scholarly journals Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

2021 ◽  
Author(s):  
Mathieu Robin ◽  
Giada J. Ferrari ◽  
Guelfirde Akguel ◽  
Johanna Von Seth ◽  
Verena J. Schuenemann ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Middle Ages ◽  
Haplotype Diversity ◽  
Mitochondrial Haplotype ◽  
Population Fluctuations ◽  
Term Survival ◽  
Alpine Ibex ◽  
Standing Variation ◽  
Near Extinction

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. A recent bottleneck event can also largely obscure our understanding of standing variation prior to the contraction. Historic population sizes can be modeled based on extant genomics, however uncertainty increases with the severity of the bottleneck. Integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern genomes. Coalescent demography simulations based on modern genomes indicate population fluctuations matching major climatic change over the past millennia. Using ancient genomes, we show that mitochondrial haplotype diversity has been reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincided with human settlement expansions in the Middle Ages. The near extinction severely reduced the mitochondrial diversity. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Contrary to expectations, we show that a second ancestral mitochondrial lineage has survived in an isolated population further south. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations.

Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle

2008 ◽  
Author(s):  
JEFF A. JOHNSON ◽  
RUTH E. TINGAY ◽  
MELANIE CULVER ◽  
FRANK HAILER ◽  
MICHÈLE L. CLARKE ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Critically Endangered ◽  
Term Survival ◽  
Long Term Survival ◽  
Low Genetic Diversity

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

scholarly journals Wolbachia-driven selective sweep in a range expanding insect species

2021 ◽  
Author(s):  
Junchen Deng ◽  
Giacomo Assandri ◽  
Pallavi Chauhan ◽  
Ryo Futahashi ◽  
Andrea Galimberti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Model Organism ◽  
Evolutionary Genetics ◽  
Mediterranean Area ◽  
Mitochondrial Haplotype ◽  
North West ◽  
Local Loss

Abstract Background Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism of the genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetic of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance in 17 I. elegans populations across Europe and Japan, and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). Results Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20 000 to 44 000 years before present, which is consistent with the end of the last glacial period about 20 000 ya. Conclusions Our findings provide an example of how endosymbiont infections ca shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which can impact geographic patterns of mitochondrial genetic diversity.

The interplay of population dynamics and the evolutionary process

1990 ◽  
Vol 330 (1257) ◽  
pp. 253-259 ◽  
Keyword(s):  
Genetic Diversity ◽  
Interspecific Interactions ◽  
Genotypic Variation ◽  
Evolutionary Process ◽  
Interactive System ◽  
Population Fluctuations ◽  
Genetic Changes ◽  
Local Extinctions ◽  
Term Maintenance

Long-term maintenance of genetic diversity is affected by ecological forces that are driven in turn by current levels of genetic variation. The strength of population regulation and the consequent patterns of population fluctuations determine the likelihood of genetic changes considered pivotal for rapid speciation. However, genetic diversity in the susceptibility to regulatory forces can reduce the magnitude of such fluctuations and minimize the likelihood of genetic revolutions. A group of populations that experiences local extinctions and recolonizations may hold lower levels of genetic diversity than in the absence of such extinctions, but local adaption, which provides enhanced genetic diversity, can reduce the likelihood of local extinctions. Tightly regulated populations experience different selection pressures than poorly regulated populations, although tighter regulation itself can evolve. When genotypic variation affects the outcome of interspecific interactions on a local scale, this effect, coupled with appropriate spatial variation, can enhance the resilience of the interactive system.

scholarly journals Wolbachia-driven selective sweep in a range expanding insect species

2021 ◽  
Author(s):  
Junchen Deng ◽  
Giacomo Assandri ◽  
Pallavi Chauhan ◽  
Ryo Futahashi ◽  
Andrea Galimberti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Model Organism ◽  
Evolutionary Genetics ◽  
Mediterranean Area ◽  
Mitochondrial Haplotype ◽  
North West ◽  
Local Loss

