scholarly journals Incipient sympatric speciation in wild barley caused by geological-edaphic divergence

2020 ◽  
Vol 3 (12) ◽  
pp. e202000827
Author(s):  
Kexin Li ◽  
Xifeng Ren ◽  
Xiaoying Song ◽  
Xiujuan Li ◽  
Yu Zhou ◽  
...  
Keyword(s):  
Wild Barley ◽  
Sympatric Speciation ◽  
Ex Situ ◽  
Effective Population ◽  
Genome Resequencing ◽  
Recombination Rates ◽  
Whole Genome Resequencing ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Sympatric speciation (SS) has been contentious since the idea was suggested by Darwin. Here, we show in wild barley SS due to geologic and edaphic divergence in “Evolution Plateau,” Upper Galilee, Israel. Our whole genome resequencing data showed SS separating between the progenitor old Senonian chalk and abutting derivative young Pleistocene basalt wild barley populations. The basalt wild barley species unfolds larger effective population size, lower recombination rates, and larger genetic diversity. Both species populations show similar descending trend ∼200,000 yr ago associated with the last glacial maximum. Coalescent demography analysis indicates that SS was local, primary, in situ, and not due to a secondary contact from ex situ allopatric population. Adaptive divergent putatively selected genes were identified in both populations. Remarkably, disease resistant genes were selected in the wet basalt population, and genes related to flowering time, leading to temporal reproductive isolation, were selected in the chalk population. The evidence substantiates adaptive ecological SS in wild barley, highlighting the genome landscape during SS with gene flow, due to geologic-edaphic divergence.

scholarly journals No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 58 ◽  
Author(s):  
Martin Irestedt ◽  
Per G. P. Ericson ◽  
Ulf S. Johansson ◽  
Paul Oliver ◽  
Leo Joseph ◽  
...  
Keyword(s):  
19Th Century ◽  
Evolutionary History ◽  
Genetic Erosion ◽  
Glacial Cycle ◽  
Genome Resequencing ◽  
Extrinsic Factors ◽  
Dramatic Decline ◽  
Whole Genome Resequencing ◽  
The 19Th Century ◽  
The Last Glacial

The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.

scholarly journals THE DYNAMICS OF HISTORICAL AND RECENT RANGE SHIFTS IN THE RUFFED GROUSE (Bonasa umbellus)

2020 ◽  
Author(s):  
Utku Perktaş
Keyword(s):  
Ecological Niche ◽  
Demographic History ◽  
Ecological Niche Modelling ◽  
Ruffed Grouse ◽  
Bonasa Umbellus ◽  
Effective Population ◽  
Niche Modelling ◽  
Range Dynamics ◽  
The Last Glacial Maximum ◽  
The Last Glacial

ABSTRACTClimate variability is the most important force affecting distributional range dynamics of common and widespread species with important impacts on biogeographic patterns. This study integrates phylogeography with distributional analyses to understand the demographic history and range dynamics of a widespread bird species, the Ruffed Grouse (Bonasa umbellus), under several climate change scenarios. For this, I used an ecological niche modelling approach, together with Bayesian based phylogeographic analysis and landscape genetics, to develop robust inferences regarding this species’ demographic history and range dynamics. The model’s predictions were mostly congruent with the present distribution of the Ruffed Grouse. However, under the Last Glacial Maximum bioclimatic conditions, the model predicted a substantially narrower distribution than the present. The predictions for the Last Glacial Maximum also showed three allopatric refugia in south-eastern and west-coast North America, and a cryptic refugium in Alaska. The prediction for the Last Interglacial showed two separate distributions to the west and east of the Rocky Mountains. In addition, the predictions for 2050 and 2070 indicated that the Ruffed Grouse will most likely show slight range shifts to the north and will become more widely distributed than in the past or present. At present, effective population connectivity throughout North America was weakly positively correlated with Fst values. That is, the species’ distribution range showed a weak isolation-by-resistance pattern. The extended Bayesian Skyline Plot analysis, which provided good resolution of the effective population size changes over the Ruffed Grouse’s history, was mostly congruent with ecological niche modelling predictions for this species. This study offers the first investigation of the late-Quaternary history of the Ruffed Grouse based on ecological niche modelling and Bayesian based demographic analysis. The species’ present genetic structure is significantly affected by past climate changes, particularly during the last 130 kybp. That is, this study offers valuable evidence of the ‘expansion–contraction’ model of North America’s Pleistocene biogeography.

scholarly journals Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1018 ◽  
Author(s):  
Andrea Giontella ◽  
Francesca Maria Sarti ◽  
Irene Cardinali ◽  
Samira Giovannini ◽  
Raffaele Cherchi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Iberian Peninsula ◽  
Inbreeding Coefficient ◽  
Historical Background ◽  
Effective Population ◽  
Horse Breed ◽  
Mitochondrial Data ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.

