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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)