Biogeographic models of gene flow in two waterfowl of the Australo‐Papuan tropics

There are many large, easy‐to‐observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source‐sink dynamics relevant to their conservation or assess risks associated with avian‐borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present‐day genetic connectivity between populations of two widely distributed waterfowl in the Australo‐Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling‐duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling‐duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling‐duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling‐duck and magpie goose is consistent with earlier suggestions that the west‐coast of Cape York Peninsula is a flyway for Australo‐Papuan anseriforms between Australia and New Guinea across Torres Strait.     

The spermatozoon of the Old Endemic Australo‐Papuan and Philippine rodents – its morphological diversity and evolution

Breed, W.G. and Leigh, C.M. 2010. The spermatozoon of the Old Endemic Australo‐Papuan and Philippine rodents – its morphological diversity and evolution.—Acta Zoologica (Stockholm) 91 : 279–294 The spermatozoon of most murine rodents contains a head in which there is a characteristic apical hook, whereas most old endemic Australian murines, which are part of a broader group of species that also occur in New Guinea and the Philippines, have a far more complex sperm form with two additional ventral processes. Here we ask the question: what is the sperm morphology of the New Guinea and Philippines species and what are the trends in evolutionary changes of sperm form within this group? The results show that, within New Guinea, most species have a highly complex sperm morphology like the Australian rodents, but within the Pogonomys Division some species have a simpler sperm morphology with no ventral processes. Amongst the Philippines species, many have a sperm head with a single apical hook, but in three Apomys species the sperm head contains two additional small ventral processes, with two others having cockle‐shaped sperm heads. When these findings are plotted on a molecular phylogeny, the results suggest that independent and convergent evolution of highly complex sperm heads containing two ventral processes has evolved in several separate lineages. These accessory structures may support the sperm head apical hook during egg coat penetration.     

The role of phylogeny and ecology in shaping morphology in 21 genera and 127 species of Australo‐Papuan myobatrachid frogs

Body shape is predicted to differ among species for functional reasons and in relation to environmental niche and phylogenetic history. We quantified morphological differences in shape and size among 98.5% of the 129 species and all 21 genera of the Australo‐Papuan endemic myobatrachid frogs to test the hypothesis that habitat type predicts body shape in this radiation. We tested this hypothesis in a phylogenetic context at two taxonomic levels: across the entire radiation and within the four largest genera. Thirty‐four external measurements were taken on 623 museum specimens representing 127 species. Data for seven key environmental variables relevant to anurans were assembled for all Australian‐distributed species based on species' distributions and 131,306 locality records. The Australo‐Papuan myobatrachid radiation showed high diversity in adult body size, ranging from minute (15 mm snout–vent length) to very large species (92 mm), and shape, particularly sin relative limb length. Five main morphological and environmental summary variables displayed strong phylogenetic signal. There was no clear relationship between body size and environmental niche, and this result persisted following phylogenetic correction. For most species, there was a better match between environment/habitat and body shape, but this relationship did not persist following phylogenetic correction. At a broad level, species fell into three broad groups based on environmental niche and body shape: 1) species in wet habitats with relatively long limbs, 2) species in arid environments with relatively short limbs (many of which are forward or backward burrowers) and 3) habitat generalist species with a conservative body shape. However, these patterns were not repeated within the four largest genera ? Crinia, Limnodynastes, Pseudophryne and Uperoleia. Each of these genera displayed a highly conservative anuran body shape, yet individual species were distributed across the full spectrum of Australian environments. Our results suggest that phylogenetic legacy is important in the evolution of body size and shape in Australian anurans, but also that the conservative body plan of many frogs works well in a wide variety of habitats.     

Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae)

