The effect of climatic changes on genetic build-up of populations and their role in promoting adaptive radiations

• Název práce v češtině: Efekt klimatických změn na genetickou strukturu populací a jejich úloha při adaptivních radiacích
• Název v anglickém jazyce: The effect of climatic changes on genetic build-up of populations and their role in promoting adaptive radiations
• Akademický rok vypsání: 2010/2011
• Typ práce: disertační práce
• Jazyk práce: angličtina
• Ústav: Katedra zoologie (31-170)
• Vedoucí / školitel: Mgr. Karel Janko, Ph.D.
• Řešitel: skrytý - zadáno vedoucím/školitelem
• Datum přihlášení: 19.11.2010
• Datum zadání: 19.11.2010
• Datum odevzdání elektronické podoby: 16.11.2021
• Datum proběhlé obhajoby: 14.01.2022
• Oponenti: Mgr. Marie Šabacká, Ph.D.

Předběžná náplň práce v anglickém jazyce

Project background: Climate changes play indeed crucial role in the evolution of biota. Well-known effect of climate-induced population fluctuation is the genetic homogenization of affected populations, which stems from repeated population bottlenecks. The opposite, less well known, but perhaps even more important effect is the induction of geographical subdivision and secondary contacts, which may result not only in splits into refugial populations (hence putatively promoting allopatric speciation) but also in creation of evolutionary novelties via interpecific hybridisations. Indeed, it is not by chance that periods of more or less frequent climatic shifts are referred to as diversity pumps. Proposed project focuses on three model systems in order to answer questions related to the above mentioned topic.
Cobitis taenia hybrid complex is a suitable model group to address the effects of repeated hybridisation on the evolution of sex and asex as well as on interactions of both groups. To date, four taxa, C. elongatoides, C. taenia, C. tanaitica and C. taurica with parapatric distribution over the Europe were documented to hybridise giving rise to virtually all-female di-, tri- and tetraploid hybrids with gynogenetic reproduction (Janko, 2007). Distant relative to all Cobitis sensu stricto (Perdices & Doadrio, 2001) - C. strumicae ? is further known to hybridise with C. elongatoides in lower Danubian area. Asexual hybrid lineages are currently distributed over much of the ranges of parental taxa and are result of repeated secondary contacts of C. elongatoides, C. tanaitica and C. taenia in upper Elbe and Odra R. and in northern Black Sea shelf area during the Pleistocene (Janko, 2005).
Notothenioidei, the most abundant and diverse suborder, resides Atlantic and South ocean. A novel adaptation, grounded in presence of anti freeze proteins, is considered to be a main agent of colonization of freezing waters. In Miocene, after the formation of Circum Antarctic current, Notothenioidei availed eradiation of Eocene fauna and underwent such adaptive radiation as is nowhere else known in the world. The Notothenioid ancestor lack swim bladder so is benthic as most of genus within suborder, heavy species. There are also pelagic, cryopelagic, mesopelagic species which evolved mechanisms of buoyancy.
?Antarctic terrestrial organisms live in even more extreme environments than the marine creatures. Not only have they to cope with expansions and contractions of the ice sheets, they also occur in fragmented and patchy habitats (less than 1% of the continental surface is ice-free) such as nunataks, coastal capes and bays, and dry valleys. All of these environments are subject to changes in ice cover that almost certainly have a significant effect on local invertebrate populations. At least one species of Antarctic nematode, Panagrolaimus davidi, is known to survive both intracellular and extracellular freezing (Wharton, 2003) and a number of others including Plectus murrayi and Plectus frigophilus show similar properties (our unpublished data). In contrast, Collembola are freezing-resistant and show no evidence of freezing tolerance (Hawes 2006). As winter air temperatures may reach a minimum of ?45°C along the coast, and ?80°C in the interior of the continent, this appears to be a risky strategy, which might be expected to affect survival individuals and local populations.
?Project aims:
The proposed post gradual project is separated into two complementary parts.
