António M. Santos

Zebu Cattle Are an Exclusive Legacy of the South Asia Neolithic

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

The timing of pigmentation lightening in Europeans

The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.

Biogeographic patterns of intertidal macroinvertebrates and their association with macroalgae distribution along the Portuguese coast

Geographical patterns in the distribution of epifaunal crustaceans (Amphipoda, Isopoda and Tanaidacea) occurring with dominant macroalgal species were investigated along the Portuguese rocky coast. Three regions, each encompassing six shores, were studied. Algal species were selected according to their geographical distribution: Mastocarpusstellatus and Chondrus crispus (north); Bifurcariabifurcata (north-centre); Plocamiumcartilagineum and Cystoseiratamariscifolia (centre-south); Corallina spp. and Codiumtomentosum (entire coast). Multivariate techniques were used to test for differences in crustacean assemblage composition between sub-regions and host algal species. A clear gradient of species substitution was observed from north to south. Differences in abundance and diversity of epifaunal crustaceans were observed between southern locations and the remaining sites. Four species were recorded for the first time in the Portuguese coast. Among the 57 taxa identified, southern distribution limits were observed for three species and northern distribution limits were observed for four species. Interestingly, the observed geographical patterns in epifaunal abundance and diversity were not related with geographical changes in the indentity of the dominant algal species.

First record of Halidrys siliquosa on the Portuguese coast: counter-intuitive range expansion?

The occurrence of the pod weed, Halidrys siliquosa , is recorded for the first time on the Portuguese coast. Several specimens of this brown algae were observed attached to the rocky surface in tide pools at 41o44′10″N 8o52′34″W, extending southward its previously known geographical distribution. The observed shift is inconsistent with general predictions of species migrations under warming climate conditions, which anticipate poleward shifts rather than southern expansions. Although more data will be required to undoubtedly uncover its cause, the recently observed range expansion raises important questions about the generalization of the previously stated biogeographic rules.

Spatial dynamics and expanded vertical niche of blue sharks in oceanographic fronts reveal habitat targets for conservation

Dramatic population declines among species of pelagic shark as a result of overfishing have been reported, with some species now at a fraction of their historical biomass. Advanced telemetry techniques enable tracking of spatial dynamics and behaviour, providing fundamental information on habitat preferences of threatened species to aid conservation. We tracked movements of the highest pelagic fisheries by-catch species, the blue shark Prionace glauca, in the North-east Atlantic using pop-off satellite-linked archival tags to determine the degree of space use linked to habitat and to examine vertical niche. Overall, blue sharks moved south-west of tagging sites (English Channel; southern Portugal), exhibiting pronounced site fidelity correlated with localized productive frontal areas, with estimated space-use patterns being significantly different from that of random walks. Tracked female sharks displayed behavioural variability in diel depth preferences, both within and between individuals. Diel depth use ranged from normal DVM (nDVM; dawn descent, dusk ascent), to reverse DVM (rDVM; dawn ascent, dusk descent), to behavioural patterns where no diel differences were apparent. Results showed that blue sharks occupy some of the most productive marine zones for extended periods and structure diel activity patterns across multiple spatio-temporal scales in response to particular habitat types. In so doing, sharks occupied an extraordinarily broad vertical depth range for their size (1.0–2.0 m fork length), from the surface into the bathypelagic realm (max. dive depth, 1160 m). The space-use patterns of blue sharks indicated they spend much of the time in areas where pelagic longlining activities are often highest, and in depth zones where these fisheries particularly target other species, which could account for the rapid declines recently reported for blue sharks in many parts of the worlds oceans. Our results provide habitat targets for blue shark conservation that may also be relevant to other pelagic species.

tcsBU: a tool to extend TCS network layout and visualization

MOTIVATION TCS is a widely used haplotype network reconstruction software, but lacks the capability of overlapping genetic with geographic structure, which is often a first step in phylogeographic analysis. RESULTS tcsBU is a web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format. AVAILABILITY AND IMPLEMENTATION tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

Movement of blue shark, Prionace glauca , in the north-east Atlantic based on mark–recapture data

A shark tagging programme along the Portuguese coast was initiated in 2001 in collaboration with the National Marine Fisheries Service. From a total of 168 blue sharks (Prionace glauca) tagged, 34 sharks were recaptured (20% return rate) providing important information on this species’ movement patterns for the area. A total of 28 sharks travelled less than 1000 km while at liberty for time periods ranging from 22 to 1294 days. The remaining ¢sh travelled long distances to north-west Africa, central Atlantic and the Bay of Biscay. Only one shark made a transatlantic migration, being recaptured 3187 km from the tagging site. North ^ south movements seem to be related to seasonal sea-surface temperature variation in the north-east Atlantic. Seasonal segregation of diierent life stages also occurs.

Invasion or invisibility: using genetic and distributional data to investigate the alien or indigenous status of the Atlantic populations of the peracarid isopod, Stenosoma nadejda (Rezig 1989).

The peracarid isopod, Stenosoma nadejda (Rezig 1989), until recently considered to be endemic of the Mediterranean region, was first reported in the Atlantic coast of southern Spain in 2001, and in 2006 abundant populations were discovered throughout the southwestern Portuguese coast. This fast expansion was intriguing because, as a direct brooder, this species has limited mechanisms for dispersal, such as rafting on seaweeds. Did S. nadejda recently extend its range into the Atlantic or was it overlooked in the past? We examined the patterns of genetic diversity and population differentiation accordingly by sequencing the cytochrome c oxidase subunit I mitochondrial gene from 75 individuals collected in five locations in Atlantic Iberia and one in the Mediterranean. Our results indicate that the newly discovered Atlantic populations of S. nadejda appear to be old and have long persisted on Atlantic shores rather than being a recent introduction. High levels of genetic diversity and geographic structure were uncovered in what was initially suspected to be an ‘invasive’ species. Recent changes in population dynamics may have made S. nadejda more conspicuous in the Atlantic shores, or a more comprehensive survey led to the recognition of this species where it was not expected.

Reproductive cycles of four species of Patella (Mollusca: Gastropoda) on the northern and central Portuguese coast

The reproductive cycles of four limpet species, Patella depressa, Patella ulyssiponensis, Patella vulgata and Patella rustica are described for several locations in northern and central Portugal. Patella depressa and P. ulyssiponensis displayed almost continual gonad activity, with two main spawning periods, September–January and March–June, and minor spawning events dispersed throughout the year. Patella vulgata and P. rustica exhibited highly synchronized reproductive cycles, with well-defined breeding and resting periods. Gonad development in P. vulgata started in September and spawning took place from November–December to March. In P. rustica development started in June and spawning occurred from September–October to December–January. Compared to the 1980s these results suggest that breeding periods are becoming longer in southern species and shorter in northern species.

The breeding ecology of the pipefish Nerophis lumbriciformis and its relation to latitude and water temperature

The breeding season of Nerophis lumbriciformis (Pisces: Syngnathidae), has not yet been determined for the southernmost part of its range. A total of 863 individuals was examined between March 1997 and November 1999. In Portugal, the breeding season of this species occurs throughout the year, with a marked reduction during summer and autumn, whilst in Britain it occurs from May to September. Despite these temporal differences, the water temperature at which breeding takes place is similar in the two areas (13–16°C). Together with preliminary laboratory observations with animals kept at different temperatures, these data support the hypothesis that the decrease in breeding activity during summer and autumn in Portugal is due to an inhibitory effect of high water temperature.