Bryant, L. M., Donnellan, S. C., Hurwood, D. A. & Fuller, S. J. (2011). Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae). —Zoologica Scripta, 40, 433–447. We inferred phylogenetic relationships and divergence date estimates among four genera of mosaic‐tailed rats from the Uromys division in Australia, New Guinea and the Solomon Islands from both mitochondrial (16S rRNA) and nuclear (AP5 and DHFR introns) nucleotide sequence data. Phylogenetic analysis of our combined data shows that Melomys species from Australia and New Guinea are monophyletic to the exclusion of Paramelomys, which last shared a common ancestor with other members of the Uromys division approximately 3 MYA. However, Melomys was found to be paraphyletic with respect to the Solomon Islands endemic Solomys, suggesting the taxonomic distinction of the latter may need revision. The radiation of this group was estimated to have occurred between 2.1 MYA and 900 000 years ago. A currently undescribed taxon, species nova, which is apparently morphologically indistinguishable from sympatric M. cervinipes, was found to be a highly distinctive lineage and was not monophyletic with Melomys from Australia or New Guinea. Australian Uromys share a sister group relationship with sp. n. and the Melomys/Solomys clade. Australian Melomys were not monophyletic with respect to New Guinean Melomys. The New Guinean M. lutillus and Australian M. burtoni appear to be conspecific, supporting a previous suggestion that M. burtoni has an extralimital distribution encompassing New Guinea as M. lutillus. This also suggests sustained contact between these taxa, most likely enabled through historical landbridges that linked the two landmasses during periods of lower sea level. Melomys rubicola, found only on Bramble Cay, 50 km south of New Guinea, is more closely related to Australian Melomys, particularly M. capensis, than to any of the New Guinean species. Results suggest that M. rubicola and M. capensis last shared a common ancestor in the early Pleistocene, a time when land bridges existed connecting Bramble Cay to Cape York. Finally, polyphyly within M. cervinipes was also detected, corresponding to reciprocally monophyletic northern and southern clades. The northern M. cervinipes clade diverged from the M. capensis/rubicola clade approximately 1.2 MYA, with this split possibly resulting from isolation across the Normanby gap in far north Queensland.     

Effects of historical forest contraction on the phylogeographic structure of Australo‐Papuan populations of the red‐legged pademelon (Macropodidae: Thylogale stigmatica)

Geographic patterns of genetic variation are strongly influenced by historical changes in species habitats. Whether such patterns are common to co‐distributed taxa may depend on the extent to which species vary in ecology and vagility. We investigated whether broad‐scale phylogeographic patterns common to a number of small‐bodied vertebrate and invertebrate species in eastern Australian forests were reflected in the population genetic structure of an Australo‐Papuan forest marsupial, the red‐legged pademelon (Macropodidae: Thylogale stigmatica). Strong genetic structuring of mtDNA haplotypes indicated the persistence of T. stigmatica populations across eastern Australia and southern New Guinea in Pleistocene refugial areas consistent with those inferred from studies of smaller, poorly dispersing species. However, there was limited divergence of haplotypes across two known historical barriers in the northeastern Wet Tropics (Black Mountain Barrier) and coastal mideastern Queensland (Burdekin Gap) regions. Lack of divergence across these barriers may reflect post‐glacial recolonization of forests from a large, central refugium in the Wet Tropics. Additionally, genetic structure is not consistent with the present delimitation of subspecies T. s. wilcoxi and T. s. stigmatica across the Burdekin Gap. Instead, the genetic division occurs further to the south in mideastern Queensland. Thus, while larger‐bodied marsupials such as T. stigmatica did persist in Pleistocene refugia common to a number of other forest‐restricted species, species‐specific local extinction and recolonization events have resulted in cryptic patterns of genetic variation. Our study demonstrates the importance of understanding individualistic responses to historical climate change in order to adequately conserve genetic diversity and the evolutionary potential of species.     

Next‐Gen phylogeography of rainforest trees: exploring landscape‐level cpDNA variation from whole‐genome sequencing

Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next‐generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun‐based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species‐specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape‐level studies. As the key laboratory‐based steps do not require prior species‐specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet‐laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.     

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome‐wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans‐Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter‐riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Comparative phylogeography of endemic cyprinids in the south-west Iberian Peninsula: evidence for a new ichthyogeographic area

The comparative phylogeography and evolutionary history of three native cyprinid genera, Squalius (subfamily Leuciscinae), Chondrostoma (subfamily Leuciscinae) and Barbus (subgenus Luciobarbus ; subfamily Cyprininae), were examined focusing mainly in the South-Western region of the Iberian Peninsula, where recently described endemic species are present with considerably restricted distribution areas. In order to accomplish that the variation at the complete cytochrome b gene (1140 bp) was analysed for specimens from the South-Western region, and also for representatives of the three genera from all over the Iberian Peninsula. Data indicate different evolutionary histories, with distinct time periods of colonization between the two cyprinid subfamilies in the Iberian Peninsula. Four new Iberian ichthyogeographic areas are accordingly proposed based on congruent phylogeographic and geological evidences: the South-Western, the South-Eastern, the Atlantic and the Mediterranean. Evidence was provided for the older isolation of the South-Western area in the Miocene during the Endorheic Drainages phase, designating a clearly defined and distinct ichthyogeographic area. A new molecular clock calibration is proposed for the subgenus Luciobarbus .     

