Implementing large genomic single nucleotide polymorphism data sets in phylogenetic network reconstructions: A case study of particularly rapid radiations of cichlid fish

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation (⁠37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.Fil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Meyer, Axel. University Of Konstanz; Alemani

Patrones parafileticos y procesos evolutivos subyacentes en los grupos de Lagartijas Patagónicas Boulengeri & Rothi (Squamata: Liolaemus).

Tesis (Grado Doctor en Ciencias Biológicas)--Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Lugar de Trabajo: Centro Nacional Patagónico, Chubut, Argentina. CENPAT-CONICET-Universidad Nacional de Córdoba. 2014 - 133 h. con Apéndices + CD. maps.; tabls.; figuras. Contiene Referencia Bibliográfica y Publicaciones Derivadas de la Tesis. Abstract en español e inglés.Existen diferentes procesos que pueden explicar la discordancia entre árboles de genes y de especies. Por un lado, la división de linaje incompleta (ILS) lleva a la retención de polimorfismos ancestrales y explica la mezcla de haplotipos entre especies o poblaciones distintas, pero la hibridación también produce patrones similares, siendo que resulta en haplotipos de un grupo que son compartidos con un grupo distinto y que difieren de los haplotipos de otras poblaciones conespecíficas. Si se utilizan marcadores moleculares que estuvieron involucrados en estos eventos (ILS o hibridación) para análisis filogenéticos o filogeográficos, darán una visión diferente de la historia poblacional de la que darían marcadores que no muestran evidencia de introgresión. Se han propuesto algunos métodos analíticos que permiten diferenciar entre ILS e hibridación, varios de ellos en el marco de la filogeografía estadística, pero distinguir entre ambos aún continua constituyendo un gran desafío en biología evolutiva. Liolaemus es un género de lagartijas muy diversificado en América del Sur Austral, del cual se describieron ~257 especies, aunque se ha sugerido en múltiples publicaciones que la diversidad real de Liolaemus se encuentra subestimada. Esto se debe a que durante mucho tiempo se consideraron especies únicas, en algunos casos con gran distribución geográfica y amplia variación cromática y morfológica, las que en realidad constituyen complejos de especies. Este es el caso de las especies descriptas como Liolaemus boulengeri y Liolaemus rothi, para los cuales se han descripto actualmente cinco especies del complejo boulengeri y seis del complejo rothi. Por otro lado, no existe consenso entre publicaciones que permitan reconocer las relaciones filogenéticas dentro del subgénero Eulaemus, tanto dentro como entre grandes grupos y en el último caso, se han observado patrones parafiléticos que involucran especies de estos dos complejos. Esto puede deberse a representaciones taxonómicas incompletas o la necesidad de incorporar mayor cantidad de datos. En base a otros estudios previos de complejos de Liolaemus, es claro que los límites de especies en este género aún no están bien definidos, y la división incompleta de linajes y la introgresión han sido propuestas como explicaciones plausibles para algunos de los diseños observados. En esta tesis se propone estudiar las relaciones filogenéticas dentro de uno de los subgéneros (Eulaemus, 144 especies), así como también estudiar las posibles causas de la parafilia observada entre los complejos boulengeri y rothi

Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)

Lack of resolution in a phylogenetic tree is usually represented as a polytomy, and often adding more data (loci and taxa) resolves the species tree. These are the ‘soft’ polytomies, but in other cases additional data fail to resolve relationships; these are the ‘hard’ polytomies. This latter case is often interpreted as a simultaneous radiation of lineages in the history of a clade. Although hard polytomies are difficult to address, model-based approaches provide new tools to test these hypotheses. Here, we used a clade of 144 species of the South American lizard clade Eulaemus to estimate phylogenies using a traditional concatenated matrix and three species tree methods: *BEAST, BEST, and minimizing deep coalescences (MDC). The different species tree methods recovered largely discordant results, but all resolved the same polytomy (e.g. very short internodes amongst lineages and low nodal support in Bayesian methods). We simulated data sets under eight explicit evolutionary models (including hard polytomies), tested these against empirical data (a total of 14 loci), and found support for two polytomies as the most plausible hypothesis for diversification of this clade. We discuss the performance of these methods and their limitations under the challenging scenario of hard polytomies.Fil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Sites, Jack W.. University Brigham Young; Estados UnidosFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

How important is it to consider lineage diversification heterogeneity in macroevolutionary studies? Lessons from the lizard family Liolaemidae

