Download 3. Identification of species, sex and individuals

3. Identification of species, sex and individuals
3.1. Species
3.1.1. What is a species?
3.1.2. Defining taxonomic groups
3.1.3. Hybrids
3.1.4. Cryptic species
3.1.5. Other applications
3.2. Sex identification
3.3. Individual identification
1
3.1. Species
3.1.1. What is a species?
• At the same time the species is
– a unit of evolution and
– a unit of classification
– Conflict: classification should be stable but evolution is not
• Examples of historical species concepts
– Typological Species Concept: species is a 'type' of organism
• "Species are as many as were created in the beginning by the
Infinite." (Linné 1758)
– Nominalistic Species Concept: a name given for convenience
• "I look at the term species, as one arbitrarily given for the sake
of convenience to a set of individuals closely resembling each
other...." (Darwin, 1859)
2
• Common concepts
– Biological species, Mayr 1963 (BSC)
• "Species are groups of interbreeding natural populations that
are reproductively isolated from other such groups.“
1. Interbreeding => a genetic unit
• species are gene pools: conspecifics (members of the same
species) resemble each other because they are related (have
common ancestors)
2. Natural Populations => an ecological unit
• Population thinking: Organisms derive their
properties from the group. Variation among
individuals is important. Species must be
understood with relation to environment and
other species.
Two individuals of Pheidole
barbata
3. Reproductively isolated => a reproductive unit
• Reproductive Isolating Mechanisms (RIMs): features that prevent
mating outside the species
• Species Recognition Mechanisms (SRMs): features that allow
recognition of potential mates
3
– Evolutionary species, Simpson, 1961 & Wiley, 1981(ESC)
•
"An evolutionary species is a single lineage of ancestor-descendant
populations, which maintains its identity from other such lineages
and which has its own evolutionary tendencies and historical fate."
1. Lineage: an ancestor-descendant series
•
•
genealogy is crucial: members of a species have a common ancestor
Phylogenetic species, Cracraft 1983 (PSC) "A ... cluster of organisms
that is diagnosably distinct from other such clusters, and within which
there is a parental pattern of ancestry and descent.“
2. Identity: a biologically distinct entity
•
Includes concepts associated with Biological
Species, the BSC is the broadest general case
of the ESC
3. Tendencies and Fate: a historical entity
•
•
•
Species have an origin
• by cladogenesis = 'splitting' of lineages
undergo evolution
• by anagenesis = change within lineages
and disappear
• by extinction = termination of lineage
4
3.1.2. Defining taxonomic groups
• Barcode of Life
– Paul Hebert et al. proposed DNA
barcoding as a way to identify
species (Biological identifications
through DNA barcodes, Proc. R. Soc. Lond. B 2003)
– Short DNA sequences as standards
• Animals: 648 bp region in the mitochondrial cytochrome c oxidase 1
gene, CO1
• Plants: two chloroplast gene regions, matK ( coding for maturase,
presumably helps splicing of introns) and rbcL (large subunit of
ribulose 1, 5 bisphosphate carboxylase/oxygenase, RUBISCO)
– Barcode of Life Database (BOLD)
• At present close to 400 000 BINs (Barcode Index Numbers ≈
species), over 4 million specimens
– FinBOL, Finnish Barcode of Life is coordinated by Marko
Mutanen at the University of Oulu
5
• Populations, subspecies or species?
– Koala, Phascoarctus cinereus: three
subspecies based on morphology, but these
are not distinguishable based on molecular
markers
• mtDNA: genetic differentiation between
populations is larger than differentiation
between subspecies (populations: FST = 0.76,
subspecies: FST = 0.55)
® Same result with microsatellites
® How management should be
planned?
Houlden et al. 1999. Mol Ecol
6
– Giraffes: distinct species?
