Imperial College London

ProfessorVincentSavolainen

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Professor of Organismic Biology
 
 
 
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Contact

 

v.savolainen CV

 
 
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Assistant

 

Ms Elisabeth Ahlstrom +44 (0)20 7594 2207

 
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Location

 

N.1-17MunroSilwood Park

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Summary

 

Publications

Publication Type
Year
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177 results found

Dures SG, Carbone C, Savolainen V, Maude G, Gottelli Det al., 2020, Ecology rather than people restrict gene flow in Okavango-Kalahari lions, Animal Conservation, Vol: 23, Pages: 502-515, ISSN: 1367-9430

© 2020 The Zoological Society of London Reduced gene exchange between animal populations may be an indicator of the effects of anthropogenic fragmentation or it may reflect natural gradients in the landscape that can also result in population fragmentation. It can be difficult, therefore, to disentangle the role of local ecology from anthropogenic factors, creating a risk of attributing a lack of gene flow as being due to human activities, leading to ill-informed management decisions. Here, we test the ecological and anthropogenic factors driving population differentiation and show how the relative influence of such effects can be identified. Using Bayesian clustering and a causal modelling approach, we combine genetic and remote sensing data to disentangle the confounding influences of ecological and anthropogenic fragmentation. We investigate a region where such confusion may arise; in and around the Okavango Delta in northern Botswana. Specifically, we used 20 microsatellites to investigate the genetic structuring of African lions Panthera leo occupying a landscape dominated by two very different environments, the wetland Okavango and the surrounding Kalahari Desert. We find that differences in ecology, rather than anthropogenic barriers, are driving genetic differences in the population and that despite their ability to disperse long distances these lion populations are differentiated into two distinct genetic groups, one inhabiting the wetland Okavango Delta and the other one inhabiting the surrounding dryland Kalahari, divided by an apparently unobstructed boundary. The genetic structure observed could easily have been misinterpreted as a response to anthropogenic disturbance reducing gene flow. This reinforces the need to consider non-anthropogenic hypotheses, such as ecological differences between habitats, when assessing possible mechanisms of gene flow and their implications for population management. As anthropogenic pressure increases in this region

Journal article

Ciezarek A, Gardner L, Savolainen V, Block Bet al., 2020, Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis, BMC Genomics, Vol: 21, ISSN: 1471-2164

BackgroundThe Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skeletal muscle, a thermal gradient exists, with deep muscles, close to the backbone, operating at elevated temperatures compared to superficial muscles near the skin. Their heart, by contrast, operates at ambient temperature, which in bluefin tunas can range widely. Cardiac function in tunas reduces in cold waters, yet the heart must continue to supply blood for metabolically demanding endothermic tissues. Physiological studies indicate Pacific bluefin tuna have an elevated cardiac capacity and increased cold-tolerance compared to warm-water tuna species, primarily enabled by increased capacity for sarcoplasmic reticulum calcium cycling within the cardiac muscles.ResultsHere, we compare tissue-specific gene-expression profiles of different cardiac and skeletal muscle tissues in Pacific bluefin tuna. There was little difference in the overall expression of calcium-cycling and cardiac contraction pathways between atrium and ventricle. However, expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, which plays a key role maintaining intracellular calcium stores, was higher in atrium than ventricle. Expression of genes involved in aerobic metabolism and cardiac contraction were higher in the ventricle than atrium. The two morphologically distinct tissues that derive the ventricle, spongy and compact myocardium, had near-identical levels of gene expression. More genes had higher expression in the cool, superficial muscle than in the warm, deep muscle in both the aerobic red muscle (slow-twitch) and anaerobic white muscle (fast-twitch), suggesting thermal compensation.ConclusionsWe find evidence of widespread transcriptomic differences between the Pacific tuna ventricle and atrium, with potentially higher rates of calcium cycling in the a

Journal article

Osborne OG, Kafle T, Brewer T, Dobreva MP, Hutton I, Savolainen Vet al., 2020, Sympatric speciation in Mountain Roses (Metrosideros) on an oceanic island, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 375, ISSN: 0962-8436

