Gene and species trees reveal mitochondrial and nuclear discordance in the Drosophila cardini group (Diptera: Drosophilidae)

Abstract. The Drosophila cardini group includes 15 species, which are subdivided into the D. cardini and D. dunni subgroups. Although many phylogenetic hypotheses have been proposed for this group during the last five decades (based on patterns of reproductive isolation, morphology of male genitalia, chromosomal inversions, isozyme variation, or molecular sequence data), these are mostly discordant with each other. We aimed to clarify some of the evolutionary patterns related to the origin of this incongruence, while also attempting to provide a better-supported phylogenetic hypothesis for the D. cardini subgroup. For this purpose, sequences from three mitochondrial and three nuclear loci were gathered for at least eight species, and both individual gene trees and joint species tree estimates were evaluated. Although there was concordance among gene trees within each of the nuclear and mitochondrial sets, considerable incongruence was revealed in the comparisons between these two data sets. The branching position of D. neocardini was the main source of incongruence, and species trees reconstructed using different approaches with and without this species were particularly incongruent. In addition to providing a better approximation of the evolutionary history of the D. cardini group, this study suggests that incomplete lineage sorting or introgression may be biasing previous species tree estimates. More generally, the results also suggest that the use of supermatrix methods can lead to an overestimation of support for the inferred relationships, and highlight the potential effects of different taxon sampling strategies in phylogenetic reconstruction.     

Frequent chloroplast capture among Isodon (Lamiaceae) species in Japan revealed by phylogenies based on variation in chloroplast and nuclear DNA

A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single-copy nuclear genes, and double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single-copy nuclear genes and the ddRAD-seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.     

Nuclear loci and coalescent methods support ancient hybridization as cause of mitochondrial paraphyly between gadwall and falcated duck (Anas spp.)

Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression ( approximately 14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.     

Distinct geographical structure across species units evidenced by chloroplast DNA haplotypes and nuclear ribosomal ITS genotypes of Corylopsis (Hamamelidaceae) in the Japanese islands

The geographical distribution of chloroplast DNA (cpDNA) haplotypes and nuclear ribosomal internal transcribed spacer (nrITS) genotypes of Japanese Corylopsis (Hamamelidaceae), which consists of four species, was investigated. Two hundred and five individuals belonging to four species from 30 populations, covering the entire geographical range, were studied. Based on approximately 1108 bp of the three non-coding regions of cpDNA, nine haplotypes were detected, and each was distinguished from adjacent haplotypes by one substitution. Based on approximately 507-bp nrITS sequences, 47 genotypes were detected, for which three clades were identified in the phylogenetic analysis. There was inconsistency between the cpDNA haplotypes, nrITS genotypes, and classification of Corylopsis taxa, possibly because of incomplete lineage sorting or introgressive hybridization. The distribution of the haplotypes was highly structured geographically, and N _ST (0.893) was significantly greater than G _ST (0.819), implying that the current distribution of Corylopsis species was structured phylogeographically during Quaternary climatic oscillations. The haplotype composition and results of analysis of molecular variance showed that the populations in Hokuriku were highly divergent, suggesting that they are long-term persistent populations arising from refugia during the Quaternary climatic oscillations. Refugial populations in Chugoku and Shikoku may have lost genetic diversity because of a bottleneck resulting from a small population size, followed by post-glacial range expansion. Pre-existing refugia may have been so small that the subsequent range expansion replaced the pre-existing genetic structure.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 501–518.     

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold‐adapted montane species, where range shifts have had a pronounced effect on population‐level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane‐restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.     

Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change

Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic 'footprints' in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene-Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post-glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation-by-distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60,000 years.     

Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.     

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced‐representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.     

Mitochondrial cytochrome b gene sequences of old world monkeys: With special reference on evolution of Asian colobines

The classification and phylogenetic relationships of the Old World monkeys are still controversial. For Asian colobines, from three to nine genera were recognized by different primatologists. In the present study, we have sequenced a 424 bp mitochondrial tRNA^Thr gene and cytochrome b gene fragment fromMacaca mulatta, Mandrillus sphinx, Mandrillus leucophaeus, Semnopithecus entellus, Trachypithecus vetulus, T. johnii, T. phayrei, T. francoisi, Pygathrix nemaeus, Rhinopithecus roxellanae, R. bieti, R. avunculus, Nasalis larvatus, andColobus polykomos in order to gain independent information on the classification and phylogenetic relationships of those species. Phylogenetic trees were constructed with parsimony analysis by weighting transversions 5 or 10 fold greater than transitions. Our results support the following conclusions: (1) the Old World monkeys are divided into two subfamilies; (2) that among the colobines,Colobus, the African group, diverged first, andNasalis andRhinopithecus form a sister clade toPygathrix; (3) that there are two clades within leaf monkeys, i.e. 1)S. entellus, T. johnii, andT. vetulus, and 2)T. phayrei andT. francoisi; (4) thatRhinopithecus avunculus, R. roxellanae, andR. bieti are closely related to each other, and they should be placed into the same subgenus; (5) thatRhinopithecus is a distinct genus; and (6) that the ancestors of Asian colobines migrated from Africa to Asia during the late Pliocene or early Pleistocene.     

