scholarly journals Conserved genomic landscapes of differentiation across Populus speciation continuum

2021 ◽  
Author(s):  
Huiying Shang ◽  
Martha Rendón-Anaya ◽  
Ovidiu Paun ◽  
David L Field ◽  
Jaqueline Hess ◽  
...  
Keyword(s):  
Substantial Contribution ◽  
Species Variation ◽  
Effective Population ◽  
Species Pairs ◽  
Population Sizes ◽  
Speciation Continuum ◽  
Positive Correlations ◽  
Multiple Species ◽  
Demographic Trajectories ◽  
Species Specific

AbstractInvestigating genome-wide variation patterns along a speciation continuum is of central importance to understand the evolutionary processes contributing to lineage diversification. To identify which forces have shaped the genomic landscapes in Populus, we resequenced 201 whole-genomes from eight closely related species, with pairs of species at different stages along the speciation continuum. Using population structure and identity by descent analyses, we show extensive introgression between some species pairs, especially those with parapatric distributions. Inference of historical changes in effective population sizes support species-specific demographic trajectories, including recent population expansions in species characterized by broad present-day distributions. We observe highly conserved genomic landscapes, either focusing on within-species (genetic diversity: π and recombination rate: ρ) or among-species variation (relative divergence: FST and absolute divergence: DXY). Independent of the stage across the divergence continuum, we recovered positive correlations between the pair π and ρ and the pair DXY and ρ across all species pairs, which is consistent with a substantial contribution of linked selection in shaping these genomic landscapes. However, the positive correlations between π and DXY became weaker as the overall divergence level (da) increased, suggesting that background selection is not the only factor at play. Positive correlations between FST and DXY in all species pairs, regardless of the rate of gene flow, also indicates the high FST could be due to divergent sorting of ancient polymorphism before speciation. Our study showcases the importance of investigating genomic patterns on multiple species across the speciation continuum to better understand the genomic landscapes of diversity and differentiation.

Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone

The Auk ◽  
2019 ◽  
Vol 136 (2) ◽  
Author(s):  
Joseph D Manthey ◽  
Stéphane Boissinot ◽  
Robert G Moyle
Keyword(s):  
Gene Flow ◽  
Contact Zone ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Effective Population ◽  
Contact Zones ◽  
Population Sizes ◽  
Speciation Continuum ◽  
Whole Genome Resequencing ◽  
Genomic Introgression

Abstract Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall’s Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

scholarly journals Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species

Heredity ◽  
2021 ◽  
Author(s):  
Jessika M. M. Neves ◽  
Zachary J. Nolen ◽  
Nidia N. Fabré ◽  
Tamí Mott ◽  
Ricardo J. Pereira
Keyword(s):  
Marine Protected Area ◽  
Demographic History ◽  
Management Strategies ◽  
Sympatric Species ◽  
Similar Species ◽  
Effective Population ◽  
Interspecific Gene Flow ◽  
Coastal Marine ◽  
Population Sizes ◽  
Species Specific

AbstractHuman overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.

scholarly journals Mitonuclear co-introgression opposes genetic differentiation between phenotypically divergent songbirds

2021 ◽  
Author(s):  
Ellen Nikelski ◽  
Alexander S. Rubtsov ◽  
Darren Irwin
Keyword(s):  
Sex Chromosome ◽  
Genomic Variation ◽  
Effective Population ◽  
Emberiza Citrinella ◽  
Genome Wide ◽  
Mitochondrial Functions ◽  
Species Pairs ◽  
Population Sizes ◽  
Nuclear Differentiation ◽  
Mtdna Introgression

Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the relative effective population sizes of these genomic components. Differential introgression can cause some species pairs to deviate dramatically from this pattern. The yellowhammer (Emberiza citrinella) and the pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance but show no mtDNA differentiation. This discordance might be explained by mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). We investigated genome-wide nuclear differentiation between yellowhammers and pine buntings and compared it to what was seen previously in the mitochondrial genome. We found clear nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further tested for preferential introgression of mitonuclear genes and detected evidence for such biased introgression in yellowhammers. Mitonuclear co-introgression can remove post-zygotic incompatibilities between species and may contribute to the continued hybridization between yellowhammers and pine buntings despite their clear morphological and genetic differences. As such, our results highlight the potential ramifications of co-introgression in species evolution.

scholarly journals Striking differences in patterns of germline mutation between mice and humans

2016 ◽  
Author(s):  
Sarah J. Lindsay ◽  
Raheleh Rahbari ◽  
Joanna Kaplanis ◽  
Thomas Keane ◽  
Matthew E. Hurles
Keyword(s):  
Mutation Rate ◽  
Germline Mutation ◽  
Purifying Selection ◽  
Germline Mutations ◽  
Spermatogonial Stem Cell ◽  
Paternal Age ◽  
Effective Population ◽  
Population Sizes ◽  
Species Specific ◽  
Biological Differences