Shifts in flowering time have the potential to act as strong prezygotic reproductive barriers in plants. We investigate the role of flowering time divergence in two species of mountain rose (Metrosideros) endemic to Lord Howe island, Australia, a minute and isolated island in the Tasman sea. Metrosideros nervulosa and M. sclerocarpa are sister species, have divergent ecological niches on the island but grow sympatrically for much of their range, and likely speciated in situ on the island. We used flowering time and population genomic analyses of population structure and selection, to investigate their evolution, with a particular focus on the role of flowering time in their speciation. Population structure analyses showed the species are highly differentiated and appear to be in the very late stages of speciation. We found flowering times of the species to be significantly displaced, with M. sclerocarpa flowering 53 days later than M. nervulosa. Furthermore, analyses of selection showed that flowering time genes are under selection between the species. Thus, prezygotic reproductive isolation is mediated by flowering time shifts in the species, and likely evolved under selection, to drive the completion of speciation within a small geographical area.

Journal article

Karrenberg S, Buerkle CA, Field DL, Savolainen Vet al., 2020, Dedication: Christian Lexer (1971-2019), PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 375, ISSN: 0962-8436

Journal article

Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AMet al., 2020, Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 375, ISSN: 0962-8436

Journal article

Steyaert M, Priestley V, Osborne O, herraiz A, Arnold R, Savolainen Vet al., 2020, Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos, Journal of Applied Ecology, ISSN: 0021-8901

Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology‐based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology‐based protocols currently used by ecological surveyors is essential to determine whether this DNA‐based approach is suitable for the long‐term monitoring of marine ecosystems.We compared metabarcoding and morphology‐based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction.Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un‐sieved samples in our metabarcoding analysis. We found that whilst metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples.Synthesis and Applications We show that metabarcoding using the cytochrome c oxidase I (COI) marker provides a more holistic, community‐based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates

Journal article

Dunn N, Savolainen V, 2020, Conservation genetics of native and European-introduced Chinese water deer (Hydropotes inermis), Zoological Journal of the Linnean Society, ISSN: 0024-4082

Journal article

Johri S, Dunn N, Chapple TK, Curnick D, Savolainen V, Dinsdale EA, Block BAet al., 2020, Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory, Mitochondrial DNA Part B: Resources, Vol: 5, Pages: 2085-2086, ISSN: 2380-2359

The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.

Journal article

Clive J, Flintham E, Savolainen V, 2020, Understanding same-sex sexual behaviour requires thorough testing rather than reinvention of theory, Nature Ecology and Evolution, Vol: 4, Pages: 784-785, ISSN: 2397-334X

Journal article

Savolainen V, Clottey VA, Doubi Bi TS, Konan JL, Quain M, Bezeng BS, Logah V, Kena AW, Osekre EA, Atuah L, Angui CMV, Ameka G, Turkson B, Boatemaa A, Anankware JP, Arwoh Boafo H, Agyei-Dwarko D, Collins CMet al., 2020, Systems thinking creates opportunities for a circular economy and sustainable palm agriculture in Africa, Current Research in Environmental Sustainability, Vol: 1, Pages: 31-34, ISSN: 2666-0490

Palm agriculture has received strong criticism in recent years due to its link with deforestation, especially in Asia. Here we propose that there is instead an opportunity for sustainable palm futures in Africa. Applying interdisciplinary systems thinking and circular production models, food and economic security can be achieved sustainably by (i) promoting integrated production of nutritionally valuable insect and fungal protein using palm crop waste; (ii) increasing resilience and productivity of crop palms in the harsh tropical climates of sub-Saharan Africa; and (iii) promoting the development of palm plantations as biodiverse agroforestry ecosystems.

Journal article

Dunn N, Johri S, Curnick D, Carbone C, Dinsdale EA, Chapple TK, Savolainen Vet al., 2020, Complete mitochondrial genome of the grey reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae), Mitochondrial DNA Part B: Resources, Vol: 5, Pages: 2080-2082, ISSN: 2380-2359

We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies’ MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).

