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See detailEvidence of a fine-scale genetic structure for the endangered Pyrenean desman (Galemys pyrenaicus) in the French Pyrenees
Gillet, François ULg; Cabria Garrido, Maria Teresa; Blanc, Frédéric et al

Poster (2014, December)

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in mountain streams of cold and well ... [more ▼]

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Pyrenean Mountains and the northern half of the Iberian Peninsula where it lives in mountain streams of cold and well-oxygenated flowing waters (Nores et al. 2007). This species is currently considered as vulnerable in the IUCN Red List (Fernandes et al. 2008) and has been suffering from habitat loss and fragmentation for decades, inevitably impacting its distribution. The ecology and biology of this species are poorly known, notably because of its elusive behavior and its primarily nocturnal activity (Stone 1987, Bertrand 1994). Its distribution area is even not definitively established. Furthermore, a recent genetic study, based on mitochondrial and intronic sequences (Igea et al. 2013), showed that the genetic variability of the Pyrenean desman is very low in the Pyrenees. In this study we investigated the potential existence of a genetic structure and gene flow at a smaller scale using 24 polymorphic microsatellites loci. As the Pyrenean desman is a very elusive species, we completed our sample collection of tissues with faeces samples coming from the French distribution area of this species. Doing so, we successfully identify 70 individuals out of 355 faeces samples. Bayesian analyses revealed a cryptic genetic structure in our data set. Three clusters were evidenced (one western, one central and one eastern) and gene flow appears to be limited between these clusters (min. Fst value of 0.2). [less ▲]

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See detailPCR-RFLP identification of the endangered Pyrenean desman, Galemys pyrenaicus (Soricomorpha, Talpidae), based on faecal DNA
Gillet, François ULg; Cabria Garrido, Maria Teresa; Némoz, Mélanie et al

in Mammalia (2014)

The Pyrenean desman is a vulnerable mammal species endemic to Pyrenees and the northern Iberian Peninsula. The presence of this elusive species can be most easily detected by sampling its faeces. However ... [more ▼]

The Pyrenean desman is a vulnerable mammal species endemic to Pyrenees and the northern Iberian Peninsula. The presence of this elusive species can be most easily detected by sampling its faeces. However, these faecal samples can be confused with those of other vertebrate species living in the same habitats. This study provides two easy and reliable methods for the identification of the Pyrenean desman faeces based on genetic analyses. The first one consists of a nested PCR and sequencing of a mitochondrial cytochrome b fragment, and the second one is an enzymatic digestion with endonucleases Alu I and Sau 3AI. The restriction patterns given by the two enzymes were found suitable for the successful discrimination of the Pyrenean desman from the other species based on species-specific sequence variations. [less ▲]

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See detailWhen morphometrics meets genetics: the case of the hazel dormouse, Muscardinus avellanarius
Mouton, Alice ULg; Renaud, Sabrina; Michaux, Johan ULg

Conference (2014, September 19)

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See detailPostglacial climate changes and rise of three ecotypes of harbor porpoises, Phocoena phocoena, in western Palearctic waters
Fontaine, Michaël; Roland, K.; Calves, I. et al

in Molecular Ecology (2014)

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See detailGenetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer)
Smitz, Nathalie ULg; Cornelis, Daniel; Chardonnet, Philippe et al

in BMC Evolutionary Biology (2014), 14

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic ... [more ▼]

Background African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the “genetic health” of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. Results The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (Ar) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (Pa) of 11), low differentiation, and an absence of an inbreeding depression signal (mean FIS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (FIS = 0.062, mean Ar = 6.160, Pa = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. Conclusions We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study. [less ▲]

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See detailNegative purifying selection drives prion and doppel protein evolution
Tsangaras, K.; Kolokotronis, S.-O.; Ulrich, R. G. et al

in Journal of Molecular Evolution (2014), 79(1-2), 12-20

The prion protein (PrP) when misfolded into the pathogenic conformer PrPSc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary ... [more ▼]

The prion protein (PrP) when misfolded into the pathogenic conformer PrPSc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene (PRNP) and doppel gene (PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2. © 2014 Springer Science+Business Media New York. [less ▲]

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See detailNuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions
Senn, H.; Ogden, R.; Frosch, C. et al

in Evolutionary Applications (2014), 7(6), 645-662

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in ... [more ▼]

Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction. © 2014 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. [less ▲]

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See detailThe genetic legacy of multiple beaver reintroductions in central Europe
Frosch, C.; Kraus, R. H. S.; Angst, C. et al

in PLoS ONE (2014), 9(5),

The comeback of the Eurasian beaver (Castor fiber) throughout western and central Europe is considered a major conservation success. Traditionally, several subspecies are recognised by morphology and ... [more ▼]

