Development and characterization of 79 nuclear markers amplifying in viviparous and oviparous clades of the European common lizard

Abstract

The European common lizard (Zootoca vivipara) is a widely distributed species across Europe and Asia exhibiting two reproductive modes (oviparity/viviparity), six major lineages and several sublineages. It has been used to tackle a large variety of research questions, nevertheless, few nuclear DNA sequence markers have been developed for this species. Here we developed 79 new nuclear DNA sequence markers using a clonation protocol. These markers were amplified in several oviparous and viviparous specimens including samples of all extant clades, to test the amplification success and their diversity. 49.4% of the markers were polymorphic and of those, 51.3% amplified in all and 94.9% amplified in 5-7 of the extant Z. vivipara clades. These new markers will be very useful for the study of the population structure, population dynamics, and micro/macro evolution of Z. vivipara. Cross-species amplification in four lizard species (Psammodromus edwardsianus, Podarcis muralis, Lacerta bilineata, and Takydromus sexlineatus) was positive in several of the markers, and six makers amplified in all five species. The large genetic distance between P. edwardsianus and Z. vivipara further suggests that these markers may as well be employed in many other species.

Reversals in complex traits uncovered as reticulation events: Lessons from the evolution of parity‐mode, chromosome morphology, and maternal resource transfer

“…It has seven well‐defined clades (Surget‐Groba et al, ), a bimodal reproductive pattern, and is a model species for the study of evolution, population dynamics, behavior, coloration, and physiology (Fitze & Le Galliard, ; Gonzalez‐Jimena & Fitze, ; Horvathova et al, ; San‐Jose, Peñalver‐Alcázar, Milá, Gonzalez‐Jimena, & Fitze, ). Because the existing genetic coverage was not sufficient for the envisaged analyses, we amplified three nuclear (nZV1, nZV2, and nZV3; Horreo, Peláez, Suárez, & Fitze, ) and three mitochondrial gene fragments (16S rDNA, 16S: Clary & Wolstenholme, ; cytochrome B, cytB: Smith & Patton, ; and NADH dehydrogenase 2, ND2: Macey, Larson, Ananjeva, Fang, & Papenfuss, ) in 24 individuals belonging to all extant clades (three individuals per clade; Surget‐Groba et al, ), except for clade B, from which 9 individuals were used, three per subclade; Horreo, Palaez, Breedveld, et al, ; Mila, Surget‐Groba, Heulin, Gosá, & Fitze, ) and two outgroups (Tables S2 and S3) following original protocols (Horreo, Peláez, Suárez, & Fitze, ). One specimen per population was used (Table S2).…”

“…It has seven well-defined clades (Surget-Groba et al, 2006), a bimodal reproductive pattern, and is a model species for the study of evolution, population dynamics, behavior, coloration, and physiology (Fitze & Le Galliard, 2011;Gonzalez-Jimena & Fitze, 2012;Horvathova et al, 2013;San-Jose, Peñalver-Alcázar, Milá, Gonzalez-Jimena, & Fitze, 2014). Because the existing genetic coverage was not sufficient for the envisaged analyses, we amplified three nuclear (Tables S2 and S3) following original protocols (Horreo, Peláez, Suárez, & Fitze, 2018). One specimen per population was used (Table S2).…”

“…nZV1, nZV2, and nZV3;Horreo, Peláez, Suárez, & Fitze, 2018) andthree mitochondrial gene fragments (16S rDNA, 16S: Clary & Wolstenholme, 1985; cytochrome B, cytB: Smith & Patton, 1991; and NADH dehydrogenase 2, ND2: Macey, Larson, Ananjeva, Fang, & Papenfuss, 1997) in 24 individuals belonging to all extant clades (three individuals per clade; Surget-Groba et al, 2001), except for clade B, from which 9 individuals were used, three per subclade; Horreo, Palaez, Breedveld, et al, 2018; Mila, Surget-Groba, Heulin, Gosá, & Fitze, 2013) and two outgroups…”

Isolation and Characterization of Interspersed Repeated Sequences in the Common Lizard, Zootoca vivipara, and Their Conservation in Squamata

“…vivipara mostly concern microsatellites [Cornetti et al, 2015a;Horreo et al, 2018], and very little is known about the organization and distribution of the repeated interspersed DNA fraction, including transposable elements (TEs). TEs represent a considerable fraction of eukaryotic genomes, including reptiles, e.g., about 40% in the agamid Pogona vitticeps [Georges et al, 2015].…”

Genetic diversity of major histocompatibility complex class I genes in Zootoca vivipara

“…Different genetic analysis has caused several differences [21][22][23][24][25][26]. At the same time, the use of molecular marker technology to explore sequence genetic polymorphism is quite concerned by researchers [27][28][29][30][31][32][33]. However, MHC molecular studies of Z. vivipara have not been reported.…”