scholarly journals Results of latest paleontological, stratigraphic and geoarchaeological research of the Volchia Griva mammoth fauna site

2018 ◽  
Vol 322 (3) ◽  
pp. 315-384 ◽  
Author(s):  
S.V. Leshchinskiy
Keyword(s):  
Western Siberia ◽  
Red Fox ◽  
Late Glacial ◽  
Forest Steppe ◽  
Large Mammals ◽  
Stone Artifacts ◽  
Articular Surfaces ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Volchia Griva is the largest site in Asia where the mammoth fauna remains are buried in situ. It is located in the Baraba forest-steppe (Western Siberia). In the 20th century, remains of at least 70 mammoths, 5 horses, 3 bisons and 1 wolf, as well as 37 stone artifacts were found here. The latest excavations of 2015–2017 on ~30 m2 revealed over 1500 bones and teeth, 95% of which belong to mammoths (at least 14 individuals), and the rest are from horses (3), bison, wolf, red fox, arctic fox, and rodents; associated artifacts – 23 items. With an average thickness of the bonebearing lens ~ 0.3–0.5 m, the local remain concentration exceeded 130/m2. The forty five crossed 14C dates were obtained from these materials, which reveal a burial period of ~20–10 ka BP. Obviously, there was the southernmost and one of the youngest mammoth refugia of Eurasia on this territory. The favorable Ca-Na geochemical landscape of the beast solonetz was the main reason for mammoth to visit the Volchia Griva. During the mineral starvation, the site attracted hundreds of large mammals, the remains of which were buried in mud baths and erosion forms. The main levels of the bone-bearing horizon have been forming for several thousand years, and that matched two waves of the megafauna’s geochemical stress in the Last Glacial Maximum and Late Glacial. Typical bone pathologies, such as exostoses, osteoporosis, erosion of articular surfaces, etc., characterize this process. These facts, together with the lack of strong evidence of hunting and butchering, indicate that the Volchia Griva was the natural mammoth death site, which was well known and used by Palaeolithic humans.

scholarly journals Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

2020 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Micheline Manseau ◽  
Cornelya F. C. Klütsch ◽  
Jean L. Polfus ◽  
Audrey Steedman ◽  
...  
Keyword(s):  
Last Glacial Maximum ◽  
High Latitude ◽  
Glacial Maximum ◽  
Effective Population ◽  
Glacial Cycles ◽  
Last Glacial ◽  
Genetic Patterns ◽  
Population Sizes ◽  
The Last Glacial Maximum ◽  
The Last Glacial

AbstractPleistocene glacial cycles influenced the diversification of high-latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. For many taxa, research has focused on genetic patterns since the Last Glacial Maximum (LGM), however glacial cycles before the LGM likely impacted genomic variation which may influence contemporary genetic patterns. We investigate diversification and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 high-coverage whole genomes coupled with larger-scale mitochondrial data. Contrary to the well-established paradigm that caribou ecotypes and contemporary genetic diversity arose from two major lineages in separate refugia during the LGM, a Beringian-Eurasian (BEL) and a North American (NAL) lineage, we found that the major diversifications of caribou occurred much earlier at around 110 kya, the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20-30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results highlight the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high-latitude species.

scholarly journals New in situ 14C data indicate the absence of nunataks in west Greenland during the Last Glacial Maximum

2019 ◽  
Vol 225 ◽  
pp. 105981 ◽  
Author(s):  
Brandon L. Graham ◽  
Jason P. Briner ◽  
Avriel D. Schweinsberg ◽  
Nathaniel A. Lifton ◽  
Ole Bennike
Keyword(s):  
Last Glacial Maximum ◽  
Glacial Maximum ◽  
West Greenland ◽  
Last Glacial ◽  
The Last Glacial Maximum ◽  
The Last Glacial

A quantitative framework for breeding and conservation of forest tree genetic resources in British Columbia

2001 ◽  
Vol 31 (4) ◽  
pp. 566-576 ◽  
Author(s):  
Alvin D Yanchuk
Keyword(s):  
British Columbia ◽  
Genetic Resources ◽  
Low Frequency ◽  
Forest Tree ◽  
Ex Situ ◽  
Individual Species ◽  
Effective Population ◽  
Breeding Populations ◽  
Conservation Plans

