Primate Paleogenomics

Veeramah, Krishna R.

doi:10.1007/13836_2018_47

Cited by 4 publications

(2 citation statements)

References 131 publications

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“…This table shows that the 31 nonhuman primates with whole-genome sequences available are mostly found in Africa, South America, and Southeast Asia, which are comparatively warm areas on Earth. The distribution of nonhuman primates today shows a positive correlation with temperature ( Veeramah 2018 ), which is also evident from the geographical location of the continents alone. It is possible that the results in this article have been biased by nonhuman primates that prefer warmer habitats.…”

Section: Resultsmentioning

confidence: 91%

“… Hofreiter et al (2015) showed that ancient nonhuman primates tended to live in conditions of high temperature and humidity. Another previous work showed that today, when the temperature is much cooler than 13 MYA, there still exists a positive correlation between primate species richness and mean annual temperature ( Veeramah 2018 ). The tendency of primates to live in habitats closer to their original environmental conditions after climate change has also previously been studied with respect to humidity.…”

Section: Resultsmentioning

confidence: 99%

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Towards understanding paleoclimate impacts on primate de novo genes

Liang

Heath

2023

G3: Genes, Genomes, Genetics

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De novo genes are genes that emerge as new genes in some species, such as primate de novo genes that emerge in certain primate species. Over the past decade, a great deal of research has been conducted regarding their emergence, origins, functions, and various attributes in different species, some of which have involved estimating the ages of de novo genes. However, limited by the number of species available for whole-genome sequencing, relatively few studies have focused specifically on the emergence time of primate de novo genes. Among those, even fewer investigate the association between primate gene emergence with environmental factors, such as paleoclimate (ancient climate) conditions. This study investigates the relationship between paleoclimate and human gene emergence at primate species divergence. Based on 32 available primate genome sequences, this study has revealed possible associations between temperature changes and the emergence of de novo primate genes. Overall, findings in this study are that de novo genes tended to emerge in the recent 13 million years when the temperature continues cooling, which is consistent with past findings. Furthermore, in the context of an overall trend of cooling temperature, new primate genes were more likely to emerge during local warming periods, where the warm temperature more closely resembled the environmental condition that preceded the cooling trend. Results also indicate that both primate de novo genes and human cancer associated genes have later origins in comparison to random human genes. Future studies can be in-depth on understanding human de novo gene emergence from an environmental perspective as well as understanding species divergence from a gene emergence perspective.

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Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Towards understanding paleoclimate impacts on primate de novo genes

Liang

Heath

2023

G3: Genes, Genomes, Genetics

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Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemurMegaladapis edwardsi

Marciniak

Mughal

Godfrey

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal “subfossil” remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

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Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant ‘subfossil’ koala lemurMegaladapis edwardsi

Marciniak

Mughal

Godfrey

et al. 2020

Preprint

View full text Add to dashboard Cite

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

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Primate Paleogenomics

Cited by 4 publications

References 131 publications

Towards understanding paleoclimate impacts on primate de novo genes

Towards understanding paleoclimate impacts on primate de novo genes

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemurMegaladapis edwardsi

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant ‘subfossil’ koala lemurMegaladapis edwardsi

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