Nucleotide sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene of lamprey classified with Lethenteron camtschaticum and the Lethenteron reissneri complex show no species-level differences

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to a high content of repeats and gene duplications in eliminated sequences and a corresponding lack of highly accurate and contiguous assemblies for these regions. Here, we present an improved assembly of the sea lamprey (Petromyzon marinus) genome that was generated using recently standardized methods that increase the contiguity and accuracy of vertebrate genome assemblies. This assembly resolves highly contiguous, somatically retained chromosomes and at least one germline-specific chromosome, permitting new analyses that reconstruct the timing, mode, and repercussions of recruitment of genes to the germline-specific fraction. These analyses reveal major roles of interchromosomal segmental duplication, intrachromosomal duplication, and positive selection for germline functions in the long-term evolution of germline-specific chromosomes.

Phylogenetics and the Cenozoic radiation of lampreys

The development of a movable jaw is one of the most important transitions in the evolutionary history of animals.¹ Jawed vertebrates rapidly diversified after appearing approximately 470 million years ago. Today, only lampreys and hagfishes represent the once dominant jawless grade^2,3,4 and comprise less than 1% of living vertebrate species. Their relationship to other vertebrates ranks among the more contentious problems in animal phylogenetics.^{5,6,7,8,9,10,11,12} Further, the phylogenetic relationships within lampreys and hagfishes remain unclear,^13,14,15 and the ages of their living lineages are largely unexplored.^16,17 Because of their importance for the genomic and developmental changes that prefigured jawed vertebrate diversity,^18,19,20,21 the evolutionary history of lampreys and hagfishes is a major frontier of organismal biology. Of these two clades, lampreys²² are more ecologically diverse, exhibiting freshwater, anadromous, and fully marine forms, as well as parasitic and nonparasitic species.^23,24 Here, we present a new phylogeny and historical biogeographic reconstruction of all living lampreys. Whereas the early diversification of this clade tracks Pangaean fragmentation, lampreys also rapidly radiated in the northern hemisphere during the mid-Cretaceous and directly after the Cretaceous-Paleogene extinction. These radiations mirrored concurrent ones in other animals and plants and coincided with changes to lamprey ecology and feeding behavior. Our results suggest that 80% of living lamprey clades appeared in the last 20 million years of Earth history. Rather than gradually accumulating since the oldest stem-group forms appeared in the early Paleozoic, living lamprey biodiversity results from diversifications extending from the Cretaceous to present.

Genetic variation and population structure among larval Lethenteron spp. within the Yukon River drainage, Alaska

The absence of information on genetic variation and population structure of lampreys Lethenteron spp. in the eastern part of their distribution limits our understanding of the migration ecology and spatial population genetic structure of the species. We examined genetic variation within and among three aggregations of Lethenteron spp. larvae in the Yukon River drainage, Alaska, using microsatellite genotypes. A total of 120 larval lampreys were genotyped at eight microsatellite loci. Global F_ST was 0.053 (95% CI 0.021-0.086), while pairwise F_ST values ranged from 0.048-0.057. Model-based Bayesian clustering analyses with sample locality priors (LOCPRIOR) identified three distinct, but admixed, genetic clusters that corresponded with the three aggregations. Estimates of contemporary gene flow indicate substantial reciprocal migration among sites consistent with no or low-fidelity natal homing. These results are largely in agreement with previous reports of historic and contemporary gene flow among Lethenteron spp. in other parts of their geographic distribution.

RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry

Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Q_lake-P  = 96.8%, F_st  = 0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Q_anad-P  = 37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations.

Distribution and ecology of lampreys Lethenteron spp. in interior Alaskan rivers

This study describes phenetic characteristics and examines the life history of anadromous Arctic lamprey Lethenteron camtschaticum and freshwater-resident Alaskan brook lamprey Lethenteron alaskense in two tributaries of the middle Yukon River, Alaska. Larval lampreys could not be identified to species using pigmentation density patterns or trunk myomere counts, but adults could be identified to species based on colouration, body size and oral-disc dentition. Although larvae were patchily distributed in both rivers, there was a greater proportion of sample locations where Lethenteron spp. were absent in upper reaches than in middle and lower reaches. Relative abundance, density and median and maximum total length (L_T ) of larvae were highly variable among sampling locations. Current velocity, substratum type and coarse woody debris were most strongly correlated with larval Lethenteron spp. density; velocity and substratum size was negatively correlated, whereas woody debris was positively correlated. Water depth, dissolved oxygen levels and specific conductance did not influence habitat selection. Length-frequency distributions, diet composition (organic detritus ≥ 98%), assimilation efficiency (>70%) and gut fullness (<0·2 mg diet ash-free dry mass) were similar for larvae, regardless of river or sampling location. These results increase understanding of Lethenteron spp. biology and ecology in interior Alaska drainages and add to the existing literature on Lethenteron spp. life history.

Redescription of the Far Eastern brook lamprey Lethenteronreissneri (Dybowski, 1869) (Petromyzontidae)

Nonparasitic Lethenteronreissneri (Dybowski) is redescribed based on four syntypes (two adults and two ammocoetes) from the Onon and Ingoda rivers, Russia, and 15 topotypic specimens (seven metamorphosing ammocoetes and eight ammocoetes) from the Onon River system, Russia and Mongolia. Posterial teeth were not mentioned in the original description, but Berg (1931) stated that they were sometimes absent, which he later (Berg 1948) changed to usually absent, based on material (some of which we have re-identified as parasitic Lethenteroncamtschaticum) from far outside of the type locality. The latter view has been widely accepted by subsequent authors. Unfortunately, the poor condition of the two adult syntypes did not permit verification of this character. However, a row of posterials was clearly visible in six of the seven topotypic metamorphosing ammocoetes and indicates their usual presence in the species. The first full description of the ammocoetes, including pigmentation, is provided. The present study restricts the distribution of Lethenteronreissneri to the Shilka and Songhua river systems within the Amur River basin, until a more geographically comprehensive study is undertaken. Additionally, in this study, feeding versus non-feeding at the adult stage, are considered to be valid taxonomic characters at the species level.

Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum

The complete mitochondrial genomes were sequenced in anadromous and resident forms of the lamprey Lethenteron camtschaticum. The sizes of the genomes in the two isolates are 16,245 and 16,295 bp. The gene arrangement, base composition, and size of the two sequenced genomes are similar to the lamprey genomes previously published. The total sequence divergence between the two genomes is very low (0.14%), supporting conspecificity of the anadromous and resident forms of L. camtschaticum. Comparison of the genomes sequenced in the present work with other genomes of lampreys available in GenBank, reveals two distinct evolutionary lineages with a genera level of divergence among the lampreys of eastern Eurasia.

Sneak male mating tactics between lampreys (Petromyzontiformes) exhibiting alternative life-history strategies

Interspecific sneak male mating tactics between paired lamprey species are described for the first time. Although alternative mating tactics among petromyzontids have been described previously, including intraspecific sneak males, the presence of sneak male tactics between parasitic and non-parasitic forms suggests that high levels of gene flow between putative lamprey species could remain high, despite large body size discrepancies.