The waters of São Tomé: a calving ground for West African humpback whales?

In the Southern Hemisphere, humpback whales Megaptera novaeangliae feed in Antarctic waters during the austral summer and migrate to their breeding grounds in subtropical and tropical waters during the winter. Historical whaling records suggest that the Archipelago of Sao Tome and Principe, located in the Gulf of Guinea, serves as a possible breeding ground. In order to investigate the temporal occurrence and group composition of humpback whales around Sao Tome Island, annual surveys were conducted during the breeding season between 2002 and 2006. A total of 186 boat-based surveys took place during this period. Data collected during each sighting included geographical positions, group size, group composition and behavioural classifications. Of the 66 groups encountered, mother/calf pairs made up a large proportion (65.15%), followed by solitary individuals (15.15%). Mother/calf pairs were seen in the region into November and resightings of identified animals indicate periods of occupancy that extended over three weeks. Few behaviours typically associated with mating activity were observed. Given the high percentage of mother/calf pairs, sometimes with very young calves, and the low frequency of mating activity, the waters of Sao Tome may primarily serve as a calving and nursing or resting area for humpback whales.Projecto Delfim; Rolas Island Resort; ECOFAC (Conservation et utilisation rationnelle des Ecosystemes Forestiers en Afrique Centrale); Wildlife Conservation Society

Do dental nonmetric traits actually work as proxies for neutral genomic data? Some answers from continental- and global-level analyses

Objectives: Crown and root traits, like those in the Arizona State University Dental Anthropology System (ASUDAS), are seemingly useful as genetic proxies. However, recent studies report mixed results concerning their heritability, and ability to assess variation to the level of genomic data. The aim is to test further if such traits can approximate genetic relatedness, among continental and global samples. Materials and Methods: First, for 12 African populations, Mantel correlations were calculated between mean measure of divergence (MMD) distances from up to 36 ASUDAS traits, and FST distances from >350,000 single nucleotide polymorphisms (SNPs) among matched dental and genetic samples. Second, among 32 global samples, MMD and FST distances were again compared. Correlations were also calculated between them and inter-sample geographic distances to further evaluate correspondence. Results: A close ASUDAS/SNP association, based on MMD and FST correlations, is evident, with rm-values between .72 globally and .84 in Africa. The same is true concerning their association with geographic distances, from .68 for a 36-trait African MMD to .77 for FST globally; one exception is FST and African geographic distances, rm = 0.49. Partial MMD/FST correlations controlling for geographic distances are strong for Africa (.78) and moderate globally (.4). Discussion: Relative to prior studies, MMD/FST correlations imply greater dental and genetic correspondence; for studies allowing direct comparison, the present correlations are markedly stronger. The implication is that ASUDAS traits are reliable proxies for genetic data—a positive conclusion, meaning they can be used with or instead of genomic markers when the latter are unavailable

Gene diversity in grevillea populations introduced in Brazil and its implication on management of genetic resources.

A variabilidade isoenzimática para seis populações de Grevillea robusta, oriundas de um teste de procedências/progenies, implantado no delineamento em blocos casualizados com 5 plantas por parcela, no Sul do Brasil, é descrita. A estrutura genética da população foi analisada utilizando-se marcadores bioquímicos, aos 5 anos de idade, especificamente para os locos MDH-3, PGM-2, DIA-2, PO-1, PO-2, SOD-1, e SKDH-1. As procedências do norte de ocorrência natural (Rathdowney e Woodenbong) apresentaram divergência genética superior, em relação à média das progênies, considerando o número de alelos por locus, (Ap), a riqueza alélica (Rs), a diversidade genética de Nei (H), e o coeficiente de endogamia (f). A endogamia foi detectada em diversos graus. A testemunha comercial apresentou o maior coeficiente de endogamia, (f = 0,4448), comparativamente à média das procedências (f = 0,2306), possivelmente devido à insuficiente amostragem populacional na região de origem (Austrália). Apesar de sua ocorrência natural restrita, observou-se correlação positiva entre divergência genética e distância geográfica entre as populações originais. A distância genética e análise de cluster, baseada no modelo bayesiano, mostrou três grupos de procedências distintos: 1) Rathdowney- QLD e Woodenbong-QLD; 2) Paddy?s Flat-NSW; e 3) Mann River-NSW, Boyd River-NSW e a testemunha comercial (material utilizado no Brasil). O agrupamento da testemunha com as procedências Mann River-NSW e Boyd River-NSW sugere um maior potencial das procedências do norte para o melhoramento genético visando à produção de madeira no Brasil, devido a sua elevada diversidade genética e baixo coeficiente de endogamia

Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species

BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. METHODOLOGY AND PRINCIPAL FINDINGS: We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS, and three from plastid genome--trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. CONCLUSIONS/SIGNIFICANCE: We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case

