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[Display omitted] • First phylogeny of Nearctic Lathrobium using a combined morphological and multi-locus molecular dataset and molecular clock analysis. • Monophyly of existing subgenera was supported, except for Abletobium Casey which was placed in synonymy with Glyptomerus Müller. • Multiple dispersal events from Palearctic to Nearctic across the Bering land bridge. • Congruent divergence patterns in endemic Appalachian lineages, with Miocene or early Pliocene origins, followed by Pleistocene speciation. The southern Appalachian Mountains are a biodiverse region with high levels of endemism. Shared biogeographic patterns among co-distributed, but independent taxa might illuminate common drivers of Appalachian endemism. Lathrobium is a Holarctic genus with 38 species described form North America, six of which are flightless and endemic to the high Appalachians. We use an integrative morphological and multi-locus molecular dataset to study phylogenetic and biogeographical relationships of Appalachian Lathrobium and test subgeneric hypotheses. A phylogeny based on 176 samples from 67 taxa supported three independent arrivals in the Appalachian Mountains. Divergence times estimated in BEAST2 were concurrent for all three lineages and fell between the Miocene or early Pliocene (16.4 – 4.6 Ma). Speciation within Appalachians occurred during the Pleistocene (2.3 – 0.1 Ma). Monophyly of existing subgenera was supported except for Abletobium Casey. Abletobium is placed in synonymy with Glyptomerus Müller. Our results reveal the importance of cold-climate refugia within the Appalachian Mountains for the persistence and in-situ diversification of endemic endogean taxa. We hypothesize that the xeric climate of the Miocene drove Lathrobium lineages into the mountains and subsequent isolation in mountaintop refugia during warm Pleistocene interglacials led to speciation. [ABSTRACT FROM AUTHOR]

(A) Distribution of sampling localities. (B) Results of the Structure analysis based on the SNPs at K = 2. (C) Principal components analysis (PCA) of 12,548 SNPs obtained from P. armandii and its relatives. (D) Phylogenetic analysis Maximum-likelihood tree constructed from the 13,906 SNPs identified in P. armandii. (E) Heat maps for the net genetic distances (Da) between different groups or species. (F) Predicted distributions of the northern and southern subdivisions using Maxent. • Cryptic speciation has occurred in Pinus armandii. • The interactions of geography and ecology led to the speciation. • Both geography and ecology contributed to the high conifer diversity in HHM. Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii , an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains. [ABSTRACT FROM AUTHOR]

The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A . janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A . janus , likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation. [ABSTRACT FROM AUTHOR]

[Display omitted] • Six cryptic species previously suggested in the White Cloud Mountain minnow Tanichthys albonubes complex were well supported. • The genetic diversity of each species in the T. albonubes complex was low with small Ne. • The highly differentiated loci among species in T. albonubes complex were evenly distributed across the genome. • The divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (N e) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex. [ABSTRACT FROM AUTHOR]

