First European record of Sticta arenosella and new Central European records of Sticta fuliginoides

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.

Graphical Abstract Highlight Research Integrated DNA barcoding and morphological variations can improve the identification of grouper species. DNA barcoding confirms the morphological identification of Plectropomus (98-100% similar). High intraspecies genetic diversity revealed within Plectropomus in Makassar Strait. Potential cryptic species identified within Plectropomus based on genetic analysis. Abstract The high economic value of groupers has made them a popular choice in both local and international markets. However, identifying grouper species is also challenging due to complex morphological variations especially in the juvenile phase. An integrative approach combining DNA barcoding and morphometric analysis was applied to improve species identification accuracy and provide additional information on grouper stocks. This research aims to gain a deeper understanding of the morphological and genetic diversity of groupers caught in the juvenile phase from the Makassar Strait. Samples of the genus Plectropomus (n=6) collected from a fish landing site in Pangkajene Kepulauan Regency were identified based on morphology and using molecular methods (DNA barcoding). Phylogenetic and haplotype network analyses were performed. For all specimens the morphometric-meristic and molecular analyses were consistent (98-100% similarity) to known P. leopardus and P. oligacanthus accessions from GenBank. However, phylogenetic analysis: P. leopardus clustered into two distinct lower-level clades, and notably, two P. areolatus (Taiwan) resolved within the P. leopardus clade, while two P. laevis (Philippines) the resolved within the P. oligacanthus clade. Haplotype network showed high intraspecific genetic diversity, with P. leopardus forming four distinct haplotype groups and P. oligacanthus forming two groups. These findings collectively indicate that misidentification may be common and highlight the urgent need for further investigation into geographic barriers to gene flow and the potential existence of cryptic species or subspecies within Plectropomus. This study is expected to provide critical support for sustainable fisheries management and the conservation of marine biodiversity in the Makassar Strait.

HIV Phylogeographic Analyses and Their Application in Prevention and Early Detection Programmes: The Case of the Tijuana–San Diego Border Region

Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.

Biogeographic regionalization can help to better understand diversity in biogeography, conservation, and macroecology. Historical regionalization schemes typically focus on species distributions, often rarely considering the rich context that phylogeographic information can provide. We investigated whether phylogeographic data could help to delineate floristic regions in the Qinghai-Tibet Plateau (QTP)-Hengduan Mountains (HDM) region by analyzing phylogeographic structure in the herb Parasyncalathium souliei (Asteraceae). We sequenced the plastid psbA-trnH and trnL-rpl32 spacer regions for 417 individuals in 36 populations across the geographic range of the species. To estimate the phylogeographic history of this species, a series of population genetic, phylogenetic, molecular dating, and haplotype network analyses were conducted, as were tested for historical demographic expansions. Using occurrence data, species distribution modeling was used to estimate geographic distributions at three time points: the present, the Mid-Holocene and the Last Glacial Maximum. Significant phylogeographic structure was evident (NST> GST; P < 0.05) among the 37 haplotypes detected. Four major haplogroups were identified based on phylogenetic analyses. Private haplotypes were restricted to geographically distinct regions that generally corresponded to previously identified biogeographic subregions within the QTP-HDM region. Our results imply Pliocene-Pleistocene diversification of P. souliei and suggest that the species may have been geographically widespread early in its history. This study may provide valuable evidence for phylogeographic regionalization using chloroplast genetic data in a common, widespread endemic species from the QTP-HDM.

Amphisbaenian paleobiogeography: Evidence of vicariance and geodispersal patterns

ABSTRACTDuring the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission.IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.

