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Understanding the genomic basis of adaptation to different abiotic environments is important in the context of climate change and resulting short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether signatures of genomic adaptation to a set of environmental parameters are concentrated in specific subsets of genes and functions in lacertid lizards and other vertebrates. We first identify 200 genes with signatures of positive diversifying selection from transcriptomes of 24 species of lacertid lizards and demonstrate their involvement in physiological and morphological adaptations to climate. To understand how functionally similar these genes are to previously predicted candidate functions for climate adaptation and to compare them with other vertebrate species, we then performed a meta-analysis of 1, 100 genes under selection obtained from -omics studies in vertebrate species adapted to different abiotic factors. We found that the vertebrate gene set formed a tightly connected interactome, which was to 23% enriched in previously predicted functions of adaptation to climate, and to a large part (18%) involved in organismal stress response. We found a much higher degree of identical genes being repeatedly selected among different animal groups (43.6%), and of functional similarity and post-translational modifications than expected by chance, and no clear functional division between genes used for ectotherm and endotherm physiological strategies. In total, 171 out of 200 genes of Lacertidae were part of this network. These results highlight an important role of a comparatively small set of genes and their functions in environmental adaptation and narrow the set of candidate pathways and markers to be used in future research on adaptation and stress response related to climate change.

Made available in DSpace on 2021-06-25T11:53:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-01 Deutsche Forschungsgemeinschaft Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) MfN Taxonomy Fund NYUAD NYUAD Research Institute Climate has a large impact on diversity and evolution of the world's biota. The Eocene-Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene-Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them-and especially A. guineensis-as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene-Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae. New York Univ Abu Dhabi, Abu Dhabi, Saadiyat Island, U Arab Emirates Univ Estadual Paulista, Dept Biodiversidade, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil Univ Vet Med Hannover, Inst Zool, Bunteweg 17, D-30559 Hannover, Germany Univ Antilles, Sorbonne Univ, Inst Systemat Evolut Biodivers ISYEB, Museum Natl Hist Nat,CNRS,Ecole Prat Hautes Etud, CP 30,57 Rue Cuvier, F-75005 Paris, France Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Invalidenstr 43, D-10115 Berlin, Germany IRD, UMR MIVEGEC, Lab Paludol & Zool Med, BP 1386, Dakar, Senegal Tech Univ Carolo Wilhelmina Braunschweig, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany Univ Estadual Paulista, Dept Biodiversidade, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil Deutsche Forschungsgemeinschaft: VE 247/11-1/MU 1760/9-1 FAPESP: 2017/26162-8 NYUAD: AD180 NYUAD Research Institute: G1205A

The lacertid genus Pedioplanis is a moderately speciose group of small-bodied, cryptically-colored lizards found in arid habitats throughout southern Africa. Previous phylogenetic work on Pedioplanis has determined its placement within the broader context of the Lacertidae, but interspecific relations within the genus remain unsettled, particularly within the P. undata species complex, a group largely endemic to Namibia. We greatly expanded taxon sampling for members of the P. undata complex and other Pedioplanis, and generated molecular sequence data from 1,937 bp of mtDNA (ND2 and cytb) and 2,015 bp of nDNA (KIF24, PRLR, RAG-1) which were combined with sequences from GenBank resulting in a final dataset of 455 individuals. Both maximum likelihood and Bayesian analyses recover similar phylogenetic results and reveal the polyphyly of P. undata and P. inornata as presently construed. We confirm that P. husabensis is sister to the group comprising the P. undata complex plus the Angolan sister species P. huntleyi + P. haackei and demonstrate that P. benguelensis lies outside of this clade in its entirety. The complex itself comprises six species including P. undata, P. inornata, P. rubens, P. gaerdesi and two previously undescribed entities. Based on divergence date estimates, the P. undata species complex began diversifying in the late Miocene (5.3 ± 1.6 MYA) with the most recent cladogenetic events dating to the Pliocene (2.6 ± 1.0 MYA), making this assemblage relatively young compared to the genus Pedioplanis as a whole, the origin of which dates back to the mid-Miocene (13.5 ± 1.8 MYA). Using an integrative approach, we here describe Pedioplanis branchisp. nov. and Pedioplanis mayerisp. nov. representing northern populations previously assigned to P. inornata and P. undata, respectively. These entities were first flagged as possible new species by Berger-Dell’mour and Mayer over thirty years ago but were never formally described. The new species are supported chiefly by differences in coloration and by unique amino acid substitutions. We provide comprehensive maps depicting historical records based on museum specimens plus new records from this study for all members of the P. undata complex and P. husabensis. We suggest that climatic oscillations of the Upper Miocene and Pliocene-Pleistocene era in concert with the formation of biogeographic barriers have led to population isolation, gene flow restrictions and ultimately cladogenesis in the P. undata complex.