[Display omitted] • Hybridization between Diphasiastrum species from Russian Far East was investigated. • Hybrids were clearly recognizable by molecular methods, but only in part by morphology. • Chloroplast microsatellites revealed apparent uniparental hybridization. • Two nuclear markers and GBS data confirmed hybridization and introgression events. • Results are in contrast to prior findings on European species and their hybrids. Hybridization occurs often in the genus Diphasiastrum (Lycopodiaceae), which corroborates reports for the two other recognized lycophyte families, Isoëtaceae and Selaginellaceae. Here we investigate the case of D. alpinum and D. sitchense from the Russian Far East (Kamchatka). Their hybrid, D. × takedae, was morphologically recognizable in 16 out of 22 accessions showing molecular signatures of hybridization; the remaining accessions displayed the morphology of either D. alpinum (3) or D. sitchense (3). We sequenced markers for chloroplast microsatellites (cp, 175 accessions from Kamchatka) and for the two nuclear markers RPB and LFY (175 and 152 accessions). A selection of 42 accessions, including all hybrid accessions, was analysed via genotyping by sequencing (GBS). We found multiple, but apparently uniparental hybridization, clearly characterized by a deviating group of haplotypes for D. sitchense and all hybrids. All accessions showing molecular signatures of hybridization in nuclear markers revealed the parental haplotype of D. sitchense , however only the LFY marker differentiated between the parent species. GBS, including 69,819 quality-filtered single nucleotid polymorphisms, unambiguously identified the hybrids and revealed introgression to occur. Most of the hybrids were F 1 , but three turned out to be backcrosses with D. alpinum (one) and with D. sitchense (two). These observations are in contrast to prior findings on three European species and their intermediates where all three hybrids turned out to be independent F 1 crosses without evidence of recent backcrossing. In this study, backcrossing was detected, which indicates a limited fertility of the hybrid taxon D. × takedae. A comparison of accessions of Kamchatkian D. alpinum with plants from Europe indicated possible cryptic speciation. Accessions from the Far East had (i) a lower DNA content (7.0 vs. 7.5 pg/2C), (ii) different prevailing cp haplotypes, and (iii) RPB genotypes, and (iv) a clearly different SNP pattern in GBS. Diphasiastrum sitchense and the similar D. nikoënse , for the latter additional accessions from Japan were investigated, appeared as forms of one diverse species, sharing genotypes in both nuclear markers, although chloroplast haplotypes and DNA content show slight variations. [ABSTRACT FROM AUTHOR]

Highlights: [•] Multilocus was first used to study evolutionary history of Bemisia tabaci. [•] Species statuses of different genetic groups were supported by Bayesian species delimitation. [•] Higher degree of mtDNA than nuclear DNA divergence was found. [•] Approximate Bayesian computation suggested there was gene flow at early stage of speciation. [•] Gene flow during speciation has a great impact on divergence dating. [ABSTRACT FROM AUTHOR]

Abstract: The Neotropical-African liverwort Marchesinia brachiata has long been regarded as a polymorphic species. This hypothesis is examined using a dataset including sequences of the nuclear internal transcribed spacer region and the plastidic trnL–trnF region of 39 Marchesinia accessions. Maximum parsimony, maximum likelihood and Bayesian analyses indicate that Marchesinia robusta is nested within M. brachiata s.l. The molecular topologies support at least three partly sympatric biological species within M. brachiata s.l., the Neotropical M. bongardiana and M. languida, and the Neotropical-African M. brachiata s.s. These species are incompletely separated by subtle differences in underleaf shape and leaf dentation. Long branches within M. brachiata s.s. suggest ongoing speciation processes that are not yet reflected in distinguishable morphological variation. Divergence time estimates based on nrITS sequence variation and the liverwort fossil record indicate an establishment of the species M. bongardiana, M. brachiata, M. languida, M. madagassa, and M. robusta in the Late Oligocene and Miocene. The intraspecific diversity shows distinctive patterns with evidence for constant accumulation of genetic diversity in M. robusta and M. brachiata whereas M. bongardiana and M. languida likely went through a recent extinction or expansion process as indicated by the bottleneck pattern of genetic diversity. The tropical American-African disjunction of M. brachiata is the result of dispersal rather than Western Gondwanan vicariance. [Copyright &y& Elsevier]

Abstract: The avian genus Saxicola is distributed throughout Africa, Asia, Europe and various islands across Oceania. Despite the fact that the group has great potential as a model to test evolutionary hypotheses due to the extensive variability in life history patterns recorded between and within species, the phylogenetic relationships among species and subspecies of this genus are poorly understood. We undertook a systematic investigation of the relationships within this genus with three main objectives in mind, (1) to test the monophyly of the genus; (2) to ascertain geographical origin and dispersal sequence; and (3) to test for monophyly within the most morphologically diverse species, S. torquata and S. caprata. We studied sequence data from the mitochondrial cytochrome b gene from 11 of the 12 recognized species and 15 of the 45 described subspecies. Four clades, two exclusively Asian, one Eurasian, and the fourth encompassing Eurasia and Africa, were identified. Based on our analyses, monophyly of the genus Saxicola is not supported and an Asian origin for the genus can be inferred. Results from DIVA analyses, tree topology and nodal age estimates suggest independent colonisation events from Asia to Africa and from Asia to the Western Palearctic, with the Sahara desert acting as a natural barrier for S. torquata. Subspecies and populations of S. torquata are not monophyletic due to S. tectes, S. dacotiae and S. leucura grouping within this complex. Subspecies and populations of S. caprata are monophyletic. Importantly, within S. torquata and S. caprata, slight morphological traits and plumage colour pattern differences used to recognize subspecies are indicative of the greater cryptic diversification that has occurred within this genus. [Copyright &y& Elsevier]