Macroevolutionary and biogeographical studies commonly apply multiple models to test state-dependent diversification. These models track the association between states of interest along a phylogeny, although many of them do not consider whether different clades might be evolving under different evolutionary drivers. Yet, they are still commonly applied to empirical studies without careful consideration of possible lineage diversification heterogeneity along the phylogenetic tree. A recent biogeographic study has suggested that orogenic uplift of the southern Andes has acted as a species pump, driving diversification of the lizard family Liolaemidae (307 described species), native to temperate southern South America. Here, we argue against the Andean uplift as main driver of evolution in this group. We show that there is a clear pattern of heterogeneous diversification in the Liolaemidae, which biases state- and environment-dependent analyses in, respectively, the GeoSSE and RPANDA programs. We show here that there are two shifts to accelerated speciation rates involving two clades that have both been classified as having Andean distributions. We incorporated the Geographic Hidden-State Speciation and Extinction model (GeoHiSSE) to accommodate unrelated diversification shifts, and also re-analyzed the data in RPANDA program after splitting biologically distinct clades for separate analyses, as well as including a more appropriate set of models. We demonstrate that the ?Andean uplift? hypothesis is not supported when the heterogeneous diversification histories among these lizards is considered. We use the Liolaemidae as an ideal system to demonstrate potential risks of ignoring clade-specific differences in diversification patterns in macroevolutionary studies. We also implemented simulations to show that, in agreement with previous findings, the HiSSE approach can effectively and substantially reduce the level of distribution- dependent models receiving the highest AIC weights in such scenarios. However, we still find a relatively high rate (15%) of distribution-dependent models receiving the highest AIC weights, and provide recommendations related to the set of models included in the analyses that reduce these rates by half. Finally, we demonstrate that trees including clades following different dependent-drivers affect RPANDA analyses by producing different outcomes, ranging from partially correct models to completely misleading results. We provide recommendations for the implementation of both programs.Fil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Sites, Jack W.. University Brigham Young; Estados UnidosFil: Morando, Mariana. Universidad Nacional de la Patagonia "San Juan Bosco"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentin

Molecular phylogenetic relationships of the Liolaemus rothi complex and a new species of lizard from Auca Mahuida Volcano (Squamata: Liolaemini)

A new species of lizard of the genus Liolaemus from Neuquén Province, western Argentina, is described. The new species is a member of the Liolaemus rothi species complex, and mitochondrial and nuclear molecular data show it as sister taxon of the clade composed of (L. hermannunezi (L. tromen + L. loboi)), differing in size, squamation, coloration, and sexual dimorphism from the other species of this group. Liolaemus sitesi sp. nov. has a dark body coloration with series of notched blotches on the dorsum, with bright spots, and a very iridescent yellow-green coloration in natural light. Liolaemus sitesi sp. nov. is found only in the Auca Mahuida volcano and is terrestrial, dwelling on the stony slopes with sandy soil between 1300 m and the volcano summit.Fil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Perez, Cristian Hernan Fulvio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Pérez, Daniel Roberto. Universidad Nacional del Comahue; ArgentinaFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

Molecular phylogeny of the “salty” <i>Liolaemus</i> species (Reptilia: Squamata): <i>anomalus</i> group, endemic of the Argentina Monte Desert

In Argentina, the Monte ecoregion extends for more than 2,000 km from NW Argentina to boreal Patagonia, and includes many salt-pans and barren flatlands colonized by the monophyletic Liolaemus anomalus group that includes seven species. Some of their external morphological characteristics and behaviors are very unusual for the genus, and this has led to a complex taxonomic history. The group is very poorly known except for a recent paper with descriptions of three species and morphological-based phylogenetic hypotheses. Of the four recognized species, two are threatened and one is vulnerable, and while the conservation status of the three recently described species is unknown, they are suspected to also be under some degree of threat. We reviewed all georeferenced localities known to produce a distribution map, and sequenced two mitochondrial and four nuclear genes, for representatives of all species. We inferred a time-calibrated species tree showing that the evolutionary history of this clade occurred entirely during the Pleistocene, with most of the divergences very recent. The climatic and geomorphological changes driving this divergence started during the Great Patagonian Glaciation, initially separating the two northwestern-most distributed species (L. pipanaco + L. pseudoanomalus) from the rest. Given the very recent evolutionary history of the group and their unique and conserved morphology, incongruent topologies among datasets are expected; a detailed genome-wide dataset will be needed to fully assess and resolve their speciation history.En Argentina, la ecorregión de Monte se extiende por más de 2.000 km desde el noroeste de Argentina hasta la Patagonia boreal, e incluye muchas salinas y llanuras áridas colonizadas por el grupo monofilético Liolaemus anomalus que incluye siete especies. Algunas de sus características y comportamientos morfológicos externos son muy inusuales para el género y esto dio lugar a una compleja historia taxonómica. Recientemente se describieron tres nuevas especies y se propusieron hipótesis filogenéticas basadas en morfología. Desde el punto de vista de su conservación, solo cuatro están categorizadas, dos amenazadas y una vulnerable, y aunque se desconoce el estado de conservación de las tres últimas especies descritas, se sospecha que se encuentran bajo algún grado de amenaza. Revisamos todas las localidades georreferenciadas conocidas para producir un mapa de distribución, y secuenciamos dos genes mitocondriales y cuatro nucleares, para representantes de todas las especies. Inferimos un árbol de especies calibrado en el tiempo que muestra que la historia evolutiva de este clado ocurrió en su totalidad durante el Pleistoceno, siendo la mayoría de las divergencias muy recientes. Los cambios climáticos y geomorfológicos que impulsaron esta divergencia ocurrieron durante la Gran Glaciación Patagónica, inicialmente separando las dos especies distribuidas más al noroeste (L. pipanaco + L. pseudoanomalus) del resto. Dada la historia evolutiva muy reciente del grupo y su morfología única y conservada, se esperan topologías incongruentes entre los conjuntos de datos. Se necesitará un conjunto de datos detallado de todo el genoma para evaluar y resolver completamente su historia de especiación.Asociación Herpetológica Argentin