Determining the susceptibility of species to changing thermal niches is a major goal for biologists. In this paper we develop an eco-physiological model of extinction risk under climate change premised on behavioral thermoregulation. Our method downscales operative environmental temperatures, which restrict hours of activity of lizards, hr , for present-day climate (1975) and future climate scenarios (2070). We apply our model using occurrence records of 20 Phrynocephalus lizards (or taxa in species complexes) drawn from literature and museum records. Our analysis is phylogenetically informed, because some clades may be more sensitive to rising temperatures. The limits for computed hr predict local extirpations among Phrynocephalus lizards at continental scales and delineate upper boundaries of thermal niches as defined by Extreme Value Distributions. Under the 8.5 Representative Concentration Pathway scenario, we predict extirpation of 64% of local populations by 2070 across 20 Phrynocephalus species, and 12 are at high risk of total extinction due to thermal limits being exceeded. In tandem with global strategies of lower CO2 emissions, we propose regional strategies for establishing new national parks to protect extinction-prone taxa by preserving high-elevation climate refugia within existing sites of species occurrence. We propose that evolved acclimatization - maternal plasticity - may ameliorate risk, but is poorly studied. Previous studies revealed that adaptive maternal plasticity by thermoregulating gravid females alter progeny thermal preferences by ±1 °C. We describe plasticity studies for extinction-prone species that could assess whether they might be buffered from climate warming - a self-rescue. We discuss an epigenetic framework for studying such maternal-effect evolution.

WOS: 000484779500005, PubMed ID: 31501432, Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genomewide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates., Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [VE 247/11-1/MU 1760/9-1, VE 247/16-1-HO3492/6-1]; Juan de la Cierva fellowships from the Spanish 'Ministerio de Economia y Competitividad' [FJCI-2014-20380, IJCI-2016-29566]; 'Rita Levi Montalcini' program for recruitment of young researchers at the University of L'Aquila; US-National Science Foundation Emerging Frontiers program [EF-1241848]; Hassan II Academy of Sciences and Technologies (ICGVSA Project); Slovenian Research Agency Research Program [P1-0255]; Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) [SNIC 2017/7-275]; [NORTE-01-0145-FEDER-000007]; [ON173025 MESTD RS], We are grateful to numerous students, field assistants and technicians who supported field and laboratory work, and to G. Jones for useful comments on the manuscript. This study was supported by the Deutsche Forschungsgemeinschaft (DFG) to M.V. and J.M. (VE 247/11-1/MU 1760/9-1), and to L.R. in the framework of the "TaxonOmics" priority program (VE 247/16-1-HO3492/6-1). J.G.-P. and I. I. were supported by Juan de la Cierva fellowships from the Spanish 'Ministerio de Economia y Competitividad' (FJCI-2014-20380 and IJCI-2016-29566), D.S. by the 'Rita Levi Montalcini' program for recruitment of young researchers at the University of L'Aquila, M.A.C. by project NORTE-01-0145-FEDER-000007, B.S. and D.B.M. by the US-National Science Foundation Emerging Frontiers program (EF-1241848), J.C.I. by project ON173025 MESTD RS, T.S., A.F., and A.S. by the Hassan II Academy of Sciences and Technologies (ICGVSA Project), A.Z. by the Slovenian Research Agency Research Program P1-0255. The computations were in part performed on the Altamira supercomputer at the Institute of Physics of Cantabria (IFCA-CSIC), Spain; the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2017/7-275; as well as the Zentraler Informations-und Datenverarbeitungsservice of the Tierarztliche Hochschule Hannover (IDS-TiHo). Further, we acknowledge the Viper High Performance Computing facility of the University of Hull and its support team, especially Ahmed Elnawasany, for facilitating computational analyses.

