188 results found
Savolainen V, 2022, Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing, New Phytologist, ISSN: 0028-646X
Dunn N, Savolainen V, Weber S, et al., 2022, Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding, Zoological Journal of the Linnean Society, Vol: 196, Pages: 593-607, ISSN: 0024-4082
As elasmobranchs are becoming increasingly threatened, efficient methods for monitoring the distribution and diversity of elasmobranch populations are required. Environmental DNA (eDNA) metabarcoding is an increasingly applied technique that enables mass identification of entire communities and is an effective method for the detection of rare and elusive species. We performed an eDNA metabarcoding survey for fish communities around a coral reef atoll in the Chagos Archipelago and assessed the diversity and distribution of elasmobranch species detected within these communities. Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed to fishes, 12 of which were elasmobranchs. There were no differences in fish communities based on the presence and absence of ASVs between sample depth (surface and 40m) or sampling habitat, but communities based on read abundance were significantly different between habitats. The dominant elasmobranch species were grey reef (Carcharhinus amblyrhynchos) and silvertip (C. albimarginatus) sharks, and elasmobranch communities were significantly different between sampling depth and habitat. Overall, we find that eDNA metabarcoding can be used to reveal the diversity of elasmobranchs within broader taxonomic assays, but further research and development of targeted metabarcoding primers may be required before it can be integrated into a toolkit for monitoring these species.
Ransome E, Hobbs F, Jones S, et al., 2022, Evaluating the transmission risk of SARS-CoV-2 from sewage pollution, Science of the Total Environment, ISSN: 0048-9697
The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated waters is poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. This study investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over eight months for SARS-CoV-2 RNA and infectious virus. Bivalves were also sampled as an indicator species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. No evidence of SARS-CoV-2 RNA or infectious virus was found in UK samples, in contrast to RNA positive samples from Serbia. Furthermore, this study shows that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for <3 days, while SARS-CoV-2 RNA is detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that detection of viral RNA alone is not an indication of pathogen spillover.
Jones S, Bell T, Coleman CM, et al., 2022, Testing bats in rehabilitation for SARS-CoV-2 before release into the wild, Conservation Science and Practice, Vol: 4, ISSN: 2578-4854
Several studies have suggested SARS-CoV-2 originated from a viral ancestor in bats, but whether transmission occurred directly or via an intermediary host to humans remains unknown. Concerns of spillover of SARS-CoV-2 into wild bat populations are hindering bat rehabilitation and conservation efforts in the United Kingdom and elsewhere. Current protocols state that animals cared for by individuals who have tested positive for SARS-CoV-2 cannot be released into the wild and must be isolated to reduce the risk of transmission to wild populations. Here, we propose a reverse transcription-quantitative polymerase chain reaction (RT-qPCR)-based protocol for detection of SARS-CoV-2 in bats, using fecal sampling. Bats from the United Kingdom were tested following suspected exposure to SARS-CoV-2 and tested negative for the virus. With current UK and international legislation, the identification of SARS-CoV-2 infection in wild animals is becoming increasingly important, and protocols such as the one developed here will help improve understanding and mitigation of SARS-CoV-2 in the future.
Shah T, Mashimba FH, Suleiman HO, et al., 2021, Phylogenetics of Ochna (Ochnaceae) and a new infrageneric classification, BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Vol: 198, Pages: 361-381, ISSN: 0024-4074
Anankware PJ, Roberts B, Cheseto X, et al., 2021, The nutritional profiles of five important edible insect species from West Africa – an analytical and literature synthesis, Frontiers in Nutrition, Vol: 8, Pages: 1-19, ISSN: 2296-861X
Background: Undernutrition is a prevalent, serious, and growing concern, particularly in developing countries. Entomophagy—the human consumption of edible insects, is a historical and culturally established practice in many regions. Increasing consumption of nutritious insect meal is a possible combative strategy and can promote sustainable food security. However, the nutritional literature frequently lacks consensus, with interspecific differences in the nutrient content of edible insects generally being poorly resolved.Aims and methods: Here we present full proximate and fatty acid profiles for five edible insect species of socio-economic importance in West Africa: Hermetia illucens (black soldier fly), Musca domestica (house fly), Rhynchophorus phoenicis (African palm weevil), Cirina butyrospermi (shea tree caterpillar), and Macrotermes bellicosus (African termite). These original profiles, which can be used in future research, are combined with literature-derived proximate, fatty acid, and amino acid profiles to analyse interspecific differences in nutrient content.Results: Interspecific differences in ash (minerals), crude protein, and crude fat contents were substantial. Highest ash content was found in H. illucens and M. domestica (~10 and 7.5% of dry matter, respectively), highest crude protein was found in C. butyrospermi and M. domestica (~60% of dry matter), whilst highest crude fat was found in R. phoenicis (~55% of dry matter). The fatty acid profile of H. illucens was differentiated from the other four species, forming its own cluster in a principal component analysis characterized by high saturated fatty acid content. Cirina butyrospermi had by far the highest poly-unsaturated fatty acid content at around 35% of its total fatty acids, with α-linolenic acid particularly represented. Amino acid analyses revealed that all five species sufficiently met human essential amino acid requirements, although C. butyrospermi was slightly limited in le
Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the ‘how’) of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. ‘the why’) for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.
