Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex

Molecular Phylogenetics and Evolution, Год журнала: 2017, Номер 111, С. 158 - 168

Опубликована: Апрель 5, 2017

Язык: Английский

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Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution

PLoS ONE, Год журнала: 2017, Номер 12(1), С. e0171053 - e0171053

Опубликована: Янв. 30, 2017

Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set still being explored. We present case study for use of genotyping-by-sequencing (GBS) resolve relationships species complex Australian arid semi-arid grasses (Triodia R.Br.), highlighting our solutions methodological challenges GBS data. merged overlapping paired-end reads then optimised locus assembly program PyRAD generate sets phylogenetic distance-based analyses. In addition traditional concatenation analyses RAxML, we also demonstrate novel summary tree (taking gene trees as input) with loci. found that while were relatively robust variation parameters, RAxML resulted well-supported conflicting topologies under different settings. Despite this conflict, multiple clades consistently supported distinct across Our improve resolution taxa Triodia basedowii compared previous based on Sanger nuclear (ITS/ETS) chloroplast (rps16-trnK spacer) markers. The genomic results partly support evidence hybridization between complex. insights will assist using similar within complexes.

Язык: Английский

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Improved sampling at the subspecies level solves a taxonomic dilemma – A case study of two enigmatic Chinese tit species (Aves, Passeriformes, Paridae, Poecile)

Molecular Phylogenetics and Evolution, Год журнала: 2016, Номер 107, С. 538 - 550

Опубликована: Дек. 10, 2016

Язык: Английский

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Sperm performance in conspecific and heterospecific female fluid

Ecology and Evolution, Год журнала: 2016, Номер 6(5), С. 1363 - 1377

Опубликована: Янв. 30, 2016

Divergent sexual selection within allopatric populations may result in divergent phenotypes, which can act as reproductive barriers between upon secondary contact. This hypothesis has been most tested on traits involved precopulatory selection, with less work focusing that after copulation and before fertilization (i.e., postcopulatory prezygotic traits), particularly internally fertilizing vertebrates. However, species also drive trait divergence, resulting reduced performance of heterospecific sperm the female tract. Such incompatibilities, arising a by-product allopatry, represent barriers, analogous to species-assortative mating preferences. Here, we for three pairs taxa diverged phenotypes moderate-to-high opportunity (barn swallows Hirundo rustica versus sand martins Riparia riparia, two subspecies bluethroats, Luscinia svecica L. s. namnetum, great tits Parus major blue Cyanistes caeruleus). We swimming fluid from outer tract females, because greatest reduction number birds occurs swim across vagina. Contrary our expectations, swam equally well conspecific suggesting do not these taxon pairs, at this stage fertilization. therefore suggest divergence allopatry is insufficient cause widespread form impaired passerine birds.

Язык: Английский

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GIbPSs: a toolkit for fast and accurate analyses of genotyping‐by‐sequencing data without a reference genome

Molecular Ecology Resources, Год журнала: 2016, Номер 16(4), С. 979 - 990

Опубликована: Фев. 9, 2016

Abstract Genotyping‐by‐sequencing ( GBS ) and related methods are increasingly used for studies of non‐model organisms from population genetic to phylogenetic scales. We present GI b PS s, a new genotyping toolkit the analysis data various protocols such as RAD , double‐digest two‐enzyme without reference genome. s can handle paired‐end is able assign reads both strands restriction fragment same locus. most suitable phylogeographic analyses. It avoids errors due indel variation by identifying discarding affected loci. creates genotype database that offers rich functionality filtering export in numerous formats. performed comparative analyses simulated real with another program, py . This program accounts aligning homologous sequences. better than several aspects. required much less computation time displayed higher accuracy. retained smaller numbers loci overall data. nevertheless delivered more complete matrices greater locus overlap between individuals sampled all individuals.

Язык: Английский

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Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations

PLoS ONE, Год журнала: 2020, Номер 15(3), С. e0230151 - e0230151

Опубликована: Март 19, 2020

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts fragmentations due to retreat into different glacial refugia. Thus, several extant bird species have diversified by surviving glaciations in hospitable refugia subsequently expanded their distribution ranges during the Holocene. Such scenario was also suggested for Eurasian Wren (Nannus troglodytes) despite lack genetic data most subspecies. Our phylogenetic multi-locus analysis comprised 18 out 28 currently accepted subspecies N. troglodytes, including all but one which are present Basin. resulting reconstruction dated onset entire Holarctic radiation three Nannus early Pleistocene. In Wren, two North African represented separate basal lineages from Maghreb (N. t. kabylorum) Libyan Cyrenaica juniperi), being only distantly related other populations. Although troglodytes appeared be paraphyletic with respect Nearctic Winter hiemalis), respective nodes did not receive strong statistical support. contrast, paraphyly Ibero-Maghrebian taxon kabylorum strongly supported. Southern Iberian populations clade Maghrebian same formed sister highly diverse European (including nominate eight further taxa). accordance pattern found birds, split western (Europe, Caucasus) an eastern (Central Asia, Sino-Himalayas, East Asia). This complex revealed cryptic diversification especially Iberio-Maghrebian region.

