Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae).

Abstract:

:Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot.

journal_name

Mol Phylogenet Evol

authors

Gutiérrez-Rodríguez J,Barbosa AM,Martínez-Solano Í

doi

10.1016/j.ympev.2017.04.022

subject

Has Abstract

pub_date

2017-07-01 00:00:00

pages

122-137

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(17)30291-9

journal_volume

112

pub_type

杂志文章
  • Structure and evolution of the mitochondrial genomes of Haematobia irritans and Stomoxys calcitrans: the Muscidae (Diptera: Calyptratae) perspective.

    abstract::We present the first two mitochondrial genomes of Muscidae dipterans for the species Haematobia irritans (the horn fly) and Stomoxys calcitrans (the stable fly). Typical insect mtDNA features are described, such as a high A+T content (79.1% and 78.9%, respectively), the preference for A+T-rich codons, and the evidence...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.05.022

    authors: Oliveira MT,Barau JG,Junqueira AC,Feijão PC,Rosa AC,Abreu CF,Azeredo-Espin AM,Lessinger AC

    更新日期:2008-09-01 00:00:00

  • A phylogenetic hypothesis for the recently diversified Ruschieae (Aizoaceae) in southern Africa.

    abstract::The Ruschieae is a large tribe of about 1600 species of succulent perennials. They form a major component of the arid parts of the Greater Cape Floristic Region, both in numbers of species and in their density of coverage. So far phylogenetic relationships within the tribe have been unresolved, largely through the pau...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.05.030

    authors: Klak C,Bruyns PV,Hanáček P

    更新日期:2013-12-01 00:00:00

  • Phylogeography of the ancient catfish family Diplomystidae: biogeographic, systematic, and conservation implications.

    abstract::The catfish family Diplomystidae is one of the earliest branching lineages within the diverse order Siluriformes and shows a deep phylogenetic split from all other extant and extinct major catfish groups. Despite its relevance in the evolution of siluriforms, phylogenetic relationships within the Diplomystidae are poo...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.01.015

    authors: Muñoz-Ramírez CP,Unmack PJ,Habit E,Johnson JB,Cussac VE,Victoriano P

    更新日期:2014-04-01 00:00:00

  • Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes.

    abstract::The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analy...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.04.013

    authors: Ingley SJ,Reina RG,Bermingham E,Johnson JB

    更新日期:2015-08-01 00:00:00

  • A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics.

    abstract::Austropurcellia, a genus of dispersal-limited arachnids endemic to isolated patches of coastal rainforest in Queensland, Australia, has a remarkable biogeographic history. The genus is a member of the family Pettalidae, which has a classical temperate Gondwanan distribution; previous work has suggested that Austropurc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.06.029

    authors: Oberski JT,Sharma PP,Jay KR,Coblens MJ,Lemon KA,Johnson JE,Boyer SL

    更新日期:2018-10-01 00:00:00

  • A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences.

    abstract::Higher-level relationships among catfishes were investigated by parsimony, maximum likelihood and Bayesian analyses of two nuclear genes across 110 catfish species representing 36 of 37 families and Conorhynchos (family incertae sedis). Analysis of 3660 aligned base pairs from the rag1 and rag2 genes confirms monophyl...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.05.044

    authors: Sullivan JP,Lundberg JG,Hardman M

    更新日期:2006-12-01 00:00:00

  • Relationships among the Neotropical Candirus (Trichomycteridae, Siluriformes) and the evolution of parasitism based on analysis of mitochondrial and nuclear gene sequences.

    abstract::Phylogenetic relationships among the trichomycterid catfishes are investigated for the first time using molecular sequence data. Data derived from mitochondrial and nuclear DNA sequences for representatives of 17 genera were analyzed to test previous hypotheses of relationships among trichomycterid subfamilies, the mo...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.02.016

    authors: Fernández L,Schaefer SA

    更新日期:2009-08-01 00:00:00

  • Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography.

    abstract::The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of w...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.03.015

    authors: Versieux LM,Barbará T,Wanderley Md,Calvente A,Fay MF,Lexer C

    更新日期:2012-07-01 00:00:00

  • Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails.

    abstract::Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.04.008

    authors: Wikström N,Pryer KM

    更新日期:2005-09-01 00:00:00

  • The effects of sampling on delimiting species from multi-locus sequence data.

