Deryn Alpers

Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach.

Parsimony analysis of matK and rbcL sequence data, together with a nonmolecular database, yielded a well-resolved phylogeny of Cupressaceae sensu lato. Monophyly of Cupressaceae sensu stricto is well supported, and separate northern and southern hemisphere subclades are resolved, with Tetraclinis within the northern subclade; there is no support for any of the tribes sensu Li. Taxodiaceae comprise five separate lineages. Chamaecyparis nootkatensis falls within Cupressus, clustering with a robust clade of New World species. Libocedrus Florin is paraphyletic and should incorporate Pilgerodendron. Evolution of several characters of wood and leaf anatomy and chemistry is discussed in light of this estimate of the phylogeny; numerous parallelisms are apparent. A new infrafamilial classification is proposed in which seven subfamilies are recognized: Callitroideae Saxton, Athrotaxidoideae Quinn, Cunninghamioideae (Sieb. & Zucc.) Quinn, Cupressoideae Rich. ex Sweet, Sequoioideae (Luerss.) Quinn, Taiwanioideae (Hayata) Quinn, Taxodioideae Endl. ex K. Koch. The rbcL sequence for Taxodium distichum is corrected, and the implications for a previously published estimate of the minimum rate of divergence of the gene since the Miocene are highlighted.

Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method

The highly endangered northern hairy‐nosed wombat (Lasiorhinus krefftii) is extremely difficult to study in the wild, and its numbers correspondingly difficult to estimate. Disturbance to the animals caused by trapping and radio‐tracking may not only constitute an excessive risk to the population’s viability, but may also yield biased data. The results of a pilot study are presented, which clearly show noninvasive genotyping to be a highly feasible and reliable alternative censusing method for L. krefftii. The protocol can identify individual wombats from single hairs collected remotely at burrow entrances, using: (i) a panel of microsatellite markers giving individual‐specific genotypes; and (ii) a Y‐linked sexing marker in combination with a single‐copy X‐linked amplification control. Using just the eight most variable microsatellites (of 20 available), only one in 200 pairs of full‐sibs are predicted to share the same genotype. From 12 wombat hair samples collected on tape suspended over burrow entrances, three known female, two known male and an unknown wombat of each sex were identified. The approach will allow censusing of individuals that evade capture, and will also reveal some otherwise problematic aspects of the behaviour of this elusive animal.

Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation

The roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub‐Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within‐population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.

Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield's Bronze-Cuckoo Chalcites basalis of Australia

Mitochondrial DNA (mtDNA) is being used increasingly to explore the evolution of host specificity in avian brood parasites. A stable coevolutionary equilibrium between multiple phylogenetically unrelated hosts and a brood parasitic species predicts that mtDNA diversity in the parasite should be relatively deep and phylogenetically structured. Also, the different intraspecific clades resulting from parasitism to multiple sympatric hosts should themselves occur sympatrically. However, mtDNA diversity in brood parasites is as susceptible to effects of historical population dynamics as in any species. We demonstrate the relevance of these dynamics to the use of mtDNA in understanding coevolution between an Australian brood‐parasite, Horsfield’s Bronze‐Cuckoo Chalcites basalis and its hosts, Malurus fairy‐wrens and Acanthiza thornbills. Previous ecological and behavioural analyses argue that Malurus‐ and Acanthiza‐specific host races exist in C. basalis. Yet mtDNA diversity in C. basalis is low and phylogenetically unstructured (mean sequence divergence 0.15 ± 0.07%, range 0.00%–0.31%) and tests of mtDNA neutrality and range expansion vs. population stability (Tajima’s D, Fu & Li’s F* and D*, Fu’s FS, mismatch analyses) all indicate that C. basalis has expanded its range very recently, probably within the last few tens of thousands of years following climatic amelioration after a peak of aridity in the late Pleistocene. The low mtDNA diversity and its lack of phylogenetic structure in C. basalis deny the existence of evolutionarily long‐term stable host races in C. basalis but not the possibility of recently evolved ones. They highlight the need for renewed behavioural and ecological study of the relationship between C. basalis and its hosts. Our findings illustrate the need to understand the evolutionary context in which a brood parasite and its hosts have evolved if mtDNA data are to be used in testing hypotheses concerning the origin and maintenance of host specificity. They also add to the growing body of work illustrating the use of mismatch analyses and Fu’s FS in detecting range expansions.

Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae)

A phylogeny of 19 of the 22 currently recognized species of Myiarchus tyrant-flycatchers is presented. It is based on 842bp of mitochondrial DNA (mtDNA) sequences from the ATPase subunit 8 and ATPase subunit 6 genes. Except for the morphologically distinct M. semirufus, mtDNAs of the remaining 18 species fall into either of two clades. One comprises predominantly Caribbean and Central and North American taxa (Clade I), and the other is of predominantly South American taxa (Clade II). The phylogeny is only very broadly concordant with some vocal characters and also with the limited morphological diversity for which the group is well known. Paraphyly in several species (M. swainsoni, M. tuberculifer, M. ferox, M. phaeocephalus, M. sagrae, M. stolidus) suggests that morphological evolution, albeit resulting in limited morphological diversity, has been more rapid than that of mtDNA, or that current taxonomy is faulty, or both. A South American origin for Myiarchus is likely. Dispersal and vicariance both appear to have been involved in generating the present-day distribution of some species. Relatively recent dispersal events out of South America are inferred to have brought species of Clades I and II into broad sympatry. Jamaica has been colonized independently at least twice by members of Clades I and II. The phylogeny brings a historical perspective that in turn suggests that ecological study of closely related species from within each major clade where they are sympatric will be especially rewarding.

Molecular systematics and phylogeography of New Guinean logrunners (Orthonychidae)

Abstract The logrunners (Passeriformes: Orthonychidae: Orthonyx) of the montane rainforests of New Guinea are usually treated as conspecific with the Logrunner, Orthonyx temminckii, of central eastern Australias upland subtropical rainforests. We used partial mitochondrial DNA (mtDNA) sequences (cytochrome b and ATPase 8 and 6 genes), largely derived from museum specimens and supplemented with morphometric and plumage data, to reexamine relationships within and among New Guinean and Australian populations of logrunners. The mtDNA sequences from the New Guinean populations are monophyletic and deeply divergent from Australian ones. We cannot with certainty determine whether the sister taxon of the New Guinean populations is the Chowchilla, O. spaldingii, of north-east Queenslands Wet Tropics or O. temminckii. Morphologically, the New Guinean birds are more divergent from Australian O. temminckii than has been appreciated, being significantly smaller and with far less white on their underparts. Their similarities to each other are almost certainly due to retention of ancestral plumage character states. Under any species concept their differences permit the New Guinean birds to be considered as a separate species, O. novaeguineae Meyer, 1874. Within O. novaeguineae, there is a deep phylogeographic break in the distribution of mtDNA diversity between its Vogelkop population in north-western New Guinea and its Snow Mountains and south-eastern highland populations (>5% net nucleotide diversity) in the Central Cordillera. The magnitude of this mtDNA break suggests that, as in endemic birds of the rainforests of north-eastern Queensland, vicariance has operated to fragment these birds’ populations at least since the beginning of the Pleistocene if not considerably earlier in the Plio-Miocene. The molecular divergence between Vogelkop and Central Cordillera populations is mirrored in morphology. Weak trends towards birds becoming darker and larger as one moves from west to east across New Guinea may be related to altitude. Taking a cue primarily from the patterns and magnitude of mtDNA divergence, we provisionally recommend taxonomic subdivision of O. novaeguineae.