Recent volcanism and mitochondrial DNA structuring in the lizard Gallotia atlantica from the island of Lanzarote

The phylogeography of the lacertid lizard Gallotia atlantica from the small volcanic island of Lanzarote (Canary Islands) was analysed based on 1075 bp of mitochondrial DNA (mtDNA) sequence (partial cytochrome b and ND2) for 157 individuals from 27 sites (including three sites from neighbouring islets). Levels of sequence divergence were generally low, with the most distant haplotypes separated by only 14 mutational steps. MtDNA divergence appears to coincide with formation of the middle Pleistocene lowland that united formerly separate ancient islands to form the current island of Lanzarote, allowing rejection of a two-island model of phylogeographical structure. There was evidence of large-scale population expansion after island unification, consistent with the colonization of new areas. A nested clade phylogeographical analysis (NCPA) revealed significant phylogeographical structuring. Two-step and higher-level clades each had disjunct distributions, being found to the east and west of a common area with a north-south orientation that extends between coasts in the centre-east of the island (El Jable). Other clades were almost entirely restricted to the El Jable region alone. Bayesian Markov chain Monte Carlo analyses were used to separate ongoing gene flow from historical associations. These supported the NCPA by indicating recent (75,000-150,000 years ago) east-west vicariance across the El Jable region. Lava flows covered El Jable and other parts of the central lowland at this time and likely led to population extinctions and temporary dispersal barriers, although present-day evidence suggests some populations would have survived in small refugia. Expansion of the latter appears to explain the presence of a clade located between the eastern and western components of the disjunct clades. Direct relationships between mtDNA lineages and morphology were not found, although one of two morphological forms on the island has a disjunct distribution that is broadly concordant with east-west components of the phylogeographical pattern. This work demonstrates how recent volcanic activity can cause population fragmentation and thus shape genetic diversity on microgeographical scales.     

不同地域小稻蝗mtDNA部分序列及其相互关系

测定了9个不同地理区域的小稻蝗Oxya intricata (Stal)共33个个体的线粒体DNA (mtDNA)细胞色素b基因部分序列,比较其同源性,计算核苷酸组成,并用瘤锥蝗科的曲尾似橄蝗Pseudomorphacris hollisi和斑腿蝗科的芋蝗Gesonula punctifrons作外群构建NJ分子系统树。在获得的小稻蝗432 bp的序列中, A+T约占70.3%,其中30个核苷酸位点存在变异(约占所测核苷酸的6.9%),有5个位点引起了氨基酸的变异。就每个氨基酸密码子来看,第3位点的A+T含量较高,达90.4%。由NJ树显示,小稻蝗mtDNA 细胞色素b序列不同单倍型之间有一定的分歧,形成不同的簇类关系,其分枝与地理分布没有直接的对应关系,但总体上看,这种簇类关系基本上呈平行分布,没有明显的地域性差别。     

安徽麝线粒体DNA细胞色素b基因全长序列分析

自80年代安徽麝[Moschus (moschiferus/berezovskii)anhuiensis]被发现以来,其分类地位一直众说纷纭。在本研究中,我们对安徽麝模式皮张标本进行了线粒体DNA细胞色素b基因全长序列分析。研究结果表明,安徽麝同麝属中其他种的遗传分化已经相当明显.分子系统学的分析表明,安徽麝是一个单系群,它同麝属其他种的DNA序列差异已达到种间分化的程度。因此,线粒体DNA序列的证据支持将安徽麝列为麝属中一有效种（Moschus anhuiensis),而不是前人认为的原麝或林麝的亚种。     

Mitochondrial and nuclear DNA analyses reveal population differentiation in Brazilian Creole sheep

Using ND5 sequences from mtDNA and 10 nuclear markers, we investigated the genetic differentiation of two South American Creole sheep phenotypes that historically have been bred in different biomes in southern Brazil. In total, 18 unique mtDNA haplotypes were detected, none of which was shared between the two phenotypes. Bayesian analysis also indicated two different groups (k = 2). Thus, these varieties are supported as being genotypically distinct. This situation could have resulted either from geographical isolation, associated with differences in the cultural habits of sheep farmers and in the way that flocks were managed, or more likely, from the introduction of different stocks four centuries ago.     

