Despite its usefulness, the phylogeographic method has serious shortcomings as seems to be the case for any discipline with a historical dimension. Generally, direct genetic evidence about phylogeographic divergence can be gathered only where populations currently exist. Even then, the evidence is temporally fragmented as the result of past population extinctions. These factors can obscure inferences about the prevalence and the spatial scale of cryptic speciation. Obtaining genealogical signal from genetic markers is also challenging if speciation occurred very rapidly, as is often the case in Quaternary biological radiations. Partial solutions to these shortcomings exist, but their effectiveness is dictated by the peculiarities of each biogeographic scenario. Solutions include combining traditional tree-based phylogenetic methods with estimates of demographic parameters that take into account uncertainties in phylogeographic inference [9, 10, 20–22], adding data from extinct populations [23], adding temporal samples from the same populations [24–27] and adding data from a large number of individuals, localities and fast-evolving genetic markers [21, 26–28].

Nevertheless, when combined with data from population genetics and Earth sciences, phylogeographic information can be used to answer key questions concerning past and present aspects of biodiversity and to predict future demographic scenarios. Techniques for studying cryptic diversity using DNA data are becoming cheaper and cheaper, and so finite resources can be reallocated to gather more population samples, in both time and space. Through temporal and spatial sampling a biologist is basically looking at the world as a geologist would. Phylogeographers have two main tools for looking into the past: using sophisticated models of DNA evolution they can infer from present-day data the evolutionary processes that happened in the past [20–22], or they can actually look at the past [23–27], as a geologist would when studying stratigraphic series. However, phylogeographers generally have no formal training on how to explore and interpret physical data about Earth's history. As a result, they have often inefficiently, and sometimes incorrectly, used information from disciplines such as geomorphology, sedimentology, paleoclimatology, volcanology and oceanography. Many of these fields, especially those related to Late Quaternary dynamics, have experienced technological and theoretical advances in recent years that produce data that are probably 'cryptic' to the eyes of many biologists. As a starting point, Earth scientists and phylogeographers should integrate their information to fill in temporal and spatial gaps when reconstructing the history of a particular region and its biota (Figure 1). This can be of mutual benefit to both types of specialists by guiding and rationalizing sampling (both genetic and geological) over the appropriate geographic and temporal landscape. In turn, this can produce a less fragmented picture about the patterns and processes shaping biodiversity.

Figure 1 An integration among molecular population biologists, Earth scientists and taxonomists to discover, document and understand biodiversity. The diagram exemplifies a comparative phylogeographic study but single-taxon studies are also important. Integrated scientists benefit from the flow of information that occurs from all sections of the diagram (not shown). Full size image

Justifiably or not, species as established in the current taxonomy are often used as units in biodiversity research and in conservation policy. Thus, investment towards a better resourced morphology-based taxonomy is urgently needed to implement a modern and integrated system to ensure that newly reported cryptic species will be described following their discovery [29]. Human activity has had a greater impact on biodiversity in the past 50 years than at any time in human history, and the rate of change is predicted to continue or to increase [30]. Some of the key drivers affecting the loss of biodiversity worldwide are habitat alteration, climate change, overexploitation and invasive alien species. By improving the way we discover, document and measure biodiversity, we will move towards understanding the consequences of changes in these drivers for biodiversity. For this to become a reality, biodiversity programs need to bring a spatial and temporal perspective to the forefront of their research agenda. Biologists need to dedicate more time to fieldwork (for example, the giraffe study) and expand their intellectual 'confidence zone' to better address temporal axes of diversification (for example, the frog study). The prevalence of cryptic species, even in charismatic and well studied animals like the giraffe, highlights the importance of combining multidisciplinary approaches in order to capture nature's complexity.