Djivan Prentout

New preprint about open science in eco-evo!
We sampled 110 journals, 550 articles, and assessed whether data and code are accessible: (1/5)
ecoevorxiv.org/repository/v...

#ScientificPublishing #OpenScience #ecology #conservation #EvolutionaryBiology #paleobio #systematics #archeology

Since male #cannabis plants do not produce #cannabinoids (THC and CBD) in high concentrations, identifying the sex of the plants is an important practice in agricultural applications of the plant.

1/2🧵

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📣 Two ERC-funded positions are available in the lab! If you are interested in exploring the mechanisms underlying mutation, we’d love to hear from you.

PhD: shorturl.at/Oc04N
Postdoc: shorturl.at/1ShHB

RPs and shares would be greatly appreciated!
🧪🧬🖥️ #ScienceJobs #PostdocJobs

17/ How far might this pattern extend? And which aspects are particularly constrained? With increasing genomic data from non-model organisms, it should soon be possible to test this hypothesis more broadly.

16/ The conservation of these parameters from mammals to zebra finch suggests that many mutation and recombination properties evolve under stabilizing selection in vertebrates.

15/ Despite the absence of PRDM9 in zebra finch, key recombination features—GC-biased gene conversion (59%), NCO tract length (~23 bp), and estimated NCO:CO ratio (6.7:1)—are very similar to estimates in mice and primates (e.g., tinyurl.com/ynsepayf, tinyurl.com/vrk2hjs6).

14/ As expected in the absence of PRDM9 (tinyurl.com/2tjkar3j), recombination events overlap with CpG islands more often than expected by chance (with little or no effect of TSS).

13/ In contrast, micro-chromosomes had significantly higher CO rates (4.21 cM/Mb), reflecting CO homeostasis. Both CO and NCO events were more uniformly distributed here than on macro-chromosomes.

12/ Focusing on recombination, zebra finches show a sex-averaged CO rate of 1.05 cM/Mb on macro-chromosomes. COs are enriched near telomeres, while NCOs are more evenly spread. That too resembles the pattern in mammals.

11/ Classifying mutations by developmental timing revealed a paternal germline mutation bias (1.7:1) in later stages of gametogenesis, but no sex difference in mutation rates during early development—similar to mammals (e.g., tinyurl.com/56zy44yh).

10/ We estimate a sex-averaged mutation rate per bp per generation of 5.0 × 10⁻⁹ in zebra finches, which is comparable to other mammals and birds with similar generation times (tinyurl.com/w8wzkz4x).

9/ To explore whether mutation and recombination parameters are similar in birds, we sequenced three-generation pedigrees of zebra finches, gathering information from 80 meiosis. We inferred 202 de novo mutations, 1,174 crossovers (COs), and 275 non-crossovers (NCOs).

8/ Birds, including zebra finches, offer a unique contrast to mammals: among others, they have micro-chromosomes, distinct recombination mechanisms (lacking PRDM9), and distinct developmental processes.

7/ To date, few pedigree-based studies have been conducted in non-mammalian vertebrates (but see, e.g., tinyurl.com/2vmfy8dd and tinyurl.com/w8wzkz4x).

6/ These findings suggest that a number of aspects of mutation and recombination processes may evolve under stabilizing selection in mammals. But how far does this conservation extend?

5/ Similarly, the sex-averaged recombination rate in dogs (~0.8 cM/Mb, tinyurl.com/34ye8h2s) is close to that of humans (~1.2 cM/Mb, tinyurl.com/3nvbzrmh), even though dogs have almost double the number of chromosomes and a shorter genome.

4/ For instance, the mutation rate per generation in mice (~0.5e-8, tinyurl.com/39ynhxxw) is only about half that of humans (~1.2 × 10⁻⁸, tinyurl.com/ysb48wtm) despite mice having 50 times shorter generation times.

3/ Intriguingly, studies in mammals show that mutation and recombination rates are relatively stable over time.

2/ Most mutation/recombination rate estimates come from a few model organisms (e.g., tinyurl.com/4pshvyez), pedigree sequencing (mainly in mammals, e.g., tinyurl.com/muvdh5tu), and long-read sequencing of male gametes in primates (e.g., tinyurl.com/3ncryv43).

1/ A thread about mutation and recombination in vertebrates and what we learned by studying three-generation pedigrees of zebra finches. Take home: the remarkable similarities between birds and mammals in many properties of these fundamental processes.

17/ How far might this pattern extend? And which aspects are particularly constrained? With increasing genomic data from non-model organisms, it should soon be possible to test this hypothesis more broadly.

16/ The conservation of these parameters from mammals to zebra finch suggests that many mutation and recombination properties evolve under stabilizing selection in vertebrates.

15/ Despite the absence of PRDM9 in zebra finch, key recombination features—GC-biased gene conversion (59%), NCO tract length (~23 bp), and estimated NCO:CO ratio (6.7:1)—are very similar to estimates in mice and primates (e.g., tinyurl.com/ynsepayf, tinyurl.com/vrk2hjs6).

14/ As expected in the absence of PRDM9 (tinyurl.com/2tjkar3j), recombination events overlap with CpG islands more often than expected by chance (with little or no effect of TSS).

13/ In contrast, micro-chromosomes had significantly higher CO rates (4.21 cM/Mb), reflecting CO homeostasis. Both CO and NCO events were more uniformly distributed here than on macro-chromosomes.

12/ Focusing on recombination, zebra finches show a sex-averaged CO rate of 1.05 cM/Mb on macro-chromosomes. COs are enriched near telomeres, while NCOs are more evenly spread. That too resembles the pattern in mammals.

11/ Classifying mutations by developmental timing revealed a paternal germline mutation bias (1.7:1) in later stages of gametogenesis, but no sex difference in mutation rates during early development—similar to mammals (e.g., tinyurl.com/56zy44yh).

10/ We estimate a sex-averaged mutation rate per bp per generation of 5.0 × 10⁻⁹ in zebra finches, which is comparable to other mammals and birds with similar generation times (tinyurl.com/w8wzkz4x).

9/ To explore whether mutation and recombination parameters are similar in birds, we sequenced three-generation pedigrees of zebra finches, gathering information from 80 meiosis. We inferred 202 de novo mutations, 1,174 crossovers (COs), and 275 non-crossovers (NCOs).

8/ Birds, including zebra finches, offer a unique contrast to mammals: among others, they have micro-chromosomes, distinct recombination mechanisms (lacking PRDM9), and distinct developmental processes.