Eremiadinae, one of three subfamilies of Lacertidae, are distributed throughout Asia and Africa. Previous phylogenetic studies suggested that one of the main groups of Eremiadinae (the Ethiopian clade) consist of two clades with predominately East-African and South-African distribution. Yet, especially the latter one, which includes the genera Pedioplanis, Meroles, Ichnotropis, Tropidosaura and Australolacerta, was not well supported in the molecular phylogenetic analysis. In this study, we analysed the phylogenetic relationships among the genera of the ‘South African clade’ to assess whether this group actually forms a highly supported clade and to address questions concerning the monophyly of the genera. We sequenced sections of the widely used mitochondrial genes coding for 16S rRNA, 12S rRNA and cytochrome b (altogether 2045 bp) as well as the nuclear genes c-mos, RAG-1, PRLR, KIF24, EXPH5 and RAG-2 (altogether 4473 bp). The combined data set increased the support values for several nodes considerably. Yet, the relationships among five major lineages within the ‘South African clade’ are not clearly resolved even with this large data set. We interpret this as a ‘hard polytomy’ due to fast radiation within the South African lacertids. The combined tree based on nine marker genes provides strong support for the ‘South African Clade’ and its sister group relationship with the ‘East African Clade’. Our results confirm the genus Tropidosaura as a monophylum, while Ichnotropis is paraphyletic in our trees: Ichnotropis squamulosa appears more closely related to Meroles than to Ichnotropis capensis. Furthermore, the monophyly of Meroles is questionable as well. Based on our results, I. squamulosa should be transferred from Ichnotropis into the genus Meroles. Also, the two species of Australolacerta (A. australis and A. rupicola) are very distantly related and the genus is perhaps paraphyletic, too. Finally we propose a phylogeographical scenario in the context of palaeoclimatic data and compare it with a previously postulated hypothesis.

Foraging mode of the endemic Soutpansberg rock lizard (Australolacerta rupicola) was determined by (1) measuring the number of movements per minute (MPM) and the percentage time spent moving (PTM); and (2) analysing faecal samples. Furthermore, these criteria were related to diet composition, proportion of attacks initiated while moving and foraging substrate. The results are discussed in comparison to the foraging modes of 20 other lacertid species. Values for MPM and PTM as well as faecal analysis indicate an active foraging strategy for A. rupicola. Although rock living, this species mostly forages in leaf litter where it is well camouflaged while actively searching for sedentary prey. Even in comparison to other active foragers of the family Lacertidae, A. rupicola displays the prototypic behaviour of a widely foraging lizard with very high PTM and very low MPM.

Within the genus Pedioplanis the two basal species P. laticeps and P. burchelli are phenotypically similar. In this study we examine material of both species to determine diagnostic characters and we revise the distribution of Pedioplanis laticeps . For this we used data from museum collections, literature records, as well as results from our own surveys. Careful examination of the type material of P. laticeps and P. burchelli, as well as additional specimens, confirmed several morphological characters that distinguish between the two species. A reconstruction of the taxonomic history of the species revealed that P. laticeps was described in 1845, and not in 1844 or 1849 as commonly attributed. We designate a holotype for P. burchelli , a lectotype and two paralectotypes for P. laticeps, re-describe the types of P. laticeps and P. burchelli and correct previous misidentifications. Recent literature considers P. laticeps endemic to South Africa. However, 40-year-old museum records contain specimens sampled in Namibia. Surveys in Namibia confirmed at least one extant population of P. laticeps north of the Orange River, close to an area where they were previously collected. Natural history data is very scarce for both species and a comprehensive genetic analysis, covering the entire ranges of both taxa, is urgently needed to shed light on the evolutionary history of the two sister species.