Genetic distinctness and phylogenetic relationships among Undaria species (Laminariales, Phaeophyceae) based on mitochondrial cox3 gene sequences

Genetic relationships among Undaria species and among populations of each species were studied based on DNA sequences of the mitochondrial cox3 gene. Although three Undaria species, U. peterseniana (Kjellman) Okamura, U. pinnatifida (Harvey) Suringar and U. undarioides (Yendo) Okamura, have been described based mostly on blade morphology, plants with intermediate morphologies have also been found. Multiple plants from several populations in Japan were collected. Morphological characters could identify most of the samples unambiguously. A few samples with intermediate morphologies were also collected. Mitochondrial haplotypes found in each population were different for each identified species, and each species had multiple haplotypes. In the cox3 haplotype network analysis, the numbers of steps between haplotypes within and between species were similar, and haplotypes of each species did not group together. The close genetic relationships among species strongly suggest that these species are conspecific. Alternatively, recent speciation could be possible with maintenance of ancestral polymorphisms within the species (i.e. incomplete lineage sorting). Haplotypes of samples with intermediate morphologies were different for each sample and the same as ones found in the local population, suggesting interspecific hybridizations among species.     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

从D环和细胞色素b基因序列探讨懒猴属的分子系统发育关系(英文)

本研究测定了懒猴属(Nycticebus)D环的部分序列和细胞色素b基因的全序列(1140bp),分析了该属物种之间的系统发育进化关系。在DNA水平上,序列分析结果一致地提供了新的分类学证据：支持Rataiszczak和Groves的观点,即N．intermedus只是N．pygmaeus的成体(Ratajszczak,1998;Groves,1971)。对两种序列的数据做了联合及个别分析,获得相似的系统树,支持懒猴属由两个单系群组成：第一群由N．pygmaeus聚成,第二群由N．coucang聚成。该结果也提供了新的分子遗传证据,支持懒猴属由N．coucang和N．pygmaeus两物种组成。     

Understanding the mechanisms of antitropical divergence in the seabird White‐faced Storm‐petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach

Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White‐faced Storm‐petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial Φ_ST = 0.89 (P < 0.01) and global nuclear Φ_ST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long‐term antitropical divergence in isolation. Coalescent‐based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000–600 000), both probably associated with the profound palaeo‐oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long‐distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.     

线粒体DNA 序列分析在中国水域真海豚物种鉴定中的初步应用

真海豚包括长喙真海豚( Delphinus capensis) 和短喙真海豚( D. delphis) 2 种, 而中国水域的真海豚到底是哪一个种或是否同时有两个种的存在, 并不清楚。本研究测定了12 头中国水域真海豚mtDNA 控制区(control region) 366 bp 和细胞色素b (cytochrome b , cyt b) 基因336 bp 的序列, 并与已发表的其它真海豚的序列合并分析,初步鉴定中国水域真海豚的分类地位。结果表明, 中国水域的真海豚与东太平洋的长喙真海豚有相同的鉴别位点, 且两者之间的核苷酸歧异度(控制区: 1.93 ±0.22 % , cyt b 基因: 0.68 ±0.19 %) 显著低于与短喙真海豚之间的差异(控制区: 2.92 ±0.41 % , cyt b 基因: 0.95 ±0.27 %) 。通过MEGA (molecular evolutionary genetic analysis) 软件中的邻接法(neighbor joining) 进行的系统发生分析中, 中国水域的真海豚与长喙真海豚聚成一支, 有明显较近的亲缘关系。因此, 中国水域的真海豚在分类上应归属于长喙真海豚。     

Ecological speciation in the East Maui-endemic Dubautia (Asteraceae) species

Abstract Adaptive diversification can be viewed as a balance between the conservative force of interpopulation gene flow and selection for differential environments. In this paper, we examine ecological, morphological, and genetic differentiation in a small clade consisting of four East Maui-endemic species of Dubautia : D. menziesii , D. platyphylla , D. reticulata , and D. waianapanapaensis , in the Hawaiian silversword alliance (Asteraceae). The East Maui clade is apparently recently derived (less than 1 million years ago) and is geographically restricted yet displays significant ecological and morphological differences. We used geographic data from historical herbarium specimens, measurements of plant architecture and leaf morphometrics, and measures of genetic differentiation in both microsatellite and nuclear coding loci to examine the correlation of different forms of divergence in this small species flock. We found overlap in large-scale geographic distributions, significant differentiation in most habitat factors, significant micro-satellite differentiation, and many shared alleles at nuclear coding loci suggesting on-going lineage sorting. Despite the presence of apparent hybrids in some populations, microsatellite variation is consistent with isolation among species. Using Mantel tests, we compared the direction and extent of diversification among different datasets, to determine whether ecological/morphological divergence was correlated with genetic divergence. Correlations among different datasets showed that habitat was strongly correlated with plant architecture but not leaf morphology. Taken together, these results indicate that ecological and morphological diversification has driven genetic divergence at rapidly evolving microsatellite loci, whereas there is continuing lineage sorting at neutral sites in nuclear coding loci.