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 Population structure of Czech cold-blooded breeds of horses

2011 ◽  
Vol 54 (1) ◽  
pp. 1-9
Author(s):  
L. Vostrý ◽  
Z. Čapková ◽  
J. Přibyl ◽  
B. Hofmanová ◽  
H. Vostrá Vydrová ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Czech Republic ◽  
Generation Interval ◽  
Average Value ◽  
Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

scholarly journals IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽  
1977 ◽  
Vol 86 (3) ◽  
pp. 697-713
Author(s):  
C Chevalet ◽  
M Gillois ◽  
R F Nassar
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Random Mating ◽  
Matrix Multiplication ◽  
Inbred Lines ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Mean ◽  
Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

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 Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6424 ◽  
Author(s):  
Marta Maria Ciucani ◽  
Davide Palumbo ◽  
Marco Galaverni ◽  
Patrizia Serventi ◽  
Elena Fabbri ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Genetic Variability ◽  
Late Pleistocene ◽  
Phylogenetic Analyses ◽  
Hypervariable Region ◽  
Chronological Period ◽  
Complex Population ◽  
The Last Glacial Maximum ◽  
Mitochondrial Clade ◽  
The Last Glacial

Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.

Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation

2020 ◽  
Vol 132 (1) ◽  
pp. 161-173
Author(s):  
Camila D Ritter ◽  
Laís A Coelho ◽  
João Mg Capurucho ◽  
Sergio H Borges ◽  
Cíntia Cornelius ◽  
...  
Keyword(s):  
Population Structure ◽  
Bird Species ◽  
Population History ◽  
Sister Species ◽  
White Sand ◽  
Migration Rates ◽  
History Of ◽  
The Last Glacial Maximum ◽  
Vegetation Patches ◽  
The Last Glacial

Abstract Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.

Pedigree-based analysis of genetic variability in the registered Normande cattle breed in Colombia

2017 ◽  
Vol 57 (3) ◽  
pp. 422
Author(s):  
Derly Rodríguez Sarmiento ◽  
Emanuela Tullo ◽  
Rita Rizzi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Population Size ◽  
Cattle Breed ◽  
Inbreeding Coefficient ◽  
Mating Strategies ◽  
Effective Population ◽  
Significant Difference ◽  
Genealogical Information ◽  
Over Time

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.

On thin ice: problems with Stanford and Bradley's proposed Solutrean colonisation of North America

Antiquity ◽  
2014 ◽  
Vol 88 (340) ◽  
pp. 606-613 ◽  
Author(s):  
Michael J. O'Brien ◽  
Matthew T. Boulanger ◽  
Mark Collard ◽  
Briggs Buchanan ◽  
Lia Tarle ◽  
...  
Keyword(s):  
North America ◽  
Iberian Peninsula ◽  
North Atlantic ◽  
Food Supply ◽  
Ice Shelf ◽  
Southern France ◽  
The North ◽  
The North Atlantic ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Across Atlantic ice: the origin of America's Clovis culture(Stanford & Bradley 2012) is the latest iteration of a controversial proposal that North America was first colonised by people from Europe rather than from East Asia, as most researchers accept. The authors, Dennis Stanford and Bruce Bradley, argue that Solutrean groups from southern France and the Iberian Peninsula used watercraft to make their way across the North Atlantic and into North America during the Last Glacial Maximum (LGM). According to Stanford and Bradley, this 6000km journey was facilitated by a continuous ice shelf that provided fresh water and a food supply.AcrossAtlantic ice has received a number of positive reviews. Shea (2012: 294), for example, suggests that it is “an excellent example of hypothesis-building in the best tradition of processual archaeology. It challenges American archaeology in a way that will require serious research by its opponents”. Runnels (2012) is equally enthusiastic.

scholarly journals Phylogeny of the Formicoxenus genus-group (Hymenoptera: Formicidae) reveals isolated lineages of Leptothorax acervorum in the Iberian Peninsula predating the Last Glacial Maximum

2021 ◽  
Author(s):  
Dario Ojeda ◽  
Max John ◽  
Robert L. Hammond ◽  
Riita Savolainen ◽  
Kari Vepsalainen ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Last Glacial Maximum ◽  
Social Parasitism ◽  
Glacial Maximum ◽  
Glacial Refugium ◽  
Cold Adapted ◽  
Last Glacial ◽  
Distribution Ranges ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Formicoxenus genus-group comprises six genera within the tribe Crematogastrini. The group is well known for repeated evolution of social parasitism among closely related taxa and cold-adapted species with large distribution ranges in the Nearctic and Palearctic regions. Previous analyses based on nuclear markers (ultraconserved elements, UCEs) and mitochondrial genes suggest close relationship between Formicoxenus Mayr, 1855, Leptothorax Mayr, 1855 and Harpagoxenus Forel, 1893. However, scant sampling has limited phylogenetic assessment of these genera. Also, previous phylogeographic analyses of L. acervorum (Fabricius, 1793) have been limited to its West-Palearctic range of distribution, which has provided a narrow view on recolonization, population structure and existing refugia of the species. Here, we inferred the phylogenenetic history of genera within the Formicoxenus genus-group and reconstructed the phylogeography of L. acervorum with more extensive sampling. We employed four datasets consisting of whole genomes and sequences of the COI. The topologies of previous nuclear and our inferences based on mitochondrial genomes were overall congruent. Further, Formicoxenus may not be monophyletic. We found several monophyletic lineages that do not correspond to the current species described within Leptothorax, especially in the Nearctic region. We identified a monophyletic L. acervorum lineage that comprises both Nearctic and Palearctic locations. The most recent expansion within L. acervorum probably occurred within the last 0.5 Ma with isolated populations predating the Last Glacial Maximum (LGM), which are localized in at least two refugial areas (Pyrenean and Northern plateau) in the Iberian Peninsula. The patterns recovered suggest a shared glacial refugium in the Iberian Peninsula with cold-adapted trees that currently share high-altitude environments in this region.

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