Literature synthesis
Phylogeography was conceived as a science in 1987, since then the number of publications has grown exponentially. In Brazil, the first two marine phylogeographic studies were both published in 1991 using allozymes (Aron & Solé-Cava, 1991; Russo & Solé-Cava, 1991). New publications have increased ever since. The years 2016 and 2018 presented the highest number of Brazilian marine phylogeographic publications to date (15 articles). Considering the 16 taxonomic groups assessed in this study, fishes have been the most studied taxon, accounting for 33% of all publications. This is more than the second and third most studied taxa combined (crustaceans 21%, mollusks 9%). A conspicuous publication bias towards fish phylogeographic studies is observed in the literature globally. Beheregaray (2008) reviewed all phylogeographic articles published between 1987 and 2006 and fishes were ranked second, after mammals, as the taxonomic group with the largest number of publications without much difference whether they were freshwater (45%) or marine species (55%). Turchetto-Zolet et al. (2013) reviewed all phylogeographic articles published on South America terrestrial and freshwater biota between 1987-2011 and reported fishes as the second ranked taxonomic group (13%) together with overall invertebrates and second only to plants (17%). This bias towards fishes is probably due to their economic importance as human food and ecotourism, relative easier taxonomic identification, simple life-cycle and ploidy, the availability of well-suited genetic markers, and probably, the existence of a large number of hired expertise in research institutions. Differently, otaries, Kinorhynchs and flatworms presented very localized sampling due to low number of publications (one each).
The numbers of marine vertebrate and invertebrate studies in Brazil were quite even, 47% and 49%, respectively. This is opposite to what was recorded by Beheregaray (2008) and Turchetto-Zolet et al. (2013) who observed a bias towards vertebrate studies, 57% and 70% respectively. The number of marine plants and algae studies in Brazil were quite underrepresented (4%) as they are in terrestrial and freshwater autotrophic species in South America (1% algae in Turchetto-Zolet et al., 2013), terrestrial and marine plants in eastern North America (11% in Soltis et al., 2006) and world widely in general (2% reported in Beheregaray 2008). In the past, the disparity between the number of phylogeographic studies between heterotrophic x autotrophic species was attributed in part to the faster mutation rates observed in animal markers (mitochondrial genome) compared to markers available for plant studies (Soltis et al., 2006). An increase in the number of studies addressing macroalgal phylogeography would improve our understating of population genetic histories and marine phylogeography considering they are poorly-dispersers (Kinlan & Gaines, 2003), potentially being able to identify a larger number of local and regional BGF and concordant phylogeographic patterns.
The first study using genotypic data addressing the phylogeography of a Brazilian marine species was published in 1998 (Secchi et al., 1998), 11 years after the Avise’s seminal 1987 publication. Before 1998, the only six phylogeographic studies (= four articles) addressing Brazilian marine biota used phenotypic (isozyme) data. In Brazil mitochondrial genotypic data started being utilized first in the form of fragment-based methods (e.g. Secchi et al., 1998). Between 2007-2010, RAPD, AFLP, RFLP and similar fragment-based techniques played an important role increasing the number of publications. Microsatellites remain a poorly used technique with only 29 studies (12%) published since 2001 (Beheregaray & Sunnucks, 2001). A similar pattern was observed for genome-wide techniques, such as SNPs, where only one marine study was published to date (Siccha-Ramirez et al., 2018). In the world, genome wide SNP and high-throughput DNA sequencing techniques are becoming the powerhouse in phylogeographic studies (e.g. ddRadseq, B. Peterson, Weber, Kay, Fisher, & Hoekstra, 2012).
The two most well sampled and phylogeographically well studied geopolitical states were Rio de Janeiro and São Paulo, which happens to be the two richest states and the ones that hold the largest number of research universities in the country, followed by Bahia (the state with the longest coastline). The relationship between number of phylogeographic studies and economic affluence is a well-known worldwide pattern in the phylogeographic literature (reported in Beheregaray, 2008; Turchetto-Zolet et al., 2013). The weaker studied regions of Brazil are those located in the extreme northern and southern reaches of the country, where physical accessibility is challenging. Particularly the northernmost reaches, along the Amazonian Rainforest coastline towards Amapá, west of Belém (48° 29’ 25” W) where nearly nothing is known about the phylogeographic structure of any coastal marine species. The mouth of the Amazon river is considered a strong BGF in coastal South America but studies that attributed it to explain genetic discontinuities used populations samples thousands of kilometers apart across the western Atlantic Ocean (e.g. Caribbean versus Brazilian population (see de Souza et al., 2015; Nauer et al., 2019; Santos, Hrbek, Farias, Schneider, & Sampaio, 2006).