Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

Reconstructing the recent West Nile virus lineage 2 epidemic in Europe and Italy using discrete and continuous phylogeography

West Nile virus lineage 2 (WNV-2) was mainly confined to sub-Saharan Africa until the early 2000s, when it was identified for the first time in Central Europe causing outbreaks of human and animal infection. The aim of this study was to reconstruct the origin and dispersion of WNV-2 in Central Europe and Italy on a phylodynamic and phylogeographical basis. To this aim, discrete and continuous space phylogeographical models were applied to a total of 33 newly characterised full-length viral genomes obtained from mosquitoes, birds and humans in Northern Italy in the years 2013-2015 aligned with 64 complete sequences isolated mainly in Europe. The European isolates segregated into two highly significant clades: a small one including three sequences and a large clade including the majority of isolates obtained in Central Europe since 2004. Discrete phylogeographical analysis showed that the most probable location of the root of the largest European clade was in Hungary a mean 12.78 years ago. The European clade bifurcated into two highly supported subclades: one including most of the Central/East European isolates and the other encompassing all of the isolates obtained in Greece. The continuous space phylogeographical analysis of the Italian clade showed that WNV-2 entered Italy in about 2008, probably by crossing the Adriatic sea and reaching a central area of the Po Valley. The epidemic then spread simultaneously eastward, to reach the region of the Po delta in 2013, and westward to the border area between Lombardy and Piedmont in 2014; later, the western strain changed direction southward, and reached the central area of the Po valley once again in 2015. Over a period of about seven years, the virus spread all over an area of northern Italy by following the Po river and its main tributaries

Phylogeography of New Zealand’s coastal benthos

During the past 30 years, 42 molecular studies have been undertaken in New Zealand to examine the phylogeography of coastal benthic invertebrates and plants. Here, we identify generalities and/or patterns that have emerged from this research and consider the processes implicated in generating genetic structure within populations. Studies have used various molecular markers and examined taxonomic groups with a range of life histories and dispersal strategies. Genetic disjunctions have been identified at multiple locations, with the most frequently observed division occurring between northern and southern populations at the top of the South Island. Although upwelling has been implicated as a cause of this disjunction, oceanographic evidence is lacking and alternative hypotheses exist. A significant negative correlation between larval duration and genetic differentiation (r2 = 0.39, P < 0.001, n = 29) across all studies suggests that larval duration might be used as a proxy for dispersal potential. However, among taxa with short larval durations (<10 days) there was greater variability in genetic differentiation than among taxa with longer pelagic periods. This variability implies that when larval duration is short, other factors may determine dispersal and connectivity among populations. Although there has been little congruence between the phylogeographic data and recognised biogeographic regions, recent research has resolved population subdivision at finer spatial scales corresponding more closely with existing biogeographic classifications. The use of fast-evolving and ecologically significant molecular markers in hypothesis-driven research could further improve our ability to detect population subdivision and identify the processes structuring marine ecosystems

Does habitat stability structure intraspecific genetic diversity? It’s complicated...

Regional phylogeographic studies have long been conducted in the southeastern United States for a variety of species. With some exceptions, many of these studies focus on single species or single clades of organisms, and those considering multiple species tend to focus on deep historical breaks causing differentiation. However, in many species more recent factors may be influencing genetic diversity. To understand the roles of historic and contemporary processes in structuring genetic diversity, we reanalyzed existing genetic data from Southeast of North America using approaches gleaned from phylogeographic and landscape genetic literature that were implemented across species including AMOVAs, PCoAs, Species Distribution Modelling, and tests of isolation by distance, environment, and habitat instability. Genetic variance was significantly partitioned by ecoregions, watersheds, and across phylogeographic breaks in the majority of species. Similarly, genetic variation was significantly associated with some combination of geographic or environmental distance or habitat instability in most species. Patterns of genetic variation were largely idiosyncratic across species. While habitat instability over time is significantly correlated with genetic diversity in some species, it appears generally less important than isolation by geographic or environmental distance. Our results suggest that many factors, both historical and contemporary, impact genetic diversity within a species, and more so, that these patterns aren’t always similar in closely related species. This supports the importance of species- specific factors and cautions against assumptions that closely related species will respond to historical and contemporary forces in similar ways

Phylogeographic Triangulation: Using Predator-Prey-Parasite Interactions to Infer Population History from Partial Genetic Information

Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite’s phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly

Spatial and temporal phylogeny of border disease virus in pyrenean chamois (Rupicapra p. Pyrenaica)

Border disease virus (BDV) affects a wide range of ruminants worldwide, mainly domestic sheep and goat. Since 2001 several outbreaks of disease associated to BDV infection have been described in Pyrenean chamois (Rupicapra pyrenaica pyrenaica) in Spain, France and Andorra. In order to reconstruct the most probable places of origin and pathways of dispersion of BDV among Pyrenean chamois, a phylogenetic analysis of 95 BDV 5'untranslated sequences has been performed on chamois and domestic ungulates, including novel sequences and retrieved from public databases, using a Bayesian Markov Chain Monte Carlo method. Discrete and continuous space phylogeography have been applied on chamois sequences dataset, using centroid positions and latitude and longitude coordinates of the animals, respectively. The estimated mean evolutionary rate of BDV sequences was 2.9x10(-3) subs/site/year (95% HPD: 1.5-4.6x10(-3)). All the Pyrenean chamois isolates clustered in a unique highly significant clade, that originated from BDV-4a ovine clade. The introduction from sheep (dated back to the early 90s) generated a founder effect on the chamois population and the most probable place of origin of Pyrenean chamois BDV was estimated at coordinates 42.42 N and 1.9 E. The pathways of virus dispersion showed two main routes: the first started on the early 90s of the past century with a westward direction and the second arise in Central Pyrenees. The virus spread westward for more than 125 km and southward for about 50km and the estimated epidemic diffusion rate was about 13.1 km/year (95% HPD 5.2-21.4 km/year). The strong spatial structure, with strains from a single locality segregating together in homogeneous groups, and the significant pathways of viral dispersion among the areas, allowed to reconstruct both events of infection in a single area and of migrations, occurring between neighboring areas