Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.     

Molecular phylogenetic diversity in the widespread lizard Cercosaura ocellata (Reptilia: Gymnophthalmidae) in South America

For a long time, Cercosaura ocellata was considered polytypic, with three subspecies: C. ocellata ocellata, C. ocellata petersi and C. ocellata bassleri. Recently, C. ocellata bassleri was elevated to full species, based on analysis of a few molecular samples from Peru. This species complex is widely distributed in South America, occurring in Amazonia, Cerrado, Atlantic forest and Pampa biomes. The monophyly and species diversity of C. ocellata are still unstudied. Here, we infer phylogenetic relationships and species diversity of this group analysing 2326 base pairs of three mitochondrial (12S, 16S, and ND4) and one nuclear (c-mos) genes. Our taxon sampling of 115 specimens includes 72 samples of C. ocellata and sequences of other Cercosaura species and closely related Cercosaurinae. Maximum likelihood phylogenetic analysis recovered the monophyly of Cercosaura and that of C. ocellata with strong support. Our analyses suggest that C. ocellata is a complex of cryptic species, which possibly started diversifying in Amazonia.     

Phylogeography of the Northern Alligator Lizard (Squamata,Anguidae): Hidden diversity in a western endemic

Western North America includes the California Floristic Province and the Pacific Northwest, biologically diverse regions highlighted by a complex topography, geology, climate and history. A number of animals span these regions and show distinctive patterns of dispersal, vicariance and lineage diversification. Examining phylogeographic patterns in the fauna of this area aids in our understanding of the forces that have contributed to the generation and maintenance of regional biodiversity. Here, we investigate the biogeography and population structure of the Northern Alligator Lizard (Elgaria coerulea), a wide‐ranging anguid endemic to western North America. We sequenced two mtDNA fragments (ND2 and ND4) for 181 individuals across the range of the species and analysed these data with phylogenetic approaches to infer population and biogeographic history, and date major divergences within the taxon. We further used Bayesian clustering methods to assess major patterns of population structure and performed ecological niche modelling (ENM) to aid in our interpretation of geographic structure and diversification of E. coerulea lineages. Our phylogeographic examination of E. coerulea uncovered surprising diversity and structure, recovering 10 major lineages, each with substantial geographic substructure. While some divergences within the species are relatively old (Pliocene, 5.3–2.6 mya), most intraspecific variation appears to be of more recent origin (Pleistocene, 2.6 mya‐11,700 ya). Current diversity appears to have arisen in the Sierra Nevada Mountains and spread west and north since the Pliocene. Finally, our ENMs suggest that much of the Coast Ranges in California provided ideal habitat during the Last Glacial Maxima (LGM) that has since contracted dramatically and shifted northwards, whereas significant portions of the Sierra Nevada were unsuitable during the LGM and have since become more suitable. Interestingly, E. coerulea shares a number of genetic boundaries with other sympatric taxa, suggesting common historical events and geomorphological features have shaped the biota of this region.     

The limits of cryptic diversity in groundwater: phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae)

Recent studies have revealed high local diversity and endemism in groundwaters, and showed that species with large ranges are extremely rare. One of such species is the cave shrimp Troglocaris anophthalmus from the Dinaric Karst on the western Balkan Peninsula, apparently uniform across a range of more than 500 kilometres. As such it contradicts the paradigm that subterranean organisms form localized, long-term stable populations that cannot disperse over long distances. We tested it for possible cryptic diversity and/or unexpected evolutionary processes, analysing mitochondrial (COI, 16S rRNA) and nuclear (ITS2) genes of 232 specimens from the entire range. The results of an array of phylogeographical procedures congruently suggested that the picture of a widespread, continuously distributed and homogenous T. anophthalmus was wrong. The taxon is composed of four or possibly five monophyletic, geographically defined phylogroups that meet several species delimitation criteria, two of them showing evidence of biological reproductive isolation in sympatry. COI genetic distances between phylogroups turned out to be a poor predictor, as they were much lower than the sometimes suggested crustacean threshold value of 0.16 substitutions per site. Most results confirmed the nondispersal hypothesis of subterranean fauna, but the southern Adriatic phylogroup displayed a paradoxical pattern of recent dispersal across 300 kilometres of hydrographically fragmented karst terrain. We suggest a model of migration under extreme water-level conditions, when flooded poljes could act as stepping-stones. In the north of the range (Slovenia), the results confirmed the existence of a zone of unique biogeographical conflict, where surface fauna is concordant with the current watershed, and subterranean fauna is not.     

