Quantitative analysis of connectivity in populations of a semi‐aquatic mammal using kinship categories and network assortativity

Abstract

Analysing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi‐aquatic species may be critical for their conservation. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring contemporary dispersal and quantifying the effect of specific barriers on current connectivity. In this study, we used kinship data to analyse connectivity patterns in a small semi‐aquatic mammal, the Pyrenean desman (Galemys pyrenaicus), in an area comprising two river systems with close headwaters and dams of various heights and types. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we built kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species.

The impact of bottlenecks and inbreeding on the genome of the endangered Pyrenean desman

“…Additionally, the concatenation of smaller artificial barriers as well as ecological barriers resulting from contamination and predation by invasive species in the lower parts of rivers, has confined many desman populations to the river headwaters over the past few generations (Quaglietta et al 2018). The consequence of this isolation is that desmans can only breed with other individuals of the same river, which are usually closely related as determined through relatedness networks (Escoda et al 2017;Escoda et al 2019). This, in turn, leads most desmans to have high inbreeding levels (Escoda et al 2017).…”

“…A ddRADbased study on the species revealed extremely low heterozygosity in some individuals from the eastern Pyrenees, probably as a consequence of repeated bottlenecks during the postglacial recolonization of these mountains (Querejeta et al 2016). In addition, it has been demonstrated that the isolation of populations in the upper parts of rivers due to the construction of artificial barriers, such as dams, is leading to extremely high inbreeding levels in some areas (Escoda et al 2017;Escoda et al 2019). Having the complete genome of the Pyrenean desman would allow us to study how the combination of strong population bottlenecks and high inbreeding levels is reflected in the genomic landscape of a threatened species.…”

Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity

“…Escoda, Fernández‐González, and Castresana () represent a step forward in kinship‐based methods as it uses a statistical framework that develops “null” models of the expected distribution of kin relationships between two groups under random mixing. The authors use the assortativity coefficient (AC), which has been used in network analysis to study preferential associations in human social networks (Newman, ).…”

“…Pyrenean desman ( Galemys pyrenaicus ; centre right) and the barriers to its dispersal found using kinship and network analyses in Escoda et al (). The upper panel shows the watershed divide between the Tuela and Tera rivers in Zamora (Spain) that was a natural barrier to dispersal.…”

“…Recent reviews argue that new statistical methods are required to convert this wealth of genomic data into practical management outcomes for endangered populations and species (Leroy et al, 2017). By inferring the impact of a barrier on patterns of relatedness and dispersal using genomic data and the AC, F I G U R E 1 Pyrenean desman (Galemys pyrenaicus; centre right) and the barriers to its dispersal found using kinship and network analyses in Escoda et al (2018). The upper panel shows the watershed divide between the Tuela and Tera rivers in Zamora (Spain) that was a natural barrier to dispersal.…”