Nuclear DNA Data Sets Research Articles

Population genetics reveals new introgression in the nucleus herd of min pigs.

Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs. We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs. The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content = 0.713, expected heterozygosity = 0.662, observed heterozygosity = 0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes. Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.

Phylogenomic analyses support a new infrageneric classification of Pourthiaea (Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling

AbstractIn this comprehensive study, based on extensive taxon sampling, we performed phylogenomic analyses of plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent‐based strategies, to generate an accurate phylogeny of the woody Rosaceae genus Pourthiaea. The nrDNA phylogeny of Pourthiaea strongly supports three major clades, which are consistent with morphology. However, the plastid tree provides an alternative phylogenetic topology, indicating cytonuclear discordance which could be explained by frequent hybridizations between and among the species of Pourthiaea. Considering evidence from morphology and phylogenomic data, we propose a new infrageneric classification for Pourthiaea, consisting of three sections: P. sect. Pourthiaea, P. sect. Amphidoxae sect. nov., and P. sect. Impressivenae sect. nov.

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics.

The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.

Mitogenome of the Doleschallia bisaltide and Phylogenetic Analysis of Nymphalinae (Lepidoptera, Nymphalidae)

The complete mitogenome of Doleschallia bisaltide was sequenced with a size of 16,389 bp. Gene orientation and arrangement in the newly sequenced mitogenome are the same as other mitogenomes in Lepidoptera. Except for trnS1(AGN), which lacks the dihydrouridine (DHC) arm, the other 21 tRNA genes all contain a typical cloverleaf structure. Ka/Ks ratio analysis of 13 protein-coding genes (PCGs) from 23 Nymphalinae species indicates that the evolutionary rate of COX1 was slowest, while that of ATP8, ND5, and ND6 was substantially high. Phylogenetic analysis revealed that Nymphalinae and Kallimini were nonmonophyletic. Trees constructed only from the nuclear DNA (nDNA) dataset had lower support than mitochondrial or combined datasets. The addition of RNA genes did not improve the phylogenetic signal, and nodal support decreased. These data provide important information for future studies into the phylogeny of Nymphalinae.

Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia’s adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae).

Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data—CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions—for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110–112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

Euphorbiambuinzauensis, a new succulent species in Kenya from the Synadenium group in Euphorbiasect.Monadenium (Euphorbiaceae).

Euphorbiambuinzauensis, a succulent new species of the Synadenium group in Euphorbiaceae from Makueni County, Kenya, is described and illustrated. Morphologically, it is most similar to E.pseudomollis, but differs mainly by its shrubby habit (up to 4 m), abaxial leaves surfaces with densely stellate hairs, 2–4-forked cymes, smaller bracts (ca. 2.5 × 3.0 mm), smaller cyathia (6 mm wide), crimson glands without narrow smooth margin, smaller fruits (ca. 8 × 7 mm) and ovoid seeds (ca. 1.8 × 2.2 mm). Furthermore, we performed a molecular phylogenetic analysis of the Synadenium group in Euphorbiasect.Monadenium, based on complete nuclear ribosomal DNA (nrDNA) datasets. This phylogenetic inference also supports it to be a distinct species. The new species is assessed as Endangered using the IUCN criteria.

Integrative taxonomy of the Selaginella helvetica group based on morphological, molecular and ecological data

AbstractThe Eurasian and Mediterranean Selaginella helvetica group is one of the taxonomically challenging groups in the cosmopolitan lycophyte genus Selaginella. Species of the S. helvetica group are all small plants with lax strobili composed of more or less isomorphic sporophylls (isosporophylls) that are basically non‐resupinate. Owing to the similar and minute morphological characteristics, the inapplicability of chloroplast DNA markers for species delimitation and the lack of range‐wide sampling, no comprehensive study has been conducted on these species so far. In this study, we performed phylogenetic analyses based on population‐scale sampling of 126 individuals, covering the entire geographical distribution and morphological variation of this group. Five chloroplast (rbcL, psbA, atpI, atpF, atpF‐H) and two nuclear DNA regions (26S rDNA, pgiC) were used to explore species diversity of this group. The phylogeny inferred from nuclear DNA datasets revealed nine well‐supported monophyletic groups, which provided important evidence for species delimitation and called for taxonomic revision of some taxa. However, in the chloroplast phylogeny, individuals of only three species (S. denticulata, S. helvetica, S. tamamontana) formed monophyletic groups, respectively. We further investigated genome size for each species by flow cytometry and evaluated 21 morphological characteristics of 79 herbarium specimens. MaxEnt analysis was performed to predict the potential suitable distribution of each species. As a result of total evidence, 10 taxa were recognized in the S. helvetica group. The delimitation of S. denticulata, S. laxistrobila, S. nipponica, S. pallidissima, S. prostrata, and S. tamamontana was congruent with previous taxonomical treatments. We reinstated S. shensiensis as an independent species and treated S. longistrobilina as its synonym. Selaginella helvetica (s.str.) is confined to Europe and North Asia, former records of it from the Himalaya‐Hengduan mountains represent an independent species (S. jiulongensis comb. nov.). The nuclear pgiC phylogeny and flow cytometry evidence indicated that S. pseudonipponica is an allotetraploid with S. shensiensis and S. nipponica as its parents. Our results highlight that nuclear DNA markers rather than chloroplast DNA markers are more informative in delimitation of closely related species in Selaginella.

Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation.

Here, I review phylogenetic studies of the lizard family Pygopodidae, a group of 47 extant species that diversified in Australia and New Guinea. The goal of this study was to examine published phylogenetic and phylogenomic hypotheses on pygopodids to identify the strengths and weaknesses in our understanding of their phylogeny. Many parts of the pygopodid family tree are well established by multiple independent tree inferences including: (1) all multispecies genera (i.e., Aprasia, Delma, Lialis, Pletholax, and Pygopus) are monophyletic groups; (2) the root of the pygopodid tree is located along the branch leading to the Delma clade, thus showing that Delma is the sister group to all other pygopodid genera; (3) the Aprasia repens group, Delma tincta group, and several other groups of closely related species are demonstrated to be monophyletic entities; and (4) the monotypic Paradelma orientalis is the sister lineage to the Pygopus clade. Based on accumulated phylogenetic evidence, two taxonomic recommendations are given: Paradelma merits generic status rather than being subsumed into Pygopus as some earlier studies had suggested, and the monotypic Aclys concinna should be recognized as a member of Delma (following current practice) until future studies clarify its placement inside or outside the Delma clade. One chronic problem with phylogenetic studies of pygopodids, which has limited the explanatory power of many tree hypotheses, concerns the undersampling of known species. Although the continual addition of newly described species, especially over the past two decades, has been a major reason for these taxon sampling gaps, deficits in species sampling for ingroups and/or outgroups in several studies of pygopodid species complexes has confounded the testing of some ingroup monophyly hypotheses. Ancient hybridization between non-sister lineages may also be confounding attempts to recover the relationships among pygopodids using molecular data. Indeed, such a phenomenon can explain at least five cases of mito-nuclear discordance and conflicts among trees based on nuclear DNA datasets. Another problem has been the lack of consensus on the relationships among most pygopodid genera, an issue that may stem from rapid diversification of these lineages early in the group’s history. Despite current weaknesses in our understanding of pygopodid phylogeny, enough evidence exists to clarify many major and minor structural parts of their family tree. Accordingly, a composite tree for the Pygopodidae was able to be synthesized. This novel tree hypothesis contains all recognized pygopodid species and reveals that about half of the clades are corroborated by multiple independent tree hypotheses, while the remaining clades have less empirical support.

Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

A new genus and species for Chloantheae (Lamiaceae)

A molecular phylogeny of Chloantheae (Lamiaceae) based on a three-marker chloroplast and nuclear DNA dataset was used to test the monophyly of Lachnostachys Hook., Newcastelia F.Muell. and Physopsis Turcz. A clade consisting of at least one species from each of these genera was recovered separately from the ‘core’ Lachnostachys, Newcastelia and Physopsis clades. The members of this composite clade are here transferred to the new genus, Apatelantha T.C.Wilson & M.J.Henwood, which can be recognised by a combination of the base of the style being glabrous or with only non-glandular trichomes (glandular trichomes lacking), apex of corolla lobes (when present) acute to obtuse (not extending into an apical protrusion) and thin-textured (not distinctively thickened), pherophylls subtending three flowers, and anther connectives glabrous (sessile glands absent). A description of the new genus, together with new combinations for five species of Apatelantha, and amended descriptions of Lachnostachys, Newcastelia and Physopsis, are provided. A new species, Newcastelia clavipetala T.C.Wilson & Radunz, is described and illustrated. A taxonomic key to genera of Chloantheae, and keys to species of Lachnostachys, Newcastelia, Physopsis and Apatelantha are provided.

Genetic Divergence Across Glacial Refugia Despite Interglacial Gene Flow in a Crested Newt

MtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.

Phylogeny and biogeography of Sagittaria (Alismataceae) revisited: evidence for cryptic diversity and colonization out of South America.

