scholarly journals Mitochondrial DNA variation of the ruffed grouse (Bonasa umbellus)

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Rodney L. Honeycutt ◽  
Glenn A. Proudfoot ◽  
Nova J. Silvy
Keyword(s):  
Mitochondrial Dna ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
The United States ◽  
Mitochondrial Haplotype ◽  
Ruffed Grouse ◽  
Bonasa Umbellus ◽  
Long Distance ◽  
Mtdna Variation

Abstract Objective The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitochondrial DNA (mtDNA) variation in the ruffed grouse across western, central, and eastern parts of its distribution. We compare patterns of mtDNA variation to those characterized by morphology and ecology. Additionally, we evaluate the demographic history of the species based on mitochondrial haplotype diversity. Results Patterns of mtDNA variation revealed geographic subdivision, with populations of ruffed grouse subdivided into 3 to 4 genetically distinct groups. This subdivision partially coincided with the ranges of described subspecies. Behavioral traits prohibiting long-distance movement and barriers to dispersal in response to physiography and unsuitable habitat help explain these patterns of subdivision. Historically, the ruffed grouse probably experienced a population expansion, possibly in response to changes during the Pleistocene.

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 Mitochondrial DNA variation in the Italian Heavy Draught Horse

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8996 ◽  
Author(s):  
Hovirag Lancioni ◽  
Irene Cardinali ◽  
Andrea Giontella ◽  
Maria Teresa Antognoni ◽  
Arianna Miglio
Keyword(s):  
Mitochondrial Dna ◽  
First Generation ◽  
Central Italy ◽  
Haplotype Diversity ◽  
Developed Countries ◽  
Mitochondrial Haplotype ◽  
Published Data ◽  
Comprehensive Overview ◽  
Dna Variation ◽  
Long Time

Background In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook. Methodology To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds. Results Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.

scholarly journals Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand

2021 ◽  
Vol 32 (1) ◽  
pp. 61-80
Author(s):  
Verakiat Supmee ◽  
◽  
Apirak Songrak ◽  
Juthamas Suppapan ◽  
Pradit Sangthong ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Genetic Information ◽  
Population Genetic ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Andaman Sea ◽  
Gulf Of Thailand ◽  
The Gulf Of Thailand

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The Analysis of molecular variance (AMOVA) analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

scholarly journals Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

2020 ◽  
Vol 43 ◽  
pp. 199-207
Author(s):  
A Jha ◽  
K Vasudevan
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Founder Population ◽  
Effective Population ◽  
Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

scholarly journals Mitochondrial phylogeography of the Mediterranean horseshoe bat on the Balkan Peninsula

2019 ◽  
Vol 71 (4) ◽  
pp. 767-774
Author(s):  
Ivana Budinski ◽  
Vladimir Jovanovic ◽  
Branka Pejic ◽  
Jelena Blagojevic ◽  
Marija Rajicic ◽  
...  
Keyword(s):  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Balkan Peninsula ◽  
Glacial Refugium ◽  
Recent Population Expansion ◽  
The Balkans ◽  
Loop Region ◽  
The Mediterranean ◽  
Horseshoe Bat

The Balkan Peninsula is identified as one of the major glacial refugia in Europe during the Pleistocene, and it has served as a genetic source for post-glacial recolonization for many temperate species. The aim of this study was to investigate the genetic diversity and phylogeographic patterns of the Mediterranean horseshoe bat, Rhinolophus euryale Blasius 1853, on the Balkan Peninsula. We also analyzed its demographic history and tested the hypothesis that this region was a glacial refugium for this species. We collected 82 samples from 20 localities in the Balkans and Italy and sequenced the mitochondrial D-loop region. Our results revealed low nucleotide but high haplotype diversity, with 20 out of 24 haplotypes reported for the first time. All Balkan and Italian samples belonged to a single genetic clade in the phylogenetic reconstruction, where they clustered together with previously published samples from Turkey, southern France and North Africa. The haplotype network had a star-like pattern that is indicative of recent population expansion. Both mismatch distribution and shallow genetic differentiation also supported the scenario of a sudden demographic expansion. We estimated that expansion within this lineage commenced in the Late Pleistocene. We suggest that the Balkan Peninsula was a glacial refugium for R. euryale.