Journal article

Flintham E, Savolainen V, Mullon CDL, 2020, Dispersal alters the nature and scope of sexually antagonistic variation, Publisher: BioRxiv

Intra-locus sexual conflict, or sexual antagonism, occurs when alleles have opposing fitness effects in thetwo sexes. Previous theory suggests that sexual antagonism is a driver of genetic variation by generating bal-ancing selection. However, these studies assume that populations are well-mixed, neglecting the effects ofspatial subdivision. Here we use mathematical modelling to show that limited dispersal can fundamentallychange evolution at sexually antagonistic autosomal and X-linked loci due to inbreeding and sex-specific kincompetition. We find that if the sexes disperse at different rates, kin competition within the philopatric sexbiases intralocus conflict in favour of the more dispersive sex. Furthermore, kin competition diminishes thestrength of balancing selection relative to genetic drift, reducing genetic variation in small subdivided pop-ulations. Meanwhile, by decreasing heterozygosity, inbreeding reduces the scope for sexually antagonisticpolymorphism due to non-additive allelic effects, and this occurs to a greater extent on the X-chromosomethan autosomes. Overall, our results demonstrate that spatial structure is an important factor in predictingwhere to expect sexually antagonistic alleles. We suggest that observed interspecific and intragenomic varia-tion in sexual antagonism may be explained by sex-specific dispersal ecology and demography.

Working paper

Clive J, Wisden W, Savolainen V, 2019, The de-scent of sexuality: should we smell a rat?, Archives of Sexual Behavior: an interdisciplinary research journal, ISSN: 0004-0002

In their Target Article, Pfau, Jordan, and Breedlove (2019) proposed a connection between the transient receptor potential cation channel 2 gene (TRPC2) and same-sex sexual behavior (SSSB) in primates. This novel theory is an attractive prospect for researchers investigating sexuality in the natural world. The proposal relies on evidence from proximate mechanism studies of TRPC2 knockout (KO) experiments in mice, in which non-functional TPRC2 alters the development of an olfactory sensory structure called the vomeronasal organ (VNO), resulting in an increase of SSSB in both males and females (Axel et al., 2002; Kimchi, Xu, & Dulac, 2007). In combination with an examination of TRPC2 sequence data and evolutionary relationships across primates, Pfau et al. proposed some hypotheses for the fitness consequences of SSSB in primates. Pfau et al. speculated that primates with multi-male/multi-female societies may have evolved via improved social cohesion facilitated by an increase in SSSB, mediated by non-functional TRPC2, and/or pleiotropy between increased SSSB and reduced same-sex aggression. Here, although we support some of these ideas by providing a more complete examination of TRPC2 in primates, we also advocate greater caution when interpreting available data on SSSB.

Journal article

Coathup M, Osborne OG, Savolainen V, 2019, Speciation: how predictable is genome evolution?, eLife, Vol: 8, ISSN: 2050-084X

Similar patterns of genomic divergence have been observed in the evolution of plant species separated by oceans.

Journal article

Papadopulos AST, Igea J, Smith TP, Hutton I, Baker WJ, Butlin RK, Savolainen Vet al., 2019, Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow, Evolution, Vol: 73, Pages: 1996-2002, ISSN: 0014-3820

The idea that populations must be geographically isolated (allopatric) to evolve into separate species has persisted for a long time. It is now clear that new species can also diverge despite ongoing genetic exchange, but few accepted cases of speciation in sympatry have held up when scrutinised using modern approaches. Here, we examined evidence for speciation of the Howea palms of Lord Howe Island, Australia, in light of new genomic data. We used coalescence-based demographic models combined with double digest restriction-site associated DNA sequencing of multiple individuals and provide support for previous claims by Savolainen et al. (Nature 441: 210–213, 2006) that speciation in Howea did occur in the face of gene flow.

Journal article

Papadopulos AST, Igea J, Dunning LT, Osborne OG, Quan X, Pellicer J, Turnbull C, Hutton I, Baker WJ, Butlin RK, Savolainen Vet al., 2019, Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea, Evolution, Vol: 73, Pages: 1986-1995, ISSN: 0014-3820

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.

Journal article

Osborne OG, Ciezarek A, Wilson T, Crayn D, Hutton I, Baker WJ, Turnbull CGN, Savolainen Vet al., 2019, Speciation in Howea palms occurred in sympatry, was preceded by ancestral admixture, and was associated with edaphic and phenological adaptation, Molecular Biology and Evolution, Vol: 36, Pages: 2682-2697, ISSN: 1537-1719

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species H. belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq dataset that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridised frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridisation may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

Journal article

Ciezarek AG, Osborne OG, Shipley ON, Brooks EJ, Tracey SR, McAllister JD, Gardner LD, Sternberg MJE, Block B, Savolainen Vet al., 2019, Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 36, Pages: 84-96, ISSN: 0737-4038

