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Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including ‘non-adaptive radiations’ containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial ‘major-lineages’ diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pliocene-Pleistocene glaciation-deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study, we estimated time-calibrated phylogenetic/phylogeographic patterns in lizards of the Liolaemus lineomaculatus group and relate them to historical Miocene-to-Pleistocene events of Patagonia and the previously proposed phylogeographic patterns. Individuals from 51 localities were sequenced for the mitochondrial marker (cyt-b) and a subsample of individuals from each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one slow evolving mitochondrial gene (12S). Our analyses revealed strong phylogeographic structure among lineages and, in most cases, no signal of demographic changes through time. The lineomaculatus group is composed of three strongly supported clades (lineomaculatus, hatcheri and kolengh + silvanae), and divergence estimates suggested their origins associated with the oldest known Patagonian glaciation (7-5 Ma); subsequent diversification within the lineomaculatus clade coincided with the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade includes nine strongly genetically and geographically structured lineages, five of which are interpreted as candidate species. Our findings suggest that some Liolaemus lineages have persisted in situ, each of them in a different refugium, through several glaciation-deglaciation cycles without demographic fluctuations. We also summarize and update qualitative evidence of some shared phylogeographic breaks and refugia among plants, rodents and lizards.

Twenty‐one species of lizards are included in the southernmost clade of South America, the Liolaemus lineomaculatus section. There are two hypotheses of species‐grouping within this section, one based on morphological similarities and the other based on molecular phylogenetic relationships; although discordant, both are in use. The ‘morphological arrangement hypothesis’, which sorts the species of the section in three groups, was proposed ∼30 years ago; however, despite taxonomic changes and almost doubling the species diversity of this section since then, the hypothesis has never been tested. Here, we (1) present an updated chronological review of taxonomic changes, species descriptions, morphological groups, and genetic clades proposed for the L. lineomaculatus section, and (2) evaluate the accuracy of the ‘morphological arrangement hypothesis’. We show that the traditional practice of classifying 11 of these species in two of the three traditional morphological groups of the section (Liolaemus kingii and Liolaemus archeforus), which is not supported by molecular data, is also not supported by morphological data, and therefore should be abandoned; we suggest referring to this group of species as the L. kingii group. We characterized the Liolaemus magellanicus group based on morphology, and extend the previously published morphological characteristics of the L. lineomaculatus group. Finally, we comment on future prospects for studies of sexual dimorphism and its possible ecological implications. This paper provides a critical synthesis of our understanding of the morphological and phylogenetic patterns within the L. lineomaculatus section and presents a useful framework for future tests of taxonomic hypotheses and physiological, behavioural, and evolutionary questions within this section.  © 2013 The Linnean Society of London

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Two new species of the lineomaculatus clade of the Liolaemus lineomaculatus section are described from southern Patagonia in Argentina. Liolaemus morandae sp. nov. is found in S Chubut province and Liolaemus avilae sp. nov. inhabits NW Santa Cruz province. Several tests were performed to diagnose these new species as distinct lineages. Univariate analysis of variance (ANOVA), principal component analysis (PCA), discriminant function analysis (DFA), non-parametric multivariate analysis of variance (NPMANOVA), as well as a genetic characterization through molecular analysis of variance (AMOVA) were performed; genetic distances between described and these new species are reported. The new Liolaemus species differ from other members of the lineomaculatus group in morphometric, meristic, qualitative and genetic characters; moreover they inhabit different phytogeographical provinces and districts. With these descriptions, the number of species now recognized in the lineomaculatus section is twenty one (including one more description that is in press).

Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that 'species' within the biome are often composed of cryptic species. In order to identify biodiversity hotspots more robustly and across multiple dimensions we integrate functional, spatial and new phylogeographic data for the Cerrado lizard fauna by (a) mapping the spatial patterns of species and phylogenetic diversity; and (b) using endemism measures to identify areas of unique diversity. We then quantify the extent to which existing protected areas represent the diversity.Location: Brazilian savanna (Cerrado). Methods:We generated species distribution models using distribution records for all Cerrado lizard species. These, combined with mitochondrial DNA phylogenies and natural history data, allowed us to map species richness, phylogenetic and functional diversity and phylogenetic and weighted endemism. Phylogenetic endemism maps were then cross-referenced against protected areas to calculate the amount of evolutionary history preserved within these areas. Results:The central region of the Cerrado, a vast and climatically stable plateau, stands out as important under all biodiversity metrics. Including evolutionary relationships in biodiversity assessment, we detected four regional hotspots with high concentration of spatially restricted evolutionary diversity. Protected areas cover only 10% of the Cerrado area and hold 11.64% of the summed phylogenetic endemism of all lizards in the biome. Main Conclusions: We highlighted both stable (Chapada dos Veadeiros and Serra do Espinhaço plateaus) and environmentally heterogenous regions (Araguaia and Tocantins valleys) as hotspots of evolutionary diversity. The creation and/or manipulation of | 1131 FENKER Et al.

A new species of the Liolaemus lineomaculatus section is described from southwestern Santa Cruz Province, Argentina. The new species is a member of the monotypic magellanicus clade; morphological, molecular and geographical data are sufficient to diagnose this new species as distinct form from L. magellanicus. The new species differs from L. magellanicus in having higher number of midbody, dorsal and ventral scales, and higher number of infradigital third finger and fourth toe lamellae. The new species also differs in having smaller dorsal blotches on the hindlimbs and a more clearly defined vertebral line, fewer precloacal pores and reduced dorsal scale mucronation, compared to L. magellanicus. Liolaemus caparensis sp. nov. is the second species described for the magellanicus group, and is geographically isolated from L. magellanicus on the Campo Las Piedras Plateau, where it is sympatric with other endemic species of the L. lineomaculatus section.