Of dups and dinos : evolution at the K/Pg boundary

Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also transcriptome data sets are considered). While some genome duplications are very old and have occurred early in the evolution of dicots and monocots, or even before, others are more recent and seem to have occurred independently in many different plant lineages. Strikingly, a majority of these duplications date somewhere between 55 and 75 million years ago (mya), and thus likely correlate with the K/Pg boundary. If true, this would suggest that plants that had their genome duplicated at that time, had an increased chance to survive the most recent mass extinction event, at 66 mya, which wiped out a majority of plant and animal life, including all non-avian dinosaurs. Here, we review several processes, both neutral and adaptive, that might explain the establishment of polyploid plants, following the K/Pg mass extinction

Ecological consequences of genetic modifications : an invasion analysis approach

Biological invasions are considered as one of the greatest threats to biodiversity, as they may lead to disruption and homogenization of natural communities, and in the worst case, to native species extinctions. The introduction of gene modified organisms (GMOs) to agricultural, fisheries and forestry practices brings them into contact with natural populations. GMOs may appear as new invasive species if they are able to (1) invade into natural habitats or (2) hybridize with their wild relatives. The benefits of GMOs, such as increased yield or decreased use of insecticides or herbicides in cultivation, may thus be reduced due the potential risks they may cause. A careful ecological risk analysis therefore has to precede any responsible GMO introduction. In this thesis I study ecological invasion in relation to GMOs, and what kind of consequences invasion may have in natural populations. A set of theoretical models that combine life-history evolution, population dynamics, and population genetics were developed for the hazard identification part of ecological risks assessment of GMOs. In addition, the potential benefits of GMOs in management of an invasive pest were analyzed. In the first study I showed that a population that is fluctuating due to scramble-type density dependence (due to, e.g., nutrient competition in plants) may be invaded by a population that is relatively more limited by a resource (e.g., light in plants) that is a cause of contest-type density dependence. This result emphasises the higher risk of invasion in unstable environments. The next two studies focused on escape of a growth hormone (GH) transgenic fish into a natural population. The results showed that previous models may have given too pessimistic a view of the so called Trojan gene -effect, where the invading genotype is harmful for the population as a whole. The previously suggested population extinctions did not occur in my studies, since the changes in mating preferences caused by the GH-fish were be ameliorated by decreased level of competition. The GH-invaders may also have to exceed a threshold density before invasion can be successful. I also showed that the prevalence of mature parr (aka. sneaker) strategy among GH-fish may have clear effect on invasion outcome. The fourth study assessed the risks and developed methods against the invasion of the Colorado Potato Beetle (CPB, Leptinotarsa decemlineata). I showed that the eradication of CPB is most important for the prevention of their establishment, but the cultivation of transgenic Bt-potato could also be effective. In general, my results emphasise that invasion of transgenic species or genotypes to be possible under certain realistic conditions and resulting in competitive exclusion, population decline through outbreeding depression and genotypic displacement of native species. Ecological risk assessment should regard the decline and displacement