Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences

Ludington, Alastair J.; Sanders, Kate L.

doi:10.1111/mec.15726

Cited by 12 publications

(13 citation statements)

References 49 publications

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“…The 1,158 heterozygous alternative scaffolds covered 1.26 Gb (75.7%) of the assembly. The assembly quality of both snake genomes compares well with the other snake genomes used in the study [43][44][45][46]. The quality of both snake assemblies was sufficient for annotation and inclusion in NCBI RefSeq and Ensembl (Table 1).…”

Section: Draft Terrestrial Elapid Genomes Are Fragmented But Show High Completenessmentioning

confidence: 80%

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Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Edwards

et al. 2021

Preprint

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Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they can be exapted as coding and regulatory elements, or can promote genetic rearrangement. In so doing TEs act as a source of genetic novelty, hence understanding TE evolution within lineages is key in understanding adaptation to their environment. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. The few broad scale studies in Squamata which have been conducted found both the diversity and total number of TEs differs significantly across the entire order. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if this pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into 6 amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three transferred into the ancestral hydrophiine likely from marine species. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

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Section: Draft Terrestrial Elapid Genomes Are Fragmented But Show High Completenessmentioning

confidence: 80%

“…The quality of both snake assemblies was sufficient for annotation and inclusion in NCBI RefSeq and Ensembl (Table 1). Vonk et al [44] Kishida et al [45] This study This study Ludington and Sanders [46]…”

Section: Draft Terrestrial Elapid Genomes Are Fragmented But Show High Completenessmentioning

confidence: 85%

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Edwards

et al. 2021

Preprint

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“…(a) Ab initio repeat annotation of elapids Using RepeatModeler2 [24], we performed ab initio annotation of the four Austro-Melanisian elapid genomes: Laticauda colubrina [25], Notechis scutatus, Pseudonaja textilis and Aipysurus laevis [26]. To improve the RepeatModeler2 libraries, we manually classified consensus sequences over 200 bp using a BLAST, extend, align and trim method, described by Galbraith et al [27].…”

Section: Methodsmentioning

confidence: 99%

Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda )

et al. 2021

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Transposable elements (TEs) are self-replicating genetic sequences and are often described as important ‘drivers of evolution’. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions potentially lead to neutral or harmful outcomes, therefore host genomes have evolved machinery to suppress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonize new genomes, and since new hosts may not be able to regulate subsequent replication, these TEs may proliferate rapidly. Here, we describe HTT of the Harbinger-Snek DNA transposon into sea kraits ( Laticauda ), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids approximately 15–25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8–12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.

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“…Inbreeding depression reduces individual fitness, survival and reproduction and can lead to rapid decline and extirpation of populations [17,20,76]. Despite small F IS values, population-level changes may not be seen for many generations in longer-lived vertebrates [18,77]-such as tiger snakes, estimated at 10 years [78]. Thus, we expect to see inbreeding increase through time, especially in sites that become completely isolated from urbanisation.…”

Section: Genomic Diversity and Healthmentioning

confidence: 99%

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

et al. 2021

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Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

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Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences

Cited by 12 publications

References 49 publications

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda )

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

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