Comments on Steadman, D.W., Martin, P.S., MacPhee, R.D.E., Jull, A.J.T., McDonald, H.G., Woods, C.A., Iturralde-Vinent, M. & Hodgins, G.W.L. (2005) Asynchronous extinction of late Quaternary sloths on continents and islands. Proceedings of the National Academy of Sciences USA, 102, 11763–11768. The debate over the causes of the Pleistocene megafaunal extinction dates back to the early 19th century (Grayson, 1984), and continues to generate considerable controversy (e.g. Grayson & Meltzer, 2003; Araujo et al., 2004; De Vivo & Carmignotto, 2004; Fiedel & Haynes, 2004; Burney & Flannery, 2005; Wroe et al., 2006). Typically, protagonists in this debate can be classified into two groups. One group argues that Late Pleistocene megafaunal extinctions were primarily caused by direct and indirect human action through hunting, habitat modification or introduction of new predators (Burney & Flannery, 2005, 2006; Barnosky et al., 2004; Fiedel & Haynes, 2004). The other interpretation is that humans had at most a minor role in the megafaunal extinction, and that the loss was attributable principally to a climatic cause (Ficcarelli et al., 2003; Grayson & Meltzer, 2003, 2004; Barnosky et al., 2004; De Vivo & Carmignotto, 2004; Boeskorov, 2006; Guthrie, 2006; Wroe et al., 2006; Wroe & Field, 2006). Here we contest the position of Steadman et al. (2005), who favour the overkill hypothesis to explain the ground sloth extinction in the Americas. Although making an important contribution to the debate on extinction of the New World megafauna, Steadman et al. (2005) make some important assumptions in their analysis. Steadman et al. (2005) argue that the extinction of ground sloths in the New World was concomitant with, and a consequence of, the human occupation of the Americas. Their argument is two-fold. First, the radiocarbon dates (14C) accepted by them for the last appearance dates (LADs) of these animals roughly correspond to megafaunal extinction dates in South and North America and the West Indies. These dates coincide with the human colonization of these regions and they argue that this supports the thesis that human arrival caused extinction of the ground sloth. Second, according to Steadman et al., extinctions caused by climatic fluctuation would result in concomitant LADs across the entire continent and associated islands, as they viewed these fluctuations as being widespread and uniform, whilst they found that the LADs for the West Indies, around 4400 14C yr bp [c. 4800–5050 calibrated years before present (cal. bp); dates calibrated with calib 5.0, Stuiver et al., 2005], are much younger than those found in the continent (c. 11,000 14C yr bp; c. 12,880–12,950 cal. bp for North America and c. 10,500 14C yr bp; c. 12,390–12,640 cal. bp for South America). We contend that the chronological data presented by Steadman et al. (2005) are incomplete, especially when considering South America. While Steadman et al. (2005) suggest that there are no acceptable Holocene LADs for ground sloths, a large number of Holocene dates generated through direct dating of bone and dung remains are indeed available in the literature. Barnosky et al. (2004; supporting material) revised the radiocarbon dates available for megafaunal remains throughout the world. In South America, they listed four articles with remains of megafauna dated within the Holocene, based both on direct and indirect dates. Even when considering only the results based on direct dates of bone remains, sufficient evidence still supports Holocene LADs for subequatorial ground sloths. For instance, from Argentina, Borrero et al. (1998) presented a total of seven 14C dates consistent with a Holocene survival of megafauna, albeit two of these ages are potentially unreliable, and four were obtained from one single specimen (indeed, one of the