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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.

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.

Eremias laticeps Smith, 1845 The type specimen BMNH 1946.8.7.56 (Fig. 4), collected by Smith, matches perfectly his description and drawings (Smith 1845). However, it is evident that Smith described only one side of the voucher; femoral pores are given by Smith (1845) as 13, but are left side 13, right side 14; Smith described the freno-nasal and the freno-ocular plate (Smith 1845) as ���freno-nasal plate small, quadrangular, rather longer than deep, freno-ocular plate large and subtriangular��� (Plate 48: 3 and 3a), whereas on the right side the freno-nasal plate is small, quadrangular, rather longer than deep, and the freno-ocular plate large and subtriangular, and on the left side the freno-nasal and freno-ocular are fused (Fig. 4). This is consistent with the lithograph in Plate 48: 3 and 3a being reversed and showing the right side of the head, which as FitzSimons (1937) explained, is a consequence of this printing technique. However, this contradicts our findings regarding Plate 48: 7a (Smith 1845) depicting E. capensis. Why the description of the type specimen given by Boulenger (1921) does not match with Smith (1845) cannot be determined. All specimens of P. laticeps examined by Boulenger (1921) are still in the BMNH collection and can be assigned correctly, plus three specimens (BMNH 1988.511, BMNH 1988.513���514) subsequently presented by E. N. Arnold in 1988 (Table 2). Although BMNH 1946.8.7.56 is treated as the type of E. laticeps, it should be noted that Smith described one voucher in detail but mentioned a total of three specimens (Smith 1845), which consequently form syntypes. All other specimens in the collection of the BMNH presented by Smith or Lord Derby cannot be the one described by Smith as none has only 5 upper labials in front of the subocular (Smith 1845, Plate 48: 3a; Fig. 4 and Table 2 this work). For stability we herein designate in accordance with Articles 74.1. and 74.7. of the Code (ICZN, 1999), specimen BMNH 1946.8.7.56 as lectotype of Pedioplanis laticeps Smith, 1845, which is depicted on plate 46 figure 1 and plate 48, figures 3 and 3a of the original description. Consequently, specimens BMNH 1865.5.4.87 and BMNH 1865.5.4.88 become paralectotypes., Published as part of Sebastian Kirchhof, Johannes Penner, Mark-Oliver R��del & Johannes M��ller, 2017, Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Dum��ril & Bibron, 1839) (Squamata: Lacertidae), pp. 82-109 in Zootaxa 4318 (1) on page 89, DOI: 10.11646/zootaxa.4318.1.3, http://zenodo.org/record/886124, {"references":["Smith, A. (1845) Illustrations of the Zoology of South Africa. Reptilia. Part XXIII. Smith, Elder, and Co., London.","FitzSimons, V. F. M. (1937) Notes on the reptiles and amphibians collected and described from South Africa by Andrew Smith. Annals of the Transvaal Museum, 17, 259 - 274.","Boulenger, G. A. (1921) Monograph of the Lacertidae, Fol. II. Trustees of the British Museum of Natural History, London, 451 pp."]}

