Hybridisation and genomic diversity in British and Irish pigeons Columba livia

Human introductions of animals and plants have caused a diverse array of conservation problems, including extinction by hybridisation. This results from interbreeding of non-native and native populations, causing genomic homogenisation. A potential benefit of anthropogenic hybridisation concerns the influx of genetic variation. The Rock Dove Columba livia has been genetically replaced across much of its range by the feral pigeon. Relict populations in the British Isles have experienced varying levels of wild-feral gene flow. Introgression correlates with higher genomic diversity, potentially improving chances of persistence of relict Rock Dove populations. However, the beneficial impacts of interbreeding may be short-lived if hybridisation levels increase

The effect of divergent and parallel selection on the genomic landscape of divergence

While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories

The island syndrome in birds

The island syndrome is a widespread biological phenomenon that describes a suite of morphological, behavioural, demographic and life-history changes associated with island dwelling. These similar evolutionary responses among disparate groups of animals and plants represent a remarkable case of convergent evolution. Among animals, birds are a highly suitable group to study the island syndrome; they are a comparatively data-rich taxon, are frequent island colonisers, and sometimes display extreme adaptations such as the loss of flight. However, the avian island syndrome literature is fragmented, and multiple components are rarely considered together even though many are inextricably linked. We reviewed multi-species comparative studies, single-species or population-level studies and anecdotal accounts, to summarise and assess the support for individual components of the island syndrome for birds, and to identify suites of traits that should be considered together. The weight of evidence for island syndrome patterns in morphology is substantial, but is more partial or even anecdotal for various aspects of behaviour, life history and physiology. Full validation of the island syndrome in birds will require the less-studied components to be treated in a comparative framework, and for covarying components to be examined in an integrated way. An improved description of the scope of the syndrome will pave the way to understanding its drivers

Insular nestling growth and its relationship to parental care effort in Silvereyes, Zosterops lateralis

The rate at which avian offspring grow can have consequences for survival and reproductive output as an adult and is known to vary widely among and within species. This variation is thought to be an adaptive response to cope with environmental variation. The principal environmental factors affecting growth are food availability and predation risk, predominantly acting as constraints on parental care. Islands pose an interesting system to explore growth rate dynamics, because the characteristic insular features of high population densities and depauperate predator diversity translate into a potentially food limited environment with low predation risk. Insular environments typically produce populations with slower life history strategies and larger body size in small-bodied species, features that are likely to be mediated by growth rate. We describe the nestling growth of an insular population of Silvereyes and how it relates to parental size and parental care. Neither parental size nor parental care explained insular nestling growth rate, even though food acquisition is thought to underpin avian growth rates. This could be due to a mismatch between acquisition and allocation of resources by nestlings. Compared to a small number of mainland nestlings, the island growth curve asymptotes were significantly larger and inflection points much later, but insular growth rates were only marginally slower. This is in line with proposed insular adaptations required to produce larger body size on islands, however understanding the mechanism underlying this pattern will require data on the relationship between food quality and acquisition, and physiological allocation of resources within individuals

Genetic patterns reveal geographic drivers of divergence in silvereyes ( Zosterops lateralis)

Identifying mechanisms that drive population divergence under varying geographic and ecological scenarios can inform our understanding of evolution and speciation. In particular, analysis of genetic data from island populations with known colonisation timelines allows us to identify potential source populations of diverging island subspecies and current relationships among populations. Silvereyes (Zosterops lateralis) are a small passerine that have served as a valuable study system to investigate evolutionary patterns on both large and small geographic scales. We examined genetic relatedness and diversity of two silvereye subspecies, the mainland Z. l. cornwalli and island Z. l. chlorocephalus, and used 18 077 single nucleotide polymorphisms (SNPs), to compare locations across southeast Queensland, Australia. Although silvereyes are prolific island colonisers our findings revealed population divergence over relatively small spatial scales was strongly influenced by geographic isolation mediated by water barriers. Strong genetic connectivity was displayed between mainland sites, but minimal inter-island connectivity was shown despite comparable sampling distances. Genetic diversity analysis showed little difference in heterozygosity between island and mainland populations, but lower inbreeding scores among the island populations. Our study confirmed the range of the Z. l. chlorocephalus subspecies throughout the southern Great Barrier Reef. Our results show that water barriers and not geographic distance per se are important in driving incipient divergence in island populations. This helps to explain the relatively high number of phenotypically differentiated, but often geographically proximate, island silvereye subspecies compared to a lower number of phenotypically less well-defined Australian continental subspecies