Phylogenetic and diversity patterns of Blanus worm lizards (Squamata: Amphisbaenia): insights from mitochondrial and nuclear gene genealogies and species tree

Phylogenetic and phylogeographic patterns of amphisbaenians are poorly known. Molecular data from mitochondrial and nuclear loci are particularly needed for amphisbaenian phylogeny and taxonomy because their specializations to subterranean habits make morphology poorly informative and the occurrence of cryptic species probable. The Mediterranean genus Blanus includes five species – three of them have been recently studied mainly at the mitochondrial level. In this study, we collected mitochondrial (16S and nd4) and nuclear (mc1r and pomc) sequences from 49 specimens, including multiple individuals for each of the five species. We used multilocus coalescent‐based species‐tree inference and single‐gene analyses to estimate phylogenetic relationships among Blanus and to assess patterns of intraspecific differentiation within all the five species. Species‐tree and single‐gene phylogenies provided strong support for the Anatolian worm lizard B. strauchi lying outside a clade comprising all other congeners, with a sister relationship between the Iberian clade (B. cinereus and B. mariae) and the North African clade (B. tingitanus and B. mettetali). Mitochondrial and nuclear data supported the genetic distinctiveness of the recently described B. mariae and also indicated that the distribution of this species is wider than previously known and overlaps with B. cinereus in central Portugal. Blanus tingitanus showed two phylogeographic groups, from the northern and the southern portion of the range, respectively, having high mitochondrial and nuclear divergence and a possible contact zone in northwestern Morrocco. Finally, high genetic variation was found within B. mettetali and B. strauchi, suggesting in the latter case, the occurrence of cryptic taxa to be tested by further research.     

Evolutionary history of bulldog bats (genus Noctilio): recent diversification and the role of the Caribbean in Neotropical biogeography

We present phylogenetic relationships and phylogeographic patterns of the two species of bulldog bats, genus Noctilio. Using a comprehensive sampling of 118 individuals throughout the species distribution, we investigated the distribution of molecular variation in one nuclear and two mitochondrial markers. Phylogenetic trees do not recover Noctilio albiventris as a monophyletic group and point to three similar‐age intraspecific genetic lineages, suggesting cryptic diversity in this taxon. These lineages correspond to the subspecies previously proposed, and are strongly associated with major river basins in South America. Analyses also suggest a very recent origin for the fishing bat Noctilio leporinus, which probably originates from N. albiventris, with a population expansion corresponding to its invasion in South America. Based on our analysis, the speciation event was dated in the Pleistocene epoch and seems to be associated with the variation of the sea level in the Caribbean islands. The present work indicates how phylogeographic studies support the identification of independent evolutionary lineages, driving new systematic/taxonomic investigations, while at the same time shed light on the role of the Caribbean in shaping Neotropical bat fauna diversity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Between an ocean and a high place: coastal drainage isolation generates endemic cryptic species in the Cape kurper Sandelia capensis (Anabantiformes: Anabantidae), Cape Region,South Africa

This study investigated the range-wide phylogenetics and biogeography of the Cape kurper Sandelia capensis, a primary freshwater fish endemic to and widespread within the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that probably represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg and Diep Rivers, the Klein River Clade is endemic to the Klein River and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesised that divergences within S. capensis sensu lato probably occurred because of isolation of coastal drainages by persistent drainage divides or vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via river capture or some other mode of transdivide dispersal or dispersal during periods of low sea level via palaeoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited palaeoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realised, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.     

Origins and patterns of endemic diversity in two specialized lizard lineages from the Australian Monsoonal Tropics (Oedura spp.)

Aim

Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia.

Location

Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia).