Over the last decade, forest tree breeders have become aware of the need for gene conservation, but have struggled with methods that would meaningfully integrate breeding and conservation populations. Gene Namkoong has provided the most guidance in this area by defining the role of in- and ex-situ populations in forest tree gene resource management and, particularly, the need for this to be dynamic in time and space. However, once conservation plans for individual species in British Columbia were considered, it became clear that more quantitative structure was needed to provide a framework for attaining practical management objectives. This paper attempts to provide such a framework and show how breeding and conservation populations can be integrated into a continuum of genetic resources. First, capturing only one copy of an allele is likely not satisfactory to meet conservation objectives, and sampling targets should be set higher (e.g., 20) so as to avoid potential problems of inbreeding at later stages in the program. Second, there seems to be a large problem with conserving very low frequency alleles that are recessive, but this occurs in nature as well. Third, in situ populations should be large enough and in a state to persist on their own over several generations, so the more recent effective population size numbers proposed by Lynch (1996) (i.e., ~1000) need to be considered. Fourth, while breeding populations of moderate size (~80) will contain adequate amounts of quantitative genetic variation, they will also contain 20 copies of dominant alleles at frequencies of ~0.20 or higher. Fifth, maintaining and rejuvenating strategic ex-situ test populations now seems to be the only way to conserve low- to mid-frequency alleles that will (i) be reduced in progressive breeding populations by drift and, (ii) over time, not be in desirable genetic backgrounds in in situ populations. Sixth, any reliance on locating mutants in production populations seems generally remote and cannot be relied upon except in a very few situations, although mutation will be important in breeding and in reserves in situ.

scholarly journals Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example

2022 ◽  
Author(s):  
Daria Martchenko ◽  
Aaron Shafer
Keyword(s):  
Isolation By Distance ◽  
Demographic History ◽  
Genomic Region ◽  
Whole Genome ◽  
Summary Statistics ◽  
Effective Population ◽  
Genome Resequencing ◽  
Reduced Representation ◽  
Whole Genome Resequencing ◽  
Population Demographic

Genomic approaches to the study of population demography rely on accurate SNP calling and by-proxy the site frequency spectrum (SFS). Two main questions for the design of such studies remain poorly investigated: do reduced genomic sequencing summary statistics reflect that of whole genome, and how do sequencing strategies and derived summary statistics impact demographic inferences? To address those questions, we applied the ddRAD sequencing approach to 254 individuals and whole genome resequencing approach to 35 mountain goat (Oreamnos americanus) individuals across the species range with a known demographic history. We identified SNPs with 5 different variant callers and used ANGSD to estimate the genotype likelihoods (GLs). We tested combinations of SNP filtering by linkage disequilibrium (LD), minor allele frequency (MAF) and the genomic region. We compared the resulting suite of summary statistics reflective of the SFS and quantified the relationship to demographic inferences by estimating the contemporary effective population size (Ne), isolation-by-distance and population structure, FST, and explicit modelling of the demographic history with δaδi. Filtering had a larger effect than sequencing strategy, with the former strongly influencing summary statistics. Estimates of contemporary Ne and isolation-by-distance patterns were largely robust to the choice of sequencing, pipeline, and filtering. Despite the high variance in summary statistics, whole genome and reduced representation approaches were overall similar in supporting a glacial induced vicariance and low Ne in mountain goats. We discuss why whole genome resequencing data is preferable, and reiterate support the use of GLs, in part because it limits user-determined filters.

scholarly journals Microbial Fe(III) reduction as a potential iron source from Holocene sediments beneath Larsen Ice Shelf

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaewoo Jung ◽  
Kyu-Cheul Yoo ◽  
Brad E. Rosenheim ◽  
Tim M. Conway ◽  
Jae Il Lee ◽  
...  
Keyword(s):  
Low Grade ◽  
Ice Shelf ◽  
Ice Shelves ◽  
Holocene Sediments ◽  
Shelf Sediments ◽  
Larsen Ice Shelf ◽  
Limited Surface ◽  
The Last Glacial Maximum ◽  
The Last Glacial

AbstractRecent recession of the Larsen Ice Shelf C has revealed microbial alterations of illite in marine sediments, a process typically thought to occur during low-grade metamorphism. In situ breakdown of illite provides a previously-unobserved pathway for the release of dissolved Fe2+ to porewaters, thus enhancing clay-rich Antarctic sub-ice shelf sediments as an important source of Fe to Fe-limited surface Southern Ocean waters during ice shelf retreat after the Last Glacial Maximum. When sediments are underneath the ice shelf, Fe2+ from microbial reductive dissolution of illite/Fe-oxides may be exported to the water column. However, the initiation of an oxygenated, bioturbated sediment under receding ice shelves may oxidize Fe within surface porewaters, decreasing dissolved Fe2+ export to the ocean. Thus, we identify another ice-sheet feedback intimately tied to iron biogeochemistry during climate transitions. Further constraints on the geographical extent of this process will impact our understanding of iron-carbon feedbacks during major deglaciations.

scholarly journals Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tetsuo Kon ◽  
Liyi Pei ◽  
Ryota Ichikawa ◽  
Chunyan Chen ◽  
Ping Wang ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Living Environment ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Resequencing ◽  
Genetic Population ◽  
Whole Genome Resequencing ◽  
Sea Area

AbstractLarge yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

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