of the wild genotype by an introduced one as a consequence that is as serious as the population extinction. It will also be crucial to take into account different kinds of behavioural differences among species when assessing the possible hazards that GMOs may cause if escaped. The benefits found of GMO crops effectiveness in pest management may also be too optimistic since CPB may evolve resistance to Bt-toxin. The models in this thesis could be further applied in case specific risk assessment of GMOs by supplementing them with detailed data of the species biology, the effect of the transgene introduced to the species, and also the characteristics of the populations or the environments in the risk of being invaded.Tulokaslajit ovat yksi luonnon monimuotoisuutta pahiten uhkaavista tekijöistä elinympäristöjen tuhoutumisen ohella. Tulokaslajit voivat kilpailla samoista resursseista alueen alkuperäislajien kanssa, joka voi johtaa jopa alkuperäislajin syrjäytymiseen alueelta. Toisaalta tulokkaat voivat myös risteytyä sukulaislajiensa kanssa, jolloin alkuperäislaji voi lopulta sulautua tulokaspopulaatioon, mikäli tulokkaan tai syntyvän risteymän kelpoisuus on parempi kuin alkuperäislajin. Maan- ja vesiviljelyn tuottavuuden tehostamiseksi kehitetyt muuntogeeniset organismit (GMO), kuten tuholaisen kestävät viljelyskasvit tai kasvuhormonilisätyt kalat, voivat kehittyä uusiksi tulokaslajeiksi, mikäli ne pystyvät runsastumaan luonnonympäristöissä tai risteytymään villien sukulaistensa kanssa. Siksi arvioitaessa GMO lajikkeista saatavaa hyötyä verrattuna tavanomaisiin lajikkeisiin, on myös niihin liittyvät riskitekijät otettava huomioon. Väitöskirjassani selvitin, minkälaiset ominaisuudet GMO lajikkeissa voisivat johtaa niiden levittäytymiseen ympäristöön ja minkälaisia vaikutuksia sillä voisi olla alueen alkuperäislajistolle populaatioekologisten ja -geneettisten mallien avulla. Toisaalta tarkastelin olisiko GMO- lajikkeen torjuntateho parempi tuholaislajin leviämistä vastaan, kuin tavanomaiset menetelmät. Tulokset osoittivat, että epävakaan dynamiikan omaava alkuperäispopulaatio on altis dynamiikaltaan vakaan tulokaslajin invaasiolle. Invaasioalttius on siten suurin esim. häirityissä ja ravinnekilpailun rajoittamissa kasvipopulaatioissa. Häiriöitä sietävä ja valorajoitteinen tulokaslaji (tai GMO lajike) voi jopa syrjäyttää tällaisen alkuperäispopulaation kilpailussa. Tarkastellessani kasvuhormonimuunnellun kalan mahdollisuutta levittäytyä luonnonpopulaatioon risteytymisen kautta havaitsin, että GMO lajike voi syrjäyttää alkuperäislajikkeen, jos GMO muotoa suositaan seksuaalivalinnassa. Risteytyminen voi johtaa myös koko populaation koon pienenemiseen, jos GMO:n elinkyky on heikompi kuin alkuperäislajikkeen (ns. Troijan geeni efekti). Havaitsin myös, että alkuperäislajikkeen ja GMO:n erilainen pariutumiskäyttäytyminen vaikuttaa invaasion onnistumiseen ja lopputulokseen. Toisaalta havaitsin, että tuholaisenkestävän GMO perunan viljely tavanomaisen perunan tilalla voi olla tehokas torjuntakeino koloradonkuoriaisen levittäytymistä vastaan entistä pohjoisemmille elinalueille ilmastonlämpenemisen myötä. Muuntogeeniset organismit näyttävät siis voivan kehittyä uusiksi tulokaslajeiksi ja syrjäyttää tai heikentää alkuperäislajien populaatioita joko kilpailun tai risteytymisen kautta tietyissä olosuhteissa. Nämä uhkatekijät on otettava huomioon ekologisessa riskinarvioinnissa ennen GMO lajikkeen käyttöönottoa. Myös muut tekijät, kuten tuhohyönteisten kehittyminen vastustuskykyisiksi tuholaistenkestäville GMO lajikkeille, voivat heikentää GMO lajikkeista saatavaa hyötyä. Kehitettyjen mallien soveltaminen tapauskohtaiseen riskinarviointiin edellyttäisi kuitenkin niiden täydentämistä yksityiskohtaisilla tiedoilla geenimuunneltavien kohdelajien biologiasta, muuntogeenin vaikutuksista kohdelajeissa sekä sen ympäristön erityispiirteistä, jonne GMO:n arvellaan voivan levittäytyä uutena tulokaslajina