Journal article

Ciezarek A, Osbourne O, Shipley ON, Brooks EJ, Tracey S, McAllister J, Gardner L, Sternberg MJE, Block B, Savolainen Vet al., 2018, Diversification of characteristics related to regional endothermy in Thunnus tunas, Molecular Biology and Evolution, ISSN: 1537-1719

Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas, among the most threatened, but commercially important, fishes worldwide are renowned regional endotherms, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tuna, such as yellowfin, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than temperate bluefin tuna. Thereby, they are more resilient to fisheries, whereas bluefins have declined steeply. Despite the importance of these traits to not only fisheries, but response to climate change, little is known of the genetic processes underlying the diversification of tuna. In collecting and analysing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation has driven the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme which underlies thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, β-oxidation and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.

Journal article

Herraiz A, Stokes L, Turnbull C, Hutton I, Baker W, Savolainen Vet al., 2018, Developing a new variety of kentia palms (Howea forsteriana): up-regulation of cytochrome b561 and chalcone synthase is associated with the red coloration of the stems, Botany Letters, Vol: 165, Pages: 241-247, ISSN: 2381-8115

The kentia palm (Howea forsteriana) is endemic to a 12 km2 volcanic island in the Tasman Sea, Lord Howe Island. It is one of the most traded houseplants in the world. The typical kentia palm presents a dark green-coloured stem. Note that the stem is made of leaf rachis and petioles, which are intermingled towards the base. However, we discovered on Lord Howe Island a new biological variety that has a red stem. Red-stemmed palm species are known and highly demanded as decorative plants. However, these red palm horticultural varieties require tropical or subtropical conditions to grow, hence commercialization is limited. Thus, a red-stemmed variety of H. forsteriana may have tremendous market potential. Nonetheless, palm trees grow generally slowly and often reach maturity at 15–20 years old or later, which may make conventional strategies unsuitable for the propagation of a new variety. This difficulty needs to be addressed before commercialization can be achieved. Here, we found that anthocyanin is responsible for the red colouration of the stem in the new variety. Using RNA sequencing and quantitative PCR, we identified two gene isoforms displaying altered expression associated with this red colouration, encoding a cytochrome b561 and a chalcone synthase. The latter protein is known to be part of the anthocyanin biosynthesis pathway, which plays a central role in pigmentation in plants. The levels of cytochrome b561 transcripts accumulated were found to be well correlated with an increased anthocyanin concentration in the red stems.

Journal article

Esin A, Bergendahl LT, Savolainen V, Marsh JA, Warnecke Tet al., 2017, The genetic basis and evolution of red blood cell sickling in deer, Nature Ecology and Evolution, Vol: 2, Pages: 367-376, ISSN: 2397-334X

Crescent-shaped red blood cells, the hallmark of sickle-cell disease, present a striking departure from the biconcave disc shape normally found in mammals. Characterized by increased mechanical fragility, sickled cells promote haemolytic anaemia and vaso-occlusions and contribute directly to disease in humans. Remarkably, a similar sickle-shaped morphology has been observed in erythrocytes from several deer species, without obvious pathological consequences. The genetic basis of erythrocyte sickling in deer, however, remains unknown. Here, we determine the sequences of human β-globin orthologues in 15 deer species and use protein structural modelling to identify a sickling mechanism distinct from the human disease, coordinated by a derived valine (E22V) that is unique to sickling deer. Evidence for long-term maintenance of a trans-species sickling/non-sickling polymorphism suggests that sickling in deer is adaptive. Our results have implications for understanding the ecological regimes and molecular architectures that have promoted convergent evolution of sickling erythrocytes across vertebrates.

Journal article

Osborne OG, De-Kayne R, Bidartondo MI, Hutton I, Baker WJ, Turnbull CGN, Savolainen Vet al., 2017, Arbuscular mycorrhizal fungi promote coexistence and niche divergence of sympatric palm species on a remote oceanic island, New Phytologist, Vol: 217, Pages: 1254-1266, ISSN: 0028-646X