Contrasting signatures of genomic divergence during sympatric speciation

Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures. The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin(1,2). Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process(3). Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs(4), but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories(5). Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.Peer reviewe

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.Fil: Chunyan, Li. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. Chinese Academy of Sciences; República de ChinaFil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Hou, Yali. Chinese Academy of Sciences; República de ChinaFil: Geng, Qi. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; ChinaFil: Schneider, Ralf. University Of Konstanz; Alemania. Helmholtz Centre for Ocean Research Kie; AlemaniaFil: Zeixa, Gao. Huazhong Agricultural University; ChinaFil: Xiaolong, Tu. Allwegene Technologies ; ChinaFil: Xin, Wang. Chinese Academy of Sciences; República de ChinaFil: Furong, Qi. China National Center for Bioinformation; China. University of Chinese Academy of Sciences; ChinaFil: Nater, Alexander. University of Konstanz; AlemaniaFil: Kautt, Andreas F.. University of Konstanz; Alemania. Harvard University; Estados UnidosFil: Wan, Shiming. Chinese Academy of Sciences; República de ChinaFil: Yanhong, Zhang. Chinese Academy of Sciences; República de ChinaFil: Yali, Liu. Chinese Academy of Sciences; República de ChinaFil: Huixian, Zhang. Chinese Academy of Sciences; República de ChinaFil: Bo, Zhang. Chinese Academy of Sciences; República de ChinaFil: Hao, Zhang. Chinese Academy of Sciences; República de ChinaFil: Meng, Qu ,. Chinese Academy of Sciences; República de ChinaFil: Shuaishuai, Liu. Chinese Academy of Sciences; República de ChinaFil: Zeyu, Chen. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Zhong, Jia. Chinese Academy of Sciences; República de ChinaFil: Zhang, He. BGI-Shenzhen; ChinaFil: Meng, Lingfeng. BGI-Shenzhen; ChinaFil: Wang, Kai. Ludong University; ChinaFil: Yin, Jianping. Chinese Academy of Sciences; República de ChinaFil: Huang, Liangmin. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Venkatesh, Byrappa. Institute of Molecular and Cell Biology; SingapurFil: Meyer, Axel. University of Konstanz; AlemaniaFil: Lu, Xuemei. Chinese Academy of Sciences; República de ChinaFil: Lin, Qiang. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. University of Chinese Academy of Sciences; Chin

Data from: Upstream analyses create problems with DNA-based species delimitation

Genetic-based delimitation of species typically involves a multistep process in which DNA data are analyzed with a series of different programs. Although the performance of the programs associated with each step has been evaluated separately, no analysis has considered how errors in the upstream assignment of individuals to putative species impacts the accuracy of species delimited in downstream analyses, such as those associated with the coalescent-based Bayesian program bpp. Here we show that because the minimal data requirements for accurate performance in each of the separate steps involved in the delimitation process differ, the reliability of inferences about species delimited from DNA sequences can be compromised. Our results provide important insights into the practice of species delimitation. Specifically, even if users exercise the practices advocated for DNA-based delimitation, there may very well be errors in individual-species association, and consequently uncertainty in the guide tree (both derived from upstream analyses that are prerequisites for analyses with bpp), which can lead to under or overestimation of biodiversity, even though the Bayesian program bpp itself may perform very well. These results highlight the usefulness of complementary data (i.e., data in addition to genetic data), especially for the assignment of individuals to putative species, to improve the accuracy of species delimitation