scholarly journals Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9679
Author(s):  
Noorhani Syahida Kasim ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Rumeaida Mat Piah ◽  
Wahidah Mohd Arshaad ◽  
Siti Azizah Mohd Nor ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Pacific Ocean ◽  
Goodness Of Fit ◽  
Demographic History ◽  
Population Expansion ◽  
Seasonal Migration ◽  
Likelihood Method ◽  
Recent Population Expansion ◽  
D Loop ◽  
Longtail Tuna

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989–1.000; ND5 = 0.848–0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019–0.025; ND5 = 0.0017–0.003), “star-like” haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

scholarly journals Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

2020 ◽  
Author(s):  
Erinç Yurtman ◽  
Onur Özer ◽  
Eren Yüncü ◽  
Nihan Dilşad Dağtaş ◽  
Dilek Koptekin ◽  
...  
Keyword(s):  
Bronze Age ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Late Glacial ◽  
Mitochondrial Haplotype ◽  
Wild Populations ◽  
Early Neolithic ◽  
Nuclear Polymorphism ◽  
Polymorphism Data ◽  
The Bronze Age

AbstractSheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.

scholarly journals Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rekha Sharma ◽  
Sonika Ahlawat ◽  
Himani Sharma ◽  
Priyanka Sharma ◽  
Poonam Panchal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Population Expansion ◽  
Scientific Management ◽  
Ecological Zones ◽  
Sheep Breeds ◽  
Indigenous Sheep

AbstractSheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

scholarly journals Influence of Two Wolbachia Strains on Population Structure of East AfricanDrosophila simulans

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 1959-1969 ◽  
Author(s):  
Matthew D Dean ◽  
Kirrie J Ballard ◽  
Anne Glass ◽  
J William ◽  
O Ballard
Keyword(s):  
Mitochondrial Dna ◽  
East Africa ◽  
Evolutionary Dynamics ◽  
Demographic History ◽  
Wolbachia Infection ◽  
Infection Status ◽  
Background Selection ◽  
Evolutionary Forces ◽  
Mtdna Variation ◽  
Multiple Strains

AbstractDrosophila simulans is hypothesized to have originated in continental East Africa or Madagascar. In this study, we investigated evolutionary forces operating on mitochondrial DNA (mtDNA) in populations of D. simulans from Zimbabwe, Malawi, Tanzania, and Kenya. Variation in mtDNA may be affected by positive selection, background selection, demographic history, and/or any maternally inherited factor such as the bacterial symbiont Wolbachia. In East Africa, the wRi and wMa Wolbachia strains associate with the siII or siIII mitochondrial haplogroups, respectively. To ask how polymorphism relates to Wolbachia infection status, we sequenced 1776 bp of mitochondrial DNA and 1029 bp of the X-linked per locus from 79 lines. The two southern populations were infected with wRi and exhibited significantly reduced mtDNA variation, while Wolbachia-uninfected siII flies from Tanzania and Kenya showed high levels of mtDNA polymorphism. These are the first known populations of D. simulans that do not exhibit reduced mtDNA variation. We observed no mitochondrial variation in the siIII haplogroup regardless of Wolbachia infection status, suggesting positive or background selection. These populations offer a unique opportunity to monitor evolutionary dynamics in ancestral populations that harbor multiple strains of Wolbachia.

Molecular Genetic Evidence from Contemporary Populations for the Origins of Native North Americans

2016 ◽  
Author(s):  
Michael Crawford ◽  
Rohina C. Rubicz
Keyword(s):  
Mitochondrial Dna ◽  
Native American ◽  
Y Chromosome ◽  
Molecular Genetic ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Genetic Evidence ◽  
Whole Genome Sequence ◽  
Aleutian Island ◽  
Molecular Genetic Evidence

An overview of the current molecular genetic evidence for the origins of North American populations is presented, including specific examples from the authors’ work with the Aleutian Island inhabitants. Shared mitochondrial DNA and Y-chromosome DNA markers among Siberians and Native Americans point to a Pleistocene migration from Siberia into the Americas via Beringia. There was likely a later migration from Siberia to Alaska, based on the analysis of whole-genome sequence data from a Greenland Paleoeskimo that clusters this individual with Siberian populations. Coalescence date estimates for Native American mitochondrial DNA and Y-chromosome DNA haplogroups indicate that there was a population expansion approximately 15,000–18,000 that was associated with a pre-Clovis settlement of the Americas and coastal migration, and then a later expansion of circum-Arctic populations. Settlement of the Aleutian Archipelago took place via east-to-west migration of Aleut kin groups, accompanied by a clinal loss in mitochondrial DNA haplotype diversity.

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