Microbes can have profound effects on their hosts, driving natural selection, promoting speciation and determining species distributions. However, soil-dwelling microbes are rarely investigated as drivers of evolutionary change in plants.We used metabarcoding and experimental manipulation of soil microbiomes to investigate the impact of soil and root microbes in a well-known case of sympatric speciation, the Howea palms of Lord Howe Island (Australia). Whereas H. forsteriana can grow on both calcareous and volcanic soils, H. belmoreana is restricted to, but more successful on, volcanic soil, indicating a trade-off in adaptation to the two soil types.We suggest a novel explanation for this trade-off. Arbuscular mycorrhizal fungi (AMF) are significantly depleted in H. forsteriana on volcanic soil, relative to both H. belmoreana on volcanic soil and H. forsteriana on calcareous soil. This is mirrored by the results of survival experiments, where the sterilization of natural soil reduces Howea fitness in every soil–species combination except H. forsteriana on volcanic soil. Furthermore, AMF-associated genes exhibit evidence of divergent selection between Howea species.These results show a mechanism by which divergent adaptation can have knock-on effects on host–microbe interactions, thereby reducing interspecific competition and promoting the coexistence of plant sister species.

Journal article

Dunn N, Priestley V, Herraiz A, Arnold R, Savolainen Vet al., 2017, Behaviour and season affect crayfish detection and density inference using environmental DNA, Ecology and Evolution, Vol: 7, Pages: 7777-7785, ISSN: 2045-7758

Although the presence/absence of aquatic invertebrates using environmental DNA (eDNA) has been established for several species, inferring population densities has remained problematic. The invasive American signal crayfish, Pacifastacus leniusculus (Dana), is the leading cause of decline in the UK's only native crayfish species, Austropotamobius pallipes (Lereboullet). Methods to detect species at low abundances offer the opportunity for the early detection, and potential eradication, of P. leniusculus before population densities reach threatening levels in areas occupied by A. pallipes. Using a factorial experimental design with aquaria, we investigated the impacts of biomass, sex ratio, and fighting behavior on the amount of eDNA released by P. leniusculus, with the aim to infer density per aquarium depending on treatments. The amount of target eDNA in water samples from each aquarium was measured using the quantitative Polymerase Chain Reaction. We show that the presence of eggs significantly increases the concentration of crayfish eDNA per unit of mass, and that there is a significant relationship between eDNA concentration and biomass when females are egg-bearing. However, the relationship between crayfish biomass and eDNA concentration is lost in aquaria without ovigerous females. Female-specific tanks had significantly higher eDNA concentrations than male-specific tanks, and the prevention of fighting did not impact the amount of eDNA in the water. These results indicate that detection and estimate of crayfish abundance using eDNA may be more effective while females are ovigerous. This information should guide further research for an accurate estimation of crayfish biomass in the field depending on the season. Our results indicate that detection and quantification of egg-laying aquatic invertebrate species using eDNA could be most successful during periods when eggs are developing in the water. We recommend that practitioners consider the reproductive cycle o

Journal article

Savolainen V, 2017, Isabelle Olivieri (1957-2016), JOURNAL OF EVOLUTIONARY BIOLOGY, Vol: 30, Pages: 224-224, ISSN: 1010-061X

Journal article

Tang CQ, Orme CDL, Bunnefeld L, Jones FA, Powell S, Chase MW, Barraclough TG, Savolainen Vet al., 2016, Global monocot diversification: geography better explains variation in species richness than environment or biology, Botanical Journal of the Linnean Society, Vol: 183, Pages: 1-15, ISSN: 0024-4074

Monocots account for a quarter of angiosperm species richness and are among the most economically and culturally important plants, including cereals (grasses), palms, orchids and lilies. Previous investigations of correlates of monocot species diversity have varied in scale and usually concentrated on a few drivers of diversification. Here, to disentangle the correlates of monocot diversity, we reconstructed a genus-level phylogenetic tree (1987 of the 2713 genera) and compiled an extensive database of abiotic, biotic and geographical characteristics to assess whether differences in these traits correlate with the vast asymmetrical species richness among genera present in this clade. Our results support several classical biodiversity theories, including species–area relationships, and latitudinal and elevational diversity gradients. Furthermore, interactions among these factors explain an additional 10% of the variation (compared to 36% from the main effects alone). We conclude that higher species richness among monocot genera is associated with geographical variables, especially larger ranges and lower elevations, rather than physical environment or physiology.