Identifying the presence of quokkas (Setonix brachyurus) and other macropods using cytochrome b analyses from faeces

Non-invasive methods have the potential to circumvent problems associated with using more traditional techniques when surveying for rare and elusive species. In this study, non-invasive molecular-based methods have been used to analyse the scats of several species of marsupials. DNA was successfully extracted from scats of the quokka, Setonix brachyurus, and three other macropods (Macropus fuliginosus, M. irma and M. eugenii) sympatric with the quokka and with similar-appearing scats. Partial sequence from the mitochondrial cytochrome b gene from these four species and seven other macropods was used to measure genetic differentiation among them to determine whether the quokka could be unambiguously identified from the scats alone. The results confirm that molecular approaches can be used for macropod species identification using scats as the source material. The approach will have potential survey and management applications, and, more specifically, may lead to more accurate assessment of the quokkas geographic range, leading to implementation of more appropriate management strategies for its conservation.

Pooling Hair Samples to Increase DNA Yield for PCR

Hairs are useful non-invasive sources of DNA, but the DNA yield can be very small, thus promoting genotyping errors. Using multiple hairs can counter this problem, but may introduce multiple contributors to a sample if collected remotely. With microsatellite genotyping, samples representing multiple animals are obvious if three or more alleles are detected at any locus: these samples can then be removed from any analyses. However, some multiple-individual samples may have only one or two alleles at each of the loci examined. We investigated the probability of failing to identify mixed pooled samples by simulating pooled samples (10 000 replicates) from microsatellite data from the northern and southern hairy-nosed wombats (NHNW, Lasiorhinus krefftii; SHNW, L. latifrons), species with low and high genetic diversity respectively. The majority (81.7%) of the 40 000 simulated samples had three or four alleles, so were readily identified as mixed. In the remaining 1-or-2-allele SHNW samples, forensic science software (DNAMIX) correctly identified mixed versus single-individual samples for all cases when the probability of locus failure was low (P(LF) = 0.1), and 99% of samples when locus failure was high (P(LF) = 0.5). For NHNW however, the probability of failing to identify a mixed sample was too high for population size estimation (0.05), even when the probability of locus failure was low. In cases such as this, pooled samples may be adequate for less demanding tasks, such as estimation of allele proportions. However, for animal populations with at least average levels of genetic variation, pooling of samples could safely be utilised for most applications.

A set of microsatellite loci for the hairy-nosed wombats (Lasiorhinus krefftii and L. latifrons)

Luciano B. Beheregaray 1, Paul Sunnucks 2, Deryn L. Alpers3, Sam C. Banks 2 & Andrea C. Taylor2∗ 1Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; 2Department of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; 3Department of Ornithology, Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Pkwy, Philadelphia, PA 19103, USA; ∗author for correspondence (E-mail: andrea.taylor@sci.monash.edu.au)

Divergent lineages in the heath mouse (Pseudomys shortridgei) are indicative of major contraction to geographically isolated refugia on the eastern and western sides of Australia during the early Pleistocene

The heath mouse (Pseudomys shortridgei) is a locally rare species; it was considered extinct in Western Australia until its rediscovery 20 years ago. It is not often detected in faunal surveys and is confined to two ecologically distinct habitats on either side of the Australian continent. An important and immediate conservation question has been to determine the genetic diversity within each of its current habitats and to determine the differences between the geographically separate populations. Measures of genetic differentiation amongst P. shortridgei populations in their eastern (Victoria) and western (Western Australia) distribution were estimated using nuclear (microsatellite loci) and partial sequence of mitochondrial DNA (427bp Cytochrome b gene and 637bp of the D-loop). Both markers identified differences between the east- and west-coast populations. MtDNA data showed significant divergence between populations with monophyly within them, and nuclear loci investigated also showed two clear genetic clusters based on Bayesian inference. As a result of these findings, we suggest that the heath mouse comprises two highly divergent (but genetically diverse) lineages and the aridity of the Nullarbor Plain has clearly been a barrier for dispersal since the early Pleistocene (∼1.43million years ago). The populations either side of the Nullarbor Plain are genetically differentiated and should be defined as separate Evolutionary Significant Units (ESUs).