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The relationship between the genetic (cM) and the physical (Mb) position of markers in the best-order map built based on the draft sequence of the zebra finch genome. Red and blue circles indicate the female- and male-specific genetic map, respectively. The length of the x -axis reflects the total physical size of the chromosome, as given by the genome assembly. Only chromosomes with > 10 markers are included. 

The relationship between the genetic (cM) and the physical (Mb) position of markers in the best-order map built based on the draft sequence of the zebra finch genome. Red and blue circles indicate the female- and male-specific genetic map, respectively. The length of the x -axis reflects the total physical size of the chromosome, as given by the genome assembly. Only chromosomes with > 10 markers are included. 

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Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variatio...

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... one other marker in a two-point analysis. The resulting framework map consisted of 32 different linkage groups ranging from 0 to 118 cM. It contained 443 markers and covered 1341 cM in total. Linkage groups were equivalent to chromosomes 1-28 (except for chromosome 22 that was not covered in our analysis), plus the Z chromosome (Sup- plemental Fig. 2). Marker order in all linkage groups of the framework map was essentially identical to the order of markers in the physical assembly of the draft genome sequence. The only exceptions were TGU2, TGU26, and TGU28, which thus contain either assembly or linkage map errors; these chromosomes were ex- cluded from the subsequent analysis of ...
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... (Fig. 1). A closer inspection of the variation in recombination rate along chromosomes revealed a sharp increase toward telomeric regions. Moreover, there were extremely low rates of recombination in the central parts of the larger chromosomes, giving rise to a sigmoid relationship between the cumulative genetic length and physical position ( Fig. 2; Sup- plemental Figs. 2, 3). As an example, the two distal 15 Mb of chro- mosome TGU1A measured 42 and 41 cM, while the genetic dis- tance in the interior 44 Mb of this chromosome was only 6 cM. For microchromosomes (chromosomes <20 Mb) the rate of re- combination was uniformly high over the entire chromosome (Fig. 2), and was similar ...
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... length and physical position ( Fig. 2; Sup- plemental Figs. 2, 3). As an example, the two distal 15 Mb of chro- mosome TGU1A measured 42 and 41 cM, while the genetic dis- tance in the interior 44 Mb of this chromosome was only 6 cM. For microchromosomes (chromosomes <20 Mb) the rate of re- combination was uniformly high over the entire chromosome (Fig. 2), and was similar to the rate in distal parts of larger chromosomes (see below). It is also clear from the distribution that male and female rates show good concordance across most of the genome, although there is a lack of concordance in a small proportion of regions. Notably, the sharp increase in recombination toward chromosome ends ...
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... rates in the distal 5-20 Mb regions, with rates of 5-10 cM/Mb in megabase windows closest to chromosome ends, and extremely low rates in central parts of chromosomes. The combined effect leads to the peculiar sigmoid relationship between cumulative genetic distance and physical position along chromosomes observed in the larger chro- mosomes (Fig. 2). About 90% of the total amount of recom- bination in zebra finch is concentrated to »23% of the genome. For the three largest chromosomes (TGU1-TGU3), 110-150 Mb in size, the interior ''recombination desert'' extends over »100 Mb with an average rate as low as »0.1 cM/Mb over these long in- tervals. The extent of recombination deserts ...

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... Reliable tools for the detection of these chromosomes were developed that contributed to identifying chicken microchromosome syntenies across many avian groups . Indeed, until recently, the very smallest of the microchromosomes, the 'D group' (chromosomes [33][34][35][36][37][38][39] , had no sequences associated with them in the genome assembly (Figure 1a). Unlike research performed on mammalian chromosomes, hybridization across a greater evolutionary distance (i.e., beyond the phylogenetic Class) is possible with chicken chromosome paints. ...
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... cM / Mb), which explains why the association between chromosome size and recombination was non-significant. Negative associations between recombination rate and chromosome length have repeatedly been observed in different taxonomic groups, for example yeast (Kaback et al. 1992), humans and rodents (Jensen-Seaman et al. 2004), birds (Backström et al. 2010), cattle (Mouresan et al. 2019) and butterflies (Martin et al. 2019, Shipilina et al. 2022. Such a relationship is expected given that crossovers are necessary for correct segregation of chromosomes during meiosis (Pardo-Manuel de Villena and Sapienza 2001, Smith and Nambiar 2020). ...
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... The TMRCA was approximated for ROH of different length classes, where the expected length of ROH L = 100/(2 t) centimorgans (cM), where t is time back to the common ancestor in generations (see, for examples,Foote et al., 2021;Peripolli et al., 2018; Stoffel et al., 2021). Recombination rate is approximated to be 1 cM/ Mb, at the lower range of avian estimates, due to small N e across Berthelot's pipit range(Backström et al., 2010;Burri et al., 2015). As Berthelot's pipits have a relatively short generation time (~2 years), the minimum ROH length threshold of >250 kb reflects the expected1365294x, 2023, 8, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/mec.16865 ...
Preprint
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit ( Anthus berthelotii ) - a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.