SummaryRecent whole genome sequencing (WGS) studies have estimated that the human germline mutation rate per basepair per generation (∼1.2−10−8) 1,2 is substantially higher than in mice (3.5-5.4−10−9) 3,4, which has been attributed to more efficient purifying selection due to larger effective population sizes in mice compared to humans.5,6,7. In humans, most germline mutations are paternal in origin and the numbers of mutations per offspring increase markedly with paternal age 2,8,9 and more weakly with maternal age 10. Germline mutations can arise at any stage of the cellular lineage from zygote to gamete, resulting in mutations being represented in different proportion and types of cells, with the earliest embryonic mutations being mosaic in both somatic and germline cells. Here we use WGS of multi-sibling mouse and human pedigrees to show striking differences in germline mutation rate and spectra between the two species, including a dramatic reduction in mutation rate in human spermatogonial stem cell (SSC) divisions, which we hypothesise was driven by selection. The differences we observed between mice and humans result from both biological differences within the same stage of embryogenesis or gametogenesis and species-specific differences in cellular genealogies of the germline.

scholarly journals Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

2021 ◽  
Author(s):  
Cecilia Di Bernardi ◽  
Camilla Wikenros ◽  
Eva Hedmark ◽  
Luigi Boitani ◽  
Paolo Ciucci ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Multiple Species ◽  
Species Specific

scholarly journals Interacting effects of insect and ungulate herbivory on Scots pine growth

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Michelle Nordkvist ◽  
Maartje J. Klapwijk ◽  
La rs Edenius ◽  
Christer Björkman
Keyword(s):  
Plant Growth ◽  
Scots Pine ◽  
Growth Response ◽  
Insect Herbivory ◽  
Additive Effects ◽  
Significant Interaction Effect ◽  
Ungulate Herbivory ◽  
Pine Trees ◽  
Multiple Species ◽  
Species Specific

AbstractMost plants are subjected to damage from multiple species of herbivores, and the combined impact on plant growth can be non-additive. Since plant response to herbivores tends to be species specific, and change with repeated damage, the outcome likely depend on the sequence and number of attacks. There is a high likelihood of non-additive effects on plant growth by damage from mammals and insects, as mammalian herbivory can alter insect herbivore damage levels, yet few studies have explored this. We report the growth response of young Scots pine trees to sequential mammal and insect herbivory, varying the sequence and number of damage events, using an ungulate-pine-sawfly system. Combined sawfly and ungulate herbivory had both additive and non-additive effects on pine growth—the growth response depended on the combination of ungulate browsing and sawfly defoliation (significant interaction effect). Repeated sawfly herbivory reduced growth (compared to single defoliation) on un-browsed trees. However, on browsed trees, depending on when sawfly defoliation was combined with browsing, trees exposed to repeated sawfly herbivory had both higher, lower and the same growth as trees exposed to a single defoliation event. We conclude that the sequence of attacks by multiple herbivores determine plant growth response.

scholarly journals Bark traits, decomposition and flammability of Australian forest trees

2017 ◽  
Vol 65 (4) ◽  
pp. 327 ◽  
Author(s):  
Saskia Grootemaat ◽  
Ian J. Wright ◽  
Peter M. van Bodegom ◽  
Johannes H. C. Cornelissen ◽  
Veronica Shaw
Keyword(s):  
Forest Tree ◽  
Remarkable Feature ◽  
Interspecific Differences ◽  
Eucalypt Plantations ◽  
Physical Traits ◽  
Key Driver ◽  
Multiple Species ◽  
Species Specific ◽  
First Time ◽  
Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

scholarly journals Species-Specific Segregation of Gender-Associated Mitochondrial DNA Types in an Area Where Two Mussel Species (Mytilus edulis and M. trossulus) Hybridize

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1359-1367 ◽  
Author(s):  
Carlos Saavedra ◽  
Donald T Stewart ◽  
Rebecca R Stanwood ◽  
Eleftherios Zouros
Keyword(s):  
Mytilus Edulis ◽  
The Other ◽  
Allozyme Analysis ◽  
Mussel Species ◽  
Species Origin ◽  
Species Pairs ◽  
Nuclear Background ◽  
Species Specific ◽  
Dna Types ◽  
Fertile Hybrids

Abstract In each of the mussel species Mytilus edulis and M. trossulus there exist two types of mtDNA, the F type transmitted through females and the M type transmitted through males. Because the two species produce fertile hybrids in nature, F and M types of one may introgress into the other. We present the results from a survey of a population in which extensive hybridization occurs between these two species. Among specimens classified as “pure” M. edulis or “pure” M. trossulus on the basis of allozyme analysis, we observed no animal that carried the F or the M mitotype of the other species. In most animals of mixed nuclear background, an individual's mtDNA came from the species that contributed the majority of the individual's nuclear genes. Most importantly, the two mtDNA types in post-F1 male hybrids were of the same species origin. We interpret this to mean that there are intrinsic barriers to the exchange of mtDNA between these two species. Because such barriers were not noted in other hybridizing species pairs (many being even less interfertile than M. edulis and M. trossulus), their presence in Mytilus could be another feature of the unusual mtDNA system in this genus.

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