Sagittaria is a genus of ca. 40 species in the aquatic plant family Alismataceae with a nearly global distribution, and a center of diversity in the New World. Two thirds of the known species are native to the Americas, while only a few species are distributed in Africa, Asia and Europe. A previous biogeographic analysis of the genus suggested an African origin for the genus with subsequent dispersal to North America and then to East Asia. Here we expanded the taxon sampling with a focus on the New World taxa and applied species delimitation and biogeographic analyses to revise the knowledge of the phylogeny and evolution of the genus. We obtained largely similar topologies from the chloroplast DNA and nuclear DNA (ITS) data sets. The 74 accessions sampled for our analyses were delimited into 29 species and several cryptic taxa were revealed in widely distributed species. Biogeographic analysis supported basal diversification in South America and subsequent colonization to North America and Asia.

Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

AbstractThe familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.

Deep south-north genetic divergence in Godlewski\u2019s bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences

BackgroundGeological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski’s Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species.ResultsA phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2–6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth.ConclusionsOur results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.

Mitochondrial and nuclear ribosomal DNA dataset suggests that Hepatiarius sudarikovi Feizullaev, 1961 is a member of the genus Opisthorchis Blanchard, 1895 (Digenea: Opisthorchiidae).

The taxonomy and classification of the family Opisthorchiidae have been revised by several authors with the exclusion or synonymization of some genera. The genus Hepatiarius Feizullaev, 1961 accommodated two species: Hepatiarius sudarikovi Feizullaev, 1961 and H. longissimus Linstow, 1883. Recently, some experts have suppressed Hepatiarius as a junior synonym of Opisthorchis Blanchard, 1895 based on morphological features alone. Prior to the present study, no molecular data either from nuclear or from mitochondrial DNA was available for any species of this genus. In the present study, four specimens of H. sudarikovi Feizullaev, 1961 were recovered from the bile ducts of the little egret, Egretta garzetta. The complete sequences of the internal transcribed spacers (ITS-1 and ITS-2) of ribosomal DNA (rDNA) and the nearly complete mitochondrial genome sequences were determined and the phylogenetic relationship of H. sudarikovi with related taxa was assessed based on the mitochondrial (mt) DNA sequences. The sequence similarity in the ITS rDNA between H. sudarikovi and Opisthorchis felineus was higher (97.62% in ITS-1 and 96.22% in ITS-2) than with other opisthorchiids. Phylogenetic analysis using Bayesian inference (BI) based on the concatenated amino acid sequences of 12 protein-coding genes (PCGs) clustered H. sudarikovi into the clade of opisthorchiids, with O. felineus being the closest related species, which supports the affinity of H. sudarikovi with trematodes in the genus Opisthorchis. This is the first avian liver fluke whose nearly complete mitochondrial genome was sequenced. The mtDNA sequences of H. sudarikovi, in combination with its rDNA sequences, provide novel resources of genetic markers for the identification, species differentiation, and systematic studies of H. sudarikovi with other avian opisthorchiid flukes.

Evolutionary distinctiveness and conservation priority of the endangered Najas ancistrocarpa (Hydrocharitaceae)

Phylogeny is vitally important to evaluate evolutionary distinctiveness and conservation priorities of species. Najas ancistrocarpa is one of the rarest and least known East Asian species of the c. 30–40 species of the aquatic plant genus Najas (Hydrocharitaceae). We used a recently discovered collection of this nationally and regionally endangered species in Japan and East Asia to assess whether N. ancistrocarpa is a distinct species or an untypical form of other Najas species and to evaluate its conservation priority in a phylogenetic context. The sample set of our previous study, exploring worldwide phylogeny of the genus was used with N. ancistrocarpa to delimit species boundaries in Najas and obtain conservation priority scores, calculated by multiplying evolutionary distinctiveness and global extinction risks converted from Red List categories. We performed molecular phylogenetic analyses of plastid (ptDNA) and nuclear (ITS) DNA datasets, STACEY species delimitation analysis using the multilocus dataset and a measurement of conservation priority with Tuatara. Najas ancistrocarpa was consistently placed in ptDNA and ITS trees. Species delimitation analysis objectively assessed that N. ancistrocarpa is phylogenetically distinct. Phylogenetic conservation prioritization ranked N. ancistrocarpa the second highest priority species of the genus Najas. Overall, in terms of biodiversity conservation, N. ancistrocarpa represents an important Najas species in Japan and probably the world.