Abstract: The cosmopolitan family Porellaceae includes about 60 species in two or three genera: the large genus Porella and the monospecific Ascidiota and Macvicaria (alternatively Porella subg. Macvicaria). Maximum parsimony, maximum likelihood and Bayesian inference of phylogeny of a dataset including three markers (rbcL, trnL–trnF region of cp DNA, nrITS region) of 96 accessions resulted in similar topologies supporting the generic status of Ascidiota. Macvicaria is nested in a subclade of Porella. Relationships among species of Porella are in general well resolved and many terminal nodes achieve good statistical support whereas basal relationships are at best moderately supported. Multiple accessions of single species are usually placed in monophyletic lineages. Accessions of P. platyphylla split into a European and a North American clade with one accession from North America embedded within the European samples. The Macaronesian endemic P. inaequalis is closely related to the Asian species P. grandiloba. Porella obtusata and P. canariensis cannot be separated on the basis of the sequence data presented in this study. The molecular topologies indicate a range extension of the Asian P. gracillima subsp. urogea to Eastern North America and of the Neotropical P. swartziana to South Africa. Current supraspecific classifications of Porella are not reflected in the molecular topologies with a correlation between genetic variation and the geographical distribution of the related accessions rather than a correlation between genetic variation and morphology. [Copyright &y& Elsevier]

Abstract: In this paper, we performed phylogenetic analyses of Mesotriton alpestris populations from the entire range of species distribution, using fragments of two mtDNA genes, cytochrome b (309bp) and 16S rRNA (∼500bp). Sequence diversity patterns and phylogenetic analyses reveal the existence of a relict lineage (Clade A) of late Miocene origin, comprising populations from south-eastern Serbia. This lineage is proposed to be ancestor to a western and an eastern lineage, which diverged during the middle Pliocene. The western lineage is further divided in two clades (Clades B, C) of middle Pliocene origin that represent populations from Italy (B) and populations from central Europe and Iberia (C). Further subdivision, dated back to the middle-late Pliocene, was found within the eastern lineage, representing southern (Clade D) and central-northern (Clade E) Balkan populations, respectively. Extensive sequence divergence, implying greater isolation in multiple refugia, is found within eastern clades, while the western clades seem to have been involved in the colonization of central, western and north-eastern Europe from a hypothetical refugium in central Europe. The extent of divergence does not support the current taxonomy indicating cryptic speciation in the Balkans, while paedomorphic lineages were found to have been evolved during early-middle Pleistocene probably as a response to the ongoing dramatic climatic oscillations. [Copyright &y& Elsevier]

Abstract: Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two genetically significantly diverged lineages with 2.1% DNA sequence divergence. These two lineages are largely allopatric: one is mainly found in southwest China (lineage A), whereas the other ranges central and east of China to northeast Asia (lineage B). The geographic distributions of these two clades narrowly overlap near the provincial boundaries of Yunnan and Guizhou or Guangxi, probably as a consequence of population expansion and secondary contact. These two lineages were estimated to have diverged about 0.56Mya, and the estimated time of expansion was approximately 70,000 years ago for lineage A population, and 110,000 years ago for lineage B population. The present molecular analysis, together with nearly complete reproductive isolation between those two lineages, strongly suggests that the two lineages might be incipient species. [Copyright &y& Elsevier]