Abstract BackgroundEvolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism of the genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetic of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance in 17 I. elegans populations across Europe and Japan, and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). ResultsOur data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20 000 to 44 000 years before present, which is consistent with the end of the last glacial period about 20 000 ya. ConclusionsOur findings provide an example of how endosymbiont infections ca shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which can impact geographic patterns of mitochondrial genetic diversity.

scholarly journals Shedding Light on the Dark Ages: Sketching Potential Trade Relationships in Early Medieval Romania through Mitochondrial DNA Analysis of Sheep Remains

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 208
Author(s):  
Arina Acatrinei ◽  
Ioana Rusu ◽  
Cristina Mircea ◽  
Cezara Zagrean-Tuza ◽  
Emese Gál ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Middle Ages ◽  
Dna Analysis ◽  
Near East ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Archaeological Site ◽  
The Black Sea ◽  
Southeast Europe ◽  
Early Middle Ages

Southeast Europe has played an important role in shaping the genetic diversity of sheep due to its proximity to the Danubian route of transport from the Near East into Europe, as well as its possible role as a post-domestication migration network and long tradition of sheep breeding. The history of Romania and, in particular, the historical province of Dobruja, located on the shore of the Black Sea, has been influenced by its geographical position at the intersection between the great powers of the Near East and mainland Europe, with the Middle Ages being an especially animated time in terms of trade, migration, and conflict. In this study, we analyzed the mitochondrial control region of five sheep originating from the Capidava archaeological site (Dobruja, Southeast Romania), radiocarbon dated to the Early Middle Ages (5th–10th century AD), in order to better understand the genetic diversity of local sheep populations and human practices in relation to this particular livestock species. The analyses illustrate high haplotype diversity in local medieval sheep, as well as possible genetic continuity in the region. A higher tendency for North to South interaction, rather than East to West, is apparent, together with a lack of interaction along the Asian route. Continuous interaction between the First Bulgarian Empire, which occupied Dobruja starting with the 7th century AD, and the Byzantine Empire is indicated. These results might suggest expanding trade in Southeast Romania in the Early Middle Ages.

scholarly journals Conservation priorities in an endangered estuarine seahorse are informed by demographic history

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Thomas Kalama Mkare ◽  
Bettine Jansen van Vuuren ◽  
Peter R. Teske
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Demographic History ◽  
Conservation Status ◽  
Limited Range ◽  
The Other ◽  
Conservation Priorities ◽  
Population Declines ◽  
Term Survival

AbstractHistorical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world’s most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses’ demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity.

scholarly journals Wolbachia-driven selective sweep in a range expanding insect species

2021 ◽  
Author(s):  
Junchen Deng ◽  
Giacomo Assandri ◽  
Pallavi Chauhan ◽  
Ryo Futahashi ◽  
Andrea Galimberti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Model Organism ◽  
Evolutionary Genetics ◽  
Mediterranean Area ◽  
Mitochondrial Haplotype ◽  
North West ◽  
Local Loss

Abstract BackgroundEvolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism of the genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetic of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance in 17 I. elegans populations across Europe and Japan, and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). ResultsOur data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20 000 to 44 000 years before present, which is consistent with the end of the last glacial period about 20 000 ya. ConclusionsOur findings provide an example of how endosymbiont infections ca shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which can impact geographic patterns of mitochondrial genetic diversity.

scholarly journals Wolbachia-driven selective sweep in a range expanding insect species

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Junchen Deng ◽  
Giacomo Assandri ◽  
Pallavi Chauhan ◽  
Ryo Futahashi ◽  
Andrea Galimberti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Host Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Model Organism ◽  
Evolutionary Genetics ◽  
Mediterranean Area ◽  
Mitochondrial Haplotype ◽  
North West ◽  
Local Loss

Abstract Background Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. Method The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). Results Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000 years before present, which is consistent with the end of the last glacial period about 20,000 years. Conclusions Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.

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