Widespread species that occupy continents and oceanic islands provide an excellent opportunity to study evolutionary forces responsible for population divergence. Here, I use multilocus coalescent based population genetic and phylogenetic methods to infer the evolutionary history of the common chaffinch (Fringilla coelebs), a widespread Palearctic passerine species. My results showed strong population structure between Atlantic islands. However, the two European subspecies can be considered one panmictic population based on gene flow estimates. My investigation of effects of sampling on concatenated and Bayesian estimation of species tree (BEST) methods demonstrated that concatenation is more sensitive to sampling than BEST. Furthermore, concatenation can provide incorrect evolutionary relationships with high confidence when sample size is small. In conclusion, my results suggest European ancestry for the common chaffinch and Atlantic islands appear to have been colonized sequentially from north to south via Azores.

Widespread species that occupy continents and oceanic islands provide an excellent opportunity to study evolutionary forces responsible for population divergence. Here, I use multilocus coalescent based population genetic and phylogenetic methods to infer the evolutionary history of the common chaffinch (Fringilla coelebs), a widespread Palearctic passerine species. My results showed strong population structure between Atlantic islands. However, the two European subspecies can be considered one panmictic population based on gene flow estimates. My investigation of effects of sampling on concatenated and Bayesian estimation of species tree (BEST) methods demonstrated that concatenation is more sensitive to sampling than BEST. Furthermore, concatenation can provide incorrect evolutionary relationships with high confidence when sample size is small. In conclusion, my results suggest European ancestry for the common chaffinch and Atlantic islands appear to have been colonized sequentially from north to south via Azores.

Once thought to be an evolutionary dead-end, hybridization is now being detected in genomes across kingdoms, perhaps even playing an integral role in evolution. In chapter 1, I investigated the potential influences of hybridization on the evolution of a group of vagrant, asexual species in the Rhizoplaca melanophthalma species group. I sequenced the mitochondrial and nuclear genomes of 55 specimens and found well-supported nuclear phylogenies of both datasets. There were, however, multiple instances of discordance between the mitochondrial and nuclear trees, which can be caused by hybridization. PhyloNet and ABBA-BABA also detected widespread hybridization among this group. In chapter 2, I shifted to the Holarctic clade of lichen-forming fungi in Xanthoparmelia to characterize gene tree conflict and investigate the potential for hybrization. Here, I used three different tests for hybridization that account for incomplete lineage sorting "ABBA-BABA, PhyloNet, and SplitsTree" as well as PhyParts to characterize gene tree conflict. Like the Rhizoplaca species group, widespread hybridization was detected in the Holarctic clade despite robust phylogenies. My research underscores the value of investigating hybridization when studying species boundaries and evolutionary history.

Despite more than 50 years of research on the genetic basis of speciation, we still know very little about the early stages of this process. A general rule of speciation is the Haldane’s Rule, which states that postzygotic isolation is expressed earlier in the heterogametic sex: sterility and inviability in hybrids is much more likely to occur in the heterogametic sex. However, it is still unknown how long hybrid sterility takes to be established in the heterogametic sex, since most studies have focused on highly divergent species that no longer hybridize in nature. The meadow grasshopper (Chorthippus parallelus) is a suitable system to shed light on this matter because hybrid male sterility exists between subspecies that show low divergence and are still able to hybridize readily in nature. C. p. parallelus is distributed throughout Northern, Central and Eastern Europe while C. p. erythropus is restricted to the Iberian Peninsula. Both subspecies meet in the Pyrenees, where they form a narrow hybrid zone. Yet, it is unknown 1) how long ago have these subspecies diverged and 2) how have they expanded to form the hybrid zone where these incompatibilities take place. Here, we applied phylogenomic methods to estimate the time of divergence of the subspecies and to study its phylogeographic history. Using the mitogenome and known mitochondrial rates of evolution, we dated the diversification of the subspecies ≈100,000 years ago and found six ancient mitochondrial haplotypes. Implementing coalescent theory to estimate a nuclear species tree, we found evidence of sub-refugia within two or three main refugia and that the hybrid zone originated from a recent post-glacial expansion from one sub-refugia. Haldane’s rule evolved rapidly in C. parallelus, within ≈100,000 years, with demographic processes, such as population expansion. Founder effect reduced genetic diversity in C. parallelus parallelus, with the possibility of fixing incompatible alleles with C. parallelus erythropus resulting in hybrid male sterility.

