Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America

Supportive data related to the article “Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America” (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. Keywords: Species tree, Next generation sequencing, Molecular markers, Phylogeography, Non-model specie

Data from: Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae)

The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species’ range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity

Weak population structure and no genetic erosion in <i>Pilosocereus aureispinus</i>: A microendemic and threatened cactus species from eastern Brazil

<div><p>Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus <i>Pilosocereus aureispinus</i>. This species is only found in a small area of c. 300 km² of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known <i>P</i>. <i>aureispinus</i> range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., <i>H</i>_E = 0.390 to 0.525; <i>H</i>_O = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (<i>trnT-trnL</i> and <i>psbD-trnT</i>) and found no variation on a subsample of 39 individuals. We used Landsat 8 images and Normalized Difference Vegetation Index to estimate a potential extent of occurrence of c. 750 km² for this species. Our results showed that <i>P</i>. <i>aureispinus</i> is not suffering from erosion of nuclear genetic variability due to its narrow distribution. However, we advocate that because of the extremely limited extent of occurrence, the ongoing anthropogenic disturbances in its habitat, and phylogenetic distinctiveness of <i>P</i>. <i>aureispinus</i>, this species should be classified as endangered (EN) on the IUCN Red List.</p></div

Data from: Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae)

The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species’ range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity

Mean allele diversity and expected heterozygosity reported for both microendemic threatened cactus species¹ and for <i>campo rupestre</i> plant species² in studies using microsatellite markers till December 2017^*.

<p>The results of Wilcoxon’s rank sum tests (WRST) comparing whether the genetic diversity estimates of <i>Pilosocereus aureispinus</i> is significantly (<i>P</i> ≤ 0.05) larger (>), smaller (<) or not different (≈) to the reported species is shown.</p

Results of the migrant detection analysis.

<p>Results of the migrant detection analysis.</p

Integrating Cytogenetics and Population Genomics:Allopatry and Neo-Sex Chromosomes May Have Shaped the Genetic Divergence in the Erythrinus erythrinus Species Complex (Teleostei, Characiformes)

SIMPLE SUMMARY: Fish present astonishing diversity, comprising more species than the combined total of all other vertebrates. Here, we integrated cytogenetic and genomic data to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation in the fish species Erythrinus erythrinus. We hypothesized that the presence of multiple sex chromosomes has contributed to the genetic differentiation of populations, which could have potentially accelerated speciation. ABSTRACT: Diversity found in Neotropical freshwater fish is remarkable. It can even hinder a proper delimitation of many species, with the wolf fish Erythrinus erythrinus (Teleostei, Characiformes) being a notable example. This nominal species shows remarkable intra-specific variation, with extensive karyotype diversity found among populations in terms of different diploid chromosome numbers (2n), karyotype compositions and sex chromosome systems. Here, we analyzed three distinct populations (one of them cytogenetically investigated for the first time) that differed in terms of their chromosomal features (termed karyomorphs) and by the presence or absence of heteromorphic sex chromosomes. We combined cytogenetics with genomic approaches to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation. The results indicated the presence of high genetic differentiation among populations both from cytogenetic and genomic aspects, with long-distance allopatry potentially being the main agent of genetic divergence. One population showed a neo-X(1)X(2)Y sexual chromosome system and we hypothesize that this system is associated with enhanced inter-population genetic differentiation which could have potentially accelerated speciation compared to the effect of allopatry alone

Population differentiation estimates per loco.

<p>Population differentiation estimates per loco.</p

Geographic distribution of known occurrence sites for <i>P</i>. <i>aureispinus</i> (sampled sites are shown coded according to Table 1) and extent of occurrence estimates.

<p>a) Map of eastern Brazil showing the studied area (red inset), the São Francisco River course in blue and main biomes. b) Natural colour Landsat 8 image. c) NDVI image with healthy vegetation in light grey and exposed soil in dark grey showing the minimum convex polygon encompassing all occurrence points in blue. d) NDVI image showing, inside the blue contour, the estimated extent of occurrence by setting a NDVI threshold. Locality and geographic coordinates of the samples IBO1 and IBO2: Ibotirama, Bahia state, S12°05’ W43°09’ and S12°16’ W43°10’, respectively; OLB1 and OLB2: Oliveira dos Brejinhos, Bahia state, S12°22’ W42°55’ and S12°20’ W42°56’, respectively. The unsampled site IBO3 is located at Ibotirama, Bahia state, S12°13’ W43°18’.</p