sampleDownGeno2SFS_MOD

Python script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Modified from Papadopoulou and Knowles 2015 (DOI: http://dx.doi.org/10.5061/dryad.23hs1

Whitelist_STACKS

This R script creates a whitelist to input into STACKS v. 1.35, by eliminating SNPs from the last bp positions, as well as loci with exceedingly high genetic diversity based on theta

Table3.doc

<p>Fish diets have been traditionally studied through the direct visual identification of food items found in their stomachs. Stomach contents of Vandeliinae and Stegophilinae (family Trichomycteridae) parasite catfishes, however, cannot be identified by usual optical methods due to their mucophagic, lepidophagic, or hematophagic diets, in such a way that the trophic interactions and the dynamics of food webs in aquatic systems involving these catfishes are mostly unknown. The knowledge about trophic interactions, including difficult relation between parasites and hosts, are crucial to understand the whole working of food webs. In this way, molecular markers can be useful to determine the truly hosts of these catfishes, proving a preference in their feeding behavior for specific organisms and not a generalist. Sequences of cytochrome oxidase subunit 1 (COI) were successfully extracted and amplified from mucus or scales found in the stomach contents of two species of stegophilines, Homodiaetus anisitsi, and Pseudostegophilus maculatus, to identify the host species. The two species were found to be obligatory mucus-feeders and occasionally lepidophagic. Selection of host species is associated to host behavior, being constituted mainly by substrate-sifting benthivores. Characiformes are preferred hosts, but host choice depends on what characiform species are available in their environments, usually corresponding to the most abundant species. This is the first time that host species of parasitic fishes bearing mucophagous habits are identified, and demonstrates the effectiveness of the extraction and amplification of mitochondrial DNA from the ingested mucus in gut contents. The molecular markers effectively allowed determine parasite preferences and helps in better understanding the food web and trophic interaction on which fish species are involved. Despite, the methodology applied here can be used for an infinitive of organisms improving ecological trophic studies.</p

Table2.doc

<p>Fish diets have been traditionally studied through the direct visual identification of food items found in their stomachs. Stomach contents of Vandeliinae and Stegophilinae (family Trichomycteridae) parasite catfishes, however, cannot be identified by usual optical methods due to their mucophagic, lepidophagic, or hematophagic diets, in such a way that the trophic interactions and the dynamics of food webs in aquatic systems involving these catfishes are mostly unknown. The knowledge about trophic interactions, including difficult relation between parasites and hosts, are crucial to understand the whole working of food webs. In this way, molecular markers can be useful to determine the truly hosts of these catfishes, proving a preference in their feeding behavior for specific organisms and not a generalist. Sequences of cytochrome oxidase subunit 1 (COI) were successfully extracted and amplified from mucus or scales found in the stomach contents of two species of stegophilines, Homodiaetus anisitsi, and Pseudostegophilus maculatus, to identify the host species. The two species were found to be obligatory mucus-feeders and occasionally lepidophagic. Selection of host species is associated to host behavior, being constituted mainly by substrate-sifting benthivores. Characiformes are preferred hosts, but host choice depends on what characiform species are available in their environments, usually corresponding to the most abundant species. This is the first time that host species of parasitic fishes bearing mucophagous habits are identified, and demonstrates the effectiveness of the extraction and amplification of mitochondrial DNA from the ingested mucus in gut contents. The molecular markers effectively allowed determine parasite preferences and helps in better understanding the food web and trophic interaction on which fish species are involved. Despite, the methodology applied here can be used for an infinitive of organisms improving ecological trophic studies.</p

Table1.DOC

<p>Fish diets have been traditionally studied through the direct visual identification of food items found in their stomachs. Stomach contents of Vandeliinae and Stegophilinae (family Trichomycteridae) parasite catfishes, however, cannot be identified by usual optical methods due to their mucophagic, lepidophagic, or hematophagic diets, in such a way that the trophic interactions and the dynamics of food webs in aquatic systems involving these catfishes are mostly unknown. The knowledge about trophic interactions, including difficult relation between parasites and hosts, are crucial to understand the whole working of food webs. In this way, molecular markers can be useful to determine the truly hosts of these catfishes, proving a preference in their feeding behavior for specific organisms and not a generalist. Sequences of cytochrome oxidase subunit 1 (COI) were successfully extracted and amplified from mucus or scales found in the stomach contents of two species of stegophilines, Homodiaetus anisitsi, and Pseudostegophilus maculatus, to identify the host species. The two species were found to be obligatory mucus-feeders and occasionally lepidophagic. Selection of host species is associated to host behavior, being constituted mainly by substrate-sifting benthivores. Characiformes are preferred hosts, but host choice depends on what characiform species are available in their environments, usually corresponding to the most abundant species. This is the first time that host species of parasitic fishes bearing mucophagous habits are identified, and demonstrates the effectiveness of the extraction and amplification of mitochondrial DNA from the ingested mucus in gut contents. The molecular markers effectively allowed determine parasite preferences and helps in better understanding the food web and trophic interaction on which fish species are involved. Despite, the methodology applied here can be used for an infinitive of organisms improving ecological trophic studies.</p