[Display omitted] • 94 of the 145 included species are new to science. • Across phylogenetic methods robust clades are recovered. • Exact branching pattern in the backbone of the phylogeny differs between inference methods. • Cryptic speciation occurs in one Macrostomum clade. • Sperm and male copulatory organ morphology is extremely diverse. Free-living flatworms of the genus Macrostomum are small and transparent animals, representing attractive study organisms for a broad range of topics in evolutionary, developmental, and molecular biology. The genus includes the model organism M. lignano for which extensive molecular resources are available, and recently there is a growing interest in extending work to additional species in the genus. These endeavours are currently hindered because, even though >200 Macrostomum species have been taxonomically described, molecular phylogenetic information and geographic sampling remain limited. We report on a global sampling campaign aimed at increasing taxon sampling and geographic representation of the genus. Specifically, we use extensive transcriptome and single-locus data to generate phylogenomic hypotheses including 145 species. Across different phylogenetic methods and alignments used, we identify several consistent clades, while their exact grouping is less clear, possibly due to a radiation early in Macrostomum evolution. Moreover, we uncover a large undescribed diversity, with 94 of the studied species likely being new to science, and we identify multiple novel morphological traits. Furthermore, we identify cryptic speciation in a taxonomically challenging assemblage of species, suggesting that the use of molecular markers is a prerequisite for future work, and we describe the distribution of putative synapomorphies and suggest taxonomic revisions based on our finding. Our large-scale phylogenomic dataset now provides a robust foundation for comparative analyses of morphological, behavioural and molecular evolution in this genus. [ABSTRACT FROM AUTHOR]

[Display omitted] • Molecular phylogeny of the genus Linopodes was reconstructed for the first time. • Six delimitation methods performed on COI sequences revealed 7 genospecies. • Genospecies were indistinguishable by phenotypic characters (cryptic species). • Linopodes originated ca. 145 MYA and evolved as a long-term stasis (50–80 MY). Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY. [ABSTRACT FROM AUTHOR]

• The O. graminea sensu lato in southern China contains five major lineages and they shows obvious phylogeographic patterns. • Diversification of O. graminea sensu lato was affected by QTP uplifts, Climate fluctuations, and drainages changes. • Mitochondrial-nuclear discordant genetic structure was revealed in the O. graminea sensu stricto. • Species delimitation results suggested the existence of high number cryptic species in the O. graminea sensu stricto. • Multiple rapid population expansion events occurred in the evolutionary history of O. graminea sensu stricto. Understanding the process of speciation and the factors driving the geographical distribution patterns of species is of great interest in ecology and evolutionary biology. Herein, we investigated the phylogeographic patterns, speciation, demographic history and genetic structure of the widespread endemic Odorrana graminea sensu lato in Southern China and adjacent areas. A total of 439 specimens from 68 localities were sequenced and analyzed for both mitochondrial (12S and 16S rRNA) and nuclear markers (RAG-1 and ten microsatellite loci). Phylogenetic analyses of the concatenated mtDNA data revealed five major highly divergent lineages within the O. graminea sensu lato in Southern China, and these divergent lineages were highly concordant with five geographical regions. The nuclear data showed a discordant genetic structure compared to the mtDNA lineages (Clades A, B, and C) for O. graminea sensu stricto, with an admixed pattern in the RAG-1 data and two structure clusters in the microsatellite data. The species delimitation analyses, based on three methods, supported the species status of Odorrana zhaoi and Odorrana rotodora , and revealed the existence of putative cryptic species in the O. graminea sensu stricto. In addition, one statistically significant gene flow event was detected from Clade B to Clade C based on mtDNA and RAG-1 data, and the microsatellite data suggested gene flow within the O. graminea sensu stricto. Bayesian skyline plotting analyses and ecological niche modeling supported demographic and range expansions during the LGM for Clades A and C of the O. graminea sensu stricto. In addition, ecological niche models suggested the existence of ecological divergence among the three Clades (Clades A, B and C) of the O. graminea sensu stricto. The intense uplifting of the Qinghai-Tibetan Plateau, the Quaternary climate oscillations, and drainage changes may have driven the speciation, genetic structure and phylogeoraphic patterns of the O. graminea sensu lato. [ABSTRACT FROM AUTHOR]