    abstract::As a fundamental unit in biology, species are used in a wide variety of studies, and their delimitation impacts every subfield of the life sciences. Thus, it is of utmost importance that species are delimited in an accurate and biologically meaningful way. However, due to morphologically similar, cryptic species, and ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.06.031

    authors: Rittmeyer EN,Austin CC

    更新日期:2012-11-01 00:00:00

  • Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): inferences from a genomic transect and the multispecies coalescent.

    abstract::Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylog...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.08.008

    authors: Lavretsky P,McCracken KG,Peters JL

    更新日期:2014-01-01 00:00:00

  • Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae).

    abstract::Chenopodium is a large and morphologically variable genus of annual and perennial herbs with an almost global distribution. All subgenera and most sections of Chenopodium were sampled along with other genera of Chenopodieae, Atripliceae and Axyrideae across the subfamily Chenopodioideae (Chenopodiaceae), totalling to ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.10.006

    authors: Fuentes-Bazan S,Mansion G,Borsch T

    更新日期:2012-01-01 00:00:00

  • Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

    abstract::Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconst...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.09.004

    authors: Murphy NP,Framenau VW,Donnellan SC,Harvey MS,Park YC,Austin AD

    更新日期:2006-03-01 00:00:00

  • Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade.

    abstract::The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined anal...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106960

    authors: Natusch DJD,Esquerré D,Lyons JA,Hamidy A,Lemmon AR,Lemmon EM,Riyanto A,Keogh JS,Donnellan S

    更新日期:2020-09-18 00:00:00

  • Molecular evidence for the monophyly of tenrecidae (mammalia) and the timing of the colonization of Madagascar by Malagasy Tenrecs.

    abstract::Tenrecs are a diverse family of insectivores, with an Afro-Malagasian biogeographic distribution. Three subfamilies (Geogalinae, Oryzorictinae, Tenrecinae) are restricted to Madagascar and one subfamily, the otter shrews (Potamogalinae), occurs on the mainland. Morphological studies have generated conflicting hypothes...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.1055

    authors: Douady CJ,Catzeflis F,Kao DJ,Springer MS,Stanhope MJ

    更新日期:2002-03-01 00:00:00

  • Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes.

    abstract::Phylogenetic analysis of over 4600 aligned nucleotide sequences from two nuclear genes, growth hormone receptor and BRCA1, provided congruent phylogenies depicting relationships among the major lineages of rodents. Separate and combined analyses resulted in five major conclusions: (1) strong support for a monophyletic...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00304-4

    authors: Adkins RM,Walton AH,Honeycutt RL

    更新日期:2003-03-01 00:00:00

  • Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty.

    abstract::We sequenced 1709 base pairs (bp) of mitochondrial DNA including parts of cytochrome b, ND 2, and the control region (CR I, II) for seven members of the avian genus Pipilo (towhees), Melozone kieneri (rusty-crowned ground-sparrow), and Arremonops rufivirgatus (olive sparrow). A total of 457 bp was variable and 257 bp ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1998.0526

    authors: Zink RM,Weller SJ,Blackwell RC

    更新日期:1998-10-01 00:00:00

  • Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species.

    abstract::Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106688

    authors: Anderson K,Braoudakis G,Kvist S

    更新日期:2020-02-01 00:00:00

  • Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly.

    abstract::The phylogenetic position of cyclostomes, i.e., the relationships between hagfishes, lampreys, and jawed vertebrates is an unresolved problem. Anatomical data support the paraphyly of cyclostomes, whereas nuclear genes data support monophyly of cyclostomes. Previous results obtained using mitochondrial DNA are ambiguo...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2001.1045

    authors: Delarbre C,Gallut C,Barriel V,Janvier P,Gachelin G

    更新日期:2002-02-01 00:00:00

  • Diversification and repeated morphological transitions in endoparasitic cnidarians (Myxozoa: Malacosporea).

    abstract::Malacosporeans are a poorly known myxozoan clade that uniquely demonstrates a tissue level of organisation. Thus, when exploiting their invertebrate hosts (freshwater bryozoans) they occur as non-motile sacs or vermiform stages capable of active swimming. We combine phylogenetic analyses of SSU and LSU rDNA with morph...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.03.010

    authors: Hartikainen H,Gruhl A,Okamura B

    更新日期:2014-07-01 00:00:00

  • Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history.

    abstract::The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2019.106712

    authors: García-Machado E,Ponce de Léon JL,Gutiérrez-Costa MA,Michel-Salzat A,Germon I,Casane D

    更新日期:2020-03-01 00:00:00

  • Molecular phylogeny and biogeography of the spider ants, genus Leptomyrmex Mayr (Hymenoptera: Formicidae).