unreliable dates comes from this specimen; Table 1). Other reports not included in Barnosky et al. (2004) provide two direct radiocarbon ages of megafaunal bone remains from central Brazil at the Pleistocene/Holocene boundary (Table 1; Neves & Piló, 2003; Araujo et al., 2004). Politis et al. (2004; also not included in Barnosky et al., 2004) presented two additional Holocene direct radiocarbon ages of Megatherium americanum (Blumenbach) specimens (Table 1) and a third one from the Holocene/Pleistocene boundary (10,190 ± 120 14C yr bp; c. 11,820–12,020 cal. bp; Table 1), all in Argentina; and Marshall et al. (1984; also not included in Barnosky et al., 2004) reported a single Holocene age of 8910 ± 200 14C yr bp (c. 9780–10,150 cal. bp; GIF-4116) of a Scelidodon chiliensis (Lydekker) in Peru (Marshall et al., 1984;Pujos & Salas, 2004). Four of the sites where these dates were obtained are located in Argentina, while two are located in central Brazil and the last in Peru (Fig. 1). All the Argentinean sites (Arroyo Seco 2, La Moderna, Campo Laborde and Paso Otero 5) are open-air archaeological sites, i.e. the megafaunal remains are associated with prehistoric human occupations (see Borrero et al., 1998; Politis et al., 2004 for detailed descriptions). Arroyo Seco 2 is interpreted as a base camp where a large variety of activities were undertaken (Politis et al., 2004), including the exploitation of ground sloths and other megafauna by humans. However, Borrero et al. (1998) and Politis et al. (2004) do not state clearly if the two specimens (M. americanum and Equus neogeus Lund) that dated to the Holocene (Table 1) showed marks of human manipulation. The remaining open-air sites are believed to be sites used for specific activities (Politis et al., 2004): La Moderna is interpreted as an occasional megafaunal processing site, where the remains of a single glyptodont (Doedicurus clavicaudatus Owen) dated to the Holocene (Table 1) were recovered; Campo Laborde presents evidence that it was used as a hunting and processing site for ground sloths (M. americanum; Table 1); and Paso Otero 5, was also identified as a hunting and processing site for local megafauna. Archaeological and palaeontological sites in South America presenting direct Late Pleistocene/Early Holocene radiocarbon (14C) dates for megafaunal remains. Circles represent sites with no evidence of human exploitation of the megafaunal remains, whereas triangles represent sites with evidence of human exploitation of megafauna. 1, Gruta Cuvieri; 2, Escrivânia 5; 3, Gruta del Indio; 4, La Moderna; 5, Campo Laborde; 6, Arroyo Seco 2; 7, Paso Otero 5; 8, Pampa de los Fósiles. The two Brazilian sites, in contrast, are exclusively palaeontological, i.e. they are not associated with human occupations, and are located in limestone caves in the karstic region of Lagoa Santa. Gruta Cuvieri is a cave where three vertical chambers functioned as natural traps for the now extinct megafauna and other animals. The only megafauna species found so far is Catonyx cuvieri (Lund), a medium-sized ground sloth. The Holocene date presented in Table 1 was obtained from one of these ground sloths, found at the surface of one of the chambers. The other Brazilian site, Escrivânia 5, is part of a complex of caves, generically referred to as Escrivânia, representing one of the richest palaeontological limestone outcrops known at Lagoa Santa. Together with tons of animal fossil bones, in one of the chambers (Escrivânia 3) an almost complete human skeleton was also recently recovered, dated to 7650 ± 80 14C yr bp (c. 8370–8420 cal. bp; Beta 174734). The Peruvian site, Pampa de los Fósiles, is also a palaeontological site located in the Cupisnique Desert. Several archaeological sites in the region have revealed no evidence of human interaction with the megafauna in the region (Pujos & Salas, 2004). In addition to these reported dates, Steadman et al. (2005; supporting material) disqualified two other Holocene dates as unreliable (they also rejected a third date, but it has a very large margin of error). These were the only Holocene dates found in their bibliographical revision and they ‘have means that are up to 1000 years younger than means of any [of the accepted LADs] [Supplementary online material]’. As 10 reliable Holocene direct radiocarbon dates for megafauna are described here, there is no further reason to reject the dates of 8990 ± 90 14C yr bp (c. 9920–10,190 cal. bp; LP-925; Garcia, 2003) and 9560 ± 90 14C yr bp (c. 10,680–10,860 cal. bp; GrN-5772; Long et al., 1998) as unacceptable outliers. These two dates are from an Argentinean site, Gruta del Indio (Fig. 1; see Long et al., 1998; Garcia, 2003 for detailed descriptions). This site is a rockshelter, and although it presents chronological information placing humans together with megafauna in time, there is no evidence of humans exploiting the local megafauna (Long et al., 1998; Garcia, 2003). As presented in Table 1, from the 14 existing Holocene dates we found for megafaunal remains in South America eight are derived from ground sloths, which severely weakens the position of Steadman et al. (2005), that there are no acceptable Holocene LADs for ground sloths in the Americas. Assuming that human groups already inhabited South America around 12,500 14C yr bp (c. 14,300–14,950 cal. bp; Dillehay, 2000), the argument that the ground sloth LADs were concomitant with the human arrival in the New World can no longer be accepted, at least not as an immediate phenomenon. The second argument presented by Steadman et al. (2005) is that the apparent delay observed in the LADs of Central America islands, when compared with the continental ones, favours the overkill hypothesis. Delayed LADs in insular regions have been found in other parts of the world, independent of human presence (Guthrie, 2004; Boeskorov, 2006). Boeskorov (2006) showed that in northern Eurasian islands, megafauna survived into the Holocene, e.g. the mammoths of Wrangel Island. Nonetheless, the extinction of megafauna in Eurasia as a whole is believed to be primarily due to climatic changes (Barnosky et al., 2004; Boeskorov, 2006), particularly because no human presence is found in the Wrangel Islands until well after the extinction of the megafauna (Boeskorov, 2006). Although these data do not peremptorily disqualify Steadman’s argument, they do bring into question whether the overkill hypothesis is the most parsimonious explanation for megafaunal extinctions. Finally, it must be emphasized that there is a general lack of evidence of sloth remains in archaeological contexts in the Americas as a whole (but see Politis et al., 2004 for an exception), which also speaks against the overkill hypothesis. Specifically, in Lagoa Santa, despite the excavation of dozens of archaeological sites dated to the Pleistocene/Holocene transition (showing human evidence as old as 11,000–11,500 14C yr bp; c. 12,880–13,400 cal. bp; Neves et al., 1999), evidence is lacking of megafaunal use by humans, either as a source of food or raw material (Kipnis, 1998; Prous & Fogaça, 1999). In North America, a similar situation is observed. According to Grayson & Meltzer (2003), there are only two genera of megafauna (Mammuthus Burnett, 1830 and Mammut Blumenbach, 1799) known to have been hunted by humans during the Clovis period (Grayson & Meltzer, 2003). This scenario is accepted even by Fiedel & Haynes (2004), strong defenders of the overkill hypothesis. Thus, at least in South America (and most probably in North and Central America as well), the idea that ground sloths went extinct due to overkill lacks archaeological support. In conclusion, the