Ancestral mitogenome capture of the Southeast Asian banded linsang

Abstract

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.

Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA

“…2016 , 2020 ; Portik et al., 2016 , Peñalba et al., 2014 ). Additionally, variation in coverage has been observed in the capture of divergent species in previous studies ( Paijmans et al., 2020 ). Divergence between bait and target does not seem to be the sole driver of this effect.…”

“…In addition to poor DNA preservation, previous work has shown that hybridization capture fails to recover sequences that are too divergent from the bait sequences ( Paijmans et al., 2016 , 2020 ). Since no sequences from close relatives are available, we used baits designed from members of the Elephantidae as well as the American mastodon.…”

“…It has been shown that capturing mitochondrial genomes using a divergent bait sequence can lead to a loss of regions with more sequence divergence in favor of those with less sequence divergence ( Paijmans et al. 2016 , 2020 ; Portik et al., 2016 , Peñalba et al., 2014 ). Additionally, variation in coverage has been observed in the capture of divergent species in previous studies ( Paijmans et al., 2020 ).…”

Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)

“…On the same array, mitochondrial genomes for five Caprinae species were present for enrichment of samples from a different project. Prior to capture, libraries were pooled in equimolar amounts according to their mitochondrial endogenous content as determined via shotgun sequencing (Supplementary Table S3 and S4 ) 43 . Due to its already high endogenous content, the Stockholm sample was not captured.…”

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

“…A potential drawback of the evenness-of-coverage metric exists for cases when cross-species hybridisation enrichment was applied in the laboratory to enrich for a particular genetic region (e.g., mitogenome, exome). It has been shown that cross-species capture—i.e., when baits from a related species are used for enrichment—can introduce strong biases for regions with the highest sequence similarity between bait and target [ 74 , 75 ]. We utilised hybridization capture with dhole bait DNA, which means that the four samples that were post-hoc identified as wolf were captured with a cross-species capture approach.…”