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1 and Ugt5 genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of βglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences

Geographical surrogates of genetic variation for selecting island populations for conservation

Aim: Threatened species often exist in small numbers in isolated populations. Limited financial resources usually constrain conservationists to allocate funds to a subset of these populations. Because obtaining information required to maximize the amount of genetic and phenotypic variation protected can be costly and time-consuming, the utility of surrogates should be explored. This study tests the efficacy of three simple and cost-effective geographical measures in capturing genetic and phenotypic variation in fragmented populations when setting conservation priorities. Location: Vanuatu archipelago. Methods: We used neutral genetic data (mtDNA and microsatellites) and morphometric data (a proxy for functional variation) for two bird species displaying different patterns of regional population genetic structure: Zosterops flavifrons and Zosterops lateralis. We tested the performance of three geographical surrogates (maximizing: geographical distance between islands; area of islands; geographical representation of islands), in representing divergence between and diversity within populations, constrained to the number of islands being protected. Results: Maximizing geographical separation of sites provided the best surrogate for a constrained budget ( 50% of the populations), the spatially most representative sites were often more effective. Selecting islands based on size retained about half of within-population genetic diversity; however, this was not much higher than selecting the islands randomly. Main conclusions: The ability of surrogates to capture genetic or phenotypic variation varied depending on the species, genetic markers and number of islands selected. While imperfect, selection of populations based on simple geographical surrogates for genetic and phenotypic variation will generally be better than random selection for conserving the evolutionary potential of threatened populations when time and money limit a more thorough and direct analyses of genetic and phenotypic variation

Limited domestic introgression in a final refuge of the wild pigeon

Domesticated animals have been culturally and economically important throughout history. Many of their ancestral lineages are extinct or genetically en dangered following hybridization with domesticated relatives. Consequently, they have been understudied compared to the ancestral lineages of domestic plants. The domestic pigeon Columba livia, which was pivotal in Darwin’s studies, has maintained outsized cultural significance. Its role as a model organism spans the fields of behavior, genetics, and evolution. Domestic pigeons have hybridized with their progenitor, the Rock Dove, rendering the latter of dubious genetic sta tus. Here, we use genomic and morphological data from the putative Rock Doves of the British Isles to identify relictual undomesticated populations. We reveal that Outer Hebridean Rock Doves have experienced minimal levels of introgres sion. Our results outline the contemporary status of these wild pigeons, high lighting the role of hybridization in the homogenization of genetic lineages.publishedVersio

Integration of population genetics with oceanographic models reveals strong connectivity among coral reefs across Seychelles

Many countries with tropical reef systems face hard choices preserving coral reefs in the face of climate change on limited budgets. One approach to maximising regional reef resilience is targeting management efforts and resources at reefs that export large numbers of larvae to other reefs. However, this requires reef connectivity to be quantified. To map coral connectivity in the Seychelles reef system we carried out a population genomic study of the Porites lutea species complex using 241 sequenced colonies from multiple islands. To identify oceanographic drivers of this connectivity and quantify variability, we further used a 2 km resolution regional ocean simulation coupled with a larval dispersal model to predict the flow of coral larvae between reef sites. Patterns of admixture and gene flow are broadly supported by model predictions, but the realised connectivity is greater than that predicted from model simulations. Both methods detected a biogeographic dispersal barrier between the Inner and Outer Islands of Seychelles. However, this barrier is permeable and substantial larval transport is possible across Seychelles, particularly for one of two putative species found in our genomic study. The broad agreement between predicted connectivity and observed genetic patterns supports the use of such larval dispersal simulations in reef system management in Seychelles and the wider region