ground sloth overkill hypothesis, as defended by Steadman et al. (2005), is not sufficiently supported in the empirical world. As we have briefly pointed out: (1) a considerable number of reliable Holocene dates for megafaunal specimens in South America already exist, including for ground sloths; (2) the existence of late megafaunal LADs in Central America islands can be equally well explained through overkilling or environmental changes; and (3) the general lack of megafaunal killing sites and megafaunal remains in archaeological contexts is inconsistent with the overkill hypothesis. Nonetheless, it is important to emphasize that the amount of information regarding the presence of megafauna in archaeological sites is still too small to be considered as strong evidence against human predation of megafauna, and thus this piece of information must be interpreted as complementary to the others. Collectively, the data presented here are more consistent with a model explaining megafaunal extinction through climatic fluctuations, although in South America the poor chronological contextualization of the megafaunal decline does not yet allow for a percentage estimate of megafaunal genera that survived until human arrival. In North America (Grayson & Meltzer, 2002, 2003) and in Australia (Wroe et al., 2006; Wroe & Field, 2006), this percentage seems to have been small, suggesting that the megafaunal extinction was a protracted process, beginning much earlier than the human settlement of these continents. Such a decline may have been the case in South America, as only a few megafaunal genera apparently survived until the Holocene. While a human presence could have accelerated the process of extinction of the remaining megafaunal genera, climatic fluctuations could also have been responsible. Araujo et al. (2005) suggested a period of drought during the mid-Holocene in central Brazil, based on a general abandonment of the region by humans and also on palaeoenvironmental data. At least for central Brazil, megafaunal extinction could thus be also explained by the dry period that started between 8500 and 7500 14C yr bp (c. 9520–8190 cal. bp). Furthermore, according to Araujo et al. (2005) several authors recognize the existence of dry climatic periods during the early and mid-Holocene in South America. Bush et al. (2005) also found evidence suggesting the existence of this drier period in the Andes region (between 0° and 24°), although in this case it was not a single or synchronous event. Even if asynchronous, the important point here is that this dry period seems to have been a widespread phenomenon in South America. Thus, we concur with Borrero et al. (1998, p. 197) who propose that ‘people played at most a secondary role in the mega mammal extinctions, perhaps accelerating a process already underway before human arrival in South America’. We would like to thanks Rodolfo Salas for his kindness in assisting us in determining the Holocene date in Peru. Our long-term research in Lagoa Santa is funded by FAPESP (grant 04/01321-6) and by scholarships given to AH (FAPESP 04/11485-6), MH (FAPESP 04/01253-0) and to WAN (CNPQ 305918/85-0). Alex Hubbe is a graduate student at the Laboratory for Human Evolutionary Studies, Instituto de Biociências, Universidade de São Paulo. His main interests are the palaeoecology and extinction of the South America megafauna. Mark Hubbe is an investigator at the Instituto de Investigaciones Arqueológicas y Museo, Universidad Católica del Norte, Chile. His main research interest is the origin and dispersion of the First Americans. Walter Neves is the coordinator of the Laboratory for Human Evolutionary Studies, Instituto de Biociências, Universidade de São Paulo. His main research interest is the origins and adaptations of the First Americans. Editor: Mark Bush