1) In the first one, we shall attempt to solve the question how species-specific life histories affect the ability of given organism to cope with climatic changes. Namely, we shall test whether the vulnerability of organisms to climate changes and especially to glacier-mediated habitat eradication (GHE) are related to their depth and habitat preferences, which should be manifested by the differing degree of historical population oscillations and population fragmentations. To attend this topic, we shall compare the phylogeographic patterns of several available species of Notothenioid fish and terrestrial Nematodes and ideally compare the results with already available data, such as those of collembolans. If climatic shifts and ice-sheet fluctuations are the main determinants of population structure in polar organisms, we expect to find different reactions on presence of the grounded ice sheet depending on the feeding and spawning strategy. The benthic feeders are about to underwent bottleneck and pelagic species, not as common, are supposed to underwent expansion. According to the recent paper of Janko at al. 2007, we expect more recent and more dramatic demographic change of benthic feeders. Nowadays there is unfinished research, which indicates to assigns the specific pattern to each species. We also expect that freezing tolerant nematodes should be affected by less pronounced population fluctuations as compared to freezing non-tolerant collembolans.
?2) In the second part, we shall try to find and document the reticulation events in the evolutionary histories of two groups of fish characterised by rapid speciation putatively linked to Pleistocene climate shifts, i.e. Cobitis and Trematominae. We shall use two complementary approaches to detect both current hybridisation as well as past introgressions. The first approach focuses on the detection of hybrids between extant taxa and is a powerful tool to detect ongoing hybridisation. This will be realised using the analysis of recently developed microsatellite loci. The second approach is specifically aimed to detect the events leading to fixed introgressions during the evolution of the whole group and is based on the concept of Divergence-population-genetics (DPG; Machado et al. 2002); a coalescent-based method that compares divergence among species from many loci with predicted values under several models of speciation. It allows the evaluation of different evolutionary mechanisms operating on distinct parts of the genome and has recently been advocated to be suitable for detection of past introgressive events (Mallet, 2005; Seehausen, 2004).
?Methods:
Comparative phylogeography: We use mitochondrial and nuclear markers such as cyt b, ND2, S7 as well as microsatellites to explore phylogeography patterns. We use summary statistics like Mismatch distribution, Tadjima´s D, Fu F´s to resolve reaction of populations on geological changes. Parametr ? correlates with initial of expansion. We apply also model-based inference such as implemented in Fluctuate. Comparison of nuclear and mtDNA patterns is useful to disentangle sex-biased patterns.
?Detection of ongoing hybridisation will be based on microsatellite analysis for which existing markers and protocols shall be used (DeGelas, 2008; Van de Putte, 2009). We shall use NewHybrid software to statistically detect hybrid individuals in the studied dataset.
?Detection of past hybridisation event shall be based on data obtained from ongoing transcriptome-wide sequencing project, which in the case of Cobitis shall provide the applicant with the data on high amount of loci sequenced for at least 5 individuals per species (which is sufficient number to detect significant among-locus heterogeneity). In the case of Trematominae it will allow to detect high amount of variable loci for which the applicant shall design suitable specific primers and will be subsequently able to perform multilocus phylogenetic inference by PCR-sequencing approach on the whole spectre of available Trematominae species. For each gene, we will calculate levels of nucleotide diversity, ? (Nei, Li, 1979), and the proportion of segregating sites, ? (Watterson ,1975) to estimate the levels of intraspecific polymorphism. In addition, we will calculate pair wise F_ST, net nucleotide divergence as well as proportion of fixed and shared polymorphisms to estimate the level of interspecific differentiation. This procedure shall be automated in the R programming environment. Coalescent simulations as implemented in the IMa software (Nielsen, Wakeley, 2001) will be performed to estimate the level of gene flow between the species and to evaluate the potential role of incomplete lineage sorting in the observed incongruent phylogenetic signals. We shall further use this information to identify candidate speciation genes, as those are expected to show the lowest levels of introgression and the highest level of differentiation.
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