tropical speciation rates

Balanced speciation and extinction across latitudes Higher tropical extinction rates

From Rolland, J., et al. (2014). Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biology, 12(1), e1001775.

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

How many species on Earth? 1992: 1,413,000 catalogued species

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2011: Catalogued: 1,438,769 Estimate : 10,960,000 ➡ 86% undescribed Prediction based on rate of discovery at different taxonomic levels

Wilson, E. O. (1992). The diversity of life. Allen Lane.

Mora, C. et al. (2011). How many species are there on Earth and in the ocean?. PLoS biology, 9(8), e1001127.

Large uncertainties

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Millennium Ecosystem Assessment (2005). Ecosystems and Human Well-being: Biodiversity Synthesis. World Resources Institute, Washington, DC.

Most diversity still remains unknown to science

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• Most species of Eukaryota are still unknown (and may disappear before they are discovered)

Millennium Ecosystem Assessment (2005). Ecosystems and Human Well-being: Biodiversity Synthesis. World Resources Institute, Washington, DC.

The dark matter of life • Most of the diversity on earth is “invisible”: unicellular life forms • High phylogenetic diversity in microeukaryotes, bacteria and archaea with billions of years life of diversification on Earth 3·109 y

1.6–2.1·109 y

• Broad environmental range including extreme habitat (high pressure, high temperature and acidic, or hypersaline environments) ➡ High metabolic diversity relative to animals and plants

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The dark matter of life • Single cell sequencing of different environments

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Archaea

Known phyla New phyla

Bacteria ~ 11,000 cultured species ~ 10,000 sequenced species (Estimate: 1·1012 species) Rinke, C., et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499(7459), 431. Locey, K. J., & Lennon, J. T. (2016). Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences, 113(21), 5970-5975.

Protists: the other 99% of eukaryotes

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~ 40,000 catalogued species Estimate: 1.4·105 - 1.6·106 species Pawlowski, J., et al. (2012). CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS biology, 10(11), e1001419.

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The “New” species of 2018 •

Discovery rate : ~18,000 new species / year

•

Top ten list of new species in 2018 according to International Institute for Species Exploration

• • • • • • • •

A species of orang-utan in Sumatra A tadpole-like fish from the dark abysses, Pacific Ocean A tree species, Brazil, only 25 known individuals Epimeria quasimodo, an amphipod, Southern Ocean A tiny beetle that lives on the abdomen of a ant species A protist of an unknown early lineage of Eukaryota A mycoheterotrophic orchid, Ishigaki Island A marine proteobacteria nicknamed "Venus' hair”, colonizing volcanic deposits. A marsupial lion from Australia, extinct. A troglobitic ground beetle striking in the dramatic elongation of its head and prothorax, China.

• •

https://www.esf.edu/top10/

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What is biodiversity? How to qualify/quantify it?

How to measure it? How it is distributed spatially? How much is known?

What are its temporal trends?

Biodiversity has changed through time • Estimates are that 4 billion species have leaved on Earth over the last 3.5 billion years and 99% of these species are extinct • The number of species on Earth at a given time is a complex function of the past and present speciation (“birth” of new species) and extinction (death of existing species) processes – these processes are governed by laws of ecology & evolution (and geology) • There have been statis and crisis in the history of life with time periods of fast speciation and time periods of fast extinction leading to evolutionary shifts in community composition and life forms • Our understanding of this history is still very superficial and biased because of the heterogeneity of species records across regions, time periods and taxa, and of difficulty to record speciation and extinction events with fossil records

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The “Big Five” Mass extinction crisis • A mass extinction is defined as a “short-time” event (~ million years) when extinction rates peak higher than the background and where > 50-75% of the species richness has disappeared (Sepkoski & Raup 1982). End O

Late D

End P

End Tr

End K

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The “Big Five” Mass extinction crisis

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• Causes of mass extinction are multiple and some are still debated • Some mass extinction have been short-term and some have lasted longer

More recent studies suggests that the impact caused the Deccan volcanism Barnosky, A. D., et al. (2011). Has the Earth’s sixth mass extinction already arrived?. Nature, 471(7336), 51.

Late Pleistocene/early holocene extinction of megafauna (1,000-100,000 years)

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Elias, S. A., & Schreve, D. (2013). Late Pleistocene megafaunal extinctions.

Barnosky, A. D., et al. (2004). Assessing the causes of Late Pleistocene extinctions on the continents. science, 306(5693), 70-75.

Trends and extremes in “extinction rates”

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Background extinction rate

• Current expected backround extinction rate: 1 E/MSY (extinction per million species-year). Sepkoski's Compendium of Marine Fossil Animal Genera (2002)

Background rates vs. current rates of extinction

• •

Time – taxonomic data of fossils Time intervals of Myears

• •

Direct measurements Indirect measurements (models)

•

Statistical analysis of appearance – disappearance rates and correction of estimates

•

Statistical analysis and correction for sampling biases and taxonomic representativeness

•

Extinction rates over Myears, with time bins including peaks and valleys of extinction-speciation rates

•

Extinction rates over centuriesdecades, typically one contemporary estimate

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➡ Comparison corrected for time interval and heterogeneity in fossil records

Extinction rates are rising at unprecedented rates in mammals

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(extinctions per million species-year)

Projections with IUCN threaten species extinct Current estimates of Pleistocene extinction rates (2.6 My to 12 ky)

Background mean: Mean E/MSY = 1.8 Mean 500 y = 28 Current estimates of recent extinction rates (