Cryptic diversity within and amongst spring‐associated Stygobromus amphipods (Amphipoda: Crangonyctidae)

Multiple species of troglomorphic, spring‐associated Stygobromus amphipods, including the endangered, narrow‐range endemic Stygobromus pecki, occupy sites in the Edwards Plateau region of North America. Given the prevalence of cryptic diversity observed in disparate subterranean, animal taxa, we evaluated geographical genetic variation and tested whether Stygobromus contained undetected biodiversity. Nominal Stygobromus taxa were treated as hypotheses and tested with mitochondrial sequence cytochrome oxidase C subunit 1, nuclear sequence (internal transcribed spacer region 1), and AFLP data. Stygobromus pecki population structure and diversity was characterized and compared with congeners. For several Stygobromus species, the nominal taxonomy conflicted with molecular genetic data and there was strong evidence of significant cryptic diversity. Whereas S. pecki genetic diversity was similar to that of congeners, mitochondrial data identified two significantly diverged but sympatric clades. AFLP data for S. pecki indicated relatively recent and ongoing gene flow in the nuclear genome. These data for S. pecki suggest either a substantial history of isolation followed by current sympatry and ongoing admixture, or a protracted period of extremely large effective population size. This study demonstrates that Edwards Plateau Stygobromus are a complex, genetically diverse group with substantially more diversity than currently recognized. © 2013 The Linnean Society of London     

Taxonomic diversity of the terrestrial bird and mammal fauna in temperate and boreal biomes of the northern hemisphere

Abstract. Using comprehensive range information of northern Hemisphere birds and mammals, we assessed the taxonomic diversity of these two groups in four different regions: Europe, east Asia, and western and eastern North America. East Asia is the richest region in the number of bird and mammal species, genera, families and orders, except that mammal species richness is highest in western North America. Eastern North America is taxonomically the poorest region, but when only forest-associated taxa were considered in mammals taxonomic diversity is equally low in Europe and in eastern North America, and in birds, Europe is the least diverse region. Patterns in endemic taxa follow overall taxonomic diversity. The proportion of shared taxa between regions is higher among boreal species and genera than among all taxa. A comparison with tree species diversity underpins the role of east Asia as the most diverse of all northern biota. Largely congruent patterns at different taxonomic levels emphasizes the role of historical processes, such as differential extinction rate in response to paleoenvironmental fluctuations, in producing these patterns, but we stress the need for more research on the coevolution of species diversity and habitat diversity.     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Genetic diversity of the mangrove‐associated alga Bostrychia radicans/Bostrychia moritziana (Ceramiales,Rhodophyta) from southern Central America

Previous studies suggested that the biodiversity of the mangrove‐associated Bostrychia radicans/Bostrychia moritziana species complex on the Pacific coast of Central America, based on genetic and reproductive data, were low compared with similar areas on the Atlantic coast. Evolutionary scenarios were proposed based on either a recent introduction to the Pacific, or a more uniform environment leading to genetically connected populations and low differentiation between populations. We sampled more extensively in southern Mexico, Guatemala and El Salvador and sequenced the samples for the RuBisCo spacer. Our results show that genetic diversity is high in these populations. Many haplotypes retrieved are also found in the Atlantic Ocean (USA, Brazil), an observation not made before. Data suggest that populations are highly differentiated with little evidence of isolation‐by‐distance. The population at La Puntilla, El Salvador is highly differentiated from other populations. Data also suggest that diversity is reduced in a northerly direction, with only one haplotype, unique to Pacific Central America, found north of Chiapas, Mexico. This could be due to northern expansion of this unique genotype as sea surface temperatures ameliorated following the last glacial maximum. Our data do not support the previous proposition of low diversity in the east central Pacific and suggest that much of the Pacific Central America diversity is from before the closure of the Isthmus of Panama.     

Comparative phylogeography of West African amphibians and reptiles

Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be absent or idiosyncratic. We conducted a Bayesian analysis of shared evolutionary events to test models of population divergence for 20 species of anurans (frogs) and squamates (lizards and snakes) that are distributed across the Dahomey Gap, a climate change-induced savanna barrier responsible for fragmenting previously contiguous rain forests of Ghana into two regions: the Togo-Volta Hills and the Southwestern Forests. A model of asynchronous diversification is supported for anurans and squamates, suggesting that drivers of diversification are not specifically related to ecological and life history associations with habitat types. Instead, the wide variability of genetic divergence histories exhibited by these species suggests that biodiversity in this region has been shaped by diversification events that extend beyond the Holocene. Comparisons of the genealogical divergence index, a measure of the genetic divergence between populations due to the combined effects of genetic isolation and gene flow, illustrate that these populations represent a broad sampling of the speciation continuum.