Clive J, Wisden W, Savolainen V, 2021, The de-scent of sexuality: should we smell a rat?, Archives of Sexual Behavior: an interdisciplinary research journal, Vol: 50, Pages: 2283-2288, 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.
Shah T, Schneider JV, Zizka G, et al., 2021, Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits, AMERICAN JOURNAL OF BOTANY, Vol: 108, Pages: 1201-1216, ISSN: 0002-9122
Flintham E, Savolainen V, Mullon C, 2021, Dispersal alters the nature and scope of sexually antagonistic variation, The American Naturalist, Vol: 197, Pages: 543-559, ISSN: 0003-0147
Intralocus sexual conflict, or sexual antagonism, occurs when alleles have opposing fitness effects in the two sexes. Previous theory suggests that sexual antagonism is a driver of genetic variation by generating balancing selection. However, most of these studies assume that populations are well mixed, neglecting the effects of spatial subdivision. Here, we use mathematical modeling to show that limited dispersal changes evolution at sexually antagonistic autosomal and X-linked loci as a result of inbreeding and sex-specific kin competition. We find that if the sexes disperse at different rates, kin competition within the philopatric sex biases intralocus conflict in favor of the more dispersive sex. Furthermore, kin competition diminishes the strength of balancing selection relative to genetic drift, reducing genetic variation in small subdivided populations. Meanwhile, by decreasing heterozygosity, inbreeding reduces the scope for sexually antagonistic polymorphism due to nonadditive allelic effects, and this occurs to a greater extent on the X chromosome than autosomes. Overall, our results indicate that spatial structure is a relevant factor in predicting where sexually antagonistic alleles might be observed. We suggest that sex-specific dispersal ecology and demography can contribute to interspecific and intragenomic variation in sexual antagonism.
Savolainen V, Allen R, Binstead M, et al., 2021, Quick detection of a rare species: forensic swabs of survey tubes for hazel dormouse Muscardinus avellanarius urine, Methods in Ecology and Evolution, Vol: 12, Pages: 818-827, ISSN: 2041-210X
1. Effective conservation decisions rely on accurate survey data, but methods can be resource‐intensive and risk false negative results. Presence of the threatened hazel dormouse (England, UK) is typically confirmed by looking for its nest in survey tubes, over a 6‐month period. As an alternative, environmental DNA (eDNA) surveys have proven benefits in efficiency and accuracy for other taxa, but generally rely on the extraction and amplification of DNA from water, soil or sediment, which are not yet dependable samples for rare terrestrial mammals like the hazel dormouse.2. At a known occupancy site, paper‐lined survey tubes were used to capture a DNA sample. Like other species of rodent, the hazel dormouse excretes urine freely, and this was highlighted by ultraviolet torch, swabbed from the paper, extracted and hazel dormouse eDNA amplified by quantitative polymerase chain reaction (qPCR).3. Hazel dormouse presence was confirmed in this way in three out of 50 tubes within 8 days. Detection by conventional nest survey occurred on day 63 when a hazel dormouse nest was found in a single survey tube. We calculate that amplification of eDNA left behind in tubes increased survey efficiency here at least 12‐fold.4. Synthesis and applications. In this study we demonstrate that eDNA swabbed from a clean substrate placed in survey apparatus can significantly hasten the detection of a rare species. This method has the potential to broaden the application of eDNA to other terrestrial vertebrates, including surveys at large spatiotemporal scales. Beyond presence/absence, the non‐invasive DNA sample could also offer insights into sex ratio, abundance, behaviour and population genetics.
Fediajevaite J, Priestley V, Arnold R, et al., 2021, Meta-analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards, Ecology and Evolution, Vol: 11, Pages: 4803-4815, ISSN: 2045-7758
1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution a
Steyaert M, Priestley V, Osborne O, et al., 2020, Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos, Journal of Applied Ecology, Vol: 57, Pages: 2234-2245, 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
Dures SG, Carbone C, Savolainen V, et al., 2020, Ecology rather than people restrict gene flow in Okavango‐Kalahari lions, Animal Conservation, Vol: 23, Pages: 502-515, ISSN: 1367-9430
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, we recommend conservation managers consider
Ciezarek A, Gardner L, Savolainen V, et 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
Osborne OG, Kafle T, Brewer T, et 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.
Kulmuni J, Butlin RK, Lucek K, et 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
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
Johri S, Dunn N, Chapple TK, et 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.
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
Savolainen V, Clottey VA, Doubi Bi TS, et 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.
Dunn N, Johri S, Curnick D, et 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).
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.
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.
Papadopulos AST, Igea J, Smith TP, et 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.
Papadopulos AST, Igea J, Dunning LT, et 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.
Osborne OG, Ciezarek A, Wilson T, et 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.
Ciezarek AG, Osborne OG, Shipley ON, et al., 2019, Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas, Molecular Biology and Evolution, Vol: 36, Pages: 84-96, ISSN: 0737-4038
Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internallygenerated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas arecommercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain inwarm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits tonot only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processesunderlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found thatparallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. Thisincludes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributesto thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, b-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eightThunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across twospecies. Phylogeny-based metrics highlight conservation needs for some of these species.
Ciezarek A, Osbourne O, Shipley ON, et 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.
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