Comparative Phylogeography of a Coevolved Community: Concerted Population Expansions in Joshua Trees and Four Yucca Moths

Comparative phylogeographic studies have had mixed success in identifying common phylogeographic patterns among co-distributed organisms. Whereas some have found broadly similar patterns across a diverse array of taxa, others have found that the histories of different species are more idiosyncratic than congruent. The variation in the results of comparative phylogeographic studies could indicate that the extent to which sympatrically-distributed organisms share common biogeographic histories varies depending on the strength and specificity of ecological interactions between them. To test this hypothesis, we examined demographic and phylogeographic patterns in a highly specialized, coevolved community – Joshua trees (Yucca brevifolia) and their associated yucca moths. This tightly-integrated, mutually interdependent community is known to have experienced significant range changes at the end of the last glacial period, so there is a strong a priori expectation that these organisms will show common signatures of demographic and distributional changes over time. Using a database of >5000 GPS records for Joshua trees, and multi-locus DNA sequence data from the Joshua tree and four species of yucca moth, we combined paleaodistribution modeling with coalescent-based analyses of demographic and phylgeographic history. We extensively evaluated the power of our methods to infer past population size and distributional changes by evaluating the effect of different inference procedures on our results, comparing our palaeodistribution models to Pleistocene-aged packrat midden records, and simulating DNA sequence data under a variety of alternative demographic histories. Together the results indicate that these organisms have shared a common history of population expansion, and that these expansions were broadly coincident in time. However, contrary to our expectations, none of our analyses indicated significant range or population size reductions at the end of the last glacial period, and the inferred demographic changes substantially predate Holocene climate changes

Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region

Between a Rock and a Hard Place: Habitat Selection in Female-Calf Humpback Whale (Megaptera novaeangliae) Pairs on the Hawaiian Breeding Grounds

The Au'au Channel between the islands of Maui and Lanai, Hawaii comprises critical breeding habitat for humpback whales (Megaptera novaeangliae) of the Central North Pacific stock. However, like many regions where marine mega-fauna gather, these waters are also the focus of a flourishing local eco-tourism and whale watching industry. Our aim was to establish current trends in habitat preference in female-calf humpback whale pairs within this region, focusing specifically on the busy, eastern portions of the channel. We used an equally-spaced zigzag transect survey design, compiled our results in a GIS model to identify spatial trends and calculated Neu's Indices to quantify levels of habitat use. Our study revealed that while mysticete female-calf pairs on breeding grounds typically favor shallow, inshore waters, female-calf pairs in the Au'au Channel avoided shallow waters (<20 m) and regions within 2 km of the shoreline. Preferred regions for female-calf pairs comprised water depths between 40–60 m, regions of rugged bottom topography and regions that lay between 4 and 6 km from a small boat harbor (Lahaina Harbor) that fell within the study area. In contrast to other humpback whale breeding grounds, there was only minimal evidence of typical patterns of stratification or segregation according to group composition. A review of habitat use by maternal females across Hawaiian waters indicates that maternal habitat choice varies between localities within the Hawaiian Islands, suggesting that maternal females alter their use of habitat according to locally varying pressures. This ability to respond to varying environments may be the key that allows wildlife species to persist in regions where human activity and critical habitat overlap

Genome‐wide SNP data reveal improved evidence for Antarctic glacial refugia and dispersal of terrestrial invertebrates

Antarctica is isolated, surrounded by the Southern Ocean, and has experienced extreme environmental conditions for millions of years, including during recent Pleistocene glacial maxima. How Antarctic terrestrial species might have survived these glaciations has been a topic of intense interest, yet many questions remain unanswered, particularly for Antarctica’s invertebrate fauna. We examine whether genetic data from a widespread group of terrestrial invertebrates, springtails (Collembola, Isotomidae) of the genus Cryptopygus, show evidence for long‐term survival in glacial refugia along the Antarctic Peninsula. We use genome‐wide SNP analyses (via genotyping‐by‐sequencing, GBS) and mitochondrial data to examine population diversity and differentiation across more than 20 sites spanning >950 km on the Peninsula, and from islands both close to the Peninsula and up to ~1,900 km away. Population structure analysis indicates the presence of strong local clusters of diversity, and we infer that patterns represent a complex interplay of isolation in local refugia coupled with occasional successful long‐distance dispersal events. We identified wind and degree days as significant environmental drivers of genetic diversity, with windier and warmer sites hosting higher diversity. Thus, we infer that refugial areas along the Antarctic Peninsula have allowed populations of indigenous springtails to survive in situ throughout glacial periods. Despite the difficulties of dispersal in cold, desiccating conditions, Cryptopygus springtails on the Peninsula appear to have achieved multiple long‐distance colonisation events, most likely through wind‐related dispersal events