scholarly journals Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae

2021 ◽  
Author(s):  
M V Westbury ◽  
Diana Le Duc ◽  
David A Duchêne ◽  
Arunkumar Krishnan ◽  
Stefan Prost ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spotted Hyena ◽  
Genetic Changes ◽  
Slow Decline ◽  
Extant Species ◽  
Phylogenetic Discordance ◽  
Population Sizes ◽  
Low Levels ◽  
Olfactory Receptor Genes ◽  
Striped Hyena

Abstract During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species; the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analysed it together with the other three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in Ne over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialisation can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.

scholarly journals Ecological specialisation and evolutionary reticulation in extant Hyaenidae

2020 ◽  
Author(s):  
M V Westbury ◽  
Diana Le Duc ◽  
David A. Duchêne ◽  
Arunkumar Krishnan ◽  
Stefan Prost ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Species ◽  
Spotted Hyena ◽  
Genetic Changes ◽  
Slow Decline ◽  
Extant Species ◽  
Phylogenetic Discordance ◽  
Population Sizes ◽  
Olfactory Receptor Genes ◽  
Striped Hyena

AbstractDuring the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four extant genera, each of which contains only a single species. These species include the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous genome studies have analysed the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. To tackle these questions, we generated an aardwolf genome and analysed it together with those from the other three species. We provide new insights into the evolutionary relationships between the species, the genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance within the family suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection in their respective lineages, suggesting putative key adaptations to carrion or termite feeding. We also found a family-wide expansion in olfactory receptor genes suggesting that an acute sense of smell was a key early adaptation for the Hyaenidae family. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, which we putatively link to their similarly slow decline in Neover the last ∼2 million years. We found much higher levels of genetic diversity in both the spotted hyena and aardwolf and more stable population sizes through time. Taken together, these findings highlight how ecological specialisation can impact the evolutionary history, demographics, and adaptive genetic changes of a lineage.

Allozyme diversity in the endangered shrub Linderamelissifolia (Lauraceae) and its widespread congener Linderabenzoin

1996 ◽  
Vol 26 (12) ◽  
pp. 2080-2087 ◽  
Author(s):  
Mary Jo W. Godt ◽  
J.L. Hamrick
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Southeastern United States ◽  
Genotypic Diversity ◽  
Allozyme Variation ◽  
Effective Population ◽  
Allozyme Diversity ◽  
Dioecious Species ◽  
Population Sizes ◽  
Low Levels

Allozyme diversity was assessed in 15 populations of the endangered clonal shrub Linderamelissifolia (Walt.) Blume (pondberry; Lauraceae) throughout its range in the southeastern United States and in five populations of spicebush (Linderabenzoin (L.) Blume), a sexually reproducing, co-occurring congener. Low levels of allozyme variation characterize both dioecious species. Although genetic diversity was moderately high (HT = 0.239) at polymorphic loci for L. benzoin, few of the 42 loci were polymorphic (Ps = 35%; Pp = 25%), and thus overall estimates of genetic diversity were relatively low (Hes = 0.083; Hep = 0.070). Little genetic variation was detected at 27 loci within L. melissifolia (Hes = 0.025; Hep = 0.015). Nine L. melissifolia loci (33%) were polymorphic but genetic diversity was low (HT = 0.074) at these loci, and few were polymorphic within populations (mean = 6.7%). The number of multilocus genotypes detected in L. melissifolia populations ranged from 1 to 18, with a mean of 4.5. Mean genetic identities between populations within each species were high (I = 0.98 and 0.99 for L. benzoin and L. melissifolia, respectively), a result of the high numbers of monomorphic loci. Despite the high genetic similarity of populations, estimates of gene flow were low to moderate (Nm = 0.82 and 1.25 for L. melissifolia and L. benzoin, respectively). The lower genetic diversity within L. melissifolia may be primarily due to bottlenecks during its evolutionary history. The recent loss of populations and of genets within populations have probably further eroded genetic diversity. To reduce the risk of extinction, effective population sizes of L. melissifolia could be enhanced by increasing genotypic diversity within populations.

scholarly journals Genetic variation in lowland and mountain populations of Tofieldia calyculata and their ability to survive within low levels of genetic diversity

2021 ◽  
Author(s):  
Tomáš Vlasta ◽  
Zuzana Műnzbergová
Keyword(s):  
Genetic Diversity ◽  
Suitable Habitat ◽  
Herbarium Specimens ◽  
The Past ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Population Sizes ◽  
Range Periphery ◽  
Low Levels ◽  
European Mountains

Abstract Loss of genetic diversity is expected to be a common reason for decline of populations of many rare species. To what extent this is true for populations at the range periphery remains to be explored. Alpine species with peripheral lowland populations are ideal but poorly known model system to address this issue. We investigated genetic diversity and structure of populations of Tofieldia calyculata, species common in central European mountains but highly endangered in lowlands using 17 microsatellite loci. We showed that lowland populations have lower genetic diversity than mountain populations and they are not clearly differentiated from mountain populations. Species probably survived the last glaciation in refugia in margins of Alps and western Carpathians. Some lowland populations are probably relict as well and contain unique genetic information. Their low genetic diversity is likely the result the of reduction of population sizes, gene flow during the Holocene and selfing. However postglacial colonization is also a case of some lowland populations. Based on data from herbarium specimens from extinct lowland populations, we demonstrated that lowland populations had low genetic diversity also in the past and main part of the genetic diversity was lost due to extinction of whole populations. Within population genetic diversity has not changed since the last century suggesting that these populations are able to survive with low levels of genetic diversity under suitable habitat conditions. This idea is also supported by finding of large viable recent populations with very low genetic diversity. We conclude that lowland populations are unique and deserve adequate conservation.