Methods

We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non‐Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum‐likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations.

Results

Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late‐Miocene to early‐Pliocene crown ages. Microendemism and diversity were highest in high‐rainfall regions, while the most widespread lineages occurred in the central and south‐east Kimberley, and showed evidence of introgression with parapatric lineages.

Main conclusions

The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the lateMiocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid‐monsoonal interface.     

Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding

The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.     

Hidden diversity and cryptic speciation refute cosmopolitan distribution in Caprella penantis (Crustacea: Amphipoda: Caprellidae)

Caprella penantis is considered a cosmopolitan species and one of the most challenging caprellids in taxonomic terms because of its remarkable intraspecific morphological variation. This study examined DNA sequences from mitochondrial (COI) and nuclear (18S) markers together with morphological data from 25 localities of C. penantis, and closely related species Caprella dilatata and Caprella andreae, all traditionally considered part of the old ‘acutifrons’ complex. The large genetic divergence and reciprocally allopatric distributions point to the existence of a species complex of at least four species, of which one is reported as a cryptic species. This study provides the first evidence of cryptic speciation in the family Caprellidae, and questions the validity of some traditional morphological characters used to delimit species in the genus Caprella. Our results are consistent with the idea that main factors were probably isolation by distance and ecological traits, promoting diversification in C. penantis. The strong genetic structure reported for this species in the Iberian Peninsula and Moroccan coasts also suggests restriction to dispersal as well as the presence of refugial areas. These results highlight the utility of the COI and 18S genes in combination with morphological characters for shedding light on systematic questions in caprellids, and patterns of genetic connectivity.     

DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes)

To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.     

DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River,Canada

Diplostomoid metacercariae parasitize freshwater fishes worldwide and cannot be identified to species based on morphology. In this study, sequences of the barcode region of cytochrome c oxidase subunit 1 (CO1) were used to discriminate species in 1088 diplostomoids, most of which were metacercariae from fish collected in the St. Lawrence River, Canada. Forty‐seven diplostomoid species were detected, representing a large increase in known diversity. Most species suggested by CO1 sequences were supported by sequences of internal transcribed spacer (ITS) of rDNA and host and tissue specificity. Three lines of evidence indicate that physiological incompatibility between host and parasite is a more important determinant of host specificity than ecological separation of hosts and parasites in this important group of freshwater fish pathogens. First, nearly all diplostomoid species residing outside the lens of the eyes of fish are highly host specific, while all species that occur inside the lens are generalists. This can be plausibly explained by a physiological mechanism, namely the lack of an effective immune response in the lens. Second, the distribution of diplostomoid species among fish taxa reflected the phylogenetic relationships of host species rather than their ecological similarities. Third, the same patterns of host specificity were observed in separate, ecologically distinctive fish communities.     

Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists

Aim To evaluate the role of historical processes in the evolution of Sclerurus leaftossers by integrating phylogenetic and phylogeographical approaches. Location Humid forests of the Neotropical region. Methods We reconstructed the evolutionary history of Sclerurus based on DNA sequences representing all species and 20 of the 26 recognized subspecies using one autosomal nuclear locus and three protein‐coding mitochondrial gene sequences. Phylogenetic relationships were inferred using Bayesian and maximum‐likelihood methods. We used Bayesian coalescent‐based approaches to evaluate demographic changes through time, and to estimate the timing of diversification events. Based on these results, we examined the temporal accumulation of divergence events using lineage‐through‐time plots. Results The monophyly of all Sclerurus species was strongly supported except for Sclerurus mexicanus, which was paraphyletic in relation to Sclerurus rufigularis, and for the sister pair Sclerurus scansor–Sclerurus albigularis, which were not reciprocally monophyletic in the nuclear tree. We found remarkably deep phylogeographical structure within all Sclerurus species, and overall this structure was congruent with currently recognized subspecies and Neotropical areas of endemism. Diversification within Sclerurus has occurred at a relatively constant rate since the Middle Miocene. Main conclusions Our results strongly support the relevance of physiographical (e.g. Nicaragua Depression, Isthmus of Panama, Andean Cordillera, great rivers of Amazonia) and ecological barriers (open vegetation corridor) and ecological gradients (elevational zonation) to the diversification of Neotropical forest‐dwelling organisms. Despite the high congruence among the spatial patterns identified, the variance in divergence times suggests multiple speciation events occurring independently across the same barrier, and a role for dispersal. The phylogenetic patterns and cryptic diversity uncovered in this study demonstrate that the current taxonomy of Sclerurus underestimates the number of species.     