    abstract::This study provides the first phylogenetic reconstruction of the ant genus Leptomyrmex Mayr, a prominent endemic component of rain forest and wet sclerophyll forest in Australia, New Guinea and New Caledonia. Five genes are used to reconstruct phylogeny and estimate of ages of diversification in order to test congruen...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.03.004

    authors: Lucky A

    更新日期:2011-05-01 00:00:00

  • Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences.

    abstract::Nucleotide sequences of the small subunit ribosomal RNA (18S) gene were used to investigate evolutionary relationships within the Fungi. The inferred tree topologies are in general agreement with traditional classifications in the following ways: (1) the Chytridiomycota and Zygomycota appear to be basal groups within ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/1055-7903(92)90020-h

    authors: Bruns TD,Vilgalys R,Barns SM,Gonzalez D,Hibbett DS,Lane DJ,Simon L,Stickel S,Szaro TM,Weisburg WG

    更新日期:1992-09-01 00:00:00

  • The mitogenome phylogeny of Adephaga (Coleoptera).

    abstract::The beetle suborder Adephaga consists of several aquatic ('Hydradephaga') and terrestrial ('Geadephaga') families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenom...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.06.009

    authors: López-López A,Vogler AP

    更新日期:2017-09-01 00:00:00

  • Phylogenetic relationships of the endosymbionts of mealybugs (Homoptera: Pseudococcidae) based on 16S rDNA sequences.

    abstract::A portion of the gene coding for the 16S ribosomal RNA from the endosymbionts of three species of mealybugs [Pseudococcus longispinus (Targioni-Tozzetti), Pseudococcus maritimus (Ehrhorn), and Dysmicoccus neobrevipes (Beardsley)] was cloned, sequenced, and compared to a homologous fragment from bacteria representative...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/1055-7903(92)90032-c

    authors: Munson MA,Baumann P,Moran NA

    更新日期:1992-03-01 00:00:00

  • Phylogenetic relationship of silkmoths inferred from sequence data of the arylphorin gene.

    abstract::A portion of the arylphorin gene from 11 silkmoth species belonging to the families Saturniidae and Bombycidae was amplified by a polymerase chain reaction. Approximately 460 bp corresponding to the third exon, the third intron, and the fourth exon were successfully amplified, sequenced, and compared. Sequences corres...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1995.1021

    authors: Shimada T,Kurimoto Y,Kobayashi M

    更新日期:1995-09-01 00:00:00

  • A multi-locus timetree of surgeonfishes (Acanthuridae, Percomorpha), with revised family taxonomy.

    abstract::We present the most comprehensive time-calibrated, species-level hypothesis of the timing of Acanthuridae (surgeonfishes and allies) evolution based on 76% of the extant diversity and nine genes. We recover two major acanthurid clades, Nasinae and Acanthurinae, and infer a much more recent Nasinae crown age (17 Ma) co...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.03.014

    authors: Sorenson L,Santini F,Carnevale G,Alfaro ME

    更新日期:2013-07-01 00:00:00

  • Range-wide phylogeography of Juniperus thurifera L., a presumptive keystone species of western Mediterranean vegetation during cold stages of the Pleistocene.

    abstract::We investigate the range-wide population structure and phylogeography of thuriferous juniper (Juniperus thurifera L.), a species with a highly disjunct distribution in the western Mediterranean. We genotyped a total of 327 individuals from 20 populations using amplified fragment length polymorphisms (AFLP). Different ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.03.018

    authors: Terrab A,Schönswetter P,Talavera S,Vela E,Stuessy TF

    更新日期:2008-07-01 00:00:00

  • Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome.

    abstract::Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear par...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.07.019

    authors: Zhang X,Unmack PJ,Kuchling G,Wang Y,Georges A

    更新日期:2017-10-01 00:00:00

  • Parthenogenesis through the ice ages: A biogeographic analysis of Caucasian rock lizards (genus Darevskia).

    abstract::Darevskia rock lizards include both sexual and parthenogenetic species, mostly distributed in the heterogeneous and ecologically diverse Caucasus. The parthenogenetic species originated via directional hybridogenesis, with only some of the sexual species known to serve as parentals. However, it remains unclear when an...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 历史文章,杂志文章

    doi:10.1016/j.ympev.2016.05.035

    authors: Freitas S,Rocha S,Campos J,Ahmadzadeh F,Corti C,Sillero N,Ilgaz Ç,Kumlutaş Y,Arakelyan M,Harris DJ,Carretero MA

    更新日期:2016-09-01 00:00:00