Язык: Английский

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Species-level divergences in multiple functional traits between the two endemic subspecies of Blue Chaffinches Fringilla teydea in Canary Islands

BMC Zoology, Год журнала: 2016, Номер 1(1)

Опубликована: Авг. 18, 2016

One of the biggest challenges in avian taxonomy is delimitation allopatric species because their reproductive incompatibility cannot be directly studied wild. Instead, has to inferred from multiple, divergent character sets that indicate a low likelihood populations amalgamating upon secondary contact. A set quantitative criteria for been developed taxonomy. Here, we report broad multi-trait comparison two insular subspecies Blue Chaffinch Fringilla teydea, endemic pine forests Tenerife (ssp. teydea) and Gran Canaria polatzeki) Canary Islands. We found taxa were reciprocally monophyletic whole mitogenomes Z chromosome introns. The genetic distance indicates around 1 Mya evolution. There diagnostic differences body morphometrics, song plumage reflectance spectra, whose combined divergence score (=11) exceeds threshold level (=7) by Tobias et al. (Ibis 152:724–746, 2010). Moreover, marked sperm lengths with little range overlap. Relatively long intra- intermale CV compared other passerines suggest mating system high levels competition (extrapair paternity) these taxa. large divergences multiple functional traits qualify rank, i.e., (Fringilla polatzeki). encourage wider use might signal at postcopulatory prezygotic stage, especially competition.

Язык: Английский

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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation

Heredity, Год журнала: 2020, Номер 125(1-2), С. 73 - 84

Опубликована: Май 26, 2020

Abstract Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes closely related species. Specifically, is often concentrated in particular genomic regions (“islands differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas rest genome homogenized by introgression. Alternatively, linked selection can produce islands allopatry without We explored influence introgression on two hybridizing goose taxa: Taiga Bean Goose ( Anser fabalis ) and Tundra A. serrirostris ). re-sequenced whole 18 individuals (9 each taxon) and, using combination population summary statistics demographic modeling, we reconstructed evolutionary history these birds. Next, quantified impact build-up maintenance differentiation. found evidence for scenario allopatric divergence (about 2.5 million years ago) followed recent secondary contact 60,000 ago). Subsequent events led high levels gene flow, mainly from into Goose. This resulted largely undifferentiated (genome-wide F ST = 0.033) with few notable peaks were scattered chromosomes. The indicated some while others arose through selection. Finally, based low differentiation, considerable morphological variation incomplete argue should be treated as subspecies.

Язык: Английский

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Spatiotemporal patterns of avian host–parasite interactions in the face of biogeographical range expansions

Molecular Ecology, Год журнала: 2020, Номер 29(13), С. 2431 - 2448

Опубликована: Май 29, 2020

Abstract Exploration of interactions between hosts and parasitic symbionts is important for our understanding the temporal spatial distribution organisms. For example, host colonization new geographical regions may alter levels infections parasite specificity, even allow to escape from co‐evolved parasites, consequently shaping distributions community structure both parasite. Here we investigate effect elevational host–parasite associations birds their vector‐transmitted haemosporidian blood parasites in two geological settings: mountains New Guinea Canary Islands. Our results demonstrate that bird communities younger have significantly lower parasitism compared those older regions. Furthermore, network analyses respond differently after arriving a region, through adaptations either expanding (Canary Islands) or retaining (New Guinea) niches. The prevalence patterns along gradients differed regions, suggesting region‐specific biotic (e.g., community) abiotic factors temperature) govern patterns. findings suggest spatiotemporal range dynamics systems are driven by multiple factors, but compositions histories particular importance.

Язык: Английский

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Longer Sperm Swim More Slowly in the Canary Islands Chiffchaff

Cells, Год журнала: 2021, Номер 10(6), С. 1358 - 1358

Опубликована: Май 31, 2021

Sperm swimming performance affects male fertilization success, particularly in species with high sperm competition. Understanding how morphology impacts is therefore important. speed hypothesized to increase total length, relative flagellum length (with the generating forward thrust), and midpiece (as contains mitochondria). We tested these hypotheses for divergence traits five island populations of Canary Islands chiffchaff (Phylloscopus canariensis). confirmed incipient mitochondrial DNA differentiation between Gran Canaria other islands. correlated negatively did not correlate (for only). The proportion motile cells increased on only. was similar across thus add a growing number studies passerine birds that do support morphology–swimming hypotheses. suggest mechanics are sufficiently different from mammalian predictions hydrodynamic models should no longer be applied this taxon. While both likely under selection passerines, relationship them requires further elucidation.

Язык: Английский

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