Cryptic diversity and unexpected evolutionary patterns in the meadow lizard,Darevskia praticola (Eversmann, 1834)

Darevskia praticola differs from the other species of the genus in having a large but disjunct distribution, covering the Balkan and the Caucasus regions. Furthermore, most Darevskia species occupy saxicolous habitats, whereas D. praticola inhabits meadows and forest environments. Here we determine the phylogeographic and phylogenetic relationships of Darevskia praticola sensu lato and evaluate the current, morphology-based taxonomy. We sequenced two mtDNA genes (Cyt-b and ND4) and two nuclear loci (MC1R and RELN) for samples collected across the species range. Because our sequences amplified with the Cyt-b primers appear to represent a nuclear pseudogene we excluded this marker from the final analysis. Our results support monophyly of D. praticola and show its division into three clades. The first divergence, dated to the Late Pliocene, is between the Balkans and the Caucasus. The Caucasus lineage is further subdivided in a western Greater Caucasus and a Transcaucasia clade, likely due to subsequent differentiation during the Pleistocene. Our findings do not support the current taxonomic arrangement within D. praticola. The main geographic divergence likely happened due to a vicariance event associated with Plio-Pleistocene climatic and vegetation oscillations.     

Onset of cryptic vicariance in the Japanese dormouse Glirulus japonicus (Mammalia, Rodentia) in the Late Tertiary, inferred from mitochondrial and nuclear DNA analysis

The sequences of the mitochondrial cytochrome b gene and restriction site variation in the spacer region of the nuclear ribosomal RNA gene [rDNA-restriction fragment length polymorphism (RFLP)] were analysed to determine the phylogeographic structure of the Japanese dormouse ( Glirulus japonicus ), which is threatened by deforestation and has been designated an endangered species in Japan. The phylogenetic tree of cytochrome b grouped G. japonicus into six geographical populations: north-eastern Honshu (I), central Honshu (II), west-central Honshu/Kii Peninsula (III), western Honshu (IV), Shikoku (V), and westernmost Honshu/Kyushu (VI); the genetic distances among these groups suggest divergence in the Late Tertiary. The lineage of group VI was located at the basal position in the phylogenetic tree, followed by the radiation of the other lineages. An rDNA-RFLP analysis of 15 restriction sites roughly supported such genetic isolation; groups I, II, III, IV, V and VI have five, two, one, one, one and four unique restriction sites, respectively, revealing four geographic groups as cryptic species: I, II, III + IV + V and VI. Our results reveal the ancient divergences of the local population, which has a complicated evolutionary history, and should be useful in developing a framework for the conservation of this species.     

Ultraviolet reflectance and cryptic sexual dichromatism in the ocellated lizard, Lacerta (Timon) lepida (Squamata: Lacertidae)

Ultraviolet (UV) colorations have garnered extensive theoretical and empirical treatment in recent years, although the majority of studies have concerned themselves with avian taxa. However, many lizards have acute visual systems with retinal photoreceptors that are sensitive to UV wavelengths, and also display UV-reflecting colour patches. In the present study, we used UV photography and full-spectrum reflectance spectrophotometry to describe intra- and intersexual colour variation in adult ocellated lizards Lacerta ( Timon ) lepida and to obtain evidence of UV-based ornamentation. We also investigated whether any colour traits correlate with morphological traits potentially related to individual quality. The results obtained show that the prominent eyespots and blue outer ventral scales (OVS) that ocellated lizards have on their flanks reflect strongly in the UV range and are best described as UV/blue in coloration. The eyespots of males are larger and cover a larger surface area than those of females. However, these differences can be entirely accounted for by sex differences in body size, with males being generally larger than females. We also found differences in the shape of reflectance curves from males and females, with the eyespots and blue OVS of males being more UV-shifted than those of females. Other body regions have extremely low UV reflectance and are not sexually dichromatic. Eyespot size and the total surface area covered by eyespots increases with body size in males but not in females, suggesting that they may be signalling an intrinsic individual characteristic such as body size or male fighting ability. We also discuss the alternative and non-exclusive hypothesis that eyespots may function in lizards of both sexes as protective markings against predators.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 766–780.     