Journal article

Savolainen V, Hodgson J, 2016, Evolution of Homosexuality, Encyclopedia of Evolutionary Psychological Science, ISBN: 9783319169996

Book chapter

Ciezarek AG, Dunning LT, Jones CS, Noble LR, Humble E, Stefanni S, Savolainen Vet al., 2016, Substitutions in the glycogenin-1 gene are associated with the evolution of endothermy in sharks and tunas, Genome Biology and Evolution, Vol: 8, Pages: 3011-3021, ISSN: 1759-6653

Despite 400-450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterised by centralisation of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behaviour. Here we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total, (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology.

Journal article

Hipperson H, Dunning LT, Baker WJ, Butlin RK, Hutton I, Papadopulos AST, Smadja CM, Wilson TC, Devaux C, Savolainen Vet al., 2016, Ecological speciation in sympatric palms: 2. Pre- and post-zygotic isolation, Journal of Evolutionary Biology, Vol: 29, Pages: 2143-2156, ISSN: 1010-061X

We evaluated reproductive isolation in two species of palms (Howea) that have evolved sympatrically on Lord Howe Island (LHI, Australia). We estimated the strength of some pre- and post-zygotic mechanisms in maintaining current species boundaries. We found that flowering time displacement between species is consistent across in and ex situ common gardens and is thus partly genetically determined. On LHI, pre-zygotic isolation due solely to flowering displacement was 97% for H. belmoreana and 80% for H. forsteriana; this asymmetry results from H. forsteriana flowering earlier than H. belmoreana and being protandrous. As expected, only a few hybrids (here confirmed by genotyping) at both juvenile and adult stages could be detected in two sites on LHI, in which the two species grow intermingled (The Far Flats) or adjacently (Transit Hill). Yet, the distribution of hybrids was different between sites. At Transit Hill we found no hybrid adult trees, but 13.5% of younger palms examined there were of late hybrid classes. In contrast we found four hybrid adult trees, mostly of late hybrid classes, and only one juvenile F1 hybrid in the Far Flats. This pattern indicates that selection acts against hybrids between the juvenile and adult stages. An in situ reciprocal seed transplant between volcanic and calcareous soils also shows that early fitness components (up to 36 months) were affected by species and soil. These results are indicative of divergent selection in reproductive isolation, although it does not solely explain the current distribution of the two species on LHI.

Journal article

Swift DG, Dunning LT, Igea J, Brooks EJ, Jones CS, Noble LR, Ciezarek A, Humble E, Savolainen Vet al., 2016, Evidence of positive selection associated with placental loss in tiger sharks, BMC Evolutionary Biology, Vol: 16, ISSN: 1471-2148

BackgroundAll vertebrates initially feed their offspring using yolk reserves. In some live-bearing species these yolk reserves may be supplemented with extra nutrition via a placenta. Sharks belonging to the Carcharhinidae family are all live-bearing, and with the exception of the tiger shark (Galeocerdo cuvier), develop placental connections after exhausting yolk reserves. Phylogenetic relationships suggest the lack of placenta in tiger sharks is due to secondary loss. This represents a dramatic shift in reproductive strategy, and is likely to have left a molecular footprint of positive selection within the genome.ResultsWe sequenced the transcriptome of the tiger shark and eight other live-bearing shark species. From this data we constructed a time-calibrated phylogenetic tree estimating the tiger shark lineage diverged from the placental carcharhinids approximately 94 million years ago. Along the tiger shark lineage, we identified five genes exhibiting a signature of positive selection. Four of these genes have functions likely associated with brain development (YWHAE and ARL6IP5) and sexual reproduction (VAMP4 and TCTEX1D2).ConclusionsOur results indicate the loss of placenta in tiger sharks may be associated with subsequent adaptive changes in brain development and sperm production.

Journal article

Dunning LT, Hipperson H, Baker WJ, Butlin RK, Devaux C, Hutton I, Igea J, Papadopulos AST, Quan X, Smadja CM, Turnbull CGN, Savolainen Vet al., 2016, Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy, Journal of Evolutionary Biology, Vol: 29, Pages: 1472-1487, ISSN: 1420-9101

Ecological speciation requires divergent selection, reproductive isolation, and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. We identified loci with potential dual function in flowering time and soil adaptation, which effect on flowering time was validated by knocking orthologous genes in a model plant species. These results indicate that pleiotropy could have favoured the evolution of barrier traits in this system, despite ongoing gene flow.

Journal article

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