Minor allele frequency thresholds strongly affect population structure inference with genomic data sets

The diversity of Laurentian Great Lakes ciscoes (Coregonus artedi, sensu lato) arose via repeated local adaptive divergence including deepwater ciscoes that are now extirpated or threatened. The nigripinnis form, or Blackfin Cisco, is extirpated from the Great Lakes and remains only in Lake Nipigon. Putative nigripinnis populations were recently discovered in sympatry with artedi in a historical drainage system of glacial Lake Algonquin, the precursor of lakes Michigan and Huron. Given the apparent convergence on Great Lakes form, we labeled this form blackfin. Here, we test the hypothesis that nigripinnis may have colonized this area from the Great Lakes as a distinct lineage. It would then represent a relict occurrence of the historical diversity of Great Lakes ciscoes. Alternatively, blackfin could have evolved in situ in several lakes. We captured more than 600 individuals in the benthic or pelagic habitat in 14 lakes in or near Algonquin Provincial Park (Ontario, Canada). Fish were compared based on habitat, morphology, and genetic variation at 6,676 SNPs. Contrary to our expectations, both cisco and blackfin belonged to an Atlantic lineage that colonized the area from the east, not from the Great Lakes. Sympatric cisco and blackfin were closely related while fish from different lakes were genetically differentiated, strongly suggesting the repeated in situ origin of each form. Across lakes, there was a continuum of ecological, morphological, and genetic differentiation that could be associated with alternative resources and lake characteristics. This study uncovers a new component of cisco diversity in inland lakes of Canada that evolved independently from ciscoes of the Laurentian Great lakes. The diversity of cisco revealed in this study and across their Canadian range presents a challenge for designating conservation units at the intraspecific level within the framework of the Committee on the Status of Endangered Wildlife in Canada (COSEWIC).

Section: Genetic Analysesmentioning

confidence: 99%

mentioning

confidence: 99%

Evolution and diversity of two cisco forms in an outlet of glacial Lake Algonquin

Piette‐Lauzière

Bell

Ridgway

et al. 2019

“…Kim et al (2011) argued that for rare SNPs (e.g., MAF < 0.01) it is not easy to differentiate between sequencing errors and a true rare allele, and alleles with less the 1% of MAF should be discarded. Linck and Battey (2019) showed that highly accurate population inferences are reached when relatively rare alleles are included (minimum allele count 2% to 8%). Therefore, in this study we set the MAF value at 2%.…”

Section: Genotypingmentioning

confidence: 99%

Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

Loureiro

Engstrom

Lim

2019

Historical events, habitat preferences, and geographic barriers might result in distinct genetic patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein, we use a genotype‐by‐sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks in comparison with highly connected ones, thus leading to different phylogeographic patterns. We show that population structures vary according to general habitat preferences, levels of population isolation, and historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.

“…These are usually discarded for population analysis, because they are deemed uninformative and may contain errors (Roesti, Salzburger, & Berner, 2012). However, careful consideration of MAF filtering was recently recommended (Linck & Battey, 2019). Therefore, we compared the distribution of alleles over the geographical regions for MAF thresholds of minimum 1 and 5% (results not shown).…”

Section: Genotype Callingmentioning

confidence: 99%

Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea

Verwimp

Vansteenbrugge²,

Derycke

et al. 2019

Nonindigenous species pose a major threat for coastal and estuarine ecosystems.Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotypingby-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. K E Y W O R D S genotyping-by-sequencing, invasion biology, Mnemiopsis leidyi, population differentiation, population genomics, Single nucleotide polymorphisms S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Verwimp C, Vansteenbrugge L, Derycke S, et al. Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea.