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A new pest of tomato, the South American tomato pinworm, Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae), was found in Kumamoto Prefecture, Japan in 2021. We examined the genetic variation in the DNA sequences of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene in 1039 individuals belonging to 39 countries including Japan. In the maximum likelihood phylogenetic tree and haplotype network, 19 haplotypes were detected in the world. Of those haplotypes, only one haplotype (Ta1) was detected from all 39 countries including neighboring countries and Japan. These results and some other information suggest that this species migrated from neighboring countries to Japan. Furthermore, we developed a Multiplex PCR using species-specific primers to discriminate T. absoluta from other gelechiid moth, Phthorimaea operculella (Zeller, 1873) (Lepidoptera: Gelechiidae). We could successfully identify the first instar larvae, fourth instar larvae, pupae, and adults of both species based on the differences in the length of amplicon bands. In addition, we were able to identify adults of both species collected from various prefectures. These results indicated that the Multiplex PCR developed in this study is useful to identify all developmental stages of both species collected in the fields. [ABSTRACT FROM AUTHOR]

Many species of shark are threatened with extinction, a consequence of overfishing to supply the shark fin and meat trade, or through bycatch. While the shark fin trade is comparatively well understood and documented, the trade in shark meat is remains understudied, even though it is larger than the fin trade in terms of value and volume. The species composition of the shark meat trade along with their geographic origin of capture remains largely unknown; this is problematic because it makes the design of effective conservation measures to prevent the overexploitation of sharks and the associated loss of biodiversity challenging. Our work here is the first to comprehensively survey of the shark meat trade in retail establishments from a region of the world that has global significance in the shark product trade. It suggests that local fishing pressure on one or few stocks or populations, rather than complex international supply chains support the trade in shark meat products destined for human consumption. Importantly, it provides a critical assessment and documentation of the species involved. This work has relevance in our efforts to protect sharks and arrest the ongoing biodiversity crisis. [ABSTRACT FROM AUTHOR]

Astylus atromaculatus Blanchard, 1843 (Coleoptera: Melyridae) is a pollinivorous beetle native to southern South America, which has invaded South Africa more than a century ago. Adults and/or larvae may occasionally damage flowers, seeds, and seedlings of various crops. Severe cattle intoxication has also been reported in Argentina, Uruguay, and South Africa following consumption of alfalfa and forage grasses infested with A. atromaculatus. Despite its economic impact, essential genetic information is lacking for this species. The present paper provides the first DNA barcode reference sequences for A. atromaculatus based on the standard 5’ fragment (658 bp) of the cytochrome c oxidase subunit I gene. The sequences obtained exhibited pairwise distances of ≤ 1.82% among them, and ~ 90% nucleotide identity with the homologous gene fragment in the morphologically similar Astylus variegatus Germar, 1824. The use of this molecular marker to explore the intraspecific variability of A. atromaculatus in central Argentina showed 21 different haplotypes, out of 32 individuals analyzed. A very high haplotype diversity (Hd = 0.962 ± 0.019) and a moderate nucleotide diversity (π = 0.00778 ± 0.00079) were recorded. The haplotype network displayed a diffuse structure due to the abundance of singletons and possible missing haplotypes, with the most common haplotype comprising only 15.6% of the specimens collected. Future research with increased sampling size and geographic coverage will allow for a better understanding of the population genetics of this pest, and consequently, for developing efficient management practices. [ABSTRACT FROM AUTHOR]

Flowering time of crops is critical for maximizing yield, quality and regional adaptability under target environments. In rice, Heading date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) proteins are the key factors of flowering time regulation in the florigen activation complex. However, effects of hd3a and rft1 mutations on the flowering time under long-day conditions are not clear. In this study, we generated single and double mutants of Hd3a and RFT1 in japonica varieties Shen Nong 9816 (SN9816) background, termed hd3a-SNs, rft1-SNs and doub-SNs, by using CRISPR/Cas9 system. The flowering time of hd3a-SN mutants was similar to wild-type (WT); but mutations of RFT1 delayed flowering time by 11 to 14 days comparing to WT under nature long day (NLD) conditions. Double mutants of Hd3a and RFT1 (doub-SNs) exhibited an extremely late flowering phenotype, and they did not flower up to 365 days after regeneration under either NLD or short-day conditions. The leaf emergency rate of RFT1 mutants was similar to WT, suggesting that the late flowering phenotype of rft1-SNs was caused by delayed floral transition, but not by retarded growth. The expression of the key floral organ identity genes was significantly decreased in rft1-SN and doub-SN mutants, resulting in late flowering phenotypes. The expression profiles, evolution and haplotypes of Hd3a and RFT1 was also analyzed. Our studies provide insight into the potential utilization of Hd3a and RFT1 gene resources to improving growth period and regional adaptability in rice breeding. [ABSTRACT FROM AUTHOR]

Sound management of coastal resources is based on science-based decisions. Bottlenose dolphins are found around Puerto Rico; however, limited information exists on the ecology, behavior, sex ratio, distribution patterns, and population structure presenting, challenges in managing the bottlenose dolphin as defined in the Marine Mammal Protection Act of 1972. We sequenced the mitochondrial control region (mtDNA-CR) of 27 live and 11 stranded dolphins from Puerto Rico, five stranded dolphins from Guadeloupe and included sequences from the North Atlantic and the Pacific Ocean. Our genetic data from the new samples indicates the presence of distinct genetic lineages (inshore—represented by coastal individuals) and worldwide-distributed form (represented by both coastal and offshore individuals) in Puerto Rico. DNA divergence between inshore/coastal and offshore haplotypes ranged from 4.34 to 6.58%. All haplotypes from Puerto Rico have been previously reported from the Caribbean and North Atlantic. Genetic analysis yielded a complex population structure without a clear geographic signal; an expected result from a highly mobile marine mammal. A clade consisting exclusively of coastal dolphins of the Caribbean and the western North Atlantic was recovered. Offshore haplotypes from the eastern and western North Atlantic were generally clustered with offshore haplotypes of the Caribbean. Coastal and offshore haplotypes from the Pacific differed from those from the Atlantic. When we partitioned the data by form (coastal vs. offshore) and ocean (Atlantic vs. Pacific), we detected significant population differentiation (FST = 0.4089), indicating limited gene flow between forms and across oceans. [ABSTRACT FROM AUTHOR]

Opuntia ficus-indica, commonly known as prickly-pear, tuna, or nopal, is a cactus species of economic significance. It is widely cultivated for its fruits and cladodes, used as both fodder and human food. The species would have been domesticated in pre-Hispanic Mexico. In Argentina, two forms are present: the horticultural (spineless, f. ficus-indica) and the wild (spiny, f. amyclaea) forms. The presence/absence of spines would be a genetically controlled trait; thus, the species would have been introduced more than once in our country. A molecular and cytogenetic study was conducted to characterize the genetic variability, infer the source of introduction in Argentina, and explore the relationship between morphotypes. Most spine samples had the Q16-H1 haplotype, except for samples from Mexico, Santiago del Estero, and Catamarca. Samples from Salta, Santiago del Estero, and Catamarca showed morphological differences from O. ficus-indica. The cytological analysis revealed that most populations are octoploid, except for one diploid population from Mexico. Although the number of individuals from Mexico was low, haplotype diversity and number of diploid individuals was higher in that country than in Argentina. The occurrence of a single haplotype of the species associated with both spineless and spiny forms in Argentina reveals a single introduction event and its subsequent dispersion mainly through asexual reproduction. The haplotype diversity found in Argentina is probably due to hybrids between O. ficus-indica and Opuntia species native to this country. [ABSTRACT FROM AUTHOR]

The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy. [ABSTRACT FROM AUTHOR]

Hyalomma anatolicum, an Anatolian hard tick is a well-recognized vector involved in the transmission of various pathogens to animals and humans. The present study elucidated the population structure and haplotype network of H. anatolicum based on the mitochondrial large subunit ribosomal RNA (16S rRNA) gene sequence. The population structure and haplotype network analysis of 75 sequences archived in the GenBank, including the 15 sequences generated herein, yielded 24 haplotypes. Haplotype 1 (Hap_1) was the predominant haplotype consisting of 45 sequences from India, China, Pakistan, Turkey, Egypt, Iraq, and Tajikistan. The complete haplotype network exhibited a stellate conformation, highlighting a recent population expansion. The overall dataset, together with the sequences corresponding to India, China, and Pakistan, showed a high haplotype (0.638 ± 0.065, 0.671 ± 0.103, 0.753 ± 0.099, and 0.854 ± 0.061, respectively) and low nucleotide (0.00407 ± 0.00090, 0.00525 ± 0.00196, 0.00680 ± 0.00233, and 0.00453 ± 0.00056, respectively) diversity, further emphasized a recent population expansion. The neutrality indices including Tajima’s D, Fu and Li’s D, and Fu and Li’s F for the complete dataset (− 2.661, − 6.008, and − 5.649, respectively) as well as for the sequences from India (− 2.223, − 3.414, and − 3.567, respectively) were negative, suggesting deviation from neutrality and a recent population expansion. The present study provided novel insights into the population structure and haplotype networks of H. anatolicum based on the mitochondrial 16S rRNA gene, and the different tests inferred a low genetic differentiation and suggested a recent population expansion of this economically important tick species. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave. [ABSTRACT FROM AUTHOR]

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species. [ABSTRACT FROM AUTHOR]

The present study was aimed to determine the phylogenetic relationship, haplotype network, and demographic dynamics of H. felis infecting the endangered Asiatic lions in Gir National Park, Gujarat, India, on the basis of partial 18S rRNA gene. The phylogenetic analysis based on the partial 18S rRNA gene sequences of H. felis exhibited the presence of two distinct genotypes of H. felis (HfG1 and HfG2) infecting the Indian wild felids, viz., the Asiatic lion, Royal Bengal tiger, and Indian leopard. The HfG1 and HfG2 genotypes exhibited 97.6–100% and 99.7–100%, and 96.9–98.7% nucleotide identity within and between themselves, respectively. The HfG1 genotype exhibited a higher genetic diversity as compared to HfG2. A total of 22 molecular signatures were identified in the 18S rRNA gene between these genotypes. Further, analysis of a total 67 sequences of H. felis (13 different host species from 13 countries of Africa, South America, Asia, and Europe) that were downloaded from GenBankTM, generated 30 haplotypes. Among all the haplotypes, Hap_17 (h=12) was the most frequent followed by Hap_12 (h=09) and Hap_4 (h=05). Out of 13 location-wise populations, India (h=12) shared the highest number of haplotypes followed by Japan (h=08), and the least number of haplotypes were found in Hungary (h=02). Population dynamics study involving neutrality tests and mismatch distribution, and genetic differentiation indices, revealed the presence of phylogeographic population structure and a constant population size indicating a uniform gene flow among the populations worldwide. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of H. felis were observed on the basis of 18S rRNA gene sequence analysis. [ABSTRACT FROM AUTHOR]

In the early twentieth century, European mouflon was introduced in Croatia, while all introductions in Slovenia occurred in the 1950s and 1960s. Although majority of the introductions were historically documented, occasional cases involving individuals of unknown origin have likely contributed to a mixed genetic pool in established colonies. To understand the impact of past management and the potential founder effects on contemporary mouflon populations, we performed the first genetic study of the species in these two countries. Utilising next-generation sequencing of both mitochondrial control region (mtDNA CR) and major histocompatibility complex (MHC DRB exon 2), our study scrutinises the genetic diversity and structure of these populations. Additionally, the origins and genetic variability of mouflon in Croatia and Slovenia were compared with reference samples from Czech Republic, Sardinia (Italy), and Corsica (France). The mtDNA haplotype network showed that the majority of mouflon from Slovenia are closely related to mouflon from Sardinia, and only few shared the same haplotypes with mouflon from Croatia. Some mouflon from mainland Croatia share identical or closely related haplotypes with individuals from the initially established population in this country (on the Brijuni Archipelago), while others belong to a distinctly different cluster. We found five MHC alleles previously reported for mouflon in Europe, and genetic diversity was similar in both studied countries. We observed an excess of the Ovar-DRB1*07012/*07012 genotype, and only a few individuals exhibited the advantageous genotypes for parasite infection (Ovar-DRB1*0114 allele and Ovar-DRB1*0324/*0114 genotype). Genetic data showed that the population origins are generally in agreement with the written historical records, although we found signals of release of extra individuals into certain colonies. [ABSTRACT FROM AUTHOR]

The results of studies of the morphology and genetics of the Baikal subendemic (Harpacticella inopinata Sars, 1908 harpacticoid) are presented. The collections of 1969 and 2017–2022 from the southern part of Lake Baikal and the Yenisei River within the city of Krasnoyarsk are used as material. It is demonstrated that morphological variability within the species is most pronounced in the structure of the antenna exopodite and the number of pores and sensilla on the integument of thoracic somites. The genetic variability of the studied H. inopinata sample is described by three clades with an average distance between them of 0.24; genetic distances between individuals within the detected genetic groups do not exceed 0.005. It is found that H. inopinata from geographically distant habitats (Lake Baikal and the Yenisei River) form a single morphological and genetic group. The analysis of genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei River, probably associated with an anthropogenic invasion. [ABSTRACT FROM AUTHOR]

The present study aimed to investigate an outbreak of Theileria annulata (T. annulata) infection in an organized dairy cattle farm in Madhya Pradesh, India, using clinical and molecular techniques. Following the deaths of two crossbred cattle in March 2021, 43 blood samples were collected from infected and apparently healthy animals and examined by blood smear and polymerase chain reaction (PCR) techniques. The blood smear examination showed that 23.25% of samples were positive for Theileria organisms, while conventional PCR targeting the 18S ribosomal RNA (18S rRNA) and T. annulata merozoite surface antigen-1 (TAMS-1) genes revealed that 32.55% of samples were positive for T. annulata. PCR targeting cytochrome b (Cytb) gene showed 46.51% of samples were positive for T. annulata. Haematological analysis confirmed clinical signs of infection in affected animals, which were treated with buparvaquone @ 2.5 mg/kg body weight intramuscularly along with supportive medicine. Two 18S rRNA gene amplicons were sequenced and analysed in a phylogenetic tree and haplotype network with 54 Indian and 38 foreign sequences. The phylogenetic tree revealed two groups with a high posterior probability and bootstrap value, while the haplotype network revealed 35 haplotypes, with haplotype 1 (H1) being the most abundant and several single haplotypes clustering around it, indicating fast and widespread expansion. Genetic diversity indices and neutrality tests confirmed that the population was expanding. These studies highlight the significance of prompt and precise diagnosis and management of T. annulata outbreaks and provide insights into its evolutionary history and population dynamics of T. annulata in India, which could aid improving disease preventive and control strategies. [ABSTRACT FROM AUTHOR]

The Spotted sardinella Amblygaster sirm are small pelagic fish that are important protein source to coastal communities in the Indo-West Pacific. In this study, a cytochrome c oxidase subunit 1 (COI) gene of A. sirm from Tanzania was amplified to assess the species’ genetic structure and demographic history. All individuals collected were identified using both morphological examination and genetic barcoding as A. sirm. A total of 19 haplotypes were found in the dataset, with low overall nucleotide (π = 0.13 ± 0.001) and moderate haplotype diversities (h = 0.45 ± 0.07). AMOVA revealed a very low and non-significant genetic differentiation in the dataset (Fst = 0.002, Фst = −0.004, p > 0.05), indicating a lack of population structure. The minimum spanning haplotype network revealed additional evidence for the lack of population structure, which grouped all the sampled haplotypes into one cluster, regardless of their geographical regions. The Tajima’s D, Fu’s Fs tests, and mismatch distribution analyses supported a hypothesis of recent demographic expansion. The lack of population structure identified suggests that the fishery should be treated as a single-stock management unit, consistent with the existing management regime for the species in Mainland Tanzania that currently does not consider genetic structure in managing the fishery. The lack of population structure suggests that populations with low genetic diversity, such as Dar es Salaam, can rebuild by recruiting from other sites if regulations against unsustainable fishing are strictly enforced. [ABSTRACT FROM AUTHOR]

Dorcadionini is a highly speciose tribe within Cerambycidae and is also one of the most challenging in terms of species identification owing to the large number of taxa, intraspecific variability or similarity between species. To support species identification and taxonomic decisions, we generated DNA barcodes for 24 species and 152 specimens. Cases of disagreement between the barcode and taxonomic species were further analysed with the 28S and internal transcribed spacer 2 (ITS2) nuclear markers. The mitochondrial variation is mostly in accordance with the traditional taxonomy except a case of haplotype sharing between Dorcadion murrayi, Dorcadion axillare and Dorcadion pusillum that suggest hybridisation events. We hypothesise that introgression is the likely explanation for part of the large morphological variability found in many other species. In Dorcadion aethiops and Dorcadion fulvum, the taxonomic subspecies are not distinguishable using molecular data, as the haplotypes are identical or very similar, while in Dorcadion equestre, the subspecific structure is in accordance with the genetic data. A low between-species divergence ranging from 0.62 to 2.38% was found in four species, in contrast with the deep intraspecific divergences in D. equestre. We use two methods for single-locus species delimitation (General Mixed Yule Coalescent and Poisson Tree Processes), but none was perfect as both have shortcomings in oversplitting or lumping species. Dorcadion fulvum fulvum is confirmed for Romania. [ABSTRACT FROM AUTHOR]

Background: Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. Objective: The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. Methods: Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. Results: Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. Conclusions: The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline. [ABSTRACT FROM AUTHOR]

Zaprionus indianus was first reported in South America in 1999 and has rapidly colonised most of the continent since. Previous studies established Brazil as the sole entry point into the continent and the source of its expansion northward, but dispersal to the southern limit of its distribution in South America has not been studied so far. In the present work we extracted DNA of 127 individuals collected in north-eastern Argentina (South America) and amplified the COII mitochondrial gene in order to describe the mitochondrial genetic diversity and shed light about the invasion history of this species into this area. Our results suggest a single Z. indianus introduction wave from Brazil has recently occurred in north-eastern Argentina. In addition, by comparison with available sequences from other locations we can state that the invasive haplotypes present in Argentina are shared with those found in Brazilian populations and are phylogenetically closer to haplotypes from Africa than those found in India. This places Brazil as the sole recipient of the invasion to the American continent and its subsequent dispersion southwards. [ABSTRACT FROM AUTHOR]

Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed. [ABSTRACT FROM AUTHOR]

The variability of the nucleotide sequences in the first domain of the mtDNA control region of Anser fabalis Latham 1787 was studied in 65 samples. A stable separation between A. f. serrirostris Swinhoe 1871 and A. f. middendorffii Severtzov 1873 was confirmed both on the phylogenetic tree and in the network of haplotypes. When comparing the sequences of A. fabalis studied earlier with those of the geese from Japan identified at the subspecies level, only one clustered with the A. f. middendorffii sequences. An assumption was made about the most likely pathways of spring migration of the geese wintering in Japan. Some geese from the Amur region were found to be similar to Anser cygnoides Linnaeus 1758. [ABSTRACT FROM AUTHOR]

Dugesia hepta Pala, Casu & Vacca, 1981 and Dugesia benazzii Lepori, 1951 are two freshwater planarian species from the islands of Corsica and Sardinia. Dugesia hepta is endemic of Sardinia and distributed in four northern hydrographic basins where it co-occurs with D. benazzii, which has a wider Tyrrhenian distribution. Although these species have been broadly studied—especially D. benazzii—as regards to their variety of reproductive patterns as well as for their karyological diversity, little is known about them from a molecular phylogenetic perspective. For the first time, we present a molecular phylogenetic tree of the two species and their populations based on two molecular markers—one mitochondrial, Cox1, and one nuclear, Dunuc12. Our results not only confirm that both species are molecularly distinct but also show that D. benazzii's Corsican and Sardinian populations could belong to separate species. Furthermore, we present the first demonstration of a natural hybridization between different species in the genus Dugesia on the basis of molecular data. [ABSTRACT FROM AUTHOR]

A subset of ornamentals grown in Serbia were surveyed for the presence of impatiens necrotic spot tospovirus (INSV) from 2008 to 2018. Out of 1578 samples tested for the presence of the virus using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), INSV was detected in 26 Begonia sp. and four Tulipa sp. samples collected in 2008 and in 10 samples of each of Begonia sp., Impatiens walleriana and I. hawkeri 'SunPatiens' and 'New Guinea' collected in 2018. INSV was not detected in any samples collected during 2009–2017. For further confirmation, the nucleotide sequence of the INSV nucleocapsid (N) gene was obtained by reverse transcription polymerase chain reaction (RT-PCR) in two and four samples collected in 2008 and 2018, respectively. The success of mechanical transmission of INSV isolates from different hosts was variable depending on isolates. Serbian INSV isolates showed very low nucleotide diversity and they were closely related to the Chinese and Japanese isolates already reported in the literature, indicating that the Serbian isolates might be of Asian origin. Phylogenetic analysis and the median-joining haplotype network of the N gene sequences showed clustering of Serbian INSV isolates in the Asian clade into two different subclades with different recent common ancestors implying two independent introductions. The sporadic occurrence of INSV with high temporal distance is a likely consequence of virus spread through the international trade in ornamental planting material. Therefore, the establishment of the virus should be considered and prevented when introducing new plant material into the country. This is also the first report of the tulip as a natural host of INSV. [ABSTRACT FROM AUTHOR]

Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The Fst pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (Fst = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event. [ABSTRACT FROM AUTHOR]

The life histories of species influence the connectivity between populations, for example the dispersal potential, fecundity, and population size. We compare the phylogeography and genetic connectivity of two sandy-beach crustaceans with contrasting dispersal potentials and population traits in Brazil, based on the 16S mitochondrial gene. While the ghost crab Ocypode quadrata possesses high fecundity, long-lived planktonic larvae, and lower population densities of adults, the isopod Excirolana braziliensis is a brooder with low fecundity and higher population densities. Phylogenetic analysis of haplotype networks yielded contrasting results for the two species. Four different lineages were observed for E. braziliensis, while O. quadrata showed a low genetic structure, sharing haplotypes over ~ 7,000 km. For the isopod, the two most frequent lineages (‘North A’ and ‘South A’ lineages) showed distribution range limits that agreed with the tropical-subtropical transition of 22°S, while the others were sympatric, less frequent, and uncommon. While the ‘North A’ showed high haplotype diversity with a high structure, the ‘South A’ showed shared haplotypes and low genetic structure. Our results suggest that the contrasting life histories affect the population connectivity and genetic structure. The genetic patterns of the two species should be considered in the management and conservation of sandy-beach ecosystems. [ABSTRACT FROM AUTHOR]

Things without names are difficult to rationalise, and so species that go without names are difficult to conserve or protect. This is a case study in resolving conflicts in historical taxonomy and ‘real’ species (identifiable and evolutionarily relevant groupings) using an approach including population genetics, natural history, and pragmatism. We report the observation that populations of a shallow-water chiton species from Washington and British Columbia demonstrate extremely high site fidelity and patchy distribution. Their limited dispersal potential and isolation could be explained by a brooding life history. This stands in direct contrast with the supposedly wide distribution of this “species”, Leptochiton rugatus (Carpenter in Pilsbry, 1892) sensu lato, from the Sea of Japan to Baja California. But this lineage has previously been suggested to comprise several cryptic species. Indeed, a haplotype network analysis using 61 individual sequences of the cytochrome oxidase c subunit I gene for L. rugatus s.l. revealed four discrete clusters which correspond to different parts of the geographic range. We infer these to represent four distinct species, at least two of which are likely novel. Leptochiton rugatus sensu stricto is herein reinterpreted as restricted to California and Baja California, and the new name L. cascadiensis sp. nov. is established for the lineage with a distribution in the Cascadia coastal bioregion from the panhandle of Alaska to Oregon. There are minor morphological differences among these species in the L. rugatus species complex, but genetic data or morphological observations alone would not have been sufficient to definitively recognise these groups as species-level lineages. The observation that different species within the complex may have different life history strategies provides important support for interpreting different populations as genuinely separate species. [ABSTRACT FROM AUTHOR]

Halyomorpha halys is an invasive stink bug pest originating from East Asia. In Europe, it was first detected in Switzerland in 2004. It is now present in thirteen countries, and seems to be spreading throughout the continent. In Italy, where it has been recorded since 2012, other than being an urban nuisance, it is causing severe damage in commercial fruit orchards. An integrated approach, using current and previous observational data in space and time and molecular information, was used to identify the genetic diversity of this pest in Europe, its invasion history, and the potential pathways of entry and diffusion. The analysis of 1175 bp of mitochondrial DNA cytochrome c oxidase I and II genes (cox1, cox2) led to the identification of twenty previously unknown haplotypes. The European distribution of H. halys is the result of multiple invasions that are still in progress, and, in some cases, it was possible to identify the specific Asian areas of origin. Moreover, secondary invasions could have occurred among European countries by a bridgehead effect. In Italy, the data were more clearly related to their temporal occurrence, allowing for a clearer reading of the patterns of invasion and dispersion. After having successfully established in localized areas, H. halys further expanded its range by an active dispersion process and/or by jump dispersal events due to passive transport. The multiple introductions from different areas of the native range together with the different patterns of diffusion of H. halys, may hamper the pest management strategies for its containment. [ABSTRACT FROM AUTHOR]

The astigmatid family Hypoderatidae includes over 80 mite species exhibiting peculiar life cycle. Deutonymphs are parasitic instars inhabiting subcutaneous or visceral tissues of birds and rodents, while all other instars are nidicolous forms. In this study we investigated genetic diversity of deutonymphs of two hypoderatid species, Neottialges evansi and Phalacrodectes gaudi, collected from 16 individuals of the great cormorant Phalacrocorax carbo in SW Poland during host post-breeding dispersal. The initial alternative hypotheses were: (1) populations of deutonymphs in both mite species found in tissues of particular bird individuals form genetically distinct populations, (2) mites are panmictic among hosts. The topologies of NJ phylogenetic trees and median-joining haplotype networks reconstructed for COI haplotypes revealed lack of hostdependent genetic structure in populations of N. evansi and P. gaudi. Furthermore, high haplotype diversity (Hd) and low nucleotide diversity (Pi) prove high genetic differentiation of both mite species. We concluded, that unlimited dispersal of mites among cormorant specimens could be explained by host specific breeding behavior: free mating between cormorants originating from different European populations and low contribution of reunited pairs in breeding colonies in subsequent breeding seasons, reuse of the same nest material by different members of the colony, and host behavior called prospecting. [ABSTRACT FROM AUTHOR]

Pedigrees illustrate the genealogical relationships among individuals, and phylogenies do the same for groups of organisms (such as species, genera, etc.). Here, I provide a brief survey of current concepts and methods for calculating and displaying genealogical relationships. These relationships have long been recognized to be reticulating, rather than strictly divergent, and so both pedigrees and phylogenies are correctly treated as networks rather than trees. However, currently most pedigrees are instead presented as 'family trees', and most phylogenies are presented as phylogenetic trees. Nevertheless, the historical development of concepts shows that networks pre-dated trees in most fields of biology, including the study of pedigrees, biology theory, and biology practice, as well as in historical linguistics in the social sciences. Trees were actually introduced in order to provide a simpler conceptual model for historical relationships, since trees are a specific type of simple network. Computationally, trees and networks are a part of graph theory, consisting of nodes connected by edges. In this mathematical context they differ solely in the absence or presence of reticulation nodes, respectively. There are two types of graphs that can be called phylogenetic networks: (1) rooted evolutionary networks, and (2) unrooted affinity networks. There are quite a few computational methods for unrooted networks, which have two main roles in phylogenetics: (a) they act as a generic form of multivariate data display; and (b) they are used specifically to represent haplotype networks. Evolutionary networks are more difficult to infer and analyse, as there is no mathematical algorithm for reconstructing unique historical events. There is thus currently no coherent analytical framework for computing such networks. [ABSTRACT FROM AUTHOR]

The brown marmorated stink bug, Halyomorpha halys, is an agricultural and household pest native of far East. In the last years, it has spread to and established in countries outside its area of origin, most notably in North America (United States and Canada), causing severe economic losses in agricultural crops. Recently, H. halys has been found in Europe (Switzerland, Germany, France, Hungary, and Greece) and since September 2012, it has also been found in Italy. However, the modalities of introduction and spreading of this pest on the Italian territory are unknown. Tracing back the diffusion modes of the species by analyzing the genetic structure and composition of populations in their initial phase of colonization could be useful also in the view to implement better pest control strategies. The present study aimed to identify the potential pathways of entry of H. halys by detecting the genetic diversity of specimens collected from Northern Italy and Canton Ticino (Southern Switzerland). The analyses of 1,175 base pairs of mtDNA cytochrome c oxidase I and II genes ( cox1 and cox2) on 42 specimens led to the identification of four combined haplotypes: one, found in Emilia Romagna region, is the same found in China and North America but never observed before in Europe. The other combined haplotypes are new but consistent in part with haplotypes previously found in Switzerland. Present data indicate that the Italian invasion may have occurred from two different pathways, both from Switzerland and from Asia and/or North America. [ABSTRACT FROM AUTHOR]

Recent molecular phylogenetic analyses have revealed that some apparently oligoxenous feather mite species are in fact monoxenous cryptic species with little morphological differentiation. In this study we analyzed two species, Zachvatkinia isolata (Avenzoariidae) and Alloptes ( Sternalloptes) stercorarii (Alloptidae) which prefer different parts of the plumage of two sister species of birds: arctic skua ( Stercorarius parasiticus) and long-tailed skua ( S. longicaudus) breeding on tundra in the High Arctic archipelago of Svalbard. Given that there are no reports about hybridization events between the host species, we expected that both skuas would have a species-specific acarofauna. The genetic distances among DNA-barcode sequences (COI and 28S rDNA), phylogenetic tree topologies, and haplotype networks of the COI sequences of mites suggested extensive gene flow in Z. isolata between and within populations inhabiting both skua species, whereas the Alloptes populations were host specific and sufficiently genetically separated as to warrant species-level status. The discrepancy in the genetic structure of Alloptes and Zachvatkinia populations suggests frequent but transient contacts between the two skua species in which the probability of mite exchange is much higher for Zachvatkinia, which is present in high numbers and inhabits exposed parts of primary flight feathers, than for the less abundant Alloptes that lives primarily in more protected and inaccessible parts of the plumage. We discuss the possible nature of these contacts between host species and the area(s) where they might take place. The star-like structures in the haplotype network as well as high haplotype diversity and low nucleotide diversity observed in Z. isolata are concordant with the known dispersal strategy of feather mites: vertical colonization of new host individuals followed by rapid growth of founder populations. [ABSTRACT FROM AUTHOR]

Zaprionus indianus, also known as the African fig fly, is an invasive pest of a variety of commercial and native fruit. The species was first reported in Brazil in 1999, but has established itself in much of the New World within the last 10-15 years. We used nucleotide sequences from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene to examine haplotype relationships, population structure, and infer the colonization history of Z. indianus in Mexico and Panama. Construction of a haplotype network showed that six COI haplotypes, obtained from flies collected at six localities in Mexico and one in Panama, clustered into three distinct clades. Clade composition was generally consistent in flies from Panama to northwestern Mexico, and analysis of molecular variance indicated no significant structure among populations. Three of the six haplotypes from Mexico and Panama were identical to previously reported haplotypes from Brazil. None of the six haplotypes, however, were shared with previously reported haplotypes from potential source populations in the Old World. The results of our genetic analysis suggest that the invasion of Z. indianus into Central America and Mexico most probably includes a northward migration of individuals from Brazil, with the possibility of at least one additional introduction of Z. indianus to the New World. Additional sequence data from potential source populations in the Old World will be required to confidently determine the number of introductions of Z. indianus into the New World, and to identify the geographic source. [ABSTRACT FROM AUTHOR]

Chromolaena odorata is a native of America while a weed in many parts of tropical and subtropical regions in the world. Research into the invasion mechanisms of C. odorata contributes to a broader understanding of factors that facilitate plant adaptation, and also helps developing effective management strategies. In this study, we used three DNA fragments and six microsatellite loci: (1) to compare genetic diversity of C. odorata in its native and invaded regions; (2) to elucidate the invasive routes and identify possible source locations of C. odorata from America to Asia, with attempt to evaluate the possible mechanisms facilitating the successful invasion of this species. Despite two recorded independent introductions, DNA sequence data revealed only one single haplotype of C. odorata present throughout tropical Asia. All six microsatellite loci consistently exhibited extremely low genetic diversity in Asian populations compared to those from native ranges. Our results implied that there was likely only a single introduction to Asia, and Trinidad, Tobago and adjacent areas in the West Indies were the most likely source location of that introduction. The successful invasion of C. odorata in Asia may have been facilitated by the genotype with strong competitive ability. [ABSTRACT FROM AUTHOR]

Halyomorpha halys has recently established in countries outside of its Asian area of origin. In the North Eastern USA, this pest causes severe economic loss in agricultural crops. Breeding populations have been confirmed in Switzerland and Canada; however, their pathways of entry and genetic diversity remain unknown. To determine invasion pathways and source population(s), the diversity of specimens from Asia, North America, and Europe was investigated. Genetic diversity in Asia was higher than that in the Canada and Switzerland. Although three haplotypes were detected among Canadian H. halys, one haplotype dominated. In contrast, two out of three haplotypes were found frequently among Swiss samples. Based on molecular data and interception records it appears likely that H. halys in Canada is derived from the movement of established US populations. Further, North American populations likely originated from the Hebei/Beijing regions of China. The area of origin of the Swiss samples remains unclear. Although the dominant haplotype in Switzerland was consistent with Asian samples collected in the Hebei and Beijing provinces, it was not the dominant haplotype in these regions and further sampling is necessary to its confirm the distribution and abundance in the area of origin. The remaining two haplotypes were unique to Switzerland and no matches were found among our Asian samples. Interestingly, no haplotypes were shared between the North American and Swiss samples, indicating that the two invasions were separate and distinct events and did not result from the movement of goods and materials between USA and Europe. [ABSTRACT FROM AUTHOR]

Colpomenia peregrina is an annual brown macroalga found in temperate waters worldwide. To understand population differentiation and to reconstruct pathways of colonization/introduction, we analyzed variation in two mitochondrial protein-coding genes, cytochrome c oxidase subunit III ( cox3) and ATP synthase F0 subunit 6 ( atp6), and cp RuBisCO spacer. A total of 359 cox3, 342 atp6, and 38 RuBisCO spacer sequences from Colpomenia peregrina were obtained for samples collected at 28 sites from 12 countries. The combined cox3 + atp6 sequences (1,231 bp) revealed 99 polymorphic sites and 69 haplotypes. An mt haplotype network revealed four distinct groups, separated by 7 to 26 mutation steps. NW Pacific populations were present in each group (but dominant in one), whereas SW Pacific and the Atlantic populations each were present in one group. The network and phylogenetic analyses, along with patterns of genetic diversity, suggested a NW Pacific center of origin, expanding first to the SW Pacific, then the NE Pacific, and most recently to the north Atlantic. A generalized skyline plot revealed a dramatic population expansion of the species ca. 20 kya. [ABSTRACT FROM AUTHOR]

Nemerteans (ribbon worms) constitute an abundant and occasionally conspicuous group of benthic invertebrates in the Southern Ocean. Although recent work has confirmed that this group is far more diverse than previously recognized, the Antarctic nemertean fauna remains poorly understood when compared to other geographic regions. In most cases, the taxonomic information on the known nemertean fauna is incomplete for this region and/or has been inappropriately documented. As a consequence, many of the species described are considered species inquirendae. Among the nearly 50 species described so far for the Southern Ocean, two hoplonemerteans are known to brood eggs in cocoons: Amphiporus incubator Joubin, and Amphiporus michaelseni Bürger, . Here, we redescribe Antarctonemertes valida (Bürger, ), a senior synonym of A. michaelseni, and describe a new congeneric species, Antarctonemertes riesgoae sp. nov. Both species show a similar reproductive strategy by brooding their cocoons, and similar external appearance, but clearly differ in other aspects of their morphology, such as the cephalic coloration pattern and the number of proboscidial nerves. We provide novel information about their life habitus, reproductive behaviour, internal anatomy, and their phylogenetic placement within hoplonemerteans using one nuclear (28S rRNA) and two mitochondrial [cytochrome c oxidase subunit I (COI) and 16S rRNA] markers. We also provide a parsimony haplotype network using 16S rRNA, COI, and the internal transcribed spacer region 2 (ITS-2) showing a clear distinction between individuals of both species. Our results stress the need of combining molecular and morphological information when dealing with closely related species of nemerteans. [ABSTRACT FROM AUTHOR]

Haminoea japonica is an opisthobranch mollusk with a large non-indigenous range. This species is a vector for a parasite that causes the human skin disease cercarial dermatitis, and may have negative effects on populations of native species. Molecular evidence from the mitochondrial cytochrome c oxidase I gene and the histone 3 nuclear gene indicates that previously published morphology-based hypotheses on the spread of H. japonica out of Japan are correct. The most likely explanation for the current range of the species, which includes Japan, Korea, France, Spain, Italy, Canada and the USA is a recent, human-mediated dispersal from Japanese populations. The highest levels of nucleotide and haplotype diversity are found in Japan. Non-indigenous populations have low levels of genetic diversity (indicating bottlenecking). Haplotypes that were detected in the non-indigenous range of H. japonica have only been found in two localities in the native range; these two localities are in north-eastern Japan. In addition, the haplotype network structure and Spatial Analysis of Molecular Variance results confirm the origins of non-indigenous populations most likely trace to north-eastern Japan, which is where most Pacific oyster exports to North America also originated. Because there are no major shipping ports in north-eastern Japan, ballast water is less likely to be the mechanism of dispersal. The results of this study provide important data for the development of policies and regulations aimed to prevent further spread of this species in non-indigenous ranges. [ABSTRACT FROM AUTHOR]

Cylindrocladium parasiticum is an important pathogen of peanut ( Arachis hypogaea) causing the disease Cylindrocladium black rot. The genetic structure of this haploid pathogen was determined for populations associated with peanut in Georgia, USA. Ten polymorphic microsatellite markers were used to determine genetic and genotypic diversity among three sub-populations representing the geographic distribution of peanut production in Georgia. Among 200 isolates collected, only 10 unique multilocus haplotypes were identified, with one multilocus haplotype occurring 176 times. Although no evidence for random mating was observed, the existence of loops in a constructed haplotype network hint at the possibility of recombination events. The absence of random mating might therefore be attributed to the homothallic nature of C. parasiticum as well as the clonality of the population, without excluding the possible occurrence of recombination. Cylindrocladium parasiticum thus appears to consist of a genetically homogeneous population throughout Georgia with mainly clonal reproduction or inbreeding contributing to the observed population genetic structure. [ABSTRACT FROM AUTHOR]

Phylogeographic analysis of Dasyscyphella longistipitata (Hyaloscyphaceae, Helotiales), which occurs on decaying Fagus crenata cupules, was carried out. The ITS-5.8S regions of the 120 isolates from 12 sites in areas across Japan revealed 38 haplotypes, the majority of which comprised the haplotype designated H12 (42.5%). H12 was found in isolates from all sites, followed by H28 and H10, which were detected in isolates from 10 and 7 sites, respectively. Thirty-two haplotypes were obtained in single isolates. In the haplotype network, H12 was the root, and it formed interior clades with H28 and H10. Genetic diversity was higher in northern and southern Japan, but genetic distance was not correlated with geographical distance, nor with the phylogenetic clades of F. crenata. Therefore, it was concluded that D. longistipitata forms a genetic continuum that covers all of the areas in which it is distributed in Japan, with variations being generated in local populations from the major haplotypes. [ABSTRACT FROM AUTHOR]

In the US, clonal growth of Fallopia japonica, Fallopia sachalinensis and their hybrid Fallopia x bohemica (Polygonaceae) is prominent, yet sexual reproduction and hybridization contribute to the genetic complexity of swarms. The contribution to this diversity from multiple introductions is unknown. Using 800 bp of the non-coding chloroplast marker accD-rbcL, we compared 21 Japanese haplotypes with 46 US samples from 11 states, 2 Canadian samples, and 6 European samples from 4 countries, in order to investigate if there were repeated introductions from Asia. While most North American and all European haplotypes accessions in our collection matched a single widespread haplotype, we identified 8 other haplotypes. Three haplotypes of F. japonica (including the widespread haplotype) and one F. sachalinensis matched previously identified Japanese haplotypes, supporting the hypothesis of multiple introductions in the US. Five additional US haplotypes were detected once. Four of these differed from Japanese haplotypes by one single nucleotide polymorphism (SNP), possibly indicating a recent in situ change. The fifth haplotype represents a garden cultivar, which differed from all F. japonica haplotypes. It therefore appears that the US genetic diversity of these taxa has three sources: intra-specific reproduction, inter-specific reproduction, and multiple sources of introduction. [ABSTRACT FROM AUTHOR]

Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (23.2 kb) per plant in a 31 plant diversity panel. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by θ and π was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and within-locus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Rare, highly diverged alleles were observed, involving at least seven tomato lines and five loci. Some of these may represent introgressions that originated both from natural hybridization with Solanum pimpinellifolium L. and from crosses with S. pimpinellifolium and additional wild relatives for crop improvement. The former was reported from classical field studies carried out by CM Rick; the latter has been extensively documented in the crop, particularly for transfer of disease resistance alleles. Extensive introgression and frequent bottlenecks within S. lycopersicum will pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.Heredity (2009) 103, 257–267; doi:10.1038/hdy.2009.58; published online 13 May 2009 [ABSTRACT FROM AUTHOR]

The wild common bean ( Phaseolus vulgaris) is widely but discontinuously distributed from northern Mexico to northern Argentina on both sides of the Isthmus of Panama. Little is known on how the species has reached its current disjunct distribution. In this research, chloroplast DNA polymorphisms in seven non-coding regions were used to study the history of migration of wild P. vulgaris between Mesoamerica and South America. A penalized likelihood analysis was applied to previously published Leguminosae ITS data to estimate divergence times between P. vulgaris and its sister taxa from Mesoamerica, and divergence times of populations within P. vulgaris. Fourteen chloroplast haplotypes were identified by PCR-RFLP and their geographical associations were studied by means of a Nested Clade Analysis and Mantel Tests. The results suggest that the haplotypes are not randomly distributed but occupy discrete parts of the geographic range of the species. The current distribution of haplotypes may be explained by isolation by distance and by at least two migration events between Mesoamerica and South America: one from Mesoamerica to South America and another one from northern South America to Mesoamerica. Age estimates place the divergence of P. vulgaris from its sister taxa from Mesoamerica at or before 1.3 Ma, and divergence of populations from Ecuador-northern Peru at or before 0.6 Ma. As these ages are taken as minimum divergence times, the influence of past events, such as the closure of the Isthmus of Panama and the final uplift of the Andes, on the migration history and population structure of this species cannot be disregarded. [ABSTRACT FROM AUTHOR]