排序方式: 共有22条查询结果,搜索用时 15 毫秒
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Jun Huang Yuttapong Thawornwattana Tom Flouri James Mallet Ziheng Yang 《Molecular biology and evolution》2022,39(12)
Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models. Here we use mathematical analysis and computer simulation to examine estimation bias and issues of interpretation when the model of gene flow is misspecified in analysis of genomic datasets, for example, if introgression is assigned to the wrong lineages. In the case of two species, we establish a correspondence between the migration rate in the continuous migration model and the introgression probability in the introgression model. When gene flow occurs continuously through time but in the analysis is assumed to occur at a fixed time point, common evolutionary parameters such as species divergence times are surprisingly well estimated. However, the time of introgression tends to be estimated towards the recent end of the period of continuous gene flow. When introgression events are assigned incorrectly to the parental or daughter lineages, introgression times tend to collapse onto species divergence times, with introgression probabilities underestimated. Overall, our analyses suggest that the simple introgression model is useful for extracting information concerning between-specific gene flow and divergence even when the model may be misspecified. However, for reliable inference of gene flow it is important to include multiple samples per species, in particular, from hybridizing species. 相似文献
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Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult
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Sarah J. Jacobs Casey Kristofferson Simon Uribe‐Convers Maribeth Latvis David C. Tank 《Molecular ecology》2018,27(10):2397-2413
Using multiple, independent approaches to molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential by‐product of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized, and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence. We advocate that incongruence within a line of evidence should be accounted for before comparing across lines of evidence that can themselves be incongruent. Additionally, it is not uncommon for empiricists working in nonmodel systems to be data‐limited, generating some concern for the adequacy of available data to address the question of interest. With conservation and management decisions often hinging on the status of species, it seems prudent to understand the capabilities of approaches we use given the data we have. Here, we apply two molecular species delimitation approaches, spedeSTEM and BPP, to the Castilleja ambigua (Orobanchaceae) species complex, a relatively young plant lineage in western North America. Upon finding incongruence in our delimitation, we employed a post hoc simulation study to examine the power of these approaches to delimit species. Given the data we collected, we find that spedeSTEM lacks the power to delimit while BPP is capable, thus allowing us to address incongruence before proceeding in delimitation. We suggest post hoc simulation studies like this compliment empirical delimitation and serve as a means of exploring conflict within a line of evidence and dealing with it appropriately. 相似文献
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在大鼠观察了牛胰多肽(BPP)对由蛋白胨和雨蛙素引起的大鼠胰外分泌的影响。向十二指肠灌入25%蛋白胨后90min 时,对照组的蛋白排出量约为其基础值的10倍,而1、3、5及10ug/kg BPP 剂量组的蛋白排出量分別为对照组的47%、33%、29%及29%。在灌注剂量为3μg/kg 雨蛙素后60min 时,对照组的蛋白排出量约为其基础值的14倍,但3、5及10μg/kgBPP 剂量组的蛋白排出量分別为对照组的74%、68%及55%。各组胰淀粉酶浓度的变化和其蛋白排出量变化相平行。胰液量的增加不受 BPP 影响。结果提示,BPP 能抑制胰酶的大量分泌,并有剂量依从关系,但不抑制胰液量。 相似文献
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Stephan C Hamacher M Blüggel M Körting G Chamrad D Scheer C Marcus K Reidegeld KA Lohaus C Schäfer H Martens L Jones P Müller M Auyeung K Taylor C Binz PA Thiele H Parkinson D Meyer HE Apweiler R 《Proteomics》2005,5(14):3560-3562
The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined. 相似文献
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Myriapods are among the earliest arthropods and may have evolved to become part of the terrestrial biota more than 400 million years ago. A noticeable lack of mitochondrial genome data from Pauropoda hampers phylogenetic and evolutionary studies within the subphylum Myriapoda. We sequenced the first complete mitochondrial genome of a microscopic pauropod, Pauropus longiramus (Arthropoda: Myriapoda), and conducted comprehensive mitogenomic analyses across the Myriapoda. The pauropod mitochondrial genome is a circular molecule of 14,487 bp long and contains the entire set of thirty-seven genes. Frequent intergenic overlaps occurred between adjacent tRNAs, and between tRNA and protein-coding genes. This is the first example of a mitochondrial genome with multiple intergenic overlaps and reveals a strategy for arthropods to effectively compact the mitochondrial genome by overlapping and truncating tRNA genes with neighbor genes, instead of only truncating tRNAs. Phylogenetic analyses based on protein-coding genes provide strong evidence that the sister group of Pauropoda is Symphyla. Additionally, approximately unbiased (AU) tests strongly support the Progoneata and confirm the basal position of Chilopoda in Myriapoda. This study provides an estimation of myriapod origins around 555 Ma (95% CI: 444-704 Ma) and this date is comparable with that of the Cambrian explosion and candidate myriapod-like fossils. A new time-scale suggests that deep radiations during early myriapod diversification occurred at least three times, not once as previously proposed. A Carboniferous origin of pauropods is congruent with the idea that these taxa are derived, rather than basal, progoneatans. 相似文献
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The true identity of Obama (Platyhelminthes: Geoplanidae) flatworm spreading across Europe
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Fernando Carbayo Marta Álvarez‐Presas Hugh D. Jones Marta Riutort 《Zoological Journal of the Linnean Society》2016,177(1):5-28
Since 2008 there have been many records in Europe (British Isles, Spain, France, Italy) of a large terrestrial planarian morphologically very similar to the Brazilian species Obama marmorata. Sequences of mitochondrial (Cox1) and nuclear (18S, 28S, ITS‐1 and EF) genes from European specimens and some from Brazil indicate that they belong to a species different from that of other specimens also collected in Brazil. Moreover, the phylogenetic results show that they are not sister‐species. Histological sections of both Brazilian and European specimens reveal subtle morphological differences between the two species. Obama marmorata is confined to Brazil, and the second, herein described new species, O bama nungara sp. nov. , is found in Brazil and Europe. These cryptic species may be syntopic in areas in Brazil. The new species occurs in human‐modified environments both in Brazil and in Europe. We also conclude that the specimens from Spain and Argentina identified previously as Obama marmorata belong to the new species. 相似文献
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The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius
arcticus Kuwert, 1890, and three morphological variants of Hydrobius
fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius
fuscipes
var.
fuscipes and Hydrobius
fuscipes
var.
subrotundus being sympatric. Hydrobius
arcticus and Hydrobius
fuscipes
var.
rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius
fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius
fuscipes
var.
fuscipes from Hydrobius
fuscipes
var.
subrotundus, but characters in the literature for Hydrobius
arcticus and Hydrobius
fuscipes
var.
rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius
arcticus and the three morphological variants of Hydrobius
fuscipes are separate species and Hydrobius
rottenbergii Gerhardt, 1872, stat. n. and Hydrobius
subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided. 相似文献