A phylogenetic network is a generalization of the concept of a phylogenetic tree. In contrast to a phylogenetic tree, a phylogenetic network can show incompatible phylogenetic information on a single diagram using reticulations. Phylogenetic network methods would be helpful to analyze genes with complex evolutionary histories such as recombination, hybridization, and gene conversion. In this study, phylogenetic network analyses using mtDNAs of hominoids, OXTR genes of hominoids, and ABO genes of gibbons (three different data sets) are described with examples. Furthermore, how a recombination event is illustrated in a phylogenetic network is explained using hypothetical data. The phylogenetic network revealed the following pattern: a recombinant allele had a short external branch and was located on a diagonal with the outgroup allele and the two parental alleles were located on another diagonal with long external branches.

Identification of major routes of HIV transmission throughout Mesoamerica

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine etal. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

North America-Eurasia and South America-Africa were certainly joined in the classic reconstruction of Pangaea by Middle Triassic time. The line of collision and suture included the Appalachian Quachita-Marathon orogenic trend in the United States extending southwestward into what is now northeastern and southeastern Mexico and into Guatemala. Widespread continentality prevailed and there was no Gulf of Mexico or Caribbean Sea. In Late Triassic time and continuing into Early Jurassic time this construct began to founder by initial rifting between South America-Africa and North America. No oceanic crust was formed, however, thus Africa-South America were still completely connected by land or shallow sea to North America until mid-Jurassic time. During this same uppermost Triassic to Middle Jurassic period a largely continental magmatic arc was draped across the Pacific margin of southwestern North America and apparently continued unbroken into northwestern South America. Sometime in the Middle Jurassic oceanic crust began to form by seafloor spreading in the central Atlantic and Gulf of Mexico as separation of South America-Africa from North America accelerated. Once this dense crust began to form the trailing margins of the continents subsided below sea-level and construction of the Atlantic and Gulf coast continental shelves began. Evidence is quite conclusive that this ocean floor spreading did not reach the Pacific Ocean, but was transformed from the southwestern corner of the newly opened Gulf of Mexico northwestward across Mexico via a complex left-slip transform fault system that reached the Pacific margin near Los Angeles. In Early Cretaceous time spreading continued in the central Atlantic but extended southward into the southern Atlantic. As the main axis of spreading extended into the south Atlantic, spreading ceased in the Gulf of Mexico. The south Atlantic spreading initiated separation of South America from Africa, but they probably remained in partial contact via ridge-ridge transform faults until Late Cretaceous time. South America must have finally completely separated from North America in Early Cretaceous time, probably via a rift along the eastern edge of Yucatan and the Nicaraguan rise. By Late Jurassic time the Pacific continental margin arc had waned and was replaced by a complex, largely oceanic, magmatic arc whose position relative to southwestern North America and northwestern South America is not known. What we do know is that by Late Cretaceous-Early Tertiary time it had accreted against the Pacific margins of both. Connections between the continents are also not known but could have included a largely submarine magmatic arc, parts of which may have subsequently dispersed eastward as the Greater Antilles. Much of what is now Middle America is apparently underlain by oceanic crust at least as young as Late Cretaceous in age. By Late Cretaceous time the Greater Antilles magmatic arc seems to have fully formed and subsequently moved northeastward as a northeast-facing subduction system during Late CretaceousEarly Tertiary Laramide time. The Greater Antilles arc-trench system ceased activity in Late Eocene time as it collided with Florida and the Bahama platform and as Laramide orogeny waned throughout western North America. This was followed by a major plate reorganization in the Caribbean-Middle America region nearly 40 m.y. B.P. which established the Caribbean plate more or less as we know it today. The principal change was initiation of the Lesser Antilles magmatic arc as an east-facing subduction system that began to consume Atlantic ocean floor. Also, a west-facing subduction system may have formed about this time along a proto-Central American western margin of the Caribbean plate. However, much of what is now Central America may have initially been off southern Mexico. The northern and southern margins of the Caribbean plate evolved into complex transform and transpressive systems as North and South America moved westward past a nearly stationary Caribbean plate. These motions significantly fragmented the Greater Antilles into their present array. There is no evidence for any complete land connection between North and South America via the Greater and/or Lesser Antilles throughout later Mesozoic or Tertiary time. Nor is there any evidence for complete land connection via Central America and the Isthmus of Panama before Neogene time.

This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863−869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.

Due to the morphological variability, the identification of moss species can be difficult when the plant grows in submerged environments. The taxonomic status of an aquatic moss found in lakes of the Soya Coast region, East Antarctica, had been controversial, and then, it was investigated by molecular phylogenetic and haplotype network analysis of two chloroplast regions (rps4 and trnL-F) and/or the nuclear ribosomal ITS region. Based on the results of the analyses, the moss was assigned to the genus Leptobryum and determined to be conspecific with Leptobryum wilsonii (Mitt.) Broth. described from South America. Almost no genetic variation was observed between all samples from Antarctic lakes and some samples of L. wilsonii from Chile. Molecular and geohistorical evidence suggests that immigration of L. wilsonii into Antarctic lakes took place during the Holocene via long-distance dispersal from South America. This study gives a clear example of the widespread assumption that most of the Antarctic moss species are post-glacial immigrants.

The fourth biennial meeting of the International Biogeography Society (IBS) in Merida, Yucatan in January 2009 represented a double opportunity for Mexican biologists. First, it fostered the integration of the large community of Mexican biogeographers with the activities of the IBS. Second, the meeting allowed us to welcome a large number of delegates from distant parts of the world who were able to visit what has been considered an obligate destination for nature lovers and cultural tourists alike: the Yucatan peninsula. As Edward O. Wilson pointed out, besides economic power every country has two additional and important types of wealth: cultural and natural. Cultural richness is a naturally embedded component of the Mexican way of life.