Abstract Both demographic histories and natural selection complicate the speciation process. There is a need to jointly study the effects of natural selection on so called magic traits that can cause reproductive isolation such as climatic adaptation, and its interaction with neutral demographic histories. Closely related incipient coniferous species offer us a great system for this effort. I used genetic variation at one set of climate-related candidate genes and another set of reference loci and cytoplasmic genomic fragments of two closely related parapatric pine species: Pinus massoniana Lamb. and Pinus hwangshanensis Hisa. Population genetic analyses were used to measure genetic variation and detect signals of ancient and recent selection. Speciation parameters including migration rates and divergence times at candidate genes and reference loci were compared under the Isolation with migration model. Hierarchical Approximate Bayesian Computation (ABC) was used to define demographic and speciation models. Intra- and interspecific genetic variation at cytoplasmic and nuclear intronic sequences were compared between parapatric populations and allopatric populations to distinguish the effects of introgression and incomplete lineage sorting in generating shared genetic variation between the species. The results showed that ancient selection were shared by the lineages leading to the species while recent selection has been species-specific. Candidate genes had significant lower migration rates compared to reference loci. Recent differential climatic selection might counteract against gene flow at underlying genes, which therefore favors divergence between the two pines through ecological speciation. Shared mitotypes were randomly distributed across species’ ranges, which therefore supported the incomplete lineage sorting hypothesis, but the shared nuclear intronic variation distributed more frequently in parapatric populations than in allopatric populations, supported the introgression hypothesis. ABC and species’ distribution modeling also supported the secondary gene flow model. The three genomes had different rates of mutation and gene flow might mirror different phases of the speciation continuum. The results in this thesis are valuable for understanding evolution in general and for other applied purposes such as tree breeding and climate change adaptation. / Tiivistelmä Luonnonvalinta ja populaatioiden historian demografia tekevät lajiutumisesta monimutkaisen tapahtumaketjun. Luonnonvalinnan ja demografisten tekijöiden vuorovaikutusta on paras tutkia samanaikaisesti, kun tarkastellaan lajiutumiseen vaikuttavia ominaisuuksia. Tällaisia ovat esimerkiksi ilmastoon sopeutumiseen liittyvät ominaisuudet. Lähisukuiset havupuulajit tarjoavat erinomaiset mahdollisuudet tähän työhön. Tutkin geneettistä muuntelua yhtäältä ilmastosopeutumiseen liittyvissä ns. ehdokasgeeneissä ja toisaalta neutraaleiksi oletetuissa verrokkigeeneissä sekä sytoplasman genomeissa kahdessa lähisukuisessa mäntylajissa Pinus massoniana Lamb. ja Pinus hwangshanensis Hisa, joiden populaatiot esiintyvät joskus erillään toisistaan (allopatrisesti), toisinaan vierekkäin (parapatrisesti). Mittasin muuntelun määrää ja etsin merkkejä valinnan vaikutuksesta. Vertasin erilaisia lajiutumismallien parametrejä verrokki- ja ehdokasgeeneissä. Käytin simulaatioita etsiäkseni parhaat demografiset ja lajiutumiseen liittyvät mallit. Vertasin kloroplastien ja mitokondrioiden genomien sekvenssien lajinsisäistä ja lajien välistä muuntelua allopatrisissa ja parapatrisissa populaatioissa tutkiakseni onko lajien yhteinen muuntelu seurausta siitä että lajien eriytymisestä on kulunut vain vähän aikaa vai siitä että sen jälkeen on tapahtunut geenivirtaa. Kauan sitten tapahtunut valinta on vaikuttanut samalla tavalla kumpaankin lajiin, osin koska tutkimus kohdistui myös niiden yhteiseen edeltäjälinjaan. Äskettäinen valinta taas oli suuremmassa määrin kummallekin lajille ominaista. Viime aikojen ilmastoon liittyvä valinta on voinut vähentää geenivirtaa ehdokasgeeneissä, mikä voisi edistää ekologista lajiutumista. Tuman DNA:n muuntelu jakautuminen tuki sitä mahdollisuutta että lajien yhteinen geneettinen muuntelu johtuu äskettäisestä geenivirrasta, ei vain siitä että lajiutuminen on niin varhaisessa vaiheessa. Mitokondrioiden geeneissä lajeilla yhtä paljon yhteistä muuntelua sekä allopatrisissa että parapatrisissa populaatioissa, mikä tukee sen sijaan eriytymisen jälkeistä epätäydellistä muuntelun erilaistumista. Eri genomit heijastavat lajiutumisprosessin eri vaiheita. Väitöskirjan tulokset ovat osaltaan tuottaneet uutta tietoa lajiutumisesta ja valinnasta. Lisäksi niillä on merkitystä ilmastomuutoksen vaikutusten ymmärtämisessä ja metsänjalostuksessa.

Phylogenetics is the research of ancestor-descendant relationships among different groups of organisms, for example, species or populations of interest. The datasets involved are usually sequence alignments of various subsets of taxa for various genes. A major task of phylogenetics is often to combine estimated gene trees from many loci sampled from the genes into an overall estimate species tree topology. Eventually, one can construct the tree of life that depicts the ancestor-descendant relationships for all known species around the world. If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated overall species tree topology. In this study, we assume that gene tree discordance is solely due to incomplete lineage sorting under the multispecies coalescent model (Degnan and Rosenberg, 2009). If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated species tree topology. In addition, we examine the performance of the most commonly used supertree method (Wilkinson et al., 2009), namely matrix representation with parsimony (MRP), to explore its statistical properties in this setting. In particular, we show that MRP is not statistically consistent. That is, an estimated species tree topology other than the true species tree topology is more likely to be returned by MRP as the number of gene trees increases. For some situations, using longer branch lengths, randomly deleting taxa or even introducing mutation can improve the performance of MRP so that the matching species tree topology is recovered more often. In conclusion, MRP is a supertree method that is able to handle large amounts of conflict in the input gene trees. However, MRP is not statistically consistent, when using gene trees arise from the multispecies coalescent model to estimate species trees.