Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Gopalakrishnan, Shyam; Sinding, Mikkel‐Holger S.; Ramos‐Madrigal, Jazmín; Niemann, Jonas; Castruita, José Alfredo Samaniego; Vieira, Filipe Garrett; Carøe, Christian; Manuel, Marc de; Kuderna, Lukas F. K.; Serres, Aitor; González-Basallote, Víctor Manuel; Yan-hu, Liu; Wang, Guodong; Mirarab, Siavash; Fernandes, Carlos A.; Gaubert, Philippe; Koepfli, Klaus‐Peter; Budd, Jane; Rueness, Eli Knispel; Sillero, Claudio; Heide‐Jørgensen, Mads Peter; Petersen, B. A.; Sicheritz-Pontén, Thomas; Bachmann, Lutz; Wiig, Øystein; Hansen, Anders J.; Gilbert, Martin

doi:10.1016/j.cub.2019.11.009

Cited by 29 publications

(63 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our interpretation is that a mitochondrial introgression occurred at 6.2-5.2 Mya from an ancestor of Canis species to the lineage leading to Lupulella mesomelas . In agreement with the genomic study of Gopalakrishnan et al (2019), which concluded to pervasive gene flow among Canis species, our results suggest that interspecies hybridization has been also frequent in the early evolutionary history of canid genera in Africa.…”

Section: Discussionsupporting

confidence: 91%

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

Hassanin

Veron

Ropiquet

et al. 2020

Preprint

View full text Add to dashboard Cite

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

show abstract

Section: Discussionsupporting

confidence: 91%

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

Hassanin

Veron

Ropiquet

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Whatever the source of this ancestry, estimates of the admixture proportion from this deeply diverging population are estimated to be ~12%. Our results, taken together with previous research [52], reveal that canids are an ideal system in which to study how gene flow can shape speciation in a genus, and highlight the need for greater study of ancient gray wolf populations.…”

Section: Resultssupporting

confidence: 69%

Genomic approaches reveal an endemic sub-population of gray wolves in Southern China

Wang

Zhang

Wang

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Despite being one of the most widely distributed terrestrial mammals, the history of gray wolves (Canis lupus) in China is not well understood as their habitats have been destroyed with growing economic development. Using six specimens from wolf skins in Chinese Natural History museums, we sequenced their genome using a modified ancient DNA procedure. Using whole genome sequence analysis, we showed that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau (Canis lupus chanco) and Northern China, suggesting that SC gray wolves may form a distinct sub-population. Of SC gray wolves, one wolf from Zhejiang carries a genetic component from a canid that must have diverged earlier from other wolves than jackals did, perhaps through gene flow from a population related to or further diverged from wolves than the dhole, a species distributed in Southern China and Southeast Asia. This may indicate that interspecific gene flow likely played an important role in shaping the speciation patterns and population structure in the genus Canis. Our study is the first to survey museum genomes of gray wolves from Southern China, revealing the presence of an endemic population with ancient interspecific gene flow from a population related to the dhole, and highlighting how sequencing the paleogenome from museum specimens can help us to study extinct species.

show abstract

“…Therefore, the positive correlations observed among f D , the inferred frequency of archaic segments, and d XY provided good support that regions of high D. punctatus ancestry in the Atlantic are responsible for increased divergence between D. labrax lineages. Admittedly, past gene flow may also have occurred with another now extinct species rather than with D. punctatus , as previously shown for other species (Meyer et al 2012; Barlow et al 2018; Gopalakrishnan et al 2018; Foote et al. 2019; Kuhlwilm et al.…”

Section: Discussionmentioning

confidence: 73%

The contribution of ancient admixture to reproductive isolation between European sea bass lineages

et al. 2020

View full text Add to dashboard Cite

Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype‐resolved whole‐genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.

show abstract

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Cited by 29 publications

References 0 publications

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

Genomic approaches reveal an endemic sub-population of gray wolves in Southern China

The contribution of ancient admixture to reproductive isolation between European sea bass lineages

Contact Info

Product

Resources

About