Population genomic analysis of North American eastern wolves (Canic lycaon) support their conservation priority status

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them

Behavioral mechanisms of reproductive isolation in avian hybrid zones

Sexual signals and mating behaviors influence whether sympatric species interbreed, and can therefore promote or impede behavioral reproductive isolation between species in secondary contact. Traditionally, research on sexual selection and hybridization has focused on the importance of interspecific mate choice and species discrimination from the perspective of choosy females, and competition from the lens of aggressive and indiscriminate males. I examined two different avian systems to compare the role of male and female competition on hybridization: white-crowned sparrows on the west coast of the US, and sex-role reversed jacanas in Panama. Using genomics and experimental field techniques, I tested morphological, behavioral, and historical factors that influence patterns of gene flow between lineages. I found that contrary to traditional expectations, divergence in male competitive signals can promote reproductive isolation, and female competition can facilitate hybridization

Evolutionary Inference from Admixed Genomes: Implications of Hybridization for Biodiversity Dynamics and Conservation

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in a shifting adaptive landscape. Chapter I employed population genomic approaches to examine potential effects of habitat modification on species boundary stability in co-occurring endemic fishes of the Colorado River basin (Gila robusta and G. cypha). Results showed how one potential outcome of hybridization might drive species decline: via a breakdown in selection against interspecific heterozygotes and subsequent genetic erosion of parental species. Chapter II explored long-term contributions of hybridization in an evolutionarily recent species complex (Gila) using a combination of phylogenomic and phylogeographic modelling approaches. Massively parallel computational methods were developed (and so deployed) to categorize sources of phylogenetic discordance as drivers of systematic bias among a panel of species tree inference algorithms. Contrary to past evidence, we found that hypotheses of hybrid origin (excluding one notable example) were instead explained by gene-tree discordance driven by a rapid radiation. Chapter III examined patterns of local ancestry in the endangered red wolf genome (Canis rufus) – a controversial taxon of a long-standing debate about the origin of the species. Analyses show how pervasive autosomal introgression served to mask signatures of prior isolation—in turn misleading analyses that led the species to be interpreted as of recent hybrid origin. Analyses also showed how recombination interacts with selection to create a non-random, structured genomic landscape of ancestries with, in the case of the red wolf, the ‘original’ species tree being retained only in low-recombination ‘refugia’ of the X chromosome. The final three chapters present bioinformatic software that I developed for my dissertation research to facilitate molecular approaches and analyses presented in Chapters I–III. Chapter IV details an in-silico method for optimizing similar genomic methods as used herein (RADseq of reduced representation libraries) for other non-model organisms. Chapter V describes a method for parsing genomic datasets for elements of interest, either as a filtering mechanism for downstream analysis, or as a precursor to targeted-enrichment reduced-representation genomic sequencing. Chapter VI presents a rapid algorithm for the definition of a ‘most parsimonious’ set of recombinational breakpoints in genomic datasets, as a method promoting local ancestry analyses as utilized in Chapter III. My three case studies and accompanying software promote three trajectories in modern hybridization research: How does hybridization impact short-term population persistence? How does hybridization drive macroevolutionary trends? and How do outcomes of hybridization vary in the genome? In so doing, my research promotes a deeper understanding of the role that hybridization has and will continue to play in governing the evolutionary fates of lineages at both contemporary and historic timescales

Assessing the Genetic Status and Factors Leading to the Decline of the Roanoke Bass (Ambloplites Cavifrons)

Although numerous factors have led to the staggering declines in freshwater biodiversity throughout the United States and the world, habitat alteration and introduced species pose some of the greatest challenges to conservation efforts. Learning more about how these two factors lead to the decline of an endemic organism could help prevent the future loss of unique species and the premature conclusion of evolutionary trajectories. Roanoke bass (Ambloplites cavifrons) is a sport fish endemic to portions of the Roanoke, Chowan, Tar, and Neuse river basins of North Carolina and Virginia. This species has been in decline for many years, and it is believed that their continued existence is threatened by competition, and potentially hybridization and introgression with their introduced relative, the rock bass (Ambloplites rupestris). In addition to interactions with this invasive species, significant alteration of habitat is likely also a contributing factor in the decline of A. cavifrons. This study seeks to evaluate the relative contributions of these various factors to the decline of A. cavifrons. I utilized a combination of nuclear markers and mitochondrial sequence data to address the question of whether or not the two species are hybridizing in areas of syntopy, and furthermore to determine whether hybrids are fertile and able to breed back with the parental species. In addition, I identified extant populations of A. cavifrons throughout their historic range, and evaluated the genetic diversity of these populations and correlated these values with changes to the landscape in the form of alterations to watershed land use and the construction of impoundments. My results indicate large portions of the historic range of A. cavifrons no longer contain the species, and that remaining populations occur at the stream level and exist in isolation from one another. Obtaining this information allows for a better understanding of the current state of this unique species, provides information that may help managers prevent its disappearance from its native range, and affords insight into the interactions of an introduced and a native species in a landscape that has been heavily altered by human activity

Widespread hybridization between Invasive bleak (Alburnus alburnus) and Iberian chub (Squalius spp.): A neglected conservation threat

Hybridization between native and nonnative fish species is a major conservation issue, especially in ecosystems with high levels of endemism, such as Iberian streams. To date, hybridization with the invasive bleak Alburnus alburnus has been reported for the Iberian chub Squalius alburnoides and S. pyrenaicus and in scattered locations only. However, the bleak is spreading in the region, potentially increasing the risks of hybridization with other Squalius species. To gather a more comprehensive picture on the current geography of hybridization, we compiled records on hybrids between bleak and chub in Portugal and conducted genetical assessments of hybrids between bleak and S. carolitertii. We found that hybridization with bleak is widespread throughout Portuguese river basins and involves at least S. alburnoides, S. pyrenaicus and S. carolitertii. Hybridization with bleak may not only cause waste of reproductive effort and damage the genetic integrity of these endemic species but also promote shifts in the reproductive dynamics of the S. alburnoides hybrid complex, which includes individuals with various ploidy levels and combinations of parental genomes, reproducing sexually and asexually. We recommend that future studies characterize the fitness of bleak hybrids and their ecological and genetic interactions with native fish, in order to design effective conservation measures