• All extant giraffes (Giraffa camelopardalis) are currently considered
to represent a single species, classified into multiple subspecies
• Geographic variation in traits such as the pelage pattern, is clearly
evident across the range in the sub-Saharan Africa
• Abrupt transition zones between different pelage types are typically
not associated with extrinsic
barriers to gene flow, thus
suggesting reproductive
isolation between the types
Brown et al. BMC Biology 2007 5:57
7
• Petrels, Pterodroma heraldica, neglecta and
arminjoniana (ulappaliitäjiä)
– Dark and a light colour varieties in heraldica
– Assortative mating
– Genetically distinct – at present divided into
different species heraldica and atrata
– Complex multi-species hybridizations?
Haplotype network
cytochrome b-gene
Brown et al. 2011. PLoS ONE
8
• Blue tit, Cyanistes-complex
– Was previously divided into the Bluet tit and the Azure tit
– Morphology, plumage, territorial song, mitochondrial DNA, microsatellites, nuclear
sequences have been studied
– Now divided in three: Canary Blue tit (C. teneriffae), Blue tit and Azure tit
– Azure tit, C. cyanus, closer to C. caeruleus than C. teneriffae
9
Kvist et al. 2005, Illera et al. 2011, Hansson et al. 2015
3.1.3. Hybrids
– Stable hybrid zones
• Selection
• Reduced fitness of the hybrids
• Often a consequence of a secondary contact between
previously isolated populations
• Bombina bombina (kellosammakko) and B. variegata
(vuoristokellosammakko) in Poland
10
At the hybrid zone:
• Abrupt change
in allele
frequency
• Increase of
linkage
disequilibrium
• Increase in
mortality
11
– Unstable hybrid zones
• Often connected with introductions of alien species
• Invasive species may drive the original species into
extinction
• Domestic cat Felis sylvestris catus
and the European wild cat F. s.
sylvestris
• Common quail Coturnix coturnix
(viiriäinen) and Japanese quail C.
japonica (japaninviiriäinen)
–
–
Females of the common quail
respond to the song of their own
species better, but Japanese quail
females accept the both species
equally well
Hybrids have mtDNA of the
Japanese quail
12
3.1.4. Cryptic species
– Common toad Bufo bufo (rupikonna) and Natterjack toad
Bufo calamita (haisukonna)
• Usually do not co-occur, but due to changes in the habitats,
more an more in same regions
• Common toad does better in regions of co-occurrence, the
larvae of Natterjacks do not survive past the
metamorphosis ® local extinctions
• Easy to identify adults, but not the larvae ® RAPD
• Managing habitats in order to decrease interspecific
competition
Bufo bufo
Bufo calamita
13
– Common skate Dipturus batis (silorausku)
•
•
•
•
Heavily fished and population numbers
declined
Largest populations today at the west
coast of Scotland, Celtic Sea and
Norwegian coastline
Now classified as the Blue Skate (D.
flossada ‘southern’) and the Flapper
Skate (D. intermedia ‘northern’)
D. intermedia one of the most
threatened fish species at the moment
Griffits et al 2010 Proc R. Soc. B 14
3.1.5. Other applications
– Identification of the prey
/diet from faeces / guts
• DNA of a mosquito from guts of
a predatory beetle
• Diet of an extinct sloth from
coprolite
– Identification of disease
vectors
• Malaria vectors (Anophelesmosquitoes) and ITS
– Only some of Anophelesspecies carry malaria
® Where to use insecticides
15
– Forensics
• Species identification from maggots of flies from
corpses to define the time of death with RAPDmarkers
• Poaching
• Smuggling
– Endangered species
– Food control
• Microbial source tracking for pathogenic microbes
• Allergen detection
• Animal species detection and differentiation in
meat products
• GM food
16
3.2. Sex identification
• Immature individuals, which have not developed
their secondary sexual characters yet
• Species with ’identical’ sexes
• Why?