Chromosomal evolution in the Brazilian lizards of genus Leposoma (Squamata, Gymnophthalmidae) from Amazon and Atlantic rain forests: banding patterns and FISH of telomeric sequences

An extensive karyotype differentiation was found among three species of gymnophthalmid lizard genus Leposoma which occur in the tropical forest areas of Brazil. We examined the chromosomes of the Amazonic species L. guianense (LOU) and L. oswaldoi (LOS) and the Atlantic forest species L. scincoides (LSC) after conventional and differential staining, and FISH of telomeric sequences. Both Amazonic species shared very similar 2n = 44 karyotypes, including 20 biarmed macrochromosomes and 24 microchromosomes (20 M + 24 m). However, the location of Ag-NORs and the amount of constitutive heterochromatin differed in these karyotypes. The Atlantic forest species L. scincoides has a very distinct karyotype with 52 acrocentric and subtelocentric chromosomes of decreasing size. Comparative R-banding analysis revealed complete homeology of the macrochromosomes of LGU and LOS and correspondence of banding patterns between LSC acrocentrics and subtelocentrics and some arms of biarmed LGU and LOS chromosomes. Pair 1 had similar banding patterns in the three species, implying the occurrence of a pericentric inversion. Interstitial telomeric bands (ITBs) detected by FISH at the pericentromeric region of some biarmed LGU and LOS chromosomes could be remnants of chromosomal rearrangements occurred during the differentiation of the karyotypes. Robertsonian rearrangements as well as pericentric inversions events probable were involved in the karyotype evolution of these Amazon and Atlantic forests species of Leposoma.     

Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera,Podarcis pityusensis (Squamata: Lacertidae)

Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time‐calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid‐late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present‐day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.     

Phylogeographic patterns of trans-Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example

Aim To investigate the phylogeography and execute a historical‐demographic analysis of the Neotropical rattlesnake, Crotalus durissus, thereby testing the hypothesis of a Pleistocene central Amazon corridor of dry forest or savanna that partitioned the Amazonian rain forest into western and eastern portions. Location South America. Methods Using sequences of three mitochondrial genes, we estimated the phylogeography, gene and nucleotide diversity across the South American range of C. durissus. Tree topology tests were used to test alternative biogeographical hypotheses, and tests of population genetic structure and statistical parsimony networks and nested clade phylogeographic analysis (NCPA) were used to infer connectivity and historical population processes on both sides of the Amazon basin. Results Tree topology tests rejected the hypothesis of a coastal dispersal in favour of a central corridor scenario. Gene diversity was similar on both sides of the Amazon basin. Nucleotide diversity indicated that the populations from north of the Amazon basin represented ancestral populations. Analysis of molecular variance (amova ) showed that intra‐population molecular variation was greater than between regions. Historical‐demographic statistics showed significant population expansion south of the Amazon, and little differentiation in the north, indicating moderate past gene flow between north and south of the Amazon. The parsimony network connected clades from the Roraima and Guyana populations with Mato Grosso, suggesting an Amazonian central corridor, and NCPA supported allopatric fragmentation between north and south of the Amazon. Main conclusions The distribution of C. durissus on both sides of the Amazon basin is evidence of changes in the distribution of rain forest vegetation during the Pleistocene. Our results suggest a formerly continuous distribution of this rattlesnake along a central Amazonian corridor during the middle Pleistocene. Allopatric fragmentation inferred from NCPA is consistent with vicariance resulting from a subsequent closure of this habitat corridor. This study emphasizes the potential of trans‐Amazonian open formation species to inform the debate on the past distribution of rain forests in the Amazon Basin.