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[Display omitted] • Hidden introgression is detected through a large geographical cline spanning through approximately 150 km. • Sample choice, small population sizes, and linking population sizes in SNAPP can influence species tree reconstructions. • Species delimitation methods yield contrasting results within Trachydactylus hajarensis. • Dataset down sampling and species delimitation methods need to be cautiously implemented and validated to avoid contributing to taxonomic inflation. With the advent of molecular phylogenetics and the implementation of Multispecies Coalescent-based (MSC) species delimitation methods (SDM), the number of taxonomic studies unveiling and describing cryptic sibling species has greatly increased. However, speciation between early divergent lineages is often defined without evaluating population structure or gene flow, which can lead to false claims of species status and, subsequently, taxonomic inflation. In this study, we focus on the intriguing case of the Arabian gecko Trachydactylus hajarensis (Squamata: Gekkonidae). We generated mitochondrial data (12S rDNA) and genome-wide SNP data (ddRADseq) for 52 specimens to determine phylogenomic relationships, population structure and genetic diversity within this species. Then, we applied a set of different SDMs to evaluate several competing species hypotheses through the MSC. Results show that T. hajarensis is comprised by three well-defined population lineages, two of them in the Hajar Mountains of eastern Arabia, and one in Masirah Island, on the southeastern coast of Oman. Strong mito-nuclear discordances were found between populations inhabiting the Hajar Mountains, but we did not find evidence of current gene flow between them. Surprisingly, discordances in species tree topology were found when different downsampled datasets were used, and especially when linking population sizes, a commonly implemented feature in species tree reconstruction with genomic data. Different SDMs yielded different results, supporting from four species within the group, to T. hajarensis being a single species. With such contrasting results we suggest caution before splitting T. hajarensis. Overall, this study highlights the importance of sample and prior choice and the integration of several SDMs to not incur into taxonomic inflation, providing a set of already available tools to assess population structure, genetic diversity, and SDMs before describing new species. [ABSTRACT FROM AUTHOR]

The Carambola fruit fly, Bactrocera carambolae, is an invasive pest in Southeast Asia. It has been introduced into areas in South America such as Suriname and Brazil. Bactrocera carambolae belongs to the B. dorsalis species complex, and seems to be separated from B. dorsalis based on morphological and multilocus phylogenetic studies. Even though the Carambola fruit fly is an important quarantine species and has an impact on international trade, knowledge of the molecular ecology of B. carambolae, concerning species status and pest management aspects, is lacking. Seven populations sampled from the known geographical areas of B. carambolae including Southeast Asia (i.e., Indonesia, Malaysia, Thailand) and South America (i.e., Suriname), were genotyped using eight microsatellite DNA markers. Genetic variation, genetic structure, and genetic network among populations illustrated that the Suriname samples were genetically differentiated from Southeast Asian populations. The genetic network revealed that samples from West Sumatra (Pekanbaru, PK) and Java (Jakarta, JK) were presumably the source populations of B. carambolae in Suriname, which was congruent with human migration records between the two continents. Additionally, three populations of B. dorsalis were included to better understand the species boundary. The genetic structure between the two species was significantly separated and approximately 11% of total individuals were detected as admixed (0.100 ≤ Q ≤ 0.900). The genetic network showed connections between B. carambolae and B. dorsalis groups throughout Depok (DP), JK, and Nakhon Sri Thammarat (NT) populations. These data supported the hypothesis that the reproductive isolation between the two species may be leaky. Although the morphology and monophyly of nuclear and mitochondrial DNA sequences in previous studies showed discrete entities, the hypothesis of semipermeable boundaries may not be rejected. Alleles at microsatellite loci could be introgressed rather than other nuclear and mitochondrial DNA. Bactrocera carambolae may be an incipient rather than a distinct species of B. dorsalis. Regarding the pest management aspect, the genetic sexing Salaya5 strain (SY5) was included for comparison with wild populations. The SY5 strain was genetically assigned to the B. carambolae cluster. Likewise, the genetic network showed that the strain shared greatest genetic similarity to JK, suggesting that SY5 did not divert away from its original genetic makeup. Under laboratory conditions, at least 12 generations apart, selection did not strongly affect genetic compatibility between the strain and wild populations. This knowledge further confirms the potential utilization of the Salaya5 strain in regional programs of area-wide integrated pest management using SIT. [ABSTRACT FROM AUTHOR]

The ecological interactions parasitic insects have with their hosts may contribute to their prodigious diversity, which is unrivaled among animals. Many insects assumed to be polyphagous generalists have been shown to consist of several differentiated races, each occupying a different host-niche. The sunflower maggot fly, Strauzia longipennis, has long been thought to consist of two or more races due to its substantial intra-specific morphological variation. Here, we use nuclear and mitochondrial markers to test the hypothesis that S. longipennis is a complex of two or more partially reproductively isolated races. We collected S. longipennis flies as pupae from roots of Jerusalem artichoke ( Helianthus tuberosus) and as adults swept from leaves of mature H. tuberosus across the breadth of a field season. Flies were scored for morphological variety ( typica or vittigera), mitochondrial haplotype (A or B) and a panel of 176 AFLP loci. Bayesian clustering and neighbor-joining phylogenetic analyses of AFLP data supported the existence of at least three, possibly four, genetic races of Strauzia (clusters I, II, III, and V), as well as a small number of putative interracial hybrids (cluster IV). Clusters I and III each consisted of flies of both morphological varieties and both haplotype groups, while flies in cluster II were all of variety typica and all but one was of mitochondrial haplotype B. Flies in cluster II were also collected only as adults on H. tuberosus and not among flies reared from pupae collected from H. tuberosus roots, suggesting that they use a different plant as their larval host. Mean capture date was significantly different between flies of each genetic race, indicating that partial allochronic isolation may be one contemporary barrier to gene flow between races. Evidence that mitochondrial genomes and morphological traits have moved between lineages implies a model of speciation-with-gene-flow for S. longipennis races. [ABSTRACT FROM AUTHOR]

Many vertebrate taxa show genetic differentiation between populations in northern and southern California. This genetic pattern may reflect a common environmental history for these species. For example, a previous study of the California vole (Microtus californicus) showed morphological divergence between populations in northern and southern California and decreased fertility in crosses between the populations. To investigate phylogeographic differences in this species, we assessed variation in mitochondrial and nuclear DNA throughout much of its distribution from Oregon to Baja California. We generated molecular data (mitochondrial cytochrome b and nuclear acid phosphatase V intron [AP5]) for 178 individuals. Examination of these data suggests 2 phylogeographic groups that are largely discordant with the boundaries of 17 currently recognized subspecies. Estimates of pairwise genetic divergence between these groups for cytochrome b are as high as 4.46% uncorrected p. Sequence data for AP5 also indicate a division between populations of M. californicus in northern and southern California. Examination of data from the mitochondrial and nuclear markers together suggests limited gene flow between clades. These data are concordant with other studies that suggest that mountain ranges in California were important in within- and possibly between-species divergence and subsequent contact. The general distribution of each clade, combined with a geographic information system analysis of known capture sites, suggests that clade divergence may be correlated with ecological differences. Our study creates a new framework for reevaluating morphological and ecological diversity in this species, and with more diverse markers, possibly the recognition of 2 species of California voles. [ABSTRACT FROM AUTHOR]