–
–
–
–
Mating structure
Conservation
Sex allocation
Financial reasons
• Domestic animals and plants
17
• In mammals, the males are heterogametic (XY) and
females homogametic (XX)
– Sex determining region Y, SRY
• In birds and butterflies, females are heterogametic
(WZ) and males homogametic (ZZ)
– Chromobox-helicase DNA-binding gene, CHD1
– The gene is present in both chromosomes, but size of
an intron is different
18
• Methods developed even for some plants
– Hops, only females needed
for beer production
→ Growing only females is a
financial question
• One RADP-marker found among
900 tested
• Not possible for all taxa
– In reptiles (temperature)
– Drosophila (X chromosome/autosome ratio)
• X chromosome/autosome ratio 1:1 → females
1:2 → males
19
3.3. Individual identification
• Microsatellites
DNA profile from 15 loci
Forensics example
20
Willow tits, Oulu
• Applications of individual
identification
♀
– Kinship and genealogy
• Paternity analyses
♂
– Assignment of individuals to a
population
Chicks
– Mating structure
• Inbreeding
– Forensics
• Connecting a suspect to the
crime scene
• Poaching
– Conservation
• Estimation of population sizes
The only chick sharing an allele with
the male that is taking care of the
chicks
21
4. Molecular methods in behavioral
ecology
4.1. Mating structure and success
4.1.1. Male reproductive success
4.1.2. Female reproductive success
4.2. Social behaviour and collaboration
4.3. Nest and brood parasitism
22
4.1. Mating structure and success
Monogamy
Polygamy
-polygyny
-polyandry
-polygyandry
Promiscuity
(no pair bond)
Females/
Males/
breeding
breeding unit
unit
1
1
1
>1
>1
>1
1
>1
>1
>1
23
• Social breeding system is not necessarily the real
one
– First EPP (extra pair paternity) findings from the house
sparrow (Passer domesticus, varpunen)
• DNA-fingerprinting, hypervariable minisatellites (Jeffrey’s
probe)
– Reed bunting (Emberiza schoeniclus,
pajusirkku): 55% EPP
– Willow tit (Poecile montanus,
hömötiainen): 0.9 – 6.7% EPP
(minisatellites/microsatellites)
– Presently mostly studied with microsatellite markers
24
• Agile antechinus, Antechinus agilis
(leveäjalkapussikärppä)
• Males die after the
breeding season
• F = mother
• 1-8 = offspring
• In the offspring,
altogether 5 alleles
that are not shared
with the mother
Þ At least 3 fathers
¬
¬
¬
¬
¬
¬
®
• Females mate with
several males and
males with several
females
25
4.1.1. Male reproductive success
• Sexual dimorphism
– Female choice
– Competition between males
– ‘Goodness’ is advertised with some
observable traits, usually tied with a
secondary sexual character
– Variation in reproductive success is
larger in males than in females
– To test the theory, paternity must be
known
26
Dragon lizard, Ctenophorus ornatus
• Polygynous
• Territories of males larger
than those of females
• Dimorphic: males bigger
and have bigger heads
• Reproductive success
correlates with male body
and head size
• Microsatellites
27
• Lekking
– Lek paradox
• Female choice
• variation in reproductive success and sexual
dimorphism
• Why females choose, when there is no use of the
males after mating? ® Good genes
• If female chooses always the best – genetic
variation should decrease to zero
• Why the subordinate males attend the leks at all?
28
– Buff-breasted sandpiper, Tryngites subruficollis
(tundravikla)
• Minisatellites
• Variation in male reproductive
success much less than expected (one male did not
overrule?)