Lacerta capensis Smith, 1838 The specimen BMNH 1946.8.7.86 (previously IV.42.a; Fig. 3), presented by Lord Derby to the collection, is considered to be the type of Lacerta capensis Smith, 1838 (Table 1). However, after careful examination we found that neither this nor any of the other specimens presented by Smith or Lord Derby match exactly the original description provided by Smith (1838). With the exception of BMNH 1946.8.7.86, BMNH 1865.5.4.87 and BMNH 1865.5.4.88, none of the specimens collected by Smith or presented by Lord Derby (including all Southern African specimens of Lacertidae) can be the original type of L. capensis as they lack the feature mentioned in the species’ description of possessing granules surrounding the inner edges of the supraoculars. Of the three specimens that have these granules, only BMNH 1946.8.7.86 and BMNH 1865.5.4.87 have 11 or 12 femoral pores, (although BMNH 1946.8.7.86 has 11 on both legs, with one additional but underdeveloped pore on the left leg, whilst BMNH 1865.5.4.87 has 12 on both legs, including one underdeveloped pore on the left leg). Finally, BMNH 1865.5.4.87 clearly has 9 enlarged scales in the collar, as in Smith’s (1838) description, whereas BMNH 1946.8.7.86 has 10. In 1845, when Smith published drawings of E. capensis, he must have examined both these specimens as both appear to be depicted in the plates. The specimen depicted in Plate 45: 2 (Smith 1845) conforms with its colouration and pattern with BMNH 1865.5.4.87, whilst the figures 7 and 7a in Plate 48 agree with BMNH 1946.8. 7.86 in depicting an incomplete inner row of granules around the supraoculars (Fig. 3) (this is more complete in BMNH 1865.5.4.87). However, the presence of scales between the subocular and the freno-ocular shown in the drawing fits only BMNH 1946.8.7.86, assuming that the image has not been reversed in the lithographic process and that it does depict the left side of the head. As noted by FitzSimons (1937) this should not be the case and the drawing should actually be mirrored and show the opposite (right) side. This would then conflict with the number of scales between the subocular and the frenoocular in this specimen (Fig. 3, Table 2). However, as indicated in previous articles (FitzSimons 1937, Branch & Bauer 2005), these figures are not the original first description of L. capensis, and Smith’s (1945) illustrations may be based on different individuals from that used in the original description. Finally, neither BMNH 1946.8.7.86 nor BMNH 1865.5.4.87 match the total length of the type of around 8 inches [197.8 mm] given in Smith’s (1838) description, with BMNH 1946.8.7.86 measuring only 148 mm (including its original tail) and BMNH 1865.5.4.87 measuring 170 mm total length (although a few mm may be missing from the broken tail). Since the name Lacerta capensis Smith, 1838 is a primary junior homonym (and therefore unavailable following Article 57.2 of the Code; ICZN 1999), there are no nomenclatural consequences for the taxon Pedioplanis laticeps (Smith, 1845) in maintaining the current status of BMNH 1946.8.7.86 as the holotype of Lacerta capensis Smith, 1838, despite the minor inconsistencies between its scalation and that detailed in the original description., Published as part of Sebastian Kirchhof, Johannes Penner, Mark-Oliver Rödel & Johannes Müller, 2017, Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae), pp. 82-109 in Zootaxa 4318 (1) on pages 88-89, DOI: 10.11646/zootaxa.4318.1.3, http://zenodo.org/record/886124, {"references":["Smith, A. (1838) Contributions to the Natural History of Southern Africa. Art. VIII. Magazine of Natural History, 2, 92 - 94.","Smith, A. (1845) Illustrations of the Zoology of South Africa. Reptilia. Part XXIII. Smith, Elder, and Co., London.","FitzSimons, V. F. M. (1937) Notes on the reptiles and amphibians collected and described from South Africa by Andrew Smith. Annals of the Transvaal Museum, 17, 259 - 274.","Branch, W. R. & Bauer, A. M. (2005) The life and herpetological contributions of Andrew Smith. In: Smith, A. (Ed.), The Herpetological Contributions of Sir Andrew Smith. Society for the Study of Amphibians and Reptiles, Villanova, pp. 1 - 19."]}

Re-examination of the type material of Ligonirostra Stuhlmanni Pfeffer, 1893 (original spelling, now Prosymna stuhlmanni) and comparison with the sole type specimen of its synonym Stenorhabdium temporale Werner, 1909 revealed a number of significant morphological differences between these taxa. Detailed analyses of pholidosis and osteology of comparative material show that S. temporale is in fact a subjective junior synonym of Pseudorabdion longiceps (Cantor, 1847). A lectotype and a paralectotype of Ligonirostra stuhlmanni are designated and described.