Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): a geographic and phylogenetic perspective.

Abstract:

:The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.

journal_name

Mol Phylogenet Evol

authors

Eaton MJ,Martin A,Thorbjarnarson J,Amato G

doi

10.1016/j.ympev.2008.11.009

subject

Has Abstract

pub_date

2009-03-01 00:00:00

pages

496-506

issue

3

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(08)00542-3

journal_volume

50

pub_type

杂志文章
  • Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae).

    abstract::The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai'i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.11.001

    authors: Geiger JM,Ranker TA

    更新日期:2005-02-01 00:00:00

  • A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships.

    abstract::Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 speci...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(03)00118-0

    authors: Amrine-Madsen H,Koepfli KP,Wayne RK,Springer MS

    更新日期:2003-08-01 00:00:00

  • Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China.

    abstract::The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.11.005

    authors: Koju NP,He K,Chalise MK,Ray C,Chen Z,Zhang B,Wan T,Chen S,Jiang X

    更新日期:2017-02-01 00:00:00

  • Cryptic diversity in a widespread North American songbird: phylogeography of the Brown Creeper (Certhia americana).

    abstract::The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to as...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.12.003

    authors: Manthey JD,Klicka J,Spellman GM

    更新日期:2011-03-01 00:00:00

  • Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea.

    abstract::Nucleotide sequences of the nuclear c-mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe's [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(03)00191-x

    authors: Voelker G,Spellman GM

    更新日期:2004-02-01 00:00:00

  • Combination of molecular data support the existence of three main lineages in the phylogeny of aphids (Hemiptera: Aphididae) and the basal position of the subfamily Lachninae.

    abstract::The first molecular studies on the phylogeny of aphids (Hemiptera: Aphididae) bumped into a striking lack of phylogenetic structure for taxa levels higher than tribe, probably as a consequence of the rapid adaptive radiation that this group of insects went through during the Late Cretaceous. Here we present a new atte...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.12.005

    authors: Ortiz-Rivas B,Martínez-Torres D

    更新日期:2010-04-01 00:00:00

  • The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach.

    abstract::Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multip...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.06.022

    authors: Gratton P,Allegrucci G,Sbordoni V,Gandolfi A

    更新日期:2014-10-01 00:00:00

  • Gene duplication and concerted evolution of mitochondrial DNA in crane species.

    abstract::The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication i...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.09.026

    authors: Akiyama T,Nishida C,Momose K,Onuma M,Takami K,Masuda R

    更新日期:2017-01-01 00:00:00

  • Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida).

    abstract::The taxonomy and biogeographic history of the bivalve family Margaritiferidae are controversial because previous molecular studies did not provide a well-resolved phylogenetic framework for these enigmatic freshwater mussels that have extensive but disjunct distribution in North America, Eurasia and North Africa. In t...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.07.020

    authors: Bolotov IN,Vikhrev IV,Bespalaya YV,Gofarov MY,Kondakov AV,Konopleva ES,Bolotov NN,Lyubas AA

    更新日期:2016-10-01 00:00:00

  • Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae).

    abstract::Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.05.003

    authors: Ortiz D,Francke OF

    更新日期:2016-08-01 00:00:00

  • How many genera and species of woolly monkeys (Atelidae, Platyrrhine, Primates) are there? The first molecular analysis of Lagothrix flavicauda, an endemic Peruvian primate species.

    abstract::We sequenced COI and COII mitochondrial genes of 141 Neotropical woolly monkeys to provide new insights concerning their phylogeography and phylogenetic relationships. For the first time, eight individuals of the endemic and extremely rare Peruvian yellow-tailed woolly monkey (flavicauda) were sequenced at these genes...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.05.034

    authors: Ruiz-García M,Pinedo-Castro M,Shostell JM

    更新日期:2014-10-01 00:00:00

  • Return flight to the Canary Islands--the key role of peripheral populations of Afrocanarian blue tits (Aves: Cyanistes teneriffae) in multi-gene reconstructions of colonization pathways.