Stevardiinae trees

Stevardiinae phylogenies reconstructed with the software's: RAxML (concatenated and gene trees), Garli, STAR and TNT. Trees were rooted in Serrasalmus sp. and bootstraps support are shown when available

Table_1.DOCX

<p>The Pampas is a Neotropical biome formed primarily by low altitude grasslands and encompasses the southernmost portion of Brazil, Uruguay, and part of Argentina. Despite the high level of endemism, and its significant environmental heterogeneity, Pampean species are underrepresented in phylogeographic studies, especially aquatic organisms. The Pampean hydrological system resulted from a long history of tectonism, climate, and sea level changes since the Neogene. In this study, we examined the population genetic structure of Cnesterodon decemmaculatus, a freshwater fish species that occurs throughout most of the Pampa biome. We characterized mitochondrial and autosomal genetic lineages in populations sampled from Southern Brazil and Uruguay to investigate (1) the correspondence between current drainage systems and evolutionary lineages, (2) the demographic history for each genetic lineage, and (3) the temporal depth of these lineages. Overall, we found that the major evolutionary lineages in this species are strongly related to the main Pampean drainage systems, even though stream capture events may have affected the distribution of genetic lineages among drainages. There was evidence for recent population growth in the lineages occupying drainages closest to the shore, which may indicate the effect of quaternary sea-level changes. In general, divergence time estimates among evolutionary lineages were shallow, ranging from 20,000 to 800,000 years before present, indicating a geologically recent history for this group, as previously reported in other Pampean species. A Bayesian phylogeographical reconstruction suggested that an ancestral lineage probably colonized the Uruguay River Basin, and then expanded throughout the Pampas. This evolutionary scenario may represent useful starting models for other freshwater species having a similar distribution.</p

Stevardiinae concatenated alignment

Concatenated alignment with all sequences generated to reconstruct the phylogeny of Stevardiinae. The gene partitions are: myh6 = 1 - 621; ptr = 622 - 1158; rag1 = 1159 - 2520; rag2 = 2521 - 3291; coi = 3292 - 3813; 16s = 3814 - 4387; 12s = 4388 - 4816. Also, all taxa listed are identified by its name and voucher number

<i>Microglanis cottoides</i>, MZUEL 7453, 54.6 mm SL.

<p>Specimen collected in the Arroio Divisa, Camaquã River basin, Cristal, RS, 30^o54'5.6"S 52^o05'18.9"W (Photo by O.A. Shibatta).</p

Median-joining networks and Bayesian phylogenetic tree of <i>Micriglanis</i> obtained with COI data.

<p>(A) Median-Joining networks among haplotypes. Each circle represents a unique haplotype with circle sizes being proportional to their frequencies. Each color represents a species. The numbers between haplotypes correspond to mutational steps. Haplotypes: H1 = Ribeira; H2 = Guaratuba + Paranaguá + Itapocu; H3 = Paranaguá; H4 = Paranaguá; H5 = Madre; H6 = Araranguá; H7 = Araranguá; H8 = <i>M</i>. <i>cibelae</i> (Mampituba); H9 = <i>M</i>. <i>cibelae</i> (Tramandaí); H10 = Patos (Camaquã); H11 = Negro + Uruguay; H12 = Uruguay; H13 = Uruguay; H14 = <i>Microglanis</i> sp. Uruguay; H15 = <i>M</i>. <i>parahybae</i>: H16 = <i>M</i>. <i>malabarbai</i>; H17 = <i>M</i>. <i>malabarbai</i>; H18 = <i>M</i>. <i>garavelloi</i>. (B) Bayesian tree. Node bars represent the threshold time for each cladogenetic event. The values above the branches indicate the posterior probability (pp). * Individuals collected in their respective type locality.</p