scholarly journals Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

2020 ◽  
Vol 6 (48) ◽  
pp. eabc6318
Author(s):  
Ira Cooke ◽  
Hua Ying ◽  
Sylvain Forêt ◽  
Pim Bongaerts ◽  
Jan M. Strugnell ◽  
...  
Keyword(s):  
Climate Change ◽  
Population Structure ◽  
Skeletal Development ◽  
Host Population ◽  
Genomic Signatures ◽  
Long Reads ◽  
Adaptive Processes ◽  
Acropora Tenuis ◽  
Whole Genome Resequencing ◽  
Genetic Signatures

Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species’ responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.

scholarly journals Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

2020 ◽  
Author(s):  
Ira Cooke ◽  
Hua Ying ◽  
Sylvain Forêt ◽  
Pim Bongaerts ◽  
Jan Strugnell ◽  
...  
Keyword(s):  
Climate Change ◽  
Skeletal Development ◽  
Demographic History ◽  
Marine Species ◽  
Thermal Fluctuations ◽  
Coral Host ◽  
Diverse Range ◽  
Coral Holobiont ◽  
Acropora Tenuis ◽  
Signatures Of Selection

AbstractClimate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly for Acropora tenuis based on long-read sequencing, and then used shallow whole-genome resequencing of 148 Acropora tenuis colonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a diverse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case of A. tenuis holobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.

scholarly journals A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Eugenie C Yen ◽  
Shane A McCarthy ◽  
Juan A Galarza ◽  
Tomas N Generalovic ◽  
Sarah Pelan ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Parental Origin ◽  
De Novo Genome Assembly ◽  
Geographic Population ◽  
Long Reads ◽  
Tiger Moth ◽  
Innovative Solution

ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.

scholarly journals Climate change, parasitism and the structure of intertidal ecosystems

2006 ◽  
Vol 80 (2) ◽  
pp. 183-191 ◽  
Author(s):  
R. Poulin ◽  
K.N. Mouritsen
Keyword(s):  
Climate Change ◽  
Global Warming ◽  
Host Population ◽  
Intertidal Communities ◽  
Corophium Volutator ◽  
Ecological Processes ◽  
Cercarial Production ◽  
Animal Populations ◽  
Animal Communities ◽  
Intertidal Ecosystems

AbstractEvidence is accumulating rapidly showing that temperature and other climatic variables are driving many ecological processes. At the same time, recent research has highlighted the role of parasitism in the dynamics of animal populations and the structure of animal communities. Here, the likely interactions between climate change and parasitism are discussed in the context of intertidal ecosystems. Firstly, using the soft-sediment intertidal communities of Otago Harbour, New Zealand, as a case study, parasites are shown to be ubiquitous components of intertidal communities, found in practically all major animal species in the system. With the help of specific examples from Otago Harbour, it is demonstrated that parasites can regulate host population density, influence the diversity of the entire benthic community, and affect the structure of the intertidal food web. Secondly, we document the extreme sensitivity of cercarial production in parasitic trematodes to increases in temperature, and discuss how global warming could lead to enhanced trematode infections. Thirdly, the results of a simulation model are used to argue that parasite-mediated local extinctions of intertidal animals are a likely outcome of global warming. Specifically, the model predicts that following a temperature increase of less than 4°C, populations of the amphipod Corophium volutator, a hugely abundant tube-building amphipod on the mudflats of the Danish Wadden Sea, are likely to crash repeatedly due to mortality induced by microphallid trematodes. The available evidence indicates that climate-mediated changes in local parasite abundance will have significant repercussions for intertidal ecosystems. On the bright side, the marked effects of even slight increases in temperature on cercarial production in trematodes could form the basis for monitoring programmes, with these sensitive parasites providing early warning signals of the environmental impacts of global warming.

How does a Psittacanthus robustus Mart. population structure relate to a Vochysia thyrsoidea Pohl. host population?

Flora ◽  
2010 ◽  
Vol 205 (12) ◽  
pp. 797-801 ◽  
Author(s):  
Grazielle Sales Teodoro ◽  
Eduardo van den Berg ◽  
Marcela de Castro Nunes Santos ◽  
Flávia de Freitas Coelho
Keyword(s):  
Population Structure ◽  
Host Population

Host Population Structure and the Evolution of Virulence: A "Law of Diminishing Returns"

Evolution ◽  
1995 ◽  
Vol 49 (4) ◽  
pp. 743 ◽  
Author(s):  
Marc Lipsitch ◽  
Edward Allen Herre ◽  
Martin A. Nowak
Keyword(s):  
Population Structure ◽  
Host Population ◽  
Evolution Of Virulence ◽  
Diminishing Returns

scholarly journals Geographic distribution and conservation status of Eulychnia ritteri Cullmann (Cactaceae), an endemic cactus from southern Peru

2021 ◽  
Vol 28 (4) ◽  
pp. e19290
Author(s):  
Gregory Anthony Pauca-Tanco ◽  
Margarita Balvin ◽  
Paul Hoxey ◽  
Víctor Quipuscoa ◽  
Johana del Pilar Quispe-Turpo
Keyword(s):  
Climate Change ◽  
Population Structure ◽  
Population Density ◽  
Geographical Distribution ◽  
Coastal Area ◽  
Conservation Status ◽  
Northern Coast ◽  
Flower Buds ◽  
Local Fauna ◽  
Populations At Risk

Eulychnia ritteri is endemic to Peru, restricted to the northern coast of the department of Arequipa. The lack of knowledge of this species, and threats such as human activities and climate change, put the populations at risk. In this research, we examined the geographical distribution and conservation status of E. ritteri in the coastal area of the Caravelí province. In addition, the population structure and phenology in the Quebrada Vizcachani population were evaluated using plots of 10x100 m. Data on the accompanying flora and local fauna were also obtained. Eulychnia ritteri showed five populations distributed from 15°43’ to 15°47’S, with a total area of 63.62 ha (0.63 km2). The Quebrada Vizcachani population is the largest (24.5 ha) and the Cementerio population the smallest (0.018 ha). The population density evaluated is 0.06 ind/m2, where seedlings, juveniles, adults, and dead plants were 3.61, 24.09, 56.63 and 15.67% respectively. The phenology was asynchronous, the flower buds, flowers and fruits appear in the same period. The flowers and fruits were food for insects and rodents respectively, and 18 accompanying species have been recorded. Finally, E. ritteri is categorised as endangered (EN), given its geographical distribution and identified threats.

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