Phylogeny of Najas (Hydrocharitaceae) revisited: Implications for systematics and evolution

AbstractNajas (Hydrocharitaceae) is a cosmopolitan genus of 30‐40 species of aquatic plants. While an infrageneric subdivision into two subgenera is generally accepted, various sectional classifications proposed in subg. Caulinia have been controversial. Earlier analyses identified tropical Asia, which harbors more than one‐third of all species, as the area of origin for the genus, but this inference requires re‐evaluation using worldwide taxon sampling. Polyploidy has been widely observed in the genus but its correlation with phylogeny has yet to be explored. Here we applied a molecular phylogenetic approach using balanced taxon sampling (1) to test infrageneric classifications, (2) to re‐assess biogeographic origin, and (3) to explore whether and how polyploidy characterizes evolutionary lineages. Our analyses of plastid and nuclear (ITS) DNA datasets produce largely congruent results that recover the two subgenera but find little support for most sectional classifications. To overcome this shortfall, we propose a new sectional classification of subg. Caulinia. The previously inferred tropical Asian origin of the genus is rejected and, instead, North America is discerned as the ancestral area, implicating dispersal of the most recent common ancestor of Najas and its sister genera in Hydrocharitaceae from tropical Asia. Based on chromosome counts confirmed in the present study and those compiled from literature, the role of polyploidization in the evolution of Najas is shown to be relatively limited, in contrast to the extreme infraspecific chromosome variation previously reported.

Concordance in phylogeography and ecological niche modelling identify dispersal corridors for reptiles in arid Australia

AbstractAimUsing the rock‐specialist agamid Ctenophorus caudicinctus as a model, we test hypothesized biogeographical dispersal corridors for lizards in the Australian arid zone (across the western sand deserts), and assess how these dispersal routes have shaped phylogeographical structuring.LocationArid and semi‐arid Australia.MethodsWe sequenced a c. 1400 bp fragment of mtDNA (ND2) for 134 individuals of C. caudicinctus as well as a subset of each of the mtDNA clades for five nuclear loci (BDNF, BACH1, GAPD, NTF3, and PRLR). We used phylogenetic methods to assess biogeographical patterns within C. caudicinctus, including relaxed molecular clock analyses to estimate divergence times. Ecological niche modelling (Maxent) was employed to estimate the current distribution of suitable climatic envelopes for each lineage.ResultsPhylogenetic analyses identified two deeply divergent mtDNA clades within C. caudicinctus – an eastern and western clade – separated by the Western Australian sand deserts. However, divergences pre‐date the Pleistocene sand deserts. Phylogenetic analyses of the nuclear DNA data sets generally support major mtDNA clades, suggesting past connections between the western C. c. caudicinctus populations in far eastern Pilbara (EP) and the lineages to the east of the sand deserts. Ecological niche modelling supports the continued suitability of climatic conditions between the Central Ranges and the far EP for C. c. graafi.Main conclusionsEstimates of lineage ages provide evidence of divergence between eastern and western clades during the Miocene with subsequent secondary contact during the Pliocene. Our results suggest that this secondary contact occurred via dispersal between the Central Ranges and the far EP, rather than the more southerly Giles Corridor. These events precede the origins of the western sand deserts and divergence patterns instead appear associated with Miocene and Pliocene climate change.

Impact of pine invasion on the taxonomic and phylogenetic diversity of a relict Mediterranean forest ecosystem

Invasion by non-native tree species is a major driver of reduction and fragmentation of forest ecosystems, also altering biodiversity components. However, the effects of this process on the phylogenetic structure and diversity of Mediterranean woodlands are still unknown. Accordingly, we used cork oak (Quercus suber) stands invaded by self-sowing populations of maritime pine locally introduced ca. 70years ago as a model system to assess the impact on the taxonomic and phylogenetic diversity of the native seed plant community. We performed vegetation sampling of the two forest types in sites of central Italy with similar conditions. Taxonomic diversity was negatively affected by the pine at three levels (gamma, alpha, beta). Indicator species were significantly less numerous than in cork oak stands, and did not include two growth-forms such as herbs and vines. Phylogenetic diversity metrics were inferred from an evolutionary tree of seed plants based on a ITS-5.8S nuclear DNA dataset including original sequences from local plant material. Phylogenetic diversity (PD) was positively related to species and genus richness, showing a marked decrease in the pine stands. Seven major clades (orders) of angiosperm dicots were only represented in the cork oak community. Both the NRI and NTI indices showed a significant reduction of phylogenetic evenness in the pine forest. Here, the proportional increase of related taxa with acid-tolerance specialization suggests that soil acidification is a major driver for a “habitat filtering” effect causing the exclusion of several understorey species and genera of cork oak forests. Progressive thinning of the pine stands is advocated to avoid further acidification and promote the re-conversion to oak woodlands by natural regeneration. This will ultimately favor the recovery of the associated plant diversity and the restoration of a vanishing forest ecosystem of the ancient Mediterranean landscape.