• Behavioural and genetic observations did not match
– 40 % of the broods had >1 father
– Most of the males attending the leks had offspring
• No lek-paradox
29
– Black grouse, Tetrao tetrix (teeri)
• Minisatellites
• Only one father / brood
• Females prefer males, which are the
most successful at the leks
• Lek-paradox remains
– White-beared manakin, Manacus
manacus, (munkkitanssija)
• Microsatellites
• Females prefer leks with many males
• Males at a lek are composed of groups
of related kin
• Subordinate males get indirect
benefit through kin-selection
30
4.1.2. Female reproductive success
• Sperm competition
– Species, in which the females are
able to store sperm
– Often the last mating partner sires
most of the offspring
• Passive sperm-loss
• Displacement of the sperm of the
previous male by the second male
• The sperm of the last male is stored
in a better location in order to be
used in fertilization
Poecilia reticulata
– Micro- and minisatellites
31
• Advantages and disadvantages of promiscuity:
- Disadvantages
– Predation and disease risks increase
– Energy expenditure increases
+ Advantages
– Direct advantages
• More males to care the young
• Protection against predators
– Indirect advantages
• A better male might be found – better and more suitable
genes
• More genetic variation in the offspring
32
• Good genes – hypothesis:
– Good males produce more offspring
– Only a part of the males in the population
produce offspring
– Advertising goodness with sexual
ornaments
– The runaway hypothesis: female
preference for male ornamentation leads
to more and more exaggerated ornamentation
– Females may mate with a second male in
search for better genes that the social mate has
– All the broods may not have several fathers,
because the first one was already good
– Blue tit (Cyanistes caeruleus) males,
which had offspring of another male
in the brood they were caring, had
lower survival
• minisatellites
33
• Genetic incompatibility
– Genetic similarity between the
male and the female may
decrease the number of
offspring
– Sand lizard, Lacerta
agilis:
• Minisatellites
• Genetic similarity of the
parents reduces the
number of offspring
34
• Mate choice and MHC
– Major histocompatibility complex and immune response
– Females avoid breeding with males with similar MHC-loci
– Man and rat
• Odour has an effect with mate choice and odour is
correlated with MHC (Wedekind et al. 1995)
– the “sweaty T-shirt test”
– Inbreeding avoidance / increase of heterozygosity
35
– Three-spined stickleback,
Gasterosteus aculeatus (kolmipiikki)
• Females prefer males with a lot of variation
in MHC IIB-loci
• Similarity of the loci is not so important
36
4.2. Social behaviour
and collaboration
• Sex ratio in the Seychell warbler, Acrocephalus sechellensis
(Seychellien kerttunen)
– Breeding pair has usually a daughter from the previous breeding
seasons to help rearing the young
– Female lays only one egg, also the helper may lay an egg
– Less helpers in low quality territories than in good quality
– More males produced in low quality territories (80%), more
females in good quality territories (83%), and in territories with
helpers, more males are produced (80%)
– Helpers in low quality habitats may harm breeding success, so it
is better to produce the more dispersing sex (males)
37
• Wren, Malurus cyaneus (sinikurkkumaluri)
– Male offspring stay to help their parents
– Altruism and kin-selection (Hamilton’s rule)?
– But:
• Minisatellites
• EPP and replacement of the dominant female very common
• Only 53 % of the helpers help their real mothers
® no indirect benefit through kinship
• Helping may be a payment for
allowing to remain on the
territory, ‘paying the rent’
38
• Social insects
– Hymenoptera (ants, bees wasps), Isoptera (termites) and
Homoptera (aphids)
– Haplodiploid sex determination (males are haploid, females =
queens and workers are diploid)
– Queen /queens mate and found a new colony
– A queen may mate with one or several males
– Kin-selection, depending on the amount of queens and
matings, workers are differentially related
– Microsatellites: amount of queens / nest, amount of matings /
queen, relatedness of workers to each others and queens
39
4.3. Nest and brood parasitism
• Cuckoo, Cuculus canorus (käki)
– Lays eggs into nests of
several species
– Eggs different depending on the
host species, always remanding
the host’s own eggs
– ‘Arms race’ between the host and
cuckoo
Cuckoo
Host species
– The maternally inherited mtDNA of the
cuckoo correlates with the host
specificity
– Microsatellite markers, inherited from
both parents do not show correlation
40
• ’Steeling’ brood from other individuals of the same
species
– Relatively common in birds
– Who pays the price?
– Common gull, Larus canus
(kalalokki):
• Relatives often nest close
to one another in a colony
• A pair may adopt chicks
• Minisatellites
• Adopted chicks more related to the adoption parents than to the
other adults of the colony
• Kin-selection
– However, only little evidence of kin selection in brood
amalgamation
41
The common merganser, Mergus merganser (isokoskelo)