scholarly journals The formation of avian montane diversity across barriers and along elevational gradients

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
José Martín Pujolar ◽  
Mozes P. K. Blom ◽  
Andrew Hart Reeve ◽  
Jonathan D. Kennedy ◽  
Petter Zahl Marki ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Differentiation ◽  
Bird Species ◽  
Geographic Area ◽  
Effective Population ◽  
Tropical Mountains ◽  
Mountainous Regions ◽  
Pleistocene Climate ◽  
Genome Wide ◽  
Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

scholarly journals Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

2010 ◽  
Vol 365 (1543) ◽  
pp. 1127-1138 ◽  
Author(s):  
Paquita E. A. Hoeck ◽  
Jennifer L. Bollmer ◽  
Patricia G. Parker ◽  
Lukas F. Keller
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Genetic Drift ◽  
Bird Species ◽  
Effective Population ◽  
Island Size ◽  
Island Populations ◽  
Population Sizes ◽  
Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

scholarly journals Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

2019 ◽  
Vol 110 (5) ◽  
pp. 587-600
Author(s):  
A Millie Burrell ◽  
Jeffrey H R Goddard ◽  
Paul J Greer ◽  
Ryan J Williams ◽  
Alan E Pepper
Keyword(s):  
Gene Flow ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Isolated Populations ◽  
Long Distance ◽  
Population Sizes ◽  
History Of ◽  
Small Set ◽  
Nuclear Microsatellite

Abstract Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

scholarly journals Continent-wide effects of urbanization on bird and mammal genetic diversity

2019 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R.P. Kinnunen ◽  
J. Bowman ◽  
C.J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

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 Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 83 ◽  
Author(s):  
Lei Xu ◽  
Bo Zhu ◽  
Zezhao Wang ◽  
Ling Xu ◽  
Ying Liu ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Haplotype Block ◽  
Block Structure ◽  
Effective Population ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Population Sizes ◽  
Haplotype Block Structure ◽  
Selection For

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle.

scholarly journals Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 350 ◽  
Author(s):  
Haile Berihulay ◽  
Rabiul Islam ◽  
Lin Jiang ◽  
Yuehui Ma
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Chromosome 1 ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes ◽  
Trait Locus ◽  
D Values ◽  
Genome Wide Linkage Disequilibrium

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

scholarly journals Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

2021 ◽  
Author(s):  
Thomas J. Batter ◽  
Joshua P. Bush ◽  
Benjamin N. Sacks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Expansion ◽  
Active Management ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Sex Marker ◽  
Cervus Canadensis ◽  
Population Sizes ◽  
Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

scholarly journals Genetic Diversity and Population Structure of Zeugodacus Tau Walker (Diptera: Tephritidae) in Southern Thailand

2021 ◽  
Vol 18 (4) ◽  
Author(s):  
Jingyoh ZAELOR ◽  
Duangta JULSIRIKUL ◽  
Sangvorn KITTHAWEE
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Fruit Fly ◽  
Haplotype Network ◽  
Single Strand Conformation Polymorphism ◽  
Fruit Flies ◽  
Effective Population ◽  
Bottleneck Effect ◽  
Southern Thailand ◽  
Population Sizes

The population structure of a fruit fly, Zeugodacus tau, was studied by a Single-Strand Conformation Polymorphism (SSCP) technique. Twenty haplotypes of Cytochrome Oxidase unit I (COI) sequence were found in flies collected from Southern Thailand. The phylogenetic tree and haplotype network revealed gene flow across a large geographic range. With the aid of winds, their gene flow diminished population structure. The population size of Z. tau in Southern Thailand seemed to be large and stable, but the other populations in some locations had experienced a bottleneck effect, leading to local genetic differentiation. Fruit flies from the eastern areas had large effective population sizes, whereas the populations from other areas were smaller. This pattern matched the ecological niche centroid model, in which fruit flies disperse from high population areas to lower ones.

scholarly journals Distinguishing gene flow between malaria parasite populations

2021 ◽  
Author(s):  
Tyler Steven Brown ◽  
Aimee R. Taylor ◽  
Olufunmilayo Arogbokun ◽  
Caroline O. Buckee ◽  
Hsiao-Han Chang
Keyword(s):  
Gene Flow ◽  
Malaria Parasite ◽  
Sequence Data ◽  
Simulated Data ◽  
Whole Genome Sequence ◽  
Effective Population ◽  
Migration Rates ◽  
Population Sizes ◽  
And Migration ◽  
Parasite Populations

Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report evaluates numerically the ability to distinguish different levels of gene flow between malaria populations, using different amounts of real and simulated data, where data are simulated using parameters that approximate different epidemiological conditions. Specifically, using Plasmodium falciparum  whole genome sequence data and sequence data simulated for a metapopulation with different migration rates and effective population sizes, we compare two estimators of gene flow, explore the number of genetic markers and number of individuals required to reliably rank highly connected locations, and describe how these thresholds change given different effective population sizes and migration rates. Our results have implications for the design and implementation of malaria genomic surveillance efforts.

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