The comeback of the Eurasian beaver (Castor fiber) throughout western and central Europe is considered a major conservation success. Traditionally, several subspecies are recognised by morphology and mitochondrial haplotype, each linked to a relict population. During various reintroduction programs in the 20th century, beavers from multiple source localities were released and now form viable populations. These programs differed in their reintroduction strategies, i.e., using pure subspecies vs. mixed source populations. This inhomogeneity in management actions generated ongoing debates regarding the origin of present beaver populations and appropriate management plans for the future. By sequencing of the mitochondrial control region and microsatellite genotyping of 235 beaver individuals from five selected regions in Germany, Switzerland, Luxembourg, and Belgium we show that beavers from at least four source origins currently form admixed, genetically diverse populations that spread across the study region. While regional occurrences of invasive North American beavers (n = 20) were found, all but one C. fiber bore the mitochondrial haplotype of the autochthonous western Evolutionary Significant Unit (ESU). Considering this, as well as the viability of admixed populations and the fact that the fusion of different lineages is already progressing in all studied regions, we argue that admixture between different beaver source populations should be generally accepted. © 2014 Frosch et al. [less ▲]

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See detailHybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank)
Tsangaras, K.; Wales, N.; Sicheritz-Pontén, T. et al

in PLoS ONE (2014), 9(10),

Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates ... [more ▼]

Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information. [less ▲]

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See detailDiet analysis of Leopoldamys neilli, a cave-dwelling rodent in Southeast Asia, using Next-Generation Sequencing from feces
Latinne, Alice ULg; Galan, Maxime; Waengsothorn, Surachit et al

in Journal of Cave and Karst Studies (2014), 76(2), 139-145

Leopoldamys neilli is a Murinae rodent endemic to limestone karst of Thailand and the Lao PDR, but its ecology and the reasons of its endemism to karst are still totally unknown. The aim of this pilot ... [more ▼]

Leopoldamys neilli is a Murinae rodent endemic to limestone karst of Thailand and the Lao PDR, but its ecology and the reasons of its endemism to karst are still totally unknown. The aim of this pilot study was to examine the plant composition of the diet of L. neilli at the level of order and family using DNA for molecular identification and to compare it with two other forest-dwelling Leopoldamys species, L. herberti and L. sabanus. A 202bp fragment of the rbcL gene was amplified and sequenced for twenty-three fecal samples of the three species using 454 pyrosequencing. We successfully identified a total of seventeen orders and twenty-one plant families, corresponding to thirty-three putative species, in the feces of these three Leopoldamys species. Solanaceae were the most common plants in the diet of L.neilli regardless of the region and sampling season, and they were also present in feces of both L. herberti and L. sabanus. The Araceae, Fabaceae, and Apocynaceae families were also identified in feces of L. neilli collected in various regions of Thailand and at different seasons. Plants of the Oleaceae family are consumed by both L. herberti and L. sabanus but were not found in the diet of L. neilli. Further improvements of the study, such as the use of additional genes, the creation of a reference collection, the microhistological examination of plant fragments to determine which parts of the plant are consumed, and the analysis of the animal diet of Leopoldamys are suggested to enhance the quality and accuracy of the results obtained. [less ▲]

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See detailIs Leopoldamys neilli (Rodentia, Muridae) a synonym of Leopoldamys herberti? A reply to Balakirev et al. (2013)
Latinne, Alice ULg; Chaval, Yannick; Waengsothorn, Surachit et al

in Zootaxa (2013), 3731(4), 589-598

Recently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename ... [more ▼]

Recently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename several of them. According to these authors, the genetic lineage previously thought to belong to L. edwardsi (lineage L1) should be assigned to L. revertens while L. neilli (lineage L2) should be considered as a junior synonym of L. herberti. Using molecular and morphological data from a large sampling of Leopoldamys specimens, the aim of the present study was to investigate the taxonomic status of L. herberti and L. neilli. This study reveals that, contrary to Balakirev et al.’s statement, both genetic lineages L1 and L2 occur in Nakhon Ratchasima Province, close to the type locality of L. herberti. We also show that the external measurements and color pattern of L. herberti are highly similar to those of L1 specimens but are not consistent with the morphology of L2 specimens. Therefore these results strongly suggest that L. herberti should be assigned to the genetic lineage L1. Consequently L. neilli should not be considered as a junior synonym of L. herberti and this study confirms that the appropriate name of the genetic lineage L2 is L. neilli. Moreover, as our results show that L. herberti should be assigned to the lineage L1, this name has nomenclatural priority over L. revertens, the species name suggested by Balakirev et al. (2013) for this lineage. [less ▲]

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See detailDiversity and endemism of Murinae rodents in Thai limestone karsts
Latinne, Alice ULg; Waengsothorn, Surachit; Rojanadilok, Prateep et al

in Systematics and Biodiversity (2013), 11(3), 323-344

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live ... [more ▼]

