Branching out: what omics can tell us about primate evolution

Kuderna, Lukas F. K.; Esteller-Cucala, Paula

doi:10.1016/j.gde.2020.06.006

Cited by 10 publications

(11 citation statements)

References 66 publications

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“…We tested the impact of heterogeneous genome quality on PSG detection by comparing a set of metrics with the number of PSGs detected. To be objective and in the absence of NG50 and Q-score metrics for all primates, we chose to run the QUAST-LG tool on raw data to generate the quality metrics ( supplementary table 12 , Supplementary Material online) ( Kuderna et al 2020 ; Mikheenko et al 2018 ). The relative position of the analyzed genome was assessed using these metrics and a PCA; no significant association between PSG number and genome quality was observed: PCA coordinates were not detected for axis 1 (Kruskal–Wallis test, χ 2 = 5.15, P value <0.08) nor axis 2 (Kruskal–Wallis test, χ 2 = 1.5 P value <0.47).…”

Section: Resultsmentioning

confidence: 99%

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

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Delehelle

et al. 2021

Genome Biology and Evolution

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The large spectrum of hearing sensitivity observed in primates results from the impact of environmental and behavioral pressures to optimize sound perception and localization. Although evidence of positive selection in auditory genes has been detected in mammals including in Hominoids, selection has never been investigated in other primates. We analyzed 123 genes highly expressed in the inner ear of 27 primate species and tested to what extent positive selection may have shaped these genes in the order Primates tree. We combined both site and branch-site tests to obtain a comprehensive picture of the positively selected genes (PSGs) involved in hearing sensitivity, and drew a detailed description of the most affected branches in the tree. We chose a conservative approach, and thus focused on confounding factors potentially affecting PSG signals (alignment, GC-biased gene conversion, duplications, heterogeneous sequencing qualities). Using site tests, we showed that around 12% of these genes are PSGs, an α selection value consistent with average human genome estimates (10-15%). Using branch-site tests, we showed that the primate tree is heterogeneously affected by positive selection, with the black snub-nosed monkey, the bushbaby, and the orangutan, being the most impacted branches. A large proportion of these genes is inclined to shape hair cells and stereocilia, which are involved in the mechanotransduction process, known to influence frequency perception. Adaptive selection, and more specifically recurrent adaptive evolution, could have acted in parallel on a set of genes (ADGRVl, USH2A, PCDH15, PTPRQ and ATP8A2) involved in stereocilia growth and the whole complex of bundle links connecting them, in species across different habitats, including high altitude and nocturnal environments.

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Section: Resultsmentioning

confidence: 99%

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

Moreira

Croze

Delehelle

et al. 2021

Genome Biology and Evolution

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“…Anthropologists can now obtain large-scale genomic data in relatively easy and affordable ways, even for non-model organisms. [17][18][19][20] While the number of primate species for which we have high-quality annotated genomes is still relatively low (Figure 3), various types of genomic data are now available for many taxa. 17,19,20,98 These data range from hundreds or thousands of loci obtained using sequence capture techniques (e.g., exome, ultra-conserved regions) 21 to thousands of single nucleotide polymorphisms obtained using reduced representation libraries (e.g., dRAD or ddRAD) [99][100][101] or whole-genome sequencing.…”

Section: From a Single Locus To A Genomic Approachmentioning

confidence: 99%

“…[17][18][19][20] While the number of primate species for which we have high-quality annotated genomes is still relatively low (Figure 3), various types of genomic data are now available for many taxa. 17,19,20,98 These data range from hundreds or thousands of loci obtained using sequence capture techniques (e.g., exome, ultra-conserved regions) 21 to thousands of single nucleotide polymorphisms obtained using reduced representation libraries (e.g., dRAD or ddRAD) [99][100][101] or whole-genome sequencing. 22,23,102,103 Although these datasets do not necessarily include the whole genome, they represent a dramatic increase in the amount of data available to reconstruct phylogenetic relationships among primates.…”

Section: From a Single Locus To A Genomic Approachmentioning

confidence: 99%

“…[12][13][14][15][16] Second, the promises of more efficient and affordable sequencing technologies have contributed to the rapid accumulation of a vast amount of genetic data for a growing number of primate species. [17][18][19][20] Now, evidence from hundreds or even thousands of loci across the genome, not only from one or a few genes, can be combined with morphological and fossil data to simultaneously estimate tree topology and divergence times. [21][22][23] These recent developments generated great excitement in the field of molecular anthropology, phylogenetics, and paleontology.…”

Section: Introductionmentioning

confidence: 99%

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Rocks and clocks revised: New promises and challenges in dating the primate tree of life

Pozzi

Penna

2022

Evolutionary Anthropology

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In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total‐evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever‐increasing availability of genomic‐level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

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“…From a genomic perspective, relatively little is known about ring-tailed lemurs (and strepsirrhines more broadly). Genome assemblies have been published for 18 strepsirrhine species, but none of these assemblies has a contig N50 value >1 Mb, and only 3 of them are >100 kb [ 10 ]. Recently, an L. catta genome (LemCat_v1_BIUU) was assembled by the Zoonomia consortium [ 11 ]; given that it is derived from Illumina short reads, its metrics and application are still limited compared to the genome quality of recent highly contiguous assemblies [ 12 ].…”

Section: Contextmentioning

confidence: 99%

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

et al. 2022

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Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.

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Branching out: what omics can tell us about primate evolution

Cited by 10 publications

References 66 publications

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

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