scholarly journals Genetic diversity of rice stem borer (Chilo suppressalis Walker) from Northern Iran and comparison with other countries

2016 ◽  
Vol 48 (3) ◽  
pp. 360 ◽  
Author(s):  
M. Shayanmehr ◽  
E. Yoosefi-Lafooraki
Keyword(s):  
Genetic Diversity ◽  
Stem Borer ◽  
Chilo Suppressalis ◽  
Mazandaran Province ◽  
Northern Iran ◽  
Low Genetic Diversity ◽  
High Gene ◽  
Major Pest ◽  
Different Populations ◽  
Low Levels

Rice striped stem borer, <em>Chilo suppressalis</em> Walker (Lepidoptera: Crambidae) is considered the major pest of rice in Iran. Because of the serious damage on rice in Northern Iran, the present study was conducted to investigate genetic diversity within populations of <em>C. suppressalis</em>, from Mazandaran using a template of cytochrome oxidase I gene, 750 bps, (<em>COI</em>). Later the haplotypes from Iran were compared with those found in other countries. According to the results of this study, there is very low genetic diversity (two haplotypes) among different populations of this pest in populations of Northern Iran. The genetic similarity and low levels of genetic diversity of these populations suggest that the pest colonization occurred relatively recently and there is high gene flow between these populations of the province. In addition, haplotypes of Mazandaran province are different with those found in other countries. The similarity of Iranian population (Simorgh) with one population from China indicated that China might be the origin of <em>C. suppresalis</em>.

scholarly journals Enhancing (crop) plant photosynthesis by introducing novel genetic diversity

2017 ◽  
Vol 372 (1730) ◽  
pp. 20160380 ◽  
Author(s):  
Marcel Dann ◽  
Dario Leister
Keyword(s):  
Genetic Diversity ◽  
Genetic Manipulation ◽  
Plant Evolution ◽  
Crop Plants ◽  
Crop Plant ◽  
Higher Plant ◽  
Novel Approach ◽  
Population Sizes ◽  
Plant Photosynthesis ◽  
Successful Establishment

Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility. This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.

scholarly journals Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8304 ◽  
Author(s):  
Biao Xiong ◽  
Limei Zhang ◽  
Shubin Dong ◽  
Zhixiang Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Sex Ratios ◽  
Mainland China ◽  
Small Sample ◽  
Chloroplast Microsatellites ◽  
Wild Populations ◽  
Haplotype Networks ◽  
Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

scholarly journals Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

2016 ◽  
Author(s):  
Stephen R. Doyle ◽  
Catherine Bourguinat ◽  
Hugues C. Nana-Djeunga ◽  
Jonas A. Kengne-Ouafo ◽  
Sébastien D.S. Pion ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Genetic Drift ◽  
Onchocerca Volvulus ◽  
Molecular Pathways ◽  
Ivermectin Treatment ◽  
Genetic Changes ◽  
Genome Wide ◽  
Parasite Populations ◽  
Generation Sequencing

ABSTRACTBackgroundTreatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana - exposed to more than a decade of regular ivermectin treatment - have raised concern that sub-optimal responses to ivermectin’s anti-fecundity effect are becoming more frequent and may spread.Methodology/Principal FindingsPooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR.Conclusions/SignificanceThis study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait in which identical or related molecular pathways but not necessarily individual genes likely determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations.Author summaryOnchocerciasis is a human parasitic disease endemic across large areas of Sub-Saharan Africa, where more that 99% of the estimated 100 million people globally at-risk live. The microfilarial stage of Onchocerca volvulus causes pathologies ranging from mild itching to visual impairment and ultimately, irreversible blindness. Mass administration of ivermectin kills microfilariae and has an anti-fecundity effect on adult worms by temporarily inhibiting the development in utero and/or release into the skin of new microfilariae, thereby reducing morbidity and transmission. Phenotypic and genetic changes in some parasite populations that have undergone multiple ivermectin treatments in Cameroon and Ghana have raised concern that sub-optimal response to ivermectin’s anti-fecundity effect may increase in frequency, reducing the impact of ivermectin-based control measures. We used next generation sequencing of small pools of parasites to define genome-wide genetic differences between phenotypically characterised good and sub-optimal responder parasites from Cameroon and Ghana, and identified multiple genomic regions differentiating the response types. These regions were largely different between parasites from both countries but revealed common molecular pathways that might be involved in determining the extent of response to ivermectin’s anti-fecundity effect. These data reveal a more complex than previously described pattern of genetic diversity among O. volvulus populations that differ in their geography and response to ivermectin treatment.

scholarly journals Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

2013 ◽  
Vol 280 (1771) ◽  
pp. 20131945 ◽  
Author(s):  
Joana Segura ◽  
Luca Ferretti ◽  
Sebastián Ramos-Onsins ◽  
Laia Capilla ◽  
Marta Farré ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mammalian Species ◽  
Evolutionary Change ◽  
Critical Importance ◽  
Recombination Rates ◽  
Allelic Variants ◽  
Crossover Interference ◽  
Chromosomal Segregation ◽  
Low Levels ◽  
Taxonomic Groups

Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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