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live-trapped. Phylogenetic reconstructions were carried out using two mitochondrial markers (cytb, COI). A sequence-based species delimitation method completed by the analysis of the level of genetic divergence was then applied to define species boundaries within our dataset. The phylogenetic position of Niviventer hinpoon was also investigated and sequences obtained from the holotype specimen of this species were used to reliably identify samples of N. hinpoon. A total of 12 described Murinae species, corresponding to 17 deeply divergent genetic lineages, were encountered in limestone karsts of Thailand. Our study revealed an important genetic diversity within the traditionally recognized species Maxomys surifer (four highly divergent genetic lineages), Leopoldamys neilli (two highly divergent genetic lineages) and Berylmys bowersi (two highly divergent genetic lineages). These species could be considered as species complex and require further taxonomic work. This study also provides valuable information on the distribution of the two rodent species endemic to limestone karsts of Thailand, L. neilli and N. hinpoon. Leopoldamys neilli was the most abundant species encountered in Thai karsts during our survey. However, L. neilli specimens from western Thailand are genetically highly divergent from the remaining populations of L. neilli and could represent a separate species. Niviventer hinpoon, phylogenetically closely related to N. fulvescens, is much rarer and its distribution limited to central Thailand. Most of the other captured species are typically associated with forest ecosystems. This study suggests that limestone karsts play a key role in the preservation of the rodent species endemic to such habitat, but they would also provide refuges for the forest-dwelling Murinae rodents in deforested regions. [less ▲]

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See detailEvolutionary history of Leopoldamys neilli, a karst endemic rodent in Southeast Asia, and implications for its conservation
Latinne, Alice ULg; Waengsothorn, Surachit; Michaux, Johan ULg

Conference (2013, August 15)

In this study, we have investigated the phylogeography of Leopoldamys neilli, a Murinae rodent species endemic to limestone karsts in Southeast Asia, on the basis of mitochondrial and nuclear markers ... [more ▼]

In this study, we have investigated the phylogeography of Leopoldamys neilli, a Murinae rodent species endemic to limestone karsts in Southeast Asia, on the basis of mitochondrial and nuclear markers. Both mitochondrial and nuclear markers support a large-scale population structure of four main groups within L. neilli and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli during Plio-Pleistocene. This study revealed an unexpected high level of intraspecific diversity within L. neilli. Consequently, the four main L. neilli population groups should be considered as four distinct Evolutionarily Significant Units (ESUs) and require appropriate management and conservation plans. [less ▲]

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See detailDesman des Pyrénées : Quand la génétique vient compléter les connaissances naturalistes...
Gillet, François ULg; Némoz, Mélanie; Blanc, Frédéric et al

Conference (2013, January)

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See detailA new genus of rodent from wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics
Fabre, P.-H.; Pagès, Marie ULg; Musser, G. G. et al

in Zoological Journal of the Linnean Society (2013), 169(2), 408-447

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement ... [more ▼]

We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo-Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo-Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo-Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio-Pleistocene associated with several major dispersal events. We identified two independent Indo-Pacific dispersal events from both western and eastern Indo-Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London, Zoological Journal of the Linnean Society. [less ▲]

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See detailToward a Noninvasive Inuit Polar Bear Survey: Genetic Data from Polar Bear Hair Snags
Van Coeverden de Groot, Peter; Wong, Pamela; Harris, Christopher et al

in Wildlife Society Bulletin (2013), 37(2), 394-401

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See detailPan-African Genetic Structure in the African Buffalo (Syncerus caffer): Investigating Intraspecific Divergence
Smitz, Nathalie ULg; Berthouly, C.; Cornélis, D. et al

in PLoS ONE (2013), 8(2),

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present ... [more ▼]

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today. © 2013 Smitz et al. [less ▲]

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See detailCryptic diversity in brevipalpus mites (tenuipalpidae)
Navia, D.; Mendonça, R. S.; Ferragut, F. et al

in Zoologica Scripta (2013), 42(4), 406-426

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention ... [more ▼]

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention and control strategies. Flat mites of the Brevipalpus genus include several crop pests and the systematics of these mites represents a challenge for acarologists. Many of the most economically important Brevipalpus species have repeatedly been inaccurately identified. Such problematic classification has been attributed to the likely occurrence of cryptic species in the genus. In this study, we used an integrative approach that combined molecular analyses, including sequence-based species delimitation, with detailed morphological identification using traits that have recently showed to be taxonomically informative. Sequences of mitochondrial cytochrome c oxidase subunit I (COI) were obtained from individuals collected from host plants belonging to 14 genera and 13 families across 29 locations in the Americas (Brazil, Chile, USA). The phylogenetic analyses included previously published Brevipalpus sequences from GenBank, and the final data set was classified into 44 haplotypes. Six putative species were recognised by COI-based species delimitation analysis, and morphological evidence supported each of these species. The integrative approach revealed the occurrence of cryptic species in the Brevipalpus genus and contributed to the clarification of previously noted incongruences. The results presented here allow for the evaluation of taxonomic characteristics in a phylogenetic context and indicate new characters for the differentiation of Brevipalpus species. In addition, Brevipalpus incognitus n. sp. Ferragut & Navia, a cryptic species detected in this study, is described based on morphological and molecular traits. Implications of the advances in Brevipalpus systematics presented herein with respect to pest management are briefly discussed. © 2013 The Norwegian Academy of Science and Letters. [less ▲]

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