    abstract::Afrocanarian blue tits (Cyanistes teneriffae) have a scattered distribution on the Canary Islands and on the North African continent. To date, the Canary Islands have been considered the species' main Pleistocene evolutionary center, but their colonization pathways remain uncertain. We set out to reconstruct a dated m...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.02.010

    authors: Päckert M,Martens J,Hering J,Kvist L,Illera JC

    更新日期:2013-05-01 00:00:00

  • Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida).

    abstract::Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.02.018

    authors: Redmond NE,McCormack GP

    更新日期:2008-06-01 00:00:00

  • Insulin-like growth factor II intron sequences support the hominoid rate-slowdown hypothesis.

    abstract::Nucleotide sequences were obtained from the approximately 1.7 kb intron 7 of the insulin-like growth factor II gene in human and representatives of both Old World and New World monkeys and analyzed with additional published noncoding regions (both introns and flanking regions) that differ substantially in base composi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1993.1030

    authors: Ellsworth DL,Hewett-Emmett D,Li WH

    更新日期:1993-12-01 00:00:00

  • Differential expansion of the merozoite surface protein (msp)-7 gene family in Plasmodium species under a birth-and-death model of evolution.

    abstract::MSP-7 is a surface protein expressed by the Plasmodium merozoite as part of a protein-complex involved in initial interaction between merozoite and erythrocyte. Contigs of seven Plasmodium species were analyzed in order to identify all msp-7 family genes. The search identified annotated and unannotated open reading fr...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.02.017

    authors: Garzón-Ospina D,Cadavid LF,Patarroyo MA

    更新日期:2010-05-01 00:00:00

  • Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences.

    abstract::Family Catostomidae is a diverse group of benthic freshwater fishes that are distributed across North America and in parts of East Asia. In this study, the phylogenetic relationships of Catostomidae is examined using 3436 nucleotides of mitochondrial ND4 and ND5 protein coding genes and intervening tRNAs. All 13 gener...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.06.006

    authors: Doosey MH,Bart HL Jr,Saitoh K,Miya M

    更新日期:2010-03-01 00:00:00

  • The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes.

    abstract::The Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.09.022

    authors: Christe C,Caetano S,Aeschimann D,Kropf M,Diadema K,Naciri Y

    更新日期:2014-01-01 00:00:00

  • New insights into the phylogeny of Pleopeltis and related Neotropical genera (Polypodiaceae, Polypodiopsida).

    abstract::The fern family Polypodiaceae plays an important role in Neotropical epiphyte diversity. Most of its American representatives are assembled in a monophyletic clade that, apart from the grammitids, nearly exclusively comprises species restricted to the New World. The phylogenetic relationships of these ferns are still ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.05.001

    authors: Otto EM,Janssen T,Kreier HP,Schneider H

    更新日期:2009-10-01 00:00:00

  • The scale of divergence: a phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus.

    abstract::Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a mtDNA-based phylogenetic hypothesis for 92 Daphnia species from all seven continents, with a focus on North and South Americ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.11.026

    authors: Adamowicz SJ,Petrusek A,Colbourne JK,Hebert PD,Witt JD

    更新日期:2009-03-01 00:00:00

  • What's missing from avian global diversification analyses?

    abstract::The accumulation of vast numbers of molecular phylogenetic studies has contributed to huge knowledge gains in the evolutionary history of birds. This permits subsequent analyses of avian diversity, such as how and why diversification varies across the globe and among taxonomic groups. However, available genetic data f...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章,评审

    doi:10.1016/j.ympev.2014.04.023

    authors: Reddy S

    更新日期:2014-08-01 00:00:00

  • Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

    abstract::A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2014.07.012

    authors: Panero JL,Freire SE,Ariza Espinar L,Crozier BS,Barboza GE,Cantero JJ

    更新日期:2014-11-01 00:00:00

  • The evolutionary history of seahorses (Syngnathidae: Hippocampus): molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean.

    abstract::Sequence data derived from four markers (the nuclear RP1 and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 32 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(03)00214-8

    authors: Teske PR,Cherry MI,Matthee CA

    更新日期:2004-02-01 00:00:00

  • Phylogeography of the Caribbean rock iguana (Cyclura): implications for conservation and insights on the biogeographic history of the West Indies.

    abstract::The Caribbean rock iguana, Cyclura, has had an unstable intrageneric taxonomy and an unclear phylogenetic position within the family Iguanidae. We use mtDNA sequence data to address these issues and explore the phylogeographic history of the genus. ND4 to leucine tRNA sequence data were collected from multiple individ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.2000.0836

    authors: Malone CL,Wheeler T,Taylor JF,Davis SK

    更新日期:2000-11-01 00:00:00

  • A phylogeny of Adelanthaceae (Jungermanniales, Marchantiophyta) based on nuclear and chloroplast DNA markers, with comments on classification, cryptic speciation and biogeography.

    abstract::Adelanthaceae (including Jamesoniellaceae) represent a major lineage of jungermannialean liverworts that is characterized by ventral-intercalary, often flagelliform branches, succubous leaves, ovoid to cylindrical, plicate perianths with a contracted mouth, often connate bracts and bracteoles, and 4-7 stratose capsule...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.11.009

    authors: Feldberg K,Váňa J,Long DG,Shaw AJ,Hentschel J,Heinrichs J

    更新日期:2010-04-01 00:00:00

  • Low-copy nuclear DNA sequences reveal a predominance of allopolyploids in a New Zealand Asplenium fern complex.

    abstract::Recent generalisations about polyploidy in plants have been largely based on studies of angiosperms. A compelling group to compare with angiosperms is ferns, because of their high polyploidy. The bi-parental inheritance of nuclear DNA sequence markers makes them advantageous for investigating polyploid complexes, but ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.06.015

    authors: Shepherd LD,Perrie LR,Brownsey PJ

    更新日期:2008-10-01 00:00:00

  • Cenozoic tectonic and climatic events in southern Iberian Peninsula: Implications for the evolutionary history of freshwater fish of the genus Squalius (Actinopterygii, Cyprinidae).

    abstract::Southern Iberian freshwater ecosystems located at the border between the European and African plates represent a tectonically complex region spanning several geological ages, from the uplifting of the Betic Mountains in the Serravalian-Tortonian periods to the present. This area has also been subjected to the influenc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 历史文章,杂志文章

    doi:10.1016/j.ympev.2016.01.007

    authors: Perea S,Cobo-Simon M,Doadrio I

    更新日期:2016-04-01 00:00:00

  • High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex.

    abstract::Carassius auratus complex is believed to originate from East Eurasia and consist of diploid and triploid forms. Diploid form reproduces sexually, whereas triploid form possesses mixture modes of unisexual gynogenesis and sexual reproduction, which makes it a unique case to study evolutionary issues among vertebrates. ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.10.006

    authors: Jiang FF,Wang ZW,Zhou L,Jiang L,Zhang XJ,Apalikova OV,Brykov VA,Gui JF

    更新日期:2013-01-01 00:00:00

  • Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds.

    abstract::Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyr...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00215-4

    authors: Ericson PG,Christidis L,Irestedt M,Norman JA

    更新日期:2002-10-01 00:00:00

  • Molecular phylogeny of the genus Luzula DC. (Juncaceae, Monocotyledones) based on plastome and nuclear ribosomal regions: a case of incongruence, incomplete lineage sorting and hybridisation.

    abstract::The genus Luzula consists of 115 species distributed throughout the world. Luzula is monophyletic, but species relationships within the genus are difficult to determine primarily due to the similar morphology even within geographically remote taxa (especially within the section Luzula). The plastome trnL intron, trnL-...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.07.022

    authors: Záveská Drábková L,Vlček C

    更新日期:2010-11-01 00:00:00

  • Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs.

    abstract::Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.107042

    authors: Cairns NA,Cicchino AS,Stewart KA,Austin